MIT News - Evolution MIT News is dedicated to communicating to the media and the public the news and achievements of the students, faculty, staff and the greater MIT community. en Tue, 03 Sep 2019 12:18:40 -0400 Comparing primate vocalizations Study shows Old World monkeys combine items in speech — but only two and never more, unlike humans. Tue, 03 Sep 2019 12:18:40 -0400 Peter Dizikes | MIT News Office <p>The utterances of Old World monkeys, some of our primate cousins, may be more sophisticated than previously realized — but even so, they display constraints that reinforce the singularity of human language, according to a new study co-authored by an MIT linguist.&nbsp;</p> <p>The study reinterprets evidence about primate language and concludes that Old World monkeys can combine two items in a language sequence. And yet, their ability to combine items together seems to stop at two. The monkeys are not able to recombine language items in the same open-ended manner as humans, whose languages generate an infinite variety of sequences.</p> <p>“We are saying the two systems are fundamentally different,” says Shigeru Miyagawa, an MIT linguist and co-author of a new paper detailing the study’s findings.</p> <p>That might seem apparent. But the study’s precise claim — that even if other primates can combine terms, they cannot do so in the way humans do — emphasizes the profound gulf in cognitive ability between humans and some of our closest relatives.</p> <p>“If what we’re saying in this paper is right, there’s a big break between two [items in a sentence], and [the potential for] infinity,” Miyagawa adds. “There is no three, there is no four, there is no five. Two and infinity. And that is the break between a nonhuman primate and human primates.”</p> <p>The paper, “Systems underlying human and Old World monkey communications: One, two, or infinite,” is published today in the journal <em>Frontiers in Psychology</em>. The authors are Miyagawa, who is a professor of linguistics at MIT; and Esther Clarke, an expert in primate vocalization who is a member of the Behavior, Ecology, and Evolution Research (BEER) Center at Durham University in the U.K.</p> <p>To conduct the study, Miyagawa and Clarke re-evaluated recordings of Old World monkeys, a family of primates with over 100 species, including baboons, macaques, and the probiscis monkey.</p> <p>The language of some of these species has been studied fairly extensively. Research starting in the 1960s, for example, established that vervet monkeys have specific calls when they see leopards, eagles, and snakes, all of which requires different kinds of evasive action. Similarly, tamarin monkeys have one alarm call to warn of aerial predators and one to warn of ground-based predators.</p> <p>In other cases, though, Old World monkeys seem capable of combining calls to create new messages. The putty-nosed monkey of West Africa, for example, has a general alarm call, which scientists call “pyow,” and a specific alarm call warning of eagles, which is “hack.” Sometimes these monkeys combine them in “pyow-hack” sequences of varying length, a third message that is used to spur group movement.</p> <p>However, even these latter “pyow-hack” sequences start with “pyow” and end with “hack”; the terms are never alternated. Although these sequences vary in length and consequently can sound a bit different from each other, Miyagawa and Clarke break with some other analysts and think there is no “combinatorial operation” at work with putty-nosed monkey language, unlike the process through which humans rearrange terms. It is only the length of the “pyow-hack” sequence that indicates how far the monkeys will relocate.</p> <p>“The putty-nose monkey’s expression is complex, but the important thing is the overall length, which predicts behavior and predicts how far they travel,” Miyagawa says. “They start with ‘pyow’ and end up with ‘hack.’ They never go back to ‘pyow.’ Never.”</p> <p>As a result, Miyagawa adds, “Yes, those calls are made up of two items. Looking at the data very carefully it is apparent. The other thing that is apparent is that they cannot combine more than two things. We decided there is a whole different system here,” compared to human language.</p> <p>Similarly, Campbell’s monkey, also of West Africa, deploys calls that might be interpreted as evidence of human-style combination of language items, but which Miyagawa and Clarke believe are actually a simpler system. The monkeys make sounds rendered as “hok,” for an eagle alarm, and “krak,” for a leopard alarm. To each, they add an “-oo” suffix to turn those utterances into generalized aerial alarms and land alarms.</p> <p>However, that does not mean the Campbell’s monkey has developed a suffix as a kind of linguistic building block that could be part of a more open-ended, larger system of speech, the researchers conclude. Instead, its use is restricted to a small set of fixed utterances, none of which have more than two basic items in them.</p> <p>“It’s not the human system,” Miyagawa says. In the paper, Miyagawa and Clarke contend that the monkeys’ ability to combine these terms means they are merely deploying a “dual-compartment frame” which lacks the capacity for greater complexity.</p> <p>Miyagawa also notes that when the Old World monkeys speak, they seem to use a part of the brain known as the frontal operculum. Human language is heavily associated with Broca’s area, a part of the brain that seems to support more complex operations.</p> <p>If the interpretation of Old World monkey language that Miyagawa and Clarke put forward here holds up, then humans’ ability to harness Broca’s area for language may specifically have enabled them to recombine language elements as other primates cannot — by enabling us to link more than two items together in speech.&nbsp;</p> <p>“It seems like a huge leap,” Miyagawa says. “But it may have been a tiny [physiological] change that turned into this huge leap.”</p> <p>As Miyagawa acknowledges, the new findings are interpretative, and the evolutionary history of human language acquisition is necessarily uncertain in many regards. His own operating conception of how humans combine language elements follows strongly from Noam Chomsky’s idea that we use a system called “Merge,” which contains principles that not all linguists accept.</p> <p>Still, Miyagawa suggests, further analysis of the differences between human language and the language of other primates can help us better grasp how our unique language skills evolved, perhaps 100,000 years ago.</p> <p>“There’s been all this effort to teach monkeys human language that didn’t succeed,” Miyagawa notes. “But that doesn’t mean we can’t learn from them.”</p> A new study by an MIT linguist shows that the speech calls of some monkeys may be more sophisticated than realized, but are still far removed from the complexity of human language.Image: WikipediaSchool of Humanities Arts and Social Sciences, Linguistics, Evolution, Biology, Animals, Research From streams to teams Graduate student Maya Stokes, a geomorphology expert and ultimate frisbee coach, shows her passion for teaching in the field and on the field. Sun, 18 Aug 2019 00:00:00 -0400 Laura Carter | School of Science <p>If you’ve ever looked out the window of an airplane, you might have seen beautiful meandering and braided river systems cutting their way through the Earth. Fly over that same area again a few years later, and you’ll witness a different landscape. On geologic timescales, geomorphology, the study of how the Earth’s surface is shaped and evolves, involves the most rapid processes.</p> <p>“You can observe changes in the paths that rivers take or landslides that dramatically alter hillslopes in a human lifetime. Many geologic processes don’t allow you that opportunity,” says <a href="">Maya Stokes</a>, a fourth-year graduate student in the <a href="">Department of Earth, Atmospheric and Planetary Sciences</a> (EAPS) who researches rivers.</p> <p>Stokes wasn’t always interested in geomorphology, although her love for the outdoors stems from a childhood in Colorado. She entered Rice University in Houston with an interest in science and spent some time as an undergraduate trying out different fields. Fascinated by the history of the Earth and life on it, she narrowed her search down to Earth science and ecology and evolutionary biology. A class on geomorphology won her over. Being able to pursue a career that allowed her to work outside was also an enticing perk.</p> <p>At MIT, Stokes now conducts research with <a href="" target="_blank">Taylor Perron</a>, associate department head of EAPS and associate professor of geology at MIT, who is an expert in <a href="" target="_blank">riverine erosion in mountains</a>. She also collaborates with Tom Near, an evolutionary biologist at Yale University, enabling her to combine her two areas of interest. Her research focus lies at the intersection of geology and evolutionary biology. While exploring how rivers evolve over time, she simultaneously investigates how the ecosystems within those systems evolve in response.</p> <p>You can think of it like two carloads of people on a road trip. One car crosses a bridge toward a major metropolis, but shortly after, construction closes the bridge and forms a detour sending the second car traveling through a rural farmland. Those two carloads of people will have different experiences, different meals and lodging, that are unique to their car's particular pathway.</p> <p>Stokes focuses on specific pathways — freshwater environments — and the interplay of biology and streams has some dynamic features. “As shown by the recent UN report, understanding and maintaining biodiversity is a high priority goal for building a sustainable future on Earth,” she says in reference to the <a href="" target="_blank">2019 global assessment report</a> conducted by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services.</p> <p>To get more hands on, Stokes investigates how related fish are to one another in the United States. She collects both genetic and geologic datasets, processed with the help of a University of Massachusetts at Amherst geochemistry lab run by Isaac Larsen. She has been on three trips to collect data, mostly in the Appalachians, a location of which she’s grown fond, because, she explains, “The topography is rugged, the streams are clear and beautiful, and the landscape is saturated with life.”</p> <p>Specifically narrowing to the Tennessee River, Stokes and her collaborators are observing how several populations of the Greenfin darter fish (<em>Nothonotus chlorobranchius</em>) have been separated, possibly as a result of knickpoints, or sharp changes in the slope. Last year, she published a paper in <em>Geophysical Research Letters</em> that predicts a rerouting of the upper Rio Orinoco into the Rio Negro in the Amazon River basin, which is summarized in a <a href="">blog post</a> on the website of the American Geophysical Union.</p> <p>“Stokes’ ambitious project requires a blend of versatility, creativity, determination and intellectual fearlessness. I think she has that rare combination of talents,” says Perron. In order to explore the scope of her research fully, Stokes expanded her resources beyond MIT, successfully applying for funding to take short courses and field courses to achieve her research goals.</p> <p>“I love the intellectual freedom that’s been awarded to me [at MIT]. It’s made my PhD feel authentic, exciting, and very much mine. I think that the culture of intellectual independence is strong at MIT, and it’s very motivating to be around,” says Stokes. She’s grateful to have received research support from MIT’s Office of Graduate Education as a <a href="" target="_blank">Hugh Hampton Young Fellow</a> and through a fellowship from the <a href="" target="_blank">MIT Martin Family Society of Fellows for Sustainability</a>.</p> <p>Hoping to continue to investigate these questions long after her PhD, Stokes plans to become a professor of the history of the Earth and how it influences the evolution of life. MIT has provided Stokes the opportunity to build her teaching skills as a teaching assistant for incoming undergraduates at Yellowstone National Park on four occasions. Explaining the volcanic and natural history of the area, she reveled in the chance to entice new students to delve into the study of the wonderful and constantly evolving Earth. Stokes was recognized with an <a href="">Award for Excellence in Teaching</a> in EAPS earlier this year.</p> <p>Stokes’s leadership skills also led her to serve as president for the EAPS Student Advisory Council (ESAC), and to help start an initiative for a universal first-year course for all EAPS graduate students. She also worked on an initiative started by her fellow EAPS graduate student Eva Golos to allow students to provide input on faculty searches. Recently, she was honored at the MIT Office of Graduate Education’s 2019 celebration of <a href="">Graduate Women of Excellence</a>, nominated by her peers and one of three in EAPS selected based on “their exemplary leadership through example and action, service to the Institute, their dedication to mentoring and their drive to make changes to improve the student experience.” When not on trips to muddy waters, Stokes regularly joins EAPS post-work gatherings with trips to the Muddy Charles, MIT’s on-campus bar, forging deep friendships.</p> <p>Stokes still manages to spend most of her time outdoors, teaching, outside the realm of Earth science. She coaches the women’s ultimate frisbee team at MIT and plays on regionally competitive teams in the Boston area. “It’s also allowed me to interact with undergraduate students at MIT through coaching which helps me feel more tapped into the MIT community at large. I’ve learned a lot about teamwork, leadership, and teaching from the sport,” she says.</p> <p>Stokes’ advisor speculates that she will continue to stand out after she graduates with her doctorate from MIT. “She has demonstrated strong commitments to teaching undergraduates and communicating science to the public,” says Perron. “I expect that she will be a leading researcher in science working at the intersection of the physical environment and biological diversity.”</p> MIT geomorphology graduate student Maya Stokes performed fieldwork in the Chilean Altiplano in 2016. She assisted fellow MIT PhD student Christine Y. Chen with her thesis work studying the history of lakes and the paleoclimate of South America. Photo courtesy of Christine Y. ChenStudents, Graduate, postdoctoral, School of Science, EAPS, Earth and atmospheric sciences, Athletics, Student life, Leadership, Profile, Geology, Evolution, Biology, Ecology Using recent gene flow to define microbe populations New method identifies ecologically and medically relevant bacteria groups. Thu, 08 Aug 2019 10:59:59 -0400 Becky Ham | MIT News correspondent <p>Identifying species among plants and animals has been a full-time occupation for some biologists, but the task is even more daunting for the myriad microbes that inhabit the planet. Now, MIT researchers have developed a simple measurement of gene flow that can define ecologically important populations among bacteria and archaea, including pinpointing populations associated with human diseases.</p> <p>The gene flow metric separates co-existing microbes in genetically and ecologically distinct populations, Martin Polz, a professor of civil and environmental engineering at MIT, and colleagues write in the August 8 issue of <em>Cell.</em></p> <p>Polz and his colleagues also developed a method to identify parts of the genome in these populations that show different adaptations that can be mapped onto different environments. When they tested their approach on a gut bacterium, for instance, they were able to determine that different populations of the bacteria were associated with healthy individuals and patients with Crohn’s disease.</p> <p>Biologists often call a group of plants or animals a species if the group is reproductively isolated from others — that is, individuals in the group can reproduce with each other, but they can’t reproduce with others. As a result, members of a species share a set of genes that differs from other species. Much of evolutionary theory centers on species and populations, the representatives of a species in a particular area.</p> <p>But microbes “defy the classic species concept for plants and animals,” Polz explains. Microbes tend to reproduce asexually, simply splitting themselves in two rather than combining their genes with other individuals to produce offspring. Microbes are also notorious for “taking up DNA from environmental sources, such as viruses,” he says. “Viruses can transfer DNA into microbial cells and that DNA can be incorporated into their genomes.”</p> <p>These processes make it difficult to sort coexisting microbes into distinct populations based on their genetic makeup. “If we can’t identify those populations in microbes, we can’t one-to-one apply all this rich ecological and evolutionary theory that has been developed for plants and animals to microbes,” says Polz.</p> <p>If researchers want to measure an ecosystem’s resilience in the face of environmental change, for instance, they might look at how populations within species change over time. “If we don’t know what a species is, it’s very difficult to measure and assess these types of perturbations,” he adds.</p> <p>Christopher Marx, a microbiologist at the University of Idaho who was not part of the <em>Cell </em>study, says he and his colleagues “will immediately apply” the MIT researchers’ approach to their own work. “We can use this to answer the question, ‘What should we define as an ecologically important unit?’”</p> <p><strong>A yardstick for gene flow</strong></p> <p>Martin and his colleagues decided to look for another way to define ecologically meaningful populations in microbes. Led by microbiology graduate student Philip Arevalo, the researchers developed a metric of gene flow that they called PopCOGenT (Populations as Clusters Of Gene Transfer).</p> <p>PopCOGenT measures recent gene flow or gene transfer between closely related genomes. In general, microbial genomes that have exchanged DNA recently should share longer and more frequent stretches of identical DNA than if individuals were just reproducing by splitting their DNA in two. Without this sort of recent exchange, the researchers suggested, the length of these shared stretches of identical DNA would shorten as mutations insert new “letters” into the stretch.</p> <p>Two microbial strains that are not genetically identical to each other but share sizable “chunks” of identical DNA are probably exchanging more genetic material with each other than with other strains. This gene flow measurement can define distinct microbial populations, as the researchers discovered in their tests of three different kinds of bacteria.</p> <p>In <em>Vibrio</em> bacteria, for instance, closely related populations may share some core gene sequences, but they appear completely isolated from each other when viewed through this measurement of recent gene flow, Polz and colleagues found.</p> <p>Polz says that the PopCOGenT method may work better at defining microbial populations than previous studies because it focuses on recent gene flow among closely related organisms, rather than including gene flow events that may have happened thousands of years in the past.</p> <p>The method also suggests that while microbes are constantly taking in different DNA from their environment that might obscure patterns of gene flow, “it may be that this divergent DNA is really removed by selection from populations very quickly,” says Polz.</p> <p><strong>The reverse ecology approach</strong></p> <p>Microbiology graduate student David VanInsberghe then suggested a “reverse ecology” approach that could identify regions of the genome in these newly defined populations that show “selective sweeps” — places where DNA variation is reduced or eliminated, likely as a result of strong natural selection for a particular beneficial genetic variant.</p> <p>By identifying specific sweeps within populations, and mapping the distribution of these populations, the method can reveal possible adaptations that drive microbes to inhabit a particular environment or host — without any prior knowledge of their environment. When the researchers tested this approach in the gut bacterium <em>Ruminococcus gnavus</em>, they uncovered separate populations of the microbe associated with healthy people and patients with Crohn’s disease.</p> <p>Polz says the reverse ecology method is likely to be applied in the near future to studying the full diversity of the bacteria that inhabit the human body. “There is a lot of interest in sequencing closely related organisms within the human microbiome and looking for health and disease associations, and the datasets are growing.”</p> <p>He hopes to use the approach to examine the “flexible genome” of microbes. Strains of <em>E. coli</em> bacteria, for instance, share about 40 percent of their genes in a “core genome,” while the other 60 percent — the flexible part — varies between strains. “For me, it’s one of the biggest questions in microbiology: Why are these genomes so diverse in gene content?” Polz explains. “Once we can define populations as evolutionary units, we can interpret gene frequencies in these populations in light of evolutionary processes.”</p> <p>Polz and colleagues’ findings could increase estimates of microbe diversity, says Marx. “What I think is really cool about this approach from Martin’s group is that they actually suggest that the complexity that we see is even more complex than we’re giving it credit for. There may be even more types that are ecologically important out there, things that if they were plants and animals we would be calling them species.”</p> <p>Other MIT authors on the paper include Joseph Elsherbini and Jeff Gore. The research was supported, in part, by the National Science Foundation and the Simons Foundation.</p> A microscopic image of mixed bacteria from environmental samples. MIT researchers have developed a gene flow measurement that defines ecologically important populations of microbes.Image: David VanInsbergheResearch, Civil and environmental engineering, School of Science, School of Engineering, Microbes, Bacteria, Evolution, National Science Foundation (NSF) Study furthers radically new view of gene control Along the genome, proteins form liquid-like droplets that appear to boost the expression of particular genes. Thu, 08 Aug 2019 10:59:59 -0400 Anne Trafton | MIT News Office <p>In recent years, MIT scientists have developed a new model for how key genes are controlled that suggests the cellular machinery that transcribes DNA into RNA forms specialized droplets called condensates. These droplets occur only at certain sites on the genome, helping to determine which genes are expressed in different types of cells.</p> <p>In a new study that supports that model, researchers at MIT and the Whitehead Institute for Biomedical Research have discovered physical interactions between proteins and with DNA that help explain why these droplets, which stimulate the transcription of nearby genes, tend to cluster along specific stretches of DNA known as super enhancers. These enhancer regions do not encode proteins but instead regulate other genes.</p> <p>“This study provides a fundamentally important new approach to deciphering how the ‘dark matter’ in our genome functions in gene control,” says Richard Young, an MIT professor of biology and member of the Whitehead Institute.</p> <p>Young is one of the senior authors of the paper, along with Phillip Sharp, an MIT Institute Professor and member of MIT’s Koch Institute for Integrative Cancer Research; and Arup K. Chakraborty, the Robert T. Haslam Professor in Chemical Engineering, a professor of physics and chemistry, and a member of MIT’s Institute for Medical Engineering and Science and the Ragon Institute of MGH, MIT, and Harvard.</p> <p>Graduate student Krishna Shrinivas and postdoc Benjamin Sabari are the lead authors of the paper, which appears in <em>Molecular Cell </em>on Aug. 8.</p> <p><strong>“A biochemical factory”</strong></p> <p>Every cell in an organism has an identical genome, but cells such as neurons or heart cells express different subsets of those genes, allowing them to carry out their specialized functions. Previous research has shown that many of these genes are located near super enhancers, which bind to proteins called transcription factors that stimulate the copying of nearby genes into RNA.</p> <p>About three years ago, Sharp, Young, and Chakraborty joined forces to try to model the interactions that occur at enhancers. In a 2017 <em>Cell</em> paper, based on computational studies, they hypothesized that in these regions, transcription factors form droplets called phase-separated condensates. Similar to droplets of oil suspended in salad dressing, these condensates are collections of molecules that form distinct cellular compartments but have no membrane separating them from the rest of the cell.</p> <p>In a 2018 <em>Science</em> paper, the researchers showed that these <a href="">dynamic droplets</a> do form at super enhancer locations. Made of clusters of transcription factors and other molecules, these droplets attract enzymes such as RNA polymerases that are needed to copy DNA into messenger RNA, keeping gene transcription active at specific sites.</p> <p>“We had demonstrated that the transcription machinery forms liquid-like droplets at certain regulatory regions on our genome, however we didn't fully understand how or why&nbsp;these dewdrops of biological molecules only seemed to condense around specific points on our genome,” Shrinivas says.</p> <p>As one possible explanation for that site specificity, the research team hypothesized that weak interactions between intrinsically disordered regions of transcription factors and other transcriptional molecules, along with specific interactions between transcription factors and particular DNA elements, might determine whether a condensate forms at a particular stretch of DNA. Biologists have traditionally focused on “lock-and-key” style interactions between rigidly structured protein segments to explain most cellular processes, but more recent evidence suggests that weak interactions between floppy protein regions also play an important role in cell activities.</p> <p>In this study, computational modeling and experimentation revealed that the cumulative force of these weak interactions conspire together with transcription factor-DNA interactions to determine whether a condensate of transcription factors will form at a particular site on the genome. Different cell types produce different transcription factors, which bind to different enhancers. When many transcription factors cluster around the same enhancers, weak interactions between the proteins are more likely to occur. Once a critical threshold concentration is reached, condensates form.</p> <p>“Creating these local high concentrations within the crowded environment of the cell enables the right material to be in the right place at the right time to carry out the multiple steps required to activate a gene,” Sabari says. “Our current study begins to tease apart how certain regions of the genome are capable of pulling off this trick.”</p> <p>These droplets form on a timescale of seconds to minutes, and they blink in and out of existence depending on a cell’s needs.</p> <p>“It’s an on-demand biochemical factory that cells can form and dissolve, as and when they need it,” Chakraborty says. “When certain signals happen at the right locus on a gene, the condensates form, which concentrates all of the transcription molecules. Transcription happens, and when the cells are done with that task, they get rid of them.”</p> <p>“A functional condensate has to be more than the sum of its parts, and how the protein and DNA components work together is something we don't fully understand,” says Rohit Pappu, director of the Center for Science and&nbsp;Engineering of Living Systems at Washington University, who was not involved in the research. “This work gets us on the road to thinking about the interplay among protein-protein, protein-DNA, and possibly DNA-DNA interactions as determinants of the outputs of condensates.”</p> <p><strong>A new view</strong></p> <p>Weak cooperative interactions between proteins may also play an important role in evolution, the researchers proposed in a 2018 <em>Proceedings of the National Academy of Sciences</em> paper. The sequences of intrinsically disordered regions of transcription factors need to change only a little to evolve new types of specific functionality. In contrast, evolving new specific functions via “lock-and-key” interactions requires much more significant changes.</p> <p>“If you think about how biological systems have evolved, they have been able to respond to different conditions without creating new genes. We don’t have any more genes that a fruit fly, yet we’re much more complex in many of our functions,” Sharp says. “The incremental expanding and contracting of these intrinsically disordered domains could explain a large part of how that evolution happens.”</p> <p>Similar condensates appear to play a variety of other roles in biological systems, offering a new way to look at how the interior of a cell is organized. Instead of floating through the cytoplasm and randomly bumping into other molecules, proteins involved in processes such as relaying molecular signals may transiently form droplets that help them interact with the right partners.</p> <p>“This is a very exciting turn in the field of cell biology,” Sharp says. “It is a whole new way of looking at biological systems that is richer and more meaningful.”</p> <p>Some of the MIT researchers, led by Young, have&nbsp;helped form&nbsp;a company called <a href="">Dewpoint Therapeutics</a> to develop potential treatments for&nbsp;a wide variety of diseases&nbsp;by&nbsp;exploiting&nbsp;cellular condensates. There is emerging evidence that cancer cells use condensates to control sets of genes that promote cancer, and condensates have also been linked to neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) and Huntington’s disease.</p> <p>The research was funded by the National Science Foundation, the National Institutes of Health, and the Koch Institute Support (core) Grant from the National Cancer Institute.</p> MIT researchers have developed a new model of gene control, in which the cellular machinery that transcribes DNA into RNA forms specialized droplets called condensates.Image: Steven H. LeeResearch, Chemical engineering, Biology, DNA, Genetics, Cancer, Evolution, Koch Institute, Whitehead Institute, Institute for Medical Engineering and Science (IMES), School of Engineering, School of Science, National Science Foundation (NSF), National Institutes of Health (NIH) Professor Emeritus Samuel Bowring, pioneering geologist and expert in geochronology, dies at 65 A professor and mentor for more than 20 years at MIT, Bowring redefined our understanding of some of the most significant events in Earth history. Tue, 30 Jul 2019 15:50:01 -0400 Jennifer Fentress | EAPS <p>Professor Emeritus Samuel A. Bowring, a longtime MIT professor of geology, died on July 17 at age 65.</p> <p>Known for his exceptional skill as a field geologist and for innovatons in uranium-lead isotopic geochronology, Bowring worked to achieve unprecedented analytical precision and accuracy in calibrating the geologic record and reconstructing the co-evolution of life and the solid Earth.</p> <p><strong>No dates, no rates</strong></p> <p>A favorite aphorism, “No dates, no rates,” appeared in many of Bowring’s lectures and talks — meaning, to fully understand the past events preserved in the rock record you have to understand their timing. One of his earliest major contributions, which transformed what geologist know about the early evolution of the Earth, was his work in the 1980s on the Acasta gneiss complex, a rock body in northwestern Canada, pushing back the date of the oldest-known rocks to 4.03 billion years. The granitic samples he collected from an outcrop on an island in the remote Acasta River basin turned out to be rare remnants of the Earth’s earliest crust. &nbsp;</p> <p>“What is more important about the Acasta gneiss complex than its 4.03 billion year age alone is its character, which Sam recognized and documented,” said Paul Hoffman, Harvard University Sturgis Hooper Professor Emeritus of Geology and career-long Bowring collaborator and friend. Hoffman explains that the Acasta rocks, paired with Bowring’s advocacy, fundamentally changed geologists’ understanding of continental formation. Prior to Bowring’s work the prevailing view was that the continents had steadily grown over geologic time. But, with these ancient gneiss samples, Bowring was able to characterize a complex history which predated the moment of their crystallization, which points instead to a process of ongoing crustal “recycling” — where rock near the Earth’s surface, through the mechanisms of plate tectonics, is subsumed and transformed by the mantle’s convective currents. According to Hoffman, “Sam’s fascination with the creation and preservation of continental crust never left him, whether he was at Great Bear Lake, the Grand Canyon, or the High Cascades in Washington State.”</p> <p>Beyond studying the physical processes which shape the lithosphere, Bowring also sought to understand those which shape the biosphere. His work on sedimentary layers of the Precambrian/Cambrian boundary age determined the timing and rate of the pivotal biological event known as the Cambrian Explosion, beginning nearly 540 million years ago. He was able to establish that the Early Cambrian period which saw the most dramatic burst of evolutionary activity and animal diversity ever known — including the first emergence of chordates, brachiopods, and arthropods — spanned not 10 to 50 million years as was previously-believed, but instead lasted a mere 5 to 6 million years.</p> <p>Longtime friend and colleague Tim Grove, the Robert R. Shrock Professor of Earth and Planetary Sciences at MIT, wrote of the achievement in a citation for the American Geophysical Union when Bowring was awarded the Walter H. Bucher Medal in 2016: “Sam showed that during this brief time interval more phyla than have ever since existed on Earth came into existence. This represents a truly profound and astonishing new discovery about how life evolved on Earth.”</p> <p>Bowring also established the timing and duration of what has come to be known as “The Great Dying”: the largest of Earth’s five major mass extinctions, which marked the end of the Permian period and saw the elimination of over 96% of marine species and about 70% of species on land. Rocks collected by Bowring and collaborators from sites across China spanning the Permian-Triassic boundary revealed that the ecological collapse happened at breakneck speed — occurring in less than 30,000 years at a rate many times faster than previous estimates — and with little-to-no warning in geological terms.</p> <p>A world-expert in uranium-lead isotopic dating, by 2002 Bowring began to see what he later termed “the double-edged sword of high-precision geochronology.” As the field experienced rapid advancements in precision, resolution, and quantitative stratigraphic analyses, many new techniques were developing in parallel. He recognized that without calibration and intercalibration of radioisotopic dating methods and quantitative chronostratigraphy, their accuracy and capacity as individual tools for understanding deep time were diminished. In response, he and colleague Doug Erwin conceived the EARTHTIME Initiative, a community-based effort to foster collaboration across the disciplines and eliminate inter-laboratory and inter-technique biases. Bowring’s common refrain to members to “check our egos at the door” reflected his unwavering goal to push the accuracy of geochronology to new levels, and helped the initiative build consensus and develop best practices and protocols. EARTHTIME continues to lead international workshops, expanding beyond topics of calibration and standardization to engage with the broader geoscience community, seeking to understand the rock record in ever more refined and nuanced ways.</p> <p>“If the art of geochronology is the rendering of dates in their proper geologic context, Sam is our&nbsp;Michelangelo,” former MIT Department of Earth, Atmospheric and Planetary Sciences (EAPS) department head and close friend and colleague Tom Jordan said of Bowring. “He has always insisted that knowing what you are dating and why are as important as fixing the date itself; that the precision of absolute dating is most powerful when samples can be placed precisely in section.”</p> <p>Bowring’s interest in the applications of tracer isotopes to examine Earth systems also extended to their utility in tracking environmental contaminants. His lab has developed methods for not only tracing naturally-occurring sources and establishing natural regional baselines, but also for documenting variations which correlate with anthropogenic inputs associated with urbanization and industrialization.</p> <p><strong>A dedicated teacher and mentor</strong></p> <p>Bowring joined the faculty of EAPS at MIT in 1991 where, in addition to fostering the careers of over two dozen graduate students and postdocs, he demonstrated a career-long commitment to advancing undergraduate education. For more than 20 years Bowring served as a first-year and undergraduate advisor, eventually being named a Margaret MacVicar Faculty Fellow in 2006 by the Institute program which recognizes faculty for, “exemplary and sustained contributions to the teaching and education of undergraduates at MIT,” and later earning the MIT Everett Moore Baker Memorial Award for Excellence in Undergraduate Teaching in 2007. He was also deeply involved in helping to shape curricula, serving on the MIT Committee on Curriculum from 2007 to 2010. He also served as chair of the EAPS Program in Geology and Geochemistry from 1999 until 2002, at which time he became chair of the EAPS Undergraduate Committee, serving until 2015. As a field geologist, he took his keen interest in engaging students to off-campus venues, leading annual trips into the field which were fixtures in the department’s calendar — from western Massachusetts to Yellowstone to the Las Vegas desert.</p> <p>“Sam was an exceptionally effective and dedicated undergraduate educator, having gone well ‘above and beyond’ for EAPS and our students,” recalls Grove. “He took on more undergraduate teaching than any other member of our department in the last 25 years and was deeply committed to the importance of training undergraduates in the field — providing students with hands-on experience and using real-world geology to inspire and teach fundamentals.”</p> <p>Bowring also was instrumental in guiding Terrascope, a first-year learning community created jointly by EAPS and the Department of Civil and Environmental Engineering in 2002. Bowring became associate director of the program in 2006, going on to serve as director from 2008 to 2015. The nationally-recognized program, which has been the subject of several academic papers and has grown to become one of MIT’s largest first-year communities, asks students with diverse research interests to tackle complex, global problems involving sustainability, climate, and the Earth system in a series of team-oriented, student-driven classes. In 2013, Bowring and his coauthors described the innovative curriculum by saying, “Our emphasis is on using a multidisciplinary approach to show that understanding the geosciences … is important to the students' world view, whether they know it or not. We believe it is our responsibility to teach as many students as we can about the Earth system, and in our experience, Terrascope students have a greatly expanded consciousness about the Earth and humans’ effect on it.”</p> <p>Born in Portsmouth, New Hampshire, on Sept. 27, 1953, Bowring was raised in Durham, New Hampshire, where he also later attended the University of New Hampshire. After graduating in 1976 with a bachelor’s degree in geology, he went on to study at the New Mexico Institute of Mining and Technology, where he earned a master’s in 1980.</p> <p>At the University of Kansas, Bowring had the opportunity early on to work with PhD advisor Randall Van Schmus on a project in the Northwest Territories of Canada (NWT) — where he was first introduced to collaborator Hoffman — which laid the foundation for both his PhD and continuing studies in the NWT’s Proterozozoic Wopmay orogen after joining the faculty at Washington University in St. Louis (WU) in 1984. It was as an assistant professor at WU that Bowring made his seminal analysis of the Acasta gneiss from the region, along with Ian Williams from the Australian National University.</p> <p>In addition to being named a member of the National Academy of Sciences and the American Academy for the Advancement of Science, Bowring, the&nbsp;Robert R. Schrock Emeritus Professor of Geology, was a fellow of the American Geophysical Union and was recognized by the organization with both the Norman L. Bowen Award and Walter H. Bucher Medal. He was also a fellow of both the Geochemical Society and the Geological Society of America.</p> <p>He is survived by his wife of 30 years, Kristine M. (Fox) Bowring, two stepdaughters, Kelley Kintner and Sara Henrick, as well as his siblings, James Bowring, Joseph Bowring, and Margaret Ann Bowring-Price. At the family’s request, there will be no formal services.</p> Sam Bowring is seen leading the annual EAPS geology field trip to western Massachusetts, explaining the complex history preserved in the rock record there, from dinosaur footprints and Triassic fossils to the 14,000-year-old scars left by the last ice age.Photo: Helen HillFaculty, EAPS, Obituaries, Terrascope, Geology, Evolution, School of Science Uncovering the riches of traditional global medicine Researchers solve how the kava plant produces its pain-relieving and anti-anxiety molecules, demonstrate an extensible method to scale and optimize production. Tue, 23 Jul 2019 11:00:01 -0400 Greta Friar | Whitehead Institute <p>Kava (<em>Piper methysticum</em>) is a plant native to the Polynesian islands that people there have used in a calming drink of the same name in religious and cultural rituals for thousands of years. The tradition of cultivating kava and drinking it during important gatherings is a cultural cornerstone shared throughout much of Polynesia, although the specific customs — and the strains of kava — vary from island to island. Over the past few decades, kava has been gaining interest outside of the islands for its pain-relief and anti-anxiety properties as a potentially attractive alternative to drugs like opioids and benzodiazepines because kavalactones, the molecules of medicinal interest in kava, use slightly different mechanisms to affect the central nervous system and appear to be non-addictive. Kava bars have been springing up around the United States, kava supplements and teas lining the shelves at stores like Walmart, and sports figures in need of safe pain relief are touting its benefits.</p> <p>This growing usage suggests that there would be a sizeable market for kavalactone-based medical therapies, but there are roadblocks to development: for one, kava is hard to cultivate, especially outside of the tropics. Kava takes years to reach maturity and, as a domesticated species that no longer produces seeds, it can only be propagated using cuttings. This can make it difficult for researchers to get a large enough quantity of kavalactones for investigations or clinical trials.</p> <p>Now, research from Whitehead Institute member and MIT associate professor of biology <a href="">Jing-Ke Weng</a>&nbsp;and postdoc Tomáš&nbsp;Pluskal, <a href="" target="_blank">published online in&nbsp;<em>Nature Plants</em></a> July 22, describes a way to solve that problem, as well as to create kavalactone variants not found in nature that may be more effective or safer as therapeutics.</p> <div class="cms-placeholder-content-video"></div> <p>“We’re combining historical knowledge of this plant’s medicinal properties, established through centuries of traditional usage, with modern research tools in order to potentially develop new drugs,” Pluskal says.</p> <p>Weng’s lab has shown that if researchers figure out the genes behind a desirable natural molecule — in this case, kavalactones — they can clone those genes, insert them into species like yeast or bacteria that grow quickly and are easier to maintain in a variety of environments than a temperamental tropical plant, and then get these microbial bio-factories to mass produce the molecule. In order to achieve this, first Weng and Pluskal had to solve a complicated puzzle: How does kava produce kavalactones? There is no direct kavalactone gene; complex metabolites like kavalactones are created through a series of steps using intermediate molecules. Cells can combine these intermediates, snip out parts of them, and add bits onto them to create the final molecule — most of which is done with the help of enzymes, cells’ chemical reaction catalysts. So, in order to recreate kavalactone production, the researchers had to identify the complete pathway plants use to synthesize it, including the genes for all of the enzymes involved.</p> <p>The researchers could not use genetic sequencing or common gene editing tools to identify the enzymes because the kava genome is huge; it has 130 chromosomes compared to humans’ 46. Instead they turned to other methods, including sequencing the plant’s RNA to survey the genes expressed, to identify the biosynthetic pathway for kavalactones.</p> <p>“It’s like you have a lot of Lego pieces scattered on the floor,” Weng says, “and you have to find the ones that fit together to build a certain object.”</p> <p>Weng and Pluskal had a good starting point: They recognized that kavalactones had a similar structural backbone to chalcones, metabolites shared by all land plants. They hypothesized that one of the enzymes involved in producing kavalactones must be related to the one involved in producing chalcones, chalcone synthase (CHS). They looked for genes encoding similar enzymes and found two synthases that had evolved from an older CHS gene. These synthases, which they call&nbsp;<em>Pm</em>SPS1 and&nbsp;<em>Pm</em>SPS2, help to shape the basic scaffolding of kavalactones molecules.</p> <p>Then, with some trial and error, Pluskal found the genes encoding a number of the tailoring enzymes that modify and add to the molecules’ backbone to create a variety of specific kavalactones. In order to test that he had identified the right enzymes, Pluskal cloned the relevant genes and confirmed that the enzymes they encode produced the expected molecules. The team also identified key enzymes in the biosynthetic pathway of flavokavains, molecules in kava that are structurally related to kavalactones and have been shown in studies to have anti-cancer properties.</p> <p>Once the researchers had their kavalactone genes, they inserted them into bacteria and yeast to begin producing the molecules. This proof of concept for their microbial bio-factory model demonstrated that using microbes could provide a more efficient and scalable production vehicle for kavalactones. The model could also allow for the production of novel molecules engineered by combining kava genes with other genes so the microbes would produce modified kavalactones. This could allow researchers to optimize the molecules for efficiency and safety as therapeutics.</p> <p>“There’s a very urgent need for therapies to treat mental disorders, and for safer pain relief options,” Weng says. “Our model eliminates several of the bottlenecks in drug development from plants by increasing access to natural medicinal molecules and allowing for the creation of new-to-nature molecules.”</p> <p>Kava is only one of many plants around the world containing unique molecules that could be of great medicinal value. Weng and Pluskal hope that their model — combining the use of drug discovery from plants used in traditional medicine, genomics, synthetic biology, and microbial mass production — will be used to better harness the great diversity of plant chemistry around the world in order to help patients in need.</p> <p>This work was supported by grants from the Smith Family Foundation, Edward N. and Della L. Thome Memorial Foundation, the Family Larsson-Rosenquist Foundation, and the National Science Foundation. Tomáš&nbsp;Pluskal is a Simons Foundation Fellow of the Helen Hay Whitney Foundation. Jing-Ke Weng is supported by the Beckman Young Investigator Program, Pew Scholars Program in the Biomedical Sciences, and the Searle Scholars Program.</p> Kava plantsImage: Randy TravisWhitehead Institute, Biology, School of Science, Evolution, Genetics, Mental health, National Science Foundation (NSF), Research, Health, Plants Genetic study takes research on sex differences to new heights Differences in male and female gene expression, including those contributing to height differences, found throughout the body in humans and other mammals. Thu, 18 Jul 2019 14:00:00 -0400 Greta Friar | Whitehead Institute <p>Throughout the animal kingdom, males and females frequently exhibit sexual dimorphism: differences in characteristic traits that often make it easy to tell them apart. In mammals, one of the most common sex-biased traits is size, with males typically being larger than females. This is true in humans: Men are, on average, taller than women. However, biological differences among males and females aren’t limited to physical traits like height. They’re also common in disease. For example, women are much more likely to develop autoimmune diseases, while men are more likely to develop cardiovascular diseases.</p> <p>In spite of the widespread nature of these sex biases, and their significant implications for medical research and treatment, little is known about the underlying biology that causes sex differences in characteristic traits or disease. In order to address this gap in understanding, Whitehead Institute Director&nbsp;<a href="">David Page</a>&nbsp;has transformed the focus of his lab in recent years from studying the X and Y sex chromosomes to working to understand the broader biology of sex differences throughout the body. In a paper published in&nbsp;<em>Science</em>, Page, a professor of biology at MIT and a Howard Hughes Medical Institute investigator; Sahin Naqvi, first author and former MIT graduate student (now a postdoc at Stanford University); and colleagues present the results of a wide-ranging investigation into sex biases in gene expression, revealing differences in the levels at which particular genes are expressed in males versus females.</p> <div class="cms-placeholder-content-video"></div> <p>The researchers’ findings span 12 tissue types in five species of mammals, including humans, and led to the discovery that a combination of sex-biased genes accounts for approximately 12 percent of the average height difference between men and women. This finding demonstrates a functional role for sex-biased gene expression in contributing to sex differences. The researchers also found that the majority of sex biases in gene expression are not shared between mammalian species, suggesting that — in some cases — sex-biased gene expression that can contribute to disease may differ between humans and the animals used as models in medical research.</p> <p>Having the same gene expressed at different levels in each sex is one way to perpetuate sex differences in traits in spite of the genetic similarity of males and females within a species — since with the exception of the 46th&nbsp;chromosome (the Y in males or the second X in females), the sexes share the same pool of genes. For example, if a tall parent passes on a gene associated with an increase in height to both a son and a daughter, but the gene has male-biased expression, then that gene will be more highly expressed in the son, and so may contribute more height to the son than the daughter.</p> <p>The researchers searched for sex-biased genes in tissues across the body in humans, macaques, mice, rats, and dogs, and they found hundreds of examples in every tissue. They used height for their first demonstration of the contribution of sex-biased gene expression to sex differences in traits because height is an easy-to-measure and heavily studied trait in quantitative genetics.</p> <p>“Discovering contributions of sex-biased gene expression to height is exciting because identifying the determinants of height is a classic, century-old problem, and yet by looking at sex differences in this new way we were able to provide new insights,” Page says. “My hope is that we and other researchers can repeat this model to similarly gain new insights into diseases that show sex bias."</p> <p>Because height is so well studied, the researchers had access to public data on the identity of hundreds of genes that affect height. Naqvi decided to see how many of those height genes appeared in the researchers’ new dataset of sex-biased genes, and whether the genes’ sex biases corresponded to the expected effects on height. He found that sex-biased gene expression contributed approximately 1.6 centimeters to the average height difference between men and women, or 12 percent of the overall observed difference.</p> <p>The scope of the researchers’ findings goes beyond height, however. Their database contains thousands of sex-biased genes. Slightly less than a quarter of the sex-biased genes that they catalogued appear to have evolved that sex bias in an early mammalian ancestor, and to have maintained that sex bias today in at least four of the five species studied. The majority of the genes appear to have evolved their sex biases more recently, and are specific to either one species or a certain lineage, such as rodents or primates.</p> <p>Whether or not a sex-biased gene is shared across species is a particularly important consideration for medical and pharmaceutical research using animal models. For example, previous research identified certain genetic variants that increase the risk of Type 2 diabetes specifically in women; however, the same variants increase the risk of Type 2 diabetes indiscriminately in male and female mice. Therefore, mice would not be a good model to study the genetic basis of this sex difference in humans. Even when the animal appears to have the same sex difference in disease as humans, the specific sex-biased genes involved might be different. Based on their finding that most sex bias is not shared between species, Page and colleagues urge researchers to use caution when picking an animal model to study sex differences at the level of gene expression.</p> <p>“We’re not saying to avoid animal models in sex-differences research, only not to take for granted that the sex-biased gene expression behind a trait or disease observed in an animal will be the same as that in humans. Now that researchers have species and tissue-specific data available to them, we hope they will use it to inform their interpretation of results from animal models,” Naqvi says.</p> <p>The researchers have also begun to explore what exactly causes sex-biased expression of genes not found on the sex chromosomes. Naqvi discovered a mechanism by which sex-biased expression may be enabled: through sex-biased transcription factors, proteins that help to regulate gene expression. Transcription factors bind to specific DNA sequences called motifs, and he found that certain sex-biased genes had the motif for a sex-biased transcription factor in their promoter regions, the sections of DNA that turn on gene expression. This means that, for example, a male-biased transcription factor was selectively binding to the promoter region for, and so increasing the expression of, male-biased genes — and likewise for female-biased transcription factors and female-biased genes. The question of what regulates the transcription factors remains for further study — but all sex differences are ultimately controlled by either the sex chromosomes or sex hormones.</p> <p>The researchers see the collective findings of this paper as a foundation for future sex-differences research.</p> <p>“We’re beginning to build the infrastructure for a systematic understanding of sex biases throughout the body,” Page says. “We hope these datasets are used for further research, and we hope this work gives people a greater appreciation of the need for, and value of, research into the molecular differences in male and female biology.”</p> <p>This work was supported by Biogen, Whitehead Institute, National Institutes of Health, Howard Hughes Medical Institute, and generous gifts from Brit and Alexander d’Arbeloff and Arthur W. and Carol Tobin Brill.</p> This photo represents the bell curve of women's and men's heights. It was created in 1994 by Linda Strausbaugh, professor of molecular and cell biology at the University of Connecticut.Photo: Linda Strausbaugh/University of ConnecticutWhitehead Institute, School of Science, Biology, Evolution, Genetics, National Institutes of Health (NIH), Research, Animals Featured video: Saving iguanas with science and engineering Professor Otto Cordero and colleagues ask: Can microbiome engineering make the Galapagos marine iguana more resilient to climate change? Wed, 03 Jul 2019 11:40:02 -0400 MIT News Office <div class="cms-placeholder-content-video"></div> <p>All ecosystems around the globe are impacted by the interplay between herbivores and their gut microbes. Strict herbivores such as grazers are dependent on the enzymes produced by their gut microbes to digest the complex plant fibers that constitute their diet. These animals form a symbiotic relationship with their microbes, one that affects ecosystems around the globe because it allows for energy to be transferred from plants to animals.</p> <p>One of the most remarkable examples of this symbiotic relationship is found in the Galapagos islands, where marine iguanas have evolved to graze exclusively on fast-growing algae found on the shores of the archipelago’s island. Unfortunately, specialization comes at a cost: Due to their strict dependency on just one type of algae, these iguanas are highly susceptible to environmental fluctuations that change the type of algae available on the islands. In the past, El Niño events — whose intensity and frequency is exacerbated by climate change — have led to a shift in the algal species, causing up to a 90 percent loss of the iguana population.</p> <p>Associate Professor Otto Cordero of the Department of Civil and Environmental Engineering recently teamed up with researchers from the Universidad San Francisco de Quito and with Professor Itzhak Mizrahi from Ben Gurion University of the Negev. The group hypothesized that the susceptibility of the marine iguanas is caused by a loss of functional diversity in their microbiomes — in other words, that generations of a specialized diet has led to a shift in the iguana gut microbiome, favoring microorganisms that can only digest one type of algae.</p> <p>To test this idea, the team visited the islands and collected samples from various iguana colonies around the archipelago. The group plans to identify the enzymes and the microbes responsible for the algal breakdown, and to study potential microbiome interventions that could expand the iguana diet and enable them to consume other forms of algae. If successful, this would represent a novel strategy for conservation based on microbiome engineering.</p> <p><em>Submitted by: MIT Department of Civil and Environmental Engineering</em> | <em>Video by: Wild Hope Collective </em>|<em> 5 min, 33 sec</em></p> MIT Professor Otto Cordero is researching whether microbiome engineering could make the threatened Galapagos marine iguana more resilient to climate change.Featured video, Ecology, Evolution, Microbes, Animals, Climate change, Microbiology, Civil and environmental engineering, School of Engineering How a declining environment affects populations Study finds that competition between bacterial species can be upended when conditions deteriorate. Mon, 13 May 2019 23:59:59 -0400 Anne Trafton | MIT News Office <p>Stable ecosystems occasionally experience events that cause widespread death — for example, bacteria in the human gut may be wiped out by antibiotics, or ocean life may be depleted by overfishing. A new study from MIT physicists reveals how these events affect dynamics between different species within a community.</p> <p>In their studies, performed in bacteria, the researchers found that a species with a small population size under normal conditions can increase in abundance as conditions deteriorate. These findings are consistent with a theoretical model that had been previously developed but has been difficult to test in larger organisms.</p> <p>“For a single species within a complex community, an increase in mortality doesn’t necessarily mean that the net effect is that you’re going to be harmed. It could be that although the mortality itself is not good for you, the fact that your competitor species are also experiencing an increase in mortality, and they may be more sensitive to it than you are, means that you could do better,” says Jeff Gore, an MIT associate professor of physics and the senior author of the study.</p> <p>The findings in bacteria may also be applicable to larger organisms in real-world populations, which are much more difficult to study because it is usually impossible to control the conditions of the experiment the way researchers can with bacteria growing in a test tube.</p> <p>“We think that this may be happening in complex communities in natural environments, but it’s hard to do the experiments that are necessary to really nail it down. Whereas in the context of the lab, we can make very clear measurements where you see this effect in a very obvious way,” Gore says.</p> <p>Clare Abreu, an MIT graduate student, is the lead author of the study, which appeared in <em>Nature Communications </em>on May 9. Vilhelm Andersen Woltz, an MIT undergraduate, and Jonathan Friedman, a former MIT postdoc, are also authors of the paper.</p> <p><strong>Competition for resources</strong></p> <p>Microbial communities, such as those found in soil, oceans, or the human gut, usually contain thousands of different species. Gore’s lab is interested in studying the factors that determine which species are present in a given environment, and how the composition of those populations affect their functions, whether that’s cycling carbon in the ocean or helping each other resist antibiotic treatment in the gut.</p> <p>By performing controlled experiments in the lab, Gore hopes to learn how different species interact with each other, and to test hypotheses that predict how populations respond to their environment. In 2013, he discovered early signs that warn of <a href="">population collapse</a>, in yeast, and he has also studied how different species of bacteria can <a href="">protect each other</a> against antibiotics.</p> <p>“We’re using experimentally tractable, simple communities to try to determine the principles that determine which species can coexist, and how that changes in different environments,” Gore says.</p> <p>To explore whether these experimental results might be applicable to larger communities, last year Gore and his colleagues published a paper in which they showed that interactions between pairs of species that compete for resources can be used to predict, with about 90 percent accuracy, the outcome when three of the species compete with each other.</p> <p>In the new study, Gore and Abreu decided to see if they could use pairwise interactions to predict how trios of competing species would respond as environmental conditions deteriorate. To simulate this in the lab, the researchers used the process of dilution — that is, discarding a large percentage (ranging from 90 percent to 99.999999 percent) of the population at the end of each day and transferring the remainder to fresh resources. This could be analogous to real-world conditions such as overfishing or loss of habitat.</p> <p>“We’re trying to get at the general question of how an increase in mortality might change the composition of a community,” Gore says.</p> <p>The researchers studied combinations of five species of soil bacteria. In their experiments, in which they tested pairs of species at a time, they found a specific pattern that fit the predictions made by a classical model of species interactions, known as the Lotka-Volterra model.</p> <p>According to this model, declining environmental conditions should favor faster growers. The researchers found that this was the case: Even in conditions where a slower grower originally dominated the population, as the dilution rate was increased, the populations shifted until eventually the faster grower either became the larger fraction of the population or took over completely. The final outcome depends on how strong each competitor is, as well as their relative abundance in the starting population.</p> <p>The researchers also found that the results of the pairwise competitions could accurately predict what would happen when three species grew together in an environment with deteriorating conditions.</p> <p>“This is an exciting advance in our understanding of microbial ecology,” says Sean Gibbons, an assistant professor at the Institute for Systems Biology, who was not involved in the research. “The observation that nonspecific mortality rates can alter competitive outcomes is surprising, although more work needs to be done to understand whether or not dilution is having a more nuanced effect on environmental conditions.”</p> <p><strong>Population models</strong></p> <p>The Lotka-Volterra model analyzed in this study was originally developed for interactions between larger organisms. Such models are easier to test in microbial populations because it is much easier to control experimental conditions for bacteria than for, say, deer living in a forest.</p> <p>“There’s no particular reason to believe that the models are more applicable to microbes than they are to macroorganisms. It’s just that with microbes, we can study hundreds of these communities at a time, and turn the experimental knobs and make clear measurements,” Gore says. “With microorganisms, we can arrive at a clear understanding of when is it that these models are working and when is it that they’re not.”</p> <p>Gore and his students are now studying how specific environmental changes, including changes in temperature and resources, can alter the composition of microbial communities. They are also working on experimentally manipulating populations that include more than two bacterial species.</p> <p>The research was funded, in part, by the National Institutes of Health.</p> MIT researchers have shown that in microbial communities, bacterial species with a small population size under normal conditions can increase in abundance as environmental conditions deteriorate.Research, Physics, Microbes, Bacteria, Ecology, Evolution, School of Science Earliest life may have arisen in ponds, not oceans Study finds shallow bodies of water were probably more suitable for Earth’s first life forms. Fri, 12 Apr 2019 09:59:59 -0400 Jennifer Chu | MIT News Office <p>Primitive ponds may have provided a suitable environment for brewing up Earth’s first life forms, more so than oceans, a new MIT study finds.</p> <p>Researchers report that shallow bodies of water, on the order of 10 centimeters deep, could have held high concentrations of what many scientists believe to be a key ingredient for jump-starting life on Earth: nitrogen.</p> <p>In shallow ponds, nitrogen, in the form of nitrogenous oxides, would have had a good chance of accumulating enough to react with other compounds and give rise to the first living organisms. In much deeper oceans, nitrogen would have had a harder time establishing a significant, life-catalyzing presence, the researchers say.</p> <p>“Our overall message is, if you think the origin of life required fixed nitrogen, as many people do, then it’s tough to have the origin of life happen in the ocean,” says lead author Sukrit Ranjan, a postdoc in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “It’s much easier to have that happen in a pond.”</p> Ranjan and his colleagues have published their results today in the journal <em>Geochemistry, Geophysics, Geosystems.</em> The paper’s co-authors are Andrew Babbin, the Doherty Assistant Professor in Ocean Utilization in EAPS, along with Zoe Todd and Dimitar Sasselov of Harvard University, and Paul Rimmer at Cambridge University. <strong>Breaking a bond</strong></pre> If primitive life indeed sprang from a key reaction involving nitrogen, there are two ways in which scientists believe this could have happened. The first hypothesis involves the deep ocean, where nitrogen, in the form of nitrogenous oxides, could have reacted with carbon dioxide bubbling forth from hydrothermal vents, to form life’s first molecular building blocks. </pre> The second nitrogen-based hypothesis for the origin of life involves RNA — ribonucleic acid, a molecule that today helps encode our genetic information. In its primitive form, RNA was likely a free-floating molecule. When in contact with nitrogenous oxides, some scientists believe, RNA could have been chemically induced to form the first molecular chains of life. This process of RNA formation could have occurred in either the oceans or in shallow lakes and ponds. Nitrogenous oxides were likely deposited in bodies of water, including oceans and ponds, as remnants of the breakdown of nitrogen in Earth’s atmosphere. Atmospheric nitrogen consists of two nitrogen molecules, linked via a strong triple bond, that can only be broken by an extremely energetic event — namely, lightning.</pre> “Lightning is like a really intense bomb going off,” Ranjan says. “It produces enough energy that it breaks that triple bond in our atmospheric nitrogen gas, to produce nitrogenous oxides that can then rain down into water bodies.”</pre> <p>Scientists believe that there could have been enough lightning crackling through the early atmosphere to produce an abundance of nitrogenous oxides to fuel the origin of life in the ocean. Ranjan says scientists have assumed that this supply of lightning-generated nitrogenous oxides was relatively stable once the compounds entered the oceans.</p> <p>However, in this new study, he identifies two significant “sinks,” or effects that could have destroyed a significant portion of nitrogenous oxides, particularly in the oceans. He and his colleagues looked through the scientific literature and found that nitrogenous oxides in water can be broken down via interactions with the sun’s ultraviolet light, and also with dissolved iron sloughed off from primitive oceanic rocks.</p> <p>Ranjan says both ultraviolet light and dissolved iron could have destroyed a significant portion of nitrogenous oxides in the ocean, sending the compounds back into the atmosphere as gaseous nitrogen.</p> <p>“We showed that if you include these two new sinks that people hadn’t thought about before, that suppresses the concentrations of nitrogenous oxides in the ocean by a factor of 1,000, relative to what people calculated before,” Ranjan says.</p> <p><strong>“Building a cathedral”</strong></p> <p>In the ocean, ultraviolet light and dissolved iron would have made nitrogenous oxides far less available for synthesizing living organisms. In shallow ponds, however, life would have had a better chance to take hold. That’s mainly because ponds have much less volume over which compounds can be diluted. As a result, nitrogenous oxides would have built up to much higher concentrations in ponds. Any “sinks,” such as UV light and dissolved iron, would have had less of an effect on the compound’s overall concentrations.&nbsp;</p> <p>Ranjan says the more shallow the pond, the greater the chance nitrogenous oxides would have had to interact with other molecules, and particularly RNA, to catalyze the first living organisms.</p> <p>“These ponds could have been from 10 to 100 centimeters deep, with a surface area of tens of square meters or larger,” Ranjan says. “They would have been similar to Don Juan Pond in Antarctica today, which has a summer seasonal depth of about 10 centimeters.”</p> <p>That may not seem like a significant body of water, but he says that’s precisely the point: In environments any deeper or larger, nitrogenous oxides would simply have been too diluted, precluding any participation in origin-of-life chemistry. Other groups have estimated that, around 3.9 billion years ago, just before the first signs of life appeared on Earth, there may have been about 500 square kilometers of shallow ponds and lakes worldwide.</p> <p>“That’s utterly tiny, compared to the amount of lake area we have today,” Ranjan says. “However, relative to the amount of surface area prebiotic chemists postulate is required to get life started, it’s quite adequate.”</p> <p>The debate over whether life originated in ponds versus oceans is not quite resolved, but Ranjan says the new study provides one convincing piece of evidence for the former.</p> <p>“This discipline is less like knocking over a row of dominos, and more like building a cathedral,” Ranjan says. “There’s no real ‘aha’ moment. It’s more like building up patiently one observation after another, and the picture that’s emerging is that overall, many prebiotic synthesis pathways seem to be chemically easier in ponds than oceans.”</p> <p>This research was supported, in part, by the Simons Foundation and MIT.</p> Don Juan Pond in Antarctica.Image: Flickr, Pierre RoudierBiology, Chemistry, Evolution, EAPS, Earth and atmospheric sciences, Environment, Planetary science, Research, School of Science, RNA Keeping genetic engineering localized Researchers are developing a so-called &quot;daisy-chain&quot; gene-drive system that provides controls for genetic engineering of certain populations. Tue, 02 Apr 2019 17:00:01 -0400 Helen Knight | MIT Media Lab <p>Genetic engineering tools that spread genes within&nbsp;a target species have the potential to humanely control harmful pests as well as eradicate parasitic diseases such as malaria.</p> <p>The tools, known as gene drives, ensure that engineered organisms transmit desired genetic variants to their offspring. These variants could ensure, for example, that the organisms only produce male offspring, or sterile females.</p> <p>In this way, gene drives could be used to exterminate insects such as mosquitoes that carry pathogens, and that can spread malaria, dengue, and the Zika virus. Gene drives could also be used to control invasive species such as rodents that can threaten the survival of native animals.</p> <div class="cms-placeholder-content-video"></div> <p>However, previously described versions of gene drives based on the CRISPR genome editing system have the potential to spread far wider than their intended local population — to affect an entire species. The affects&nbsp;could also spread across international boundaries, potentially leading to disputes between countries where no prior agreement had been made.</p> <p>These types of concerns could significantly delay, if not altogether&nbsp;prevent, the safe testing and introduction of the technology.</p> <p>Now, in a paper published today in the&nbsp;<em>Proceedings of the National Academy of Sciences</em>, researchers at MIT and Harvard University describe a gene drive system with in-built controls.</p> <p>The CRISPR-based drive consists of a series of genetic elements arranged in a so-called daisy chain, according to&nbsp;Kevin Esvelt,&nbsp;an assistant professor of media arts and sciences and head of the Sculpting Evolution research group at the MIT Media Lab who co-led the research.</p> <p>One link within the daisy-drive system encodes the CRISPR gene editing system itself, while each of the other links encode guide RNA sequences. These guide sequences tell the CRISPR system to cut and copy the next link in the chain, Esvelt says.</p> <p>Adding more links allows the daisy drive system to spread for additional generations within the population.</p> <p>“Imagine you have a chain of daisies, and at each generation you remove the one on the end. When you run out, the daisy chain drive stops," Esvelt explains.</p> <p>In this way, a small number of genetically-engineered organisms could be released into the wild to spread the daisy-drive within&nbsp;the local population, and then stop when programmed to.</p> <p>“We’re programming the organism to do CRISPR genome editing on its own, within its reproductive cells, in each generation,” Esvelt says.</p> <p>Esvelt developed the system in collaboration with George Church, a professor of genetics at Harvard Medical School, visiting professor at the Media Lab, and a senior associate member at the Broad Institute of MIT and Harvard. Co-first authors Charleston Noble and John Min, both graduate students at Harvard Medical School, led the modelling and the molecular biology experiments designed to ensure the system is evolutionarily stable, respectively.</p> <p>“If the world is to benefit from new gene-drive technologies, we need to be very confident that we can reverse it and contain it, both theoretically and via controlled tests,” Church says.</p> <p>“Many of the applications of gene drives involve islands and other geographical isolations, at least for initial tests, including invasive species and Lyme disease,” he noted. “It would be great if these highly motivated local governments can do tests that do not automatically affect adjacent islands or mainlands. The daisy-chain drives offer this.”</p> <p>The research suggests that&nbsp;for every 100 wild counterpart, releasing&nbsp;just one engineered organism with a weak 3-link daisy-drive system, once per generation, should be enough to edit the entire population in about two generations — roughly a year in a fast-reproducing insect. That compares with existing systems that must release at least as many organisms as are already present in a local population, and sometimes 10 or 100 times as many.</p> <p>The process could take several years in species that reproduce more slowly, such as mice, but would be more humane than the existing use of rodenticides, which can also harm people and predator species, Esvelt says.</p> <p>In 2014, Esvelt and his colleagues first suggested that CRISPR-Cas9 could be used in gene-drive systems, and he&nbsp;has felt a moral responsibility to develop an alternative&nbsp;to self-propagating systems, he says. “Ideally, localization will let each community make decisions about its&nbsp;own environment, without forcing&nbsp;those decsions&nbsp;on others.</p> <p>According to Professor Luke Alphey, head of arthropod genetics at The Pirbright Institute in the UK, self-propagating drive systems can spread rapidly through target populations. However, such drive systems are also thought likely to spread to all connected populations of the target species — which is desirable if you want to modify the entire species, undesirable if you do not, he says.</p> <p>“Daisy-drives potentially provide a means to get much of the benefit of this type of gene drive, while constraining spread and also limiting persistence of the gene drive even in the target population,” Alphey says. “That is likely to be highly desirable when one wants to affect one population but not another of the same species, perhaps affecting an invasive pest population but not populations of the same species in its native range.”</p> <p>Alphey was not involved in the initial&nbsp;daisy-drive research, but is now collaborating&nbsp;with Esvelt, including&nbsp;work on the use of daisy-drives in mosquitoes.&nbsp;</p> <p>Esvelt and the&nbsp;Sculpting Evolution group are also beginning to explore the possible use of this technology to heritably immunize white-footed mice, the primary reservoir of the bacteria responsible for Lyme disease in North America. They are also setting up a research collaboration to explore the use of daisy-drives in&nbsp;<em>Cochliomyia</em>,&nbsp;also known as the New World screwworm, a parasitic fly that produces larvae that eat the living tissue of warm-blooded animals, causing considerable suffering.</p> <p>In addtition, the researchers are also investigating this technology for use in nematode worms, microscopic creatures that reproduce every three days. This will allow them to carry out laboratory-based evolutionary studies of the daisy-drive engineered organisms, with the goal of ensuring the systems cannot become self-propagating.</p> Research, Genetics, Evolution, Disease, Genetic engineering, Ethics, Media Lab, School of Architecture and Planning, Broad Institute, CRISPR New technique pinpoints milestones in the evolution of bacteria Results show bacterial genomes provide “shadow history” of animal evolution. Thu, 07 Feb 2019 23:59:59 -0500 Jennifer Chu | MIT News Office <p>Bacteria have evolved all manner of adaptations to live in every habitat on Earth. But unlike plants and animals, which can be preserved as fossils, bacteria have left behind little physical evidence of their evolution, making it difficult for scientists to determine exactly when different groups of bacteria evolved.</p> <p>Now MIT scientists have devised a reliable way to determine when certain groups of bacteria appeared in the evolutionary record. The technique could be used to identify when significant changes occurred in the evolution of bacteria, and to reveal details about the primitive environments that drove such changes in the first place.</p> <p>In a paper published online Jan. 28 in the journal <em>BMC Evolutionary Biology</em>, the researchers report using the technique to determine that, around 450 to 350 million years ago, during the Paleozoic Era, several major groups of soil bacteria acquired a specific gene from fungi that allowed them to break down chitin — a fibrous material found in the cell walls of fungi and in the exoskeletons of arthropods — and use its products to grow.</p> <p>This evolutionary adaptation in bacteria may have been driven by a significant shift in the environment. Around the same time, arthropods such as early spiders, insects, and centipedes, were moving from the oceans onto land. As these terrestrial arthropods spread and diversified, they left behind chitin, creating richer soil environments and a new opportunity for bacteria — particularly those that acquired the chitinase gene — to thrive.</p> <p>“Before this period, you would have had soils, but it might have looked like the dry valleys of Antarctica,” says Gregory Fournier, the Cecil and Ida Green Assistant Professor of Geobiology in MIT’s Department of Earth, Atmospheric, and Planetary Sciences. “With animals living in soils for the first time, that provided new opportunities for microbes to take advantage and diversify.”</p> <p>Fournier says that, by tracing certain genes such as chitinase in bacteria, scientists can gain new insight into the early history of animals and the environments in which they lived.</p> <p>“Microbes contain in their genomes a shadow history of animal life that we can use to fill gaps in our understanding of not only microbes, but also of the early history of animals,” Fournier says.</p> <p>The paper’s authors include lead author Danielle Gruen PhD ’18, now a postdoc at the National Institutes of Health, and former postdoc Joanna Wolfe, now a research scientist at Harvard University.</p> <p><strong>Missing fossils</strong></p> <p>Without a fossil record, scientists have used other techniques to lay out bacteria’s “tree of life” — a map of genetic relationships, showing many branches and splits as bacteria have evolved into hundreds of thousands of species through time. Scientists have established such maps by analyzing and comparing the gene sequences of existing bacteria.</p> <p>Using a “molecular clock” approach, they can estimate the rates at which certain genetic mutations may have occurred, and calculate the time at which two species may have diverged.</p> <p><strong>“</strong>But that can only tell you relative time, and there’s a huge uncertainty associated with these estimates,” Fournier says. “We have to anchor this tree somehow to the geological record, to absolute time.”</p> <p>The team found they could use fossils from an entirely different organism to anchor the time at which certain groups of bacteria evolved. While in the vast majority of cases, genes are passed down through generations, from parent to offspring, every so often, a gene can hop from one organism to another, via a virus or through the environment, in a process known as horizontal gene transfer. The same genetic sequence, therefore, can appear in two organisms that otherwise would have entirely different genetic histories.</p> <p>Fournier and his colleagues reasoned that if they could identify a common gene between bacteria and an entirely different organism — one with a clear fossil record — they might be able to pin bacteria’s evolution to the point at which this gene was transferred from the fossil-dated organism, to bacteria.</p> <p><strong>Splitting trees</strong></p> <p>They looked through the genome sequences of thousands of organisms and identified a single gene, chitinase, that appeared in several major bacterial groups, as well as in most species of fungi, which have a well-established fossil record.</p> <p>They then used algorithms to produce a tree of all the different species with the chitinase genes, showing the relationships between species based on mutations in their genomes. Next, they employed a molecular clock approach to determine the relative times at which each species of bacteria containing chitinase branched from its respective ancestor. They repeated this same process for fungi.</p> <p>The researchers traced chitinase in fungi to the point at which it most resembled the gene when it first appeared in bacteria, and reasoned that that must have been when fungi transferred the gene to bacteria. They then used fungi’s fossil record to pinpoint the time at which transfer likely occurred.</p> <p>They found that, following the subsequent transfer of this gene across several groups of bacteria, three major groups of soil bacteria containing the chitinase gene all diversified around 450 to 350 million years ago. This rapid burst of microbe diversity was likely in response to a similar diversification of land animals, and specifically, chitin-producing arthropods, which occurred around this same period, as the fossil record shows.</p> <p>“This result supports [the idea] that microbial groups tend to acquire genes for using resources as soon as they are available in the environment,” Fournier notes. “In principle, this approach can therefore be used to date many more groups of microbes, using the transfer of other genes that use other resources.”</p> <p>Fournier is now developing an automated pipeline for detecting useful gene transfers between bacteria and other organisms, from huge amounts of gene data. For instance, he is looking at microbial genes responsible for breaking down collagen, a compound that is produced only in animals, and is found in soft body tissues.</p> <p>“If we have a shadow history in the microbes of genes that eat soft body tissue, we could maybe reconstruct the early history of soft body tissues, which don’t preserve well in the fossil record,” Fournier says.</p> <p>This research was supported, in part, by the National Science Foundation and the Simons Foundation.</p> An exoskeleton-consuming gene found in bacteria sheds light on the first arthropods to walk the Earth.Image: MIT NewsBacteria, Biology, Evolution, EAPS, Earth and atmospheric sciences, Environment, Genetics, Microbes, Research, School of Science, National Science Foundation (NSF) Cracking a tough case Whitehead Institute and MIT researchers uncover the detailed molecular structure of the sporopollenin polymer, an inert material key for the emergence of land plants. Mon, 17 Dec 2018 11:55:00 -0500 Greta Friar | Whitehead Institute <p>For hundreds of millions of years, plants thrived in the Earth’s oceans, safe from harsh conditions found on land, such as drought and ultraviolet radiation. Then, roughly 450 million years ago, plants found a way to make the move to land: They evolved spores — small reproductive cells — and eventually pollen grains with tough, protective outer walls that could withstand the harsh conditions in the terrestrial environment until they could germinate and grow into a plant or fertilize an ovule.</p> <p>A key component of the walls is a polymer — a large molecule made up of many small subunits — called&nbsp;sporopollenin. It is durable and remains ubiquitous in all land plants to this day, but is&nbsp;absent in algae.&nbsp;Understanding the molecular composition of polymers found in nature is a fundamental pursuit of biology, with a long history tracing back to the early days of elucidating DNA and protein structures, but&nbsp;the&nbsp;toughness that makes sporopollenin so important for all land plants also makes it tough for researchers to study.</p> <p>Sporopollenin is extremely inert and resistant to reacting with other chemicals, including the ones researchers typically use to determine the structures of other plant biopolymers, such as polysaccharides, lignin, and natural rubber. Consequently, scientists have struggled for decades to figure out exactly what the sporopollenin polymer is made of. Now, in an article published today&nbsp;in the journal&nbsp;<em>Nature Plants</em>, Whitehead Institute Member Jing-Ke Weng and first author and Weng lab postdoc Fu-Shuang Li, together with collaborators Professor Mei Hong and graduate student Pyae Phyo from the Department of Chemistry, have used innovative chemical degradation methods and state-of-the-art nuclear magnetic resonance (NMR) spectroscopy to determine the chemical structure of sporopollenin.</p> <p>“Plants could not have colonized the land if they had not developed a way to withstand harsh environments,” says Weng, who is also an assistant professor of biology. “Sporopollenin helped make the terrestrial ecosystem as we know it possible.”&nbsp;</p> <p>In addition to solving a longstanding puzzle in plant chemistry, identifying the structure of sporopollenin opens the door for its potential use in a host of other applications. Sporopollenin’s inertness is a desirable attribute to replicate in the development of, for example, medical implants such as stents, which prop open clogged arteries, to prevent negative interactions between the device and the body. It could also be a good model for durable paints and coatings, such as those used on boats, where its inertness would prevent reactions with compounds in the water and so protect the ship’s hull from environmental degradation.</p> <p>Finding the shape and composition of sporopollenin was not a simple task. The first challenge was getting enough of the material to study, as pollen amounts that can be collected from most plants are minute. However, pollen from the pitch pine,&nbsp;<em>Pinus rigida</em>, is sold in bulk in China as a topping for rice cakes. So Weng used an unconventional sample collection method: He asked his parents in China to ship him copious quantities of pitch pine pollen.</p> <p>A common approach to determine a complex plant polymer’s structure is to dissolve it in solutions with specific chemical compounds that will break it apart into smaller and smaller pieces from which the complete structure can be deduced. But since sporopollenin is inert and does not react with the researchers’ usual cadre of chemicals, figuring out how to break down the molecule was a key challenge.&nbsp;</p> <p>In order to crack this problem — and make the sporopollenin dissolve more easily — Li used a specially designed grinder known as a high-energy ball mill to physically shear the tiny pollen coat into even finer pieces. Then he began testing different chemical mixtures to find ones that could break apart the sporopollenin polymer into more accessible fragments.</p> <p>The big breakthrough came when he tried a chemical degradation process called thioacidolysis, an acid-catalyzed reaction with a pinch of a special sulfur-containing compound. This allowed Li to consistently break down 50 percent&nbsp;of the total sporopollenin polymer into small pieces, with the structure of each of these pieces resolved one by one.</p> <p>To help complete the puzzle, the researchers collaborated with Mei Hong’s group in MIT’s Department of Chemistry and used magic-angle-spinning solid-state NMR spectroscopy, which can determine the chemical structures of insoluble compounds by having them interact with magnetic fields. This investigation narrowed the possible structures for sporopollenin. Combined with more chemical degradation tests to verify certain possibilities and eliminate others, it ultimately led to the complete structure.</p> <p>With the structure of sporopollenin in hand, the researchers were then able to identify aspects of this unique polymer that make it such a good protective wall for spores and pollen.</p> <p>A key finding was that sporopollenin molecules contain two types of cross-linkages —&nbsp;esters and acetals —&nbsp;that act like chemical clips, binding the chains of the molecule together. Other known plant polymers have only one main type of cross-link, and this unique characteristic likely provides the extreme chemical inertness of sporopollenin. Ester bonds are resistant to mildly acidic conditions, while acetals are resistant to basic conditions, meaning the molecule won’t break down in either type of environment in the wild or in the lab.&nbsp;</p> <p>Other components of sporopollenin that the researchers found include multiple molecules known to provide UV protection, as well as fatty acids, which are water resistant and may protect spores and pollen from drought or other changes in water availability.&nbsp;</p> <p>The researchers are now looking for differences in sporopollenin between species. Pine is not a flowering plant, but the majority of plants of interest to agriculture and medicine are, so Weng and Li are investigating how sporopollenin may have changed with the evolution of the flowering plants.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p> <p>“Since I was a student, inspired by the magnificent discovery of the structure of DNA, I have been driven to discover the fundamental forms of things in nature,” Weng says. “It has been so rewarding to illuminate the structure of this crucial biopolymer in plants.”&nbsp;</p> <p>Jing-Ke Weng’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also an assistant professor of biology at MIT.&nbsp;The research&nbsp;was supported by the Pew Scholar Program in the Biomedical Sciences and the Searle Scholars Program, and the U.S. Department of Energy.</p> The toughness of Sporopollenin, a polymer within the shells of pollen grains (seen here magnified 500X using a scanning electron microscope), has made it possible for plant life to survive on land — but has also frustrated attempts to study its fundamental composition, until now.Image: Dartmouth Electron Microscope Facility / Wikimedia CommonsSchool of Science, Chemistry, Biology, Department of Energy (DoE), Evolution, Research, Whitehead Institute, Biochemistry, Plants Surviving one of Earth’s most extreme environments New research finds a unique component of cell membranes in an archaea species conveys protection against acidic surroundings. Fri, 14 Dec 2018 15:35:02 -0500 Fatima Husain | EAPS <p>Even in Earth’s most inhospitable environments, life has taken hold.</p> <p>Extremophiles are the&nbsp;organisms most well-known for withstanding extreme temperatures, pHs, salinity, and even nutrient-starvation. They have evolved special mechanisms that enable them to survive in their environments, but getting to the bottom of that resilience requires targeted and methodical interrogation.</p> <p>At Yellowstone National Park and similar sites, extremophiles reside in environments such as acid hot springs or thermal acid soils. Here&nbsp;they are exposed, often intermittently, to some of the lowest naturally-occurring pHs on Earth, and temperatures nearing the boiling point of water. To survive in these rapidly fluctuating conditions, organisms protect themselves with complex membranes, composed of interlocked lipids linked to their backbones with strong ether bonds, rather than the ester bonds most commonly found in eukaryotes and bacteria.</p> <p>In&nbsp;<em>Sulfolobus acidocaldarius,</em> an archaeon that lives in high-acid, high-temperature environments that are common in Yellowstone, cellular membrane lipids called glycerol dialkyl glycerol tetraether&nbsp;(GDGTs) are linked to an uncommon sugar-like molecule called calditol. A group of scientists recently <a href="" target="_blank">published&nbsp;findings</a> in the&nbsp;<em>Proceedings of the National Academy of Sciences</em>&nbsp;(PNAS), identifying how calditol is made in the cell and how, specifically, it is responsible for acid-tolerance in these organisms. The work is helping&nbsp;scientists get closer to understanding how life evolved to survive in extreme environments.</p> <p><a href="">Roger Summons</a>, the Schlumberger Professor of Geobiology in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS) and one of the authors of the study, credits advances in molecular biology, bioinformatics, and targeted gene deletion strategies for enabling this discovery.</p> <p>“The era of genomics has brought a range of new tools to advance lipid biomarker research,” Summons says.&nbsp;<a href="">Paula Welander</a>, a former EAPS postdoc in the&nbsp;<a href="">Summons Lab</a>&nbsp;and now assistant professor in the Department of Earth System Science at Stanford University, directed the study that was also conducted by Zhirui Zeng and Jeremy H. Wei at Stanford, and Xiao-lei Liu, an assistant professor of organic geochemistry at the University of Oklahoma.</p> <p>“This study is an excellent example of how an interdisciplinary approach, including microbial physiologists and organic geochemists, can address outstanding questions regarding lipid biomarkers,” Welander says.</p> <p>To identify calditol’s role in the&nbsp;<em>Sulfolobus acidocaldarius</em>&nbsp;membranes, the researchers used tools in comparative genomics, gene deletion, and lipid analysis to zero in on a particular protein within the class of radical S-andenosylmethionine (SAM) enzymes that is required to synthesize calditol. When they searched for what coded that protein in calditol-producing archaeal genomes, they found just a few candidate genes.</p> <p>To test the protein’s importance for acid tolerance, the researchers created mutants — with the membrane-related genes deleted — and analyzed their lipids. By subjecting the calditol-free mutant to highly acidic conditions, the researchers were able to confirm the true function of the calditol component of the membrane. Only the naturally-occurring, calditol-producing&nbsp;Sulfolobus&nbsp;and the mutant strain with the radical-SAM gene restored, were able to grow after a significant drop in pH.</p> <p>“While Welander and colleagues have demonstrated the presence of radical-SAM lipid biosynthesis genes in bacteria, this is the first time one has been unambiguously identified in archaea,” Summons says. “Calditol-linked to membrane lipids in these organisms confer significant protective effects.”</p> <p>Adds Welander: “Researchers have hypothesized for many years that producing calditol would provide this type of protective effect, but this has not been demonstrated directly. Here we finally show this link directly.”</p> <p>Even further, the fact that a radical SAM protein is involved in linking calditol to the membranes might help scientists better understand the chemistry and evolution of membrane lipids from a wide variety of environments across the planet.</p> <p>Summons says the&nbsp;result speaks to “the possible presence of a variety of other radical chemistries to modify membrane lipids once they’ve been synthesized.”&nbsp;</p> <p>“In turn, this could help us better understand the biosynthesis of other archaea-specific lipids and help us write the evolutionary history of these strikingly distinctive membranes,” he says.</p> <p>The study was supported by&nbsp;the Simons Foundation Collaboration on the Origins of Life.</p> Extremophiles are capable of living in some of the harshest locations on Earth, such as the Grand Prismatic Spring at Yellowstone National Park.Photo: Jim Peaco/National Park ServiceSchool of Science, Bacteria, Biology, Earth and atmospheric sciences, Evolution, Genetics, Geology, Microbes, Research, EAPS, Climate, Climate change Collaboration to expand the study of microbial oceanography Simons Foundation-backed CBIOMES brings together researchers in oceanography, statistics, data science, ecology, biogeochemistry, and remote sensing. Tue, 10 Jul 2018 17:20:01 -0400 Helen Hill | EAPS <p>Microbes sustain all of Earth’s habitats, including its largest biome, the global ocean. Microbes in the sea capture solar energy, catalyze biogeochemical transformations of important elements, produce and consume greenhouse gases, and fuel the marine food web. Measuring and modeling the distribution, composition, and function of microbial communities, and their interactions with the environment, are key to understanding these fundamental processes in the ocean.</p> <p>The Simons Foundation, which provides generous funding for several lines of research within MIT's Department of Earth, Atmospheric and Planetary Sciences, recently extended its support for microbial oceanography with the establishment of the Simons Foundation Collaboration on Ocean Computational Biogeochemical Modeling of Marine Ecosystems (CBIOMES). Led by MIT professor of oceanography&nbsp;<a href="" target="_blank">Michael Follows</a>, CBIOMES draws together an multidisciplinary group of both U.S. and international investigators bridging oceanography, statistics, data science, ecology, biogeochemistry, and remote sensing.</p> <p>The goal of CBIOMES (pronounced “sea biomes”), which leverages and extends Follow’s <a href="" target="_blank">Darwin Project</a> activity, is to develop and apply quantitative models of the structure and function of marine microbial communities at seasonal and basin scales.</p> <p>As Follows explains, “Microbial communities in the sea mediate the global cycles of elements including climatically significant carbon, sulfur and nitrogen. Photosynthetic microbes in the surface ocean fix these elements into organic molecules, fueling food webs that sustain fisheries and most other life in the ocean. Sinking and subducted organic matter is remineralized and respired in the dark, sub-surface ocean, maintaining a store of carbon about three times the size of the atmospheric inventory of CO<sub>2</sub>.”</p> <p>The communities of microbes that sustain these global-scale cycles are functionally and genetically extremely diverse, non-uniformly distributed and sparsely sampled. Their biogeography reflects selection according to the relative fitness of myriad combinations of traits that govern interactions with the environment and other organisms. Trait-based theory and simulations provide tools with which to interpret biogeography and microbial mediation of biogeochemical cycles. Follows says, “Several outstanding challenges remain: Observations to constrain the biogeography of marine microbes are still sparse and based on eclectic sampling methods. Theories of the organization of the system have not been quantitatively tested, and the models used to simulate the system still lack sufficiently mechanistic biological foundations. Addressing these issues will enable meaningful, dynamic simulations and state estimation.”</p> <div class="cms-placeholder-content-video"></div> <p>CBIOMES seeks to integrate key new data sets in real-time as they are collected at sea to facilitate direct tests of theoretical predictions to synthesize an atlas of marine microbial biogeography suitable for testing a range of specific ecological theories and quantifying the skill of numerical simulations. It also aspires to develop new trait-based models and simulations of regional and global microbial communities bringing to bear the power of metabolic constraints and knowledge of macro-molecular composition; to analyze these data and models using statistical tools to interpolate and extrapolate the sparse data sets, formally quantify the skill of numerical simulations, and employ data assimilation technologies to identify and optimize compatible model frameworks. “Together, the results of these efforts will advance new theoretical approaches and lead to improved global ocean-scale predictions and regional state-estimates, constrained by observed biogeography. They will provide a quantification of the associated biogeochemical fluxes,” says Follows.</p> <p>Working with Follows on CBIOMES are principal investigators <a href="" target="_blank">Stephanie Dutkiewicz</a> of MIT; <a href="" target="_blank">Jacob Bien</a>,&nbsp;<a href="" target="_blank">Christopher Edwards</a>, and&nbsp;<a href="" target="_blank">Jed Fuhrman</a> of the University of Southern California; <a href="" target="_blank">Zoe Finkel</a>&nbsp;and&nbsp;<a href="" target="_blank">Andrew Irwin</a> of Mount Allison University in Canada; <a href="" target="_blank">Shubha Sathyendranath</a> of Plymouth Marine Laboratory in the U.K., and&nbsp;<a href="" target="_blank">Joseph Vallino</a> of the Marine Biological Laboratory.</p> <p>A meeting held at the Simons Foundation in New York City May 21 through 23 provided a first opportunity for collaborators to meet face-to-face, and provided a forum for investigators to educate one another about each others expertise and areas of activity, share initial progress, and coordinate collaborative efforts.</p> <p>Discussions centered around how to determine the biogeography of marine microbes from empirical date, the role of statistical models in determining the relationships in space and time between organisms, traits, and environments, the complimentary role of mechanistic models and how to simulate the systems that are observed, and, in the context of model-date synthesis, how to best utilize empirical data to test theory and improve simulation skill.</p> <p>“While the central question 'What is the functional biogeography of a group of organisms in the oceans?' is relatively focused, the techniques being used are extremely varied focusing a lot on computational tools, but uniquely, hand-in-hand with data collection and data compilation,” says Follows. “I am particularly excited by everyone’s enthusiasm, the number of cross-connections and collaborations already underway, and the rapid progress that is happening on many fronts.”</p> <p>Complementary to CBIOMES is the&nbsp;<a href="" target="_blank">Simons Collaboration on Ocean Processes and Ecology (SCOPE)</a>&nbsp;co-led by&nbsp;<a href="" target="_blank">Ed DeLong</a> of the MIT Department of Civil and Environmental Engineering and&nbsp;<a href="" target="_blank">David Karl</a> of the University of Hawaii. SCOPE’s focus is advancing understanding of marine biology, biogeochemistry, ecology and evolution of microbial processes by focusing on a representative ocean benchmark, Station ALOHA, located in the North Pacific Subtropical Gyre.</p> <p><a href="" target="_blank">SCOPE-Gradients</a>, a related project, with a focus on understanding transitions between the North Pacific Subtropical Gyre and neighboring ecosystems, brings a rich stream of observational data to the CBIOMES effort. The North Pacific Subpolar Gyre is a region of open ocean notable for exhibiting steep changes in environmental conditions (gradients) associated with dramatic changes in the microbial ecosystem. Several members of the SCOPE-Gradients team accompanied project principal investigator <a href="" target="_blank">Virginia Armbrust</a> of the University of Washington to the May CBIOMES meeting.</p> <p>The mission of the Simons Foundation is to advance the frontiers of research in mathematics and the basic sciences. Co-founded in New York City by Jim and Marilyn Simons, the foundation exists to support basic — or discovery-driven — scientific research undertaken in the pursuit of understanding the phenomena of our world.</p> <p>As well as&nbsp;Michael Follows, other Simons Foundation funded investigators in the MIT Department of Earth, Atmospheric and Planetary Sciences include&nbsp;<a href="" target="_blank">Tanja Bosak</a>,&nbsp;<a href="" target="_blank">Gregory Fournier</a>, and&nbsp;<a href="" target="_blank">Roger Summons</a>. Several MIT postdocs have been recipients of Simons Postdoctoral Fellowships, among them&nbsp;<a href="" target="_blank">Alexandria Johnson</a>,&nbsp;<a href="" target="_blank">Sukrit Ranjan</a>&nbsp;and&nbsp;<a href="" target="_blank">Christopher Follett</a>.</p> A computer simulation shows ecological provinces of the marine global ecosystems developed in the Follows Group at MIT. Each color represents a different combination of the most dominant phytoplankton function types (as shown in the Venn diagram at top right). Opacity indicates the total concentration of phytoplankton biomass: The darker the color, the less phytoplankton.Image: Oliver Jahn / MIT EAPSOceanography and ocean engineering, Marine biology, Ecology, Earth and atmospheric sciences, EAPS, Data, Funding, Civil and environmental engineering, School of Science, School of Engineering, Biology, Evolution Jeff Gore: A physicist exploring population dynamics of microbes MIT professor sees many “big, deep questions in biology” that benefit from study by both physicists and life scientists. Mon, 14 May 2018 23:59:59 -0400 Anne Trafton | MIT News Office <p>It’s a pretty good bet that among MIT’s physics faculty, Jeff Gore is the only one with test tubes of yeast growing in his lab.</p> <p>Gore, a biophysicist who studies population dynamics, uses yeast and other microbes to explore the fundamental rules that govern phenomena such as population collapse. His microbial communities offer a window into principles that also influence larger-scale populations that are much more difficult to study.</p> <p>“Microbes are a wonderful experimentally tractable model system to try to ask the kinds of questions we’re interested in, regarding all these phenomena that are also at play in fisheries, or in zebra populations, which are very difficult to approach experimentally,” says Gore, who recently earned tenure in MIT’s Department of Physics.</p> <p>Since joining MIT’s faculty in 2010, Gore has explored the roles of “cheaters” and “cooperators” in microbial communities, as well as perturbations that can nudge a stable population toward a tipping point that leads to collapse. The rapid timescale of microbial growth allows Gore and his students to conduct an experiment in just a few days, test their predictions, revise their models based on the experimental results, and then launch new experiments.</p> <p>“Going back and forth between experiment and modeling is a key part of how I like to do science, and it’s really only feasible, given the timescales, in these experimentally tractable organisms with short generation times,” he says.</p> <p><strong>A physical approach to biology</strong></p> <p>Gore, who grew up on a Christmas tree farm in Corvallis, Oregon, first visited MIT as a high school senior and immediately felt at home.</p> <p>“I was staying with an older graduate from my high school at one of the fraternities across the river,” he recalls. “I played ping pong with different members of the fraternity for hours, and chatted with each of them about what they were doing, what they were excited about. It definitely felt like a place that I was going to appreciate.”</p> <p>Gore began his undergraduate career as a physics major but gradually added more majors until he ended up with four concentrations, in physics, mathematics, economics, and electrical engineering.</p> <p>After graduating from MIT, Gore went to the University of California at Berkeley, where he began studying electron transport in carbon nanotubes. However, his PhD advisor left Berkeley soon after that, so he switched to a biophysics lab, where he worked on building new kinds of microscopes to look at and manipulate individual biological molecules, such as DNA.&nbsp;&nbsp;</p> <p>He found that he enjoyed applying tools and strategies from physics to try to discover patterns that underlie biological phenomena.</p> <p>“I think many physicists, probably myself included, when we first learn biology there are a lot of things to memorize, and we tend not to be very good at memorizing things, so we decide we don’t like it,” Gore says. “But over time I realized that there are a bunch of big, deep questions in biology where the approach of a physicist is complementary to the approach taken by a molecular or cell biologist.”</p> <p>He says that another appealing aspect of biophysics is that it offers the opportunity to run experiments that can be contained on a lab bench, as opposed to the huge particle colliders that are required to answer many of the fundamental questions remaining in traditional physics.</p> <p>“I like experiments, and I wanted to do experiments that could be put on a bench, where you could really have the lead in your own project,” he says. “You may not be able to find out the origin of dark matter, but you have real control over your own experiment.”</p> <p><strong>Population predictions</strong></p> <p>After finishing his PhD, Gore returned to MIT as a Pappalardo Fellow in the Department of Physics, where he began studying population dynamics of microbes. Using game theory, a mathematical approach traditionally used by economists to predict individuals’ behavior in certain situations, he set out to explore cooperative behavior, which benefits other members of a species at a cost to the individual.</p> <p>Working with yeast populations in which some members cooperate, by producing an excess of food, and others cheat, by gorging themselves on the food produced by others, Gore found that if an individual benefits even slightly by cooperating, it can survive even when surrounded by individuals that don’t cooperate. This helps to explain the perpetuation of cooperative behavior, which had puzzled biologists because if only the fittest individuals survive, genes for a behavior that benefits other members of the population more than the cooperating individual should die out.</p> <p>As a faculty member, Gore has expanded his research to include analysis of the conditions that can lead to population collapse. In 2012, he showed that he could measure a population’s risk of collapse by monitoring how quickly it recovers from small disturbances such as food shortages or overcrowding. Later, he found that monitoring variations in population density in neighboring regions — a measure that is easier to obtain — can also be used to predict risk of collapse.</p> <p>Since Gore joined MIT’s faculty, the physics department has increased its focus on the field of biophysics, hiring three more specialists in that area. That core group, along with several other biophysicists in the department, launched the Physics of Living Systems group about three years ago.</p> <p>“We’re working to develop a critical mass of faculty who are taking this physics approach to understanding biology, which is different and hopefully complementary to the approach taken by other departments,” Gore says. “There really are a distinct set of approaches to biology in different departments, which is great because the different approaches give different insights.”</p> Jeff GoreImage: Jared CharneyFaculty, Physics, School of Science, Profile, Biology, Evolution, Microbes, Alumni/ae With The Herman Project, home bakers become citizen scientists Network tracks the evolution of microbial communities in sourdough starter mixtures shared around the world. Thu, 12 Apr 2018 00:00:00 -0400 Carolyn Schmitt | Department of Civil and Environmental Engineering <p>Researchers from MIT are taking their microbial research out of the lab and into the kitchen.</p> <p>Their new <a href="">Herman Project</a> modernizes a longstanding tradition, with a digital network that tracks the evolution of sourdough starters as they are shared by home bakers around the world. By crowdsourcing information from the project’s participants, the researchers, based in the Department of Civil and Environmental Engineering (CEE), are investigating how the starters’ microbial communities change in different conditions and environments.</p> <p>Sourdough starters — a mixture of flour and water that, through the growth of bacteria, is responsible for the unique taste of sourdough bread — have traditionally been shared among friends and families. The starters, known affectionately as “Herman,” are typically shared with paper instructions for “feeding” the sourdough starter, and an accompanying letter to track the sourdough starter’s path as it is passed from person to person.</p> <p>Gabriel Leventhal, a postdoc in CEE and creator of The Herman Project, grew up participating in starter networks. Now, working with CEE Assistant Professor Otto X. Cordero and undergraduate students Sarah Weidman and Lindsey McAllister, Leventhal launched The Herman Project to create a more modern, online way to track the spread of the sourdough starters and to leverage the resulting data for science.</p> <p>“The Herman Project isn’t just doing citizen science and asking people to help us gather data. We’re giving people the opportunity to participate in the scientific process,” Leventhal says. “We plan to have feedback with the data that’s generated from the [sourdough] samples, where we can share the data and the genetic makeup of a starter, so participants can see how the starter changes over time, and potentially also do little experiments at home with their starters.”</p> <p>To help kick-start the project, Cordero and Leventhal hosted two first-year students, Weidman and McAllister, in their lab over MIT’s Independent Activities Period as part of CEE’s mini-Undergraduate Research Opportunities Program (UROP). Weidman and McAllister fine-tuned the instructions for participants, designed an accessible online platform, tested The Herman Project in its beta phase, and conducted online research for The Herman Project website.</p> <p>“My primary part was working on the instructions, and we wanted to make it more visual and look as easy as possible,” McAllister says. “We tried to make it very simple and easy to follow. I learned graphic design tools and made a big wheel that we later ended up animating to make it more interactive and highlight where in the wheel you were. Then at the end, it gave you a way to find out what our next steps would be.”</p> <p>Meanwhile, Weidman translated the complex, scientific details of sourdough into more understandable blurbs for the website. “I really liked how we were able to take what we were learning and present it to the community,” she says.</p> <p>The Herman Project works by giving each sample of “Herman,” the sourdough starter, an identification number, and using an online platform to instruct users for how to feed Herman. Herman needs to be fed with additional flour and water over four days to acclimatize to its new kitchen environment and to let the mixture ferment. Herman is then ready to be mixed with baking ingredients and cooked. Not all of the starter is used, however, and participants save some of Herman to use for future baking.</p> <p>As Herman is passed between friends, the new participants also log information on The Herman Project website, noting their location and type of flour used while growing their new starter. Each user thus adds data for the researchers to study and expand the network. In addition to participants logging their approximate location and environmental conditions of Herman as it is fed, they are also asked to share a sample of Herman with Cordero’s lab. The researchers, assisted by Weidman and McAllister, will isolate the microbes and study how the microbial communities differ across time and environments. The project's network is currently centralized in the greater Boston area, as members of Cordero’s lab begin to share Herman with their peers.</p> <p>“The Herman Project allows us to study microbial evolution in the context of communities, where multiple species coexist and interact,” Cordero explains. “This is one of the frontiers in our field. I found it really elegant and exciting that we can take advantage of the social dynamics around sourdough to ‘crowdsource’ an evolution experiment through the Herman Project.”</p> <p>The utilization of microbes such as bacteria and yeast is essential for the creation of sourdough and other fermented foods like wine and beer. For sourdough, microbes break down complex carbohydrates in the flour and water mixture and ferment the dough over a series of days. This creates carbon dioxide and produces air bubbles to help the dough rise. The process also produces lactic acid, which gives the dough its sour flavor.&nbsp;</p> <p>For The Herman Project, combining the networked information about the spread of different sourdough starters with the microbial data from the dough samples allows the researchers to analyze how microbial communities change as they transfer between different environmental conditions.</p> <p>A lot is known about how individual microbes evolve, but Leventhal and Cordero are seeking to use The Herman Project to ask questions about if and how being part of a microbial community impacts the way microbes evolve in different conditions.&nbsp;</p> <p>“I think The Herman Project could help us address many important questions,” Cordero says. “For instance, what is the impact of strain-level (within-species) diversity with respect to stability and function, are there alternative trajectories for evolution, and if so, what controls them? These are important questions to address if we want to learn how to control and design microbial consortia.”</p> <p>“Microbial communities have been used as biotechnology by human societies for millennia.&nbsp;A key difference between using microbes as engineering tools and inert components, however, is that “microbes are 'alive' — they grow, they get mutations, and they evolve. We need to understand how this influences their function as a community if we want to use them sustainably,” Leventhal says.</p> <p>Under Leventhal’s guidance, Weidman and McAllister are planning to conduct analyses of the bacteria and yeast genomes to get a complete understanding of the microbial community of each sample as part of their UROP.</p> <p>“The Herman Project is a really cool way to take something that a lot of people know about, and to investigate what’s actually happening,” McAllister says.</p> Gabriel Leventhal (right), a postdoc in the Department of Civil and Environmental Engineering, works with UROP students Sarah Weidman (left) and Lindsey McAllister (center) to analyze samples from The Herman Project, a citizen-science sourdough project. Photo: Allison Dougherty/Department of Civil and Environmental EngineeringCivil and environmental engineering, School of Engineering, Undergraduate Research Opportunities Program (UROP), Bacteria, Evolution, Microbes, Crowdsourcing Determining the timing of methanogen evolution Scientists conclude methane-producing microbes date back 3.5 billion years, supporting the hypothesis that they could have contributed to early global warming. Wed, 04 Apr 2018 13:15:00 -0400 Helen Hill | EAPS <p>Early forms of life very likely had metabolisms that transformed the primordial Earth, such as initiating the carbon cycle and producing most of the planet’s oxygen through photosynthesis. About 3.5 billion years ago, the Earth seems to have already been covered in liquid oceans, but the sun at that time was not bright or warm enough to melt ice. To explain how the oceans remained unfrozen, it has been suggested that greenhouse gases such as methane produced warming in the early atmosphere, just as they do in global warming today.</p> <p>Naturally occurring methane is mainly produced by a group of microbes, methanogenic archaea, through a metabolism called methanogenesis. While there is some evidence from carbon isotope data that sources of methane as ancient&nbsp;as 3.5 billion years old may have been biological in origin, until now there has been no solid evidence that methane-producing microbes existed early enough in Earth’s history to be responsible for keeping the early Earth warmed up.</p> <p>Now, in a <a href="" target="_blank">paper</a> published in the journal&nbsp;<em>Nature Ecology and Evolution</em>, Jo Wolfe, a postdoc in the Department of Earth, Atmospheric and Planetary Sciences (EAPS) at MIT, and Gregory Fournier, an assistant professor in EAPS, report new work combining horizontal gene transfer data with the microbial fossil record that allowed them to estimate absolute ages for methane-producing microbes on the geological timeline.</p> <p><strong>Paleontology meets genetics</strong></p> <p>Wolfe is a paleontologist specializing in how fossil and living animal species are related in the tree of life. Fournier specializes in exploring how genomes from living organisms can be used to study the early evolution of microbes. Cracking this puzzle required both areas of expertise.</p> <p>"Trace chemical evidence hints that methane and the microbes that produced it could have been present, but we didn't know whether methogenic archaea were actually present at that time," Wolfe says.</p> <p>To bridge between fossil and genomic data, Wolfe and Fournier used genomes from living microbes that preserve a record of their early history. These DNA sequences can be accessed through phylogenetic analysis and compared to one another, the researchers&nbsp;explain, in order to find the best branching “tree” that describes their evolution. As one works back along this tree, the branches represent increasingly ancient lineages of microbes that existed in Earth’s deep history. Changes along these branches can be measured, producing a molecular clock&nbsp;that&nbsp;calculates the rate of evolution along each branch, and, from that, a probabilistic estimate of the relative and absolute timing of common ancestors within the tree. A&nbsp;molecular clock requires fossils, however, which methanogens lack.&nbsp;</p> <p><strong>Calibrating the tree of life</strong></p> <p>In order to solve this difficulty, Wolfe and Fournier harnessed horizontal gene transfers, or swaps of genetic material between the ancestors of different groups of organisms. Unlike vertical transmission of DNA from parent to offspring — which is how most human genes are inherited — horizontal transfers can pass genes between distantly related microorganisms. They found that genes were donated from a group within the methanogenic archaea to the ancestor of all oxygen-producing photosynthetic cyanobacteria, which do have some fossils. Using the gene transfers and the cyanobacterial fossils together, they were able to constrain and guide the molecular clock of methane producers, and found that the methane-producing microbes were indeed over 3.5 billion years old, supporting the hypothesis that these microbes could have contributed to early global warming.</p> <p>"This is the first study to combine gene transfers and fossils to estimate absolute ages for microbes on the geological timeline," Fournier says. "Knowing the ages of microbial groups allows us to expand this powerful approach to study other events in early planetary and environmental evolution, and eventually, to build a timescale for the tree of all life."</p> <p>The&nbsp;research&nbsp;was funded by the Simons Foundation Collaboration and the National Science Foundation.</p> Artist’s view of the young Earth as it is believed to have looked 3.5 billion years agoImage: NASA GSFCSchool of Science, Earth and atmospheric sciences, Research, Climate change, EAPS, Global Warming, Greenhouse gases, Microbes, National Science Foundation (NSF), Evolution Scientists find different cell types contain the same enzyme ratios New discovery suggests that all life may share a common design principle. Thu, 29 Mar 2018 12:00:00 -0400 Justin Chen | Department of Biology <p>By studying bacteria and yeast, researchers at MIT have discovered that vastly different types of cells still share fundamental similarities, conserved across species and refined over time. More specifically, these cells contain the same proportion of specialized proteins, known as enzymes, which coordinate chemical reactions within the cell.</p> <p>To grow and divide, cells rely on a unique mixture of enzymes that perform millions of chemical reactions per second. Many enzymes, working in relay, perform a linked series of chemical reactions called a “pathway,” where the products of one chemical reaction are the starting materials for the next. By making many incremental changes to molecules, enzymes in a pathway perform vital functions such as turning nutrients into energy or duplicating DNA.</p> <p>For decades, scientists wondered whether the relative amounts of enzymes in a pathway were tightly controlled in order to better coordinate their chemical reactions. Now, researchers have demonstrated that cells not only produce precise amounts of enzymes, but that evolutionary pressure selects for a preferred ratio of enzymes. In this way, enzymes behave like ingredients of a cake that must be combined in the correct proportions and all life may share the same enzyme recipe.</p> <p>“We still don’t know why this combination of enzymes is ideal,” says Gene-Wei Li, assistant professor of biology at MIT, “but this question opens up an entirely new field of biology that we’re calling systems level optimization of pathways. In this discipline, researchers would study how different enzymes and pathways behave within the complex environment of the cell.”</p> <p>Li is the senior author of the study, which appears online in the journal <em>Cell</em> on March 29, and in print on April 19. The paper’s lead author, Jean-Benoît Lalanne, is a graduate student in the MIT Department of Physics.</p> <p><strong>An unexpected observation</strong></p> <p>For more than 100 years, biologists have studied enzymes by watching them catalyze chemical reactions in test tubes, and — more recently — using X-rays to observe their molecular structure.</p> <p>And yet, despite years of work describing individual proteins in great detail, scientists still don’t understand many of the basic properties of enzymes within the cell. For example, it is not yet possible to predict the optimal amount of enzyme a cell should make to maximize its chance of survival.</p> <p>The calculation is tricky because the answer depends not only on the specific function of the enzyme, but also how its actions may have a ripple effect on other chemical reactions and enzymes within the cell.</p> <p>“Even if we know exactly what an enzyme does,” Li says, “we still don’t have a sense for how much of that protein the cell will make. Thinking about biochemical pathways is even more complicated. If we gave biochemists three enzymes in a pathway that, for example, break down sugar into energy, they would probably not know how to mix the proteins at the proper ratios to optimize the reaction.”</p> <p>The study of the relative amounts of substances — including proteins — is known as “stoichiometry.” To investigate the stoichiometry of enzymes in different types of cells, Li and his colleagues analyzed three different species of bacteria — <em>Escherichia</em> <em>coli,</em> <em>Bacillus</em><em> subtilis,</em> and <em>Vibrio</em> <em>natriegens — </em>as well as the budding yeast <em>Saccharomyces</em><em> cerevisiae.</em> Among these cells, scientists compared the amount of enzymes in 21 pathways responsible for a variety of tasks including repairing DNA, constructing fatty acids, and converting sugar to energy. Because these species of yeast and bacteria have evolved to live in different environments and have different cellular structures, such as the presence or lack of a nucleus, researchers were surprised to find that all four cells types had nearly identical enzyme stoichiometry in all pathways examined.</p> <p>Li’s team followed up their unexpected results by detailing how bacteria achieve a consistent enzyme stoichiometry. Cells control enzyme production by regulating two processes. The first, transcription, converts the information contained in a strand of DNA into many copies of messenger RNA (mRNA). The second, translation, occurs as ribosomes decode the mRNAs to construct proteins. By analyzing transcription across all three bacterial species, Li’s team discovered that the different bacteria produced varying amounts of mRNA encoding for enzymes in a pathway.</p> <p>Different amounts of mRNA theoretically lead to differences in protein production, but the researchers found instead that the cells adjusted their rates of translation to compensate for changes in transcription. Cells that produced more mRNA slowed their rates of protein synthesis, while cells that produced less mRNA increased the speed of protein synthesis. Thanks to this compensation, the stoichiometry of enzymes remained constant across the different bacteria.</p> <p>“It is remarkable that <em>E. coli</em> and <em>B. subtilis </em>need the same relative amount of the corresponding proteins, as seen by the compensatory variations in transcription and translation efficiencies,” says Johan Elf, professor of physical biology at Uppsala University in Sweden. “These results raise interesting questions about how enzyme production in different cells have evolved."</p> <p>“Examining bacterial gene clusters was really striking,” lead author Lalanne says. “Over a long evolutionary history, these genes have shifted positions, mutated into different sequences, and been bombarded by mobile pieces of DNA that randomly insert themselves into the genome. Despite all this, the bacteria have compensated for these changes by adjusting translation to maintain the stoichiometry of their enzymes. This suggests that evolutionary forces, which we don’t yet understand, have shaped cells to have the same enzyme stoichiometry.”<br /> <br /> <strong>Searching for the stoichiometry regulating human health</strong></p> <p>In the future, Li and his colleagues will test whether their findings in bacteria and yeast extend to humans. Because unicellular and multicellular organisms manage energy and nutrients differently, and experience different selection pressures, researchers are not sure what they will discover.</p> <p>“Perhaps there will be enzymes whose stoichiometry varies, and a smaller subset of enzymes whose levels are more conserved,” Li says. “This would indicate that the human body is sensitive to changes in specific enzymes that could make good drug targets. But we won’t know until we look.”</p> <p>Beyond the human body, Li and his team believe that it is possible to find simplicity underlying the complex bustle of molecules within all cells. Like other mathematical patterns in nature, such as the the spiral of seashells or the branching pattern of trees, the stoichiometry of enzymes may be a widespread design principle of life.</p> <p>The research was funded by the National Institutes of Health, Pew Biomedical Scholars Program, Sloan Research Fellowship, Searle Scholars Program, National Sciences and Engineering Research Council of Canada, Howard Hughes Medical Institute, National Science Foundation, Helen Hay Whitney Foundation, Jane Coffin Childs Memorial Fund, and the Smith Family Foundation.</p> MIT researchers have discovered that enzymes performing the same function in yeast and bacteria may have different structures, but are present in the same relative amounts within each type of cell.Image: Haynathart/Wikimedia CommonsResearch, Bacteria, Biology, Evolution, Genetics, Microbes, Physics, DNA, RNA, School of Science New type of virus found in the ocean The unusual characteristics of these abundant, bacteria-killing viruses could lead to evolutionary insights. Wed, 24 Jan 2018 13:00:00 -0500 David L. Chandler | MIT News Office <p>A type of virus that dominates water samples taken from the world’s oceans has long escaped analysis because it has characteristics that standard tests can’t detect. However, researchers at MIT and the Albert Einstein College of Medicine have now managed to isolate and study representatives of these elusive viruses, which provide a key missing link in virus evolution and play an important role in regulating bacterial populations, as a new study reports.</p> <p>Viruses are the main predators of bacteria, and the findings suggest that the current view of bacterial virus diversity has a major blind spot. These conclusions have emerged through detailed analysis of marine samples led by MIT postdoc Kathryn Kauffman, professor of civil and environmental engineering Martin Polz, professor Libusha Kelly of Albert Einstein College of Medicine, and nine others. The results are being reported this week in the journal <em>Nature</em>.</p> <p>The newly identified viruses lack the “tail” found on most catalogued and sequenced bacterial viruses, and have several other unusual properties that have led to their being missed by previous studies. To honor that fact, the researchers named this new group the <em>Autolykiviridae</em> — after a character from Greek mythology who was storied for being difficult to catch. And, unlike typical viruses that prey on just one or two types of bacteria, these tailless varieties can infect dozens of different types, often of different species, underscoring their ecological relevance.</p> <p>This research “opens new avenues for furthering our understanding of the roles of viruses in the ocean,” says Jed Fuhrman, the McCulloch-Crosby Chair of Marine Biology at the University of Southern California, who was not involved in this work. “In a practical sense, it also shows how we need to alter some commonly used methods in order to capture these kinds of viruses for various studies,” he says. “I’d say it is an important advance in the field.”</p> <p>Current environmental models of virus-bacteria interactions are based on the well-studied tailed viruses, Kauffman explains, so they may be missing important aspects of the interactions taking place in nature.</p> <p>“We already knew that viruses are very important there,” Kauffman says, referring to the surface ocean, where the researchers’ samples were drawn, and where about 10 million viruses are found in every milliliter of water. Polz says that while “most of the viruses studied in labs have tails, most of those in the ocean don’t.” So the team decided to study one subset of tailless viruses, which infects a group of bacteria called <em>Vibrio</em>. After extensive tests, they found “that some of these were infecting unusually large numbers of hosts,” he says.</p> <p>After sequencing representatives of the <em>Autolykiviridae</em>, the researchers found “their genomes were quite different from other viruses,” Polz says. For one thing, their genomes are very short: about 10,000 bases, compared to the typical 40,000-50,000 for tailed viruses. “When we found that, we were surprised,” he says.</p> <p>With the new sequence information, the researchers were able to comb through databases and found that such viruses exist in many places. The research also showed that these viruses tend to be underrepresented in databases because of the ways samples are typically handled in labs. The methods the team developed to obtain these viruses from environmental samples could help researchers avoid such losses of information in the future. In addition, Kauffman says, typically the way researchers test for viral activity is by infecting bacteria with the viral sample and then checking the samples a day later to look for signs that patches of the bacteria have been killed off. But these particular nontailed viruses often act more slowly, and the killed-off regions don’t show up until several days have passed — so their presence was never noticed in most studies.</p> <p>The new group of viruses may especially be widespread. “We don’t think it’s ocean-specific at all,” Polz says. For example, the viruses may even be prevalent in the human biome, and they may play roles in major biogeochemical cycles, he says, such as the cycling of carbon.</p> <p>Another important aspect of theses findings is that the <em>Autolykiviridae</em> were shown to be &nbsp;members of an ancient viral lineage that is defined by specific types of capsids, the protein shell encasing the viral DNA. Though this lineage is known to be very diverse in animals and protists — and includes viruses such as the adenoviruses that infect humans, and the giant viruses that infect algae — very few viruses of this kind have been found to infect bacteria.</p> <p>“This work substantially changes the existing ideas on the composition of the ocean virome by showing that the content of small, tailless viruses … is comparable to that of the tailed viruses … that are currently thought to dominate the virosphere,” says Eugene V. Koonin, a senior investigator at the National Institutes of Health, who was not involved in this research. “This work is important also for understanding the evolution of the virus world because it shows that viruses related to the most common viruses of eukaryotes (such as adenoviruses, poxviruses, and others), at least in terms of the capsid structure, are much wider-spread in prokaryotes than previously suspected.”</p> <p>Koonin adds, “I further wonder whether the viruses reported here might only represent the tip of the proverbial iceberg, because capsid proteins can be highly diverged in sequence so that many are missed even in sensitive database searches. The findings are also of practical importance because the tailless viruses appear to play a major ecological role in the ocean, being responsible for a substantial fraction of bacteria-killing.”</p> <p>The work was supported by the National Science Foundation and the Woods Hole Oceanographic Institution’s Ocean Ventures Fund.</p> Electron microscope images of marine bacteria infected with the non-tailed viruses studied in this research. The bacterial cell walls are seen as long double lines, and the viruses are the small round objects with dark centers. Courtesy of researchers Research, Civil and environmental engineering, Biology, Biological engineering, Microbes, Bacteria, Viruses, Evolution, Ocean science, School of Engineering, School of Science, National Science Foundation (NSF) Biochemists discover mechanism that helps flu viruses evolve Influenza viruses can hijack host cellular machinery to help mutated viral proteins fold and function. Tue, 26 Sep 2017 07:59:59 -0400 Anne Trafton | MIT News Office <p>Influenza viruses mutate rapidly, which is why flu vaccines have to be redesigned every year. A new study from MIT sheds light on just how these viruses evolve so quickly, and offers a potential way to slow them down.</p> <p>The MIT team found that flu viruses’ rapid evolution relies in part on their ability to hijack some of the cellular machinery of the infected host cell — specifically, a group of proteins called chaperones, which help other proteins fold into the correct shape. When the viruses were unable to get help from these chaperones, they did not evolve as rapidly as when they could obtain extensive help from host chaperones. Moreover, the specific evolutionary trajectories followed by individual flu proteins depend on host chaperone activities.</p> <p>The findings suggest that interfering with host cell chaperones could help prevent flu viruses from becoming resistant to existing drugs and vaccines, says Matthew Shoulders, the Whitehead Career Development Associate Professor of Chemistry at MIT.</p> <p>“It’s relatively easy to make a drug that kills a virus, or an antibody that stops a virus from propagating, but it’s very hard to make one that the virus doesn’t promptly escape from once you start using it,” Shoulders says. “Our data suggest that, at some point in the future, targeting host chaperones might restrict the ability of a virus to evolve and allow us to kill viruses before they become drug resistant.”</p> <p>Shoulders is the senior author of the study, which is a collaborative effort with Leonid Mirny, a professor of physics at MIT; and Yu-Shan Lin, a professor at Tufts University. Angela Phillips, an MIT graduate student and National Science Foundation graduate fellow, is the lead author of the paper, which appears in the journal <em>eLife</em> on Sept. 26.</p> <p><strong>A little help</strong></p> <p>Flu viruses carry eight genome segments, all encoded by RNA. Of particular interest to flu researchers is the gene for the hemagglutinin protein, which is displayed on the surface of the viral envelope and interacts with cells of the infected host. Most flu vaccines target this protein, but these vaccines have to be updated every year to keep up with the protein’s ability to evolve quickly.</p> <p>However, this rapid evolution also poses a challenge for the viruses themselves. When proteins mutate, they may become unable to fold into the shape they need to assume to perform their function. Previous research, such as the pioneering work of the late Susan Lindquist, a biology professor at MIT, has shown that in many organisms, evolution of endogenous proteins depends on the ability of that organism’s chaperones to help mutated proteins fold.</p> <p>In this study, the MIT team investigated whether viruses can take advantage of their host’s chaperone proteins to help with their own evolution.</p> <p>“Viral proteins are known to interact with host chaperones, so we suspected that this interplay could have a major impact on what evolutionary pathways are available to the virus,” Shoulders says.</p> <p>To test their hypothesis, the researchers generated one set of cells with low protein-folding activity by inhibiting a key chaperone protein called heat shock protein 90 (Hsp90). In another set of cells, they used chemical genetic methods previously developed by Shoulders to enhance the levels of numerous chaperone proteins, creating a cellular environment with high protein-folding activity.</p> <p>The researchers infected both sets of cells, plus a group of cells with normal chaperone levels, with a strain of flu and then allowed the virus to evolve for nearly 200 generations. They found that the virus did indeed evolve faster in the cells with higher chaperone levels than in the cells with inhibited chaperone proteins.</p> <p>“This finding suggests that influenza will acquire new traits that might be beneficial for it faster when you have the heat shock response activated, and slower when you have key chaperones inhibited,” Shoulders says.</p> <p><strong>Blocking escape routes</strong></p> <p>The researchers also identified specific proteins that tend to become more mutated in cells with more chaperones. One of these is the hemagglutinin protein, and another is an enzyme called PA, which is a type of RNA polymerase that helps the virus copy its genes. The team also identified specific amino acids within these proteins that are more likely to become mutated in different protein-folding environments.</p> <p>“The authors develop very nice chemical genetic tools for precisely manipulating proteostasis in human cells, and the application of their methods led to a number of interesting findings,” says Jesse Bloom, a viral evolution expert and associate member of the Fred Hutchinson Cancer Research Center, who was not involved in the research. “Perhaps the most compelling is the identification of a specific mutation in influenza (H452Q in PA) that has different effects depending on whether the heat shock response is activated versus whether Hsp90 is inhibited. Identification of this mutation is proof of principle that a virus' ability to tolerate specific mutations can be affected by chaperones, providing the first link between host proteostasis and viral evolution.”</p> <p>Targeting this phenomenon could offer a way to delay viral evolution and decelerate escape from existing drugs and vaccines, the researchers say. Many chaperone inhibitors already exist, and some are now being tested in clinical trials to treat cancer and some viral infections. The new data imply that treating patients with a chaperone-inhibiting drug along with another antiviral therapy, such as a drug or vaccine, could help ensure that the virus does not evolve resistance to the therapeutic.</p> <p>The researchers believe this phenomenon is likely also found in other viruses, and they are now studying HIV, another virus that mutates rapidly. They also plan to study how a host cell’s protein-folding capacity may affect the evolution of antiviral drug or antibody resistance, using therapeutics that circulating viruses are already resistant to.</p> <p>“We can recapitulate environmental pressures like antiviral drugs in the lab, in the context of different host protein-folding environments, and see whether there’s a big impact. Our data suggest that there’s going to be, but we have to actually test it out,” Shoulders says.</p> <p>The research was funded by the Smith Family Foundation Award for Excellence in Biomedical Research and an NSF CAREER Award.</p> Virion hikers with varying levels of fitness, illustrated here as preparedness, attempt to climb Folded Peak  While some virions are too unfit to hit the trail (red), some are sufficiently fit to reach the summit without help from the park chaperones (blue). Other virions (yellow) are able to reach the summit by hijacking the park chaperones, which are also assisting certain host proteins, and some virions are unable to receive help from the park chaperones (gray). Image: Mary O’Reilly/O’Reilly Science ArtResearch, Chemistry, Microbes, School of Science, Influenza, Evolution, Health, Medicine, National Science Foundation (NSF) Technique spots warning signs of extreme events Method may help predict hotspots of instability affecting climate, aircraft performance, and ocean circulation. Fri, 22 Sep 2017 13:59:59 -0400 Jennifer Chu | MIT News Office <p>Many extreme events — from a rogue wave that rises up from calm waters, to an &nbsp;instability inside a gas turbine, to the sudden extinction of a previously hardy wildlife species — seem to occur without warning. It’s often impossible to predict when such bursts of instability will strike, particularly in systems with a complex and ever-changing mix of players and pieces.</p> <p>Now engineers at MIT have devised a framework for identifying key patterns that precede an extreme event. The framework can be applied to a wide range of complicated, multidimensional systems to pick out the warning signs that are most likely to occur in the real world.</p> <p>“Currently there is no method to explain when these extreme events occur,” says Themistoklis Sapsis, associate professor of mechanical and ocean engineering at MIT. “We have applied this framework to turbulent fluid flows, which are the Holy Grail of extreme events. They’re encountered in climate dynamics in the form of extreme rainfall, in engineering fluid flows such as stresses around an airfoil, and acoustic instabilities inside gas turbines. If we can predict the occurrence of these extreme events, hopefully we can apply some control strategies to avoid them.”</p> <p>Sapsis and MIT postdoc Mohammad Farazmand have published their results today in the journal <em>Science Advances. </em></p> <p><strong>Looking past exotic warnings</strong></p> <p>In predicting extreme events in complex systems, scientists have typically attempted to solve sets of dynamical equations — incredibly complex mathematical formulas that, once solved, can predict the state of a complex system over time.</p> <p>Researchers can plug into such equations a set of initial conditions, or values for certain variables, and solve the equations under those conditions. If the result yields a state that is considered an extreme event in the system, scientists can conclude that those initial conditions must be a precursor, or warning sign.</p> <p>Dynamical equations are formulated based on a system’s underlying physics. But Sapsis says that the physics governing many complex systems are often not well-understood and they contain important model errors. Relying on these equations to predict the state of such systems would therefore be unrealistic.</p> <p>Even in systems where the physics are well-characterized, he says there is a huge number of initial conditions one could plug into associated equations, to yield an equally huge number of possible outcomes. What’s more, the equations, based on theory, might successfully identify an enormous number of precursors for extreme events, but those precursors, or initial states, might not all occur in the real world.</p> <p>“If we just blindly take the equations and start looking for initial states that evolve to extreme events, there is a high probability we will end up with initial states that are very exotic, meaning they will never ever occur for any practical situation,” Sapsis says. “So equations contain more information than we really need.”</p> <p>Aside from equations, scientists have also looked through available data on real-world systems to pick out characteristic warning patterns. But by their nature, extreme events occur only rarely, and Sapsis says if one were to rely solely on data, they would need an enormous amount of data, over a long period of time, to be able to identify precursors with any certainty.</p> <p><strong>Searching for hotspots</strong></p> <p>The researchers instead developed a general framework, in the form of a computer algorithm, that combines both equations and available data to identify the precursors of extreme events that are most likely to occur in the real world.</p> <p>“We are looking at the equations for possible states that have very high growth rates and become extreme events, but they are also consistent with data, telling us whether this state has any likelihood of occurring, or if it’s something so exotic that, yes, it will lead to an extreme event, but the probability of it occurring is basically zero,” Sapsis says.</p> <p>In this way, the framework acts as a sort of sieve, capturing only those precursors that one would actually see in a real-world system.</p> <p>Sapsis and Farazmand tested their approach on a model of turbulent fluid flow — a prototype system of fluid dynamics that describes a chaotic fluid, such as a plume of cigarette smoke, the airflow around a jet engine, ocean and atmospheric circulation, and even the flow of blood through heart valves and arteries.</p> <p>“We used the equations describing the system, as well as some basic properties of the system, expressed through data obtained from a small number of numerical simulations, and we came up with precursors which are characteristic signals, telling us before the extreme event starts to develop, that there is something coming up,” Sapsis explains.</p> <p>They then performed a simulation of a turbulent fluid flow and looked for the precursors that their method predicted. They found the precursors developed into extreme events between 75 and 99 percent of the time, depending on the complexity of the fluid flow they were simulating.</p> <p>Sapsis says the framework is generalizable enough to apply to a wide range of systems in which extreme events may occur. He plans to apply the technique to scenarios in which fluid flows against a boundary or wall. Examples, he says, are air flows around jet planes, and ocean currents against oil risers.</p> <p>“This happens in random places around the world, and the question is being able to predict where these vortices or hotspots of extreme events will occur,” Sapsis says. “If you can predict where these things occur, maybe you can develop some control techniques to suppress them.”</p> <p>This research was supported, in part, by the Office of Naval Research, the Air Force Office of Scientific Research, and the Army Research Office.</p> Engineers at MIT have devised a framework for identifying key patterns that precede an extreme event.Computer modeling, Fluid dynamics, Mechanical engineering, Oceanography and ocean engineering, Climate, Evolution, Oil and gas, Research, School of Engineering, Weather A genomic take on geobiology Researchers in Greg Fournier’s geobiology lab are seeking to calibrate the ancient history of life on Earth using genomic analysis. Mon, 05 Jun 2017 16:30:02 -0400 Helen Hill | EAPS <p>Scientists know that atmospheric oxygen irreversibly accumulated on Earth around 2.3 billion years ago, at a time known as the&nbsp;<a href="" target="_blank">Great Oxidation Event</a>, or GOE. Prior to that time all life was microbial, and most, if not all, environments were anoxic (that is, contained no oxygen). Oxygen was first produced some time before the GOE through the evolution of a group of photosynthetic bacteria known as <a href="" target="_blank">cyanobacteria</a>. Releasing oxygen as a by-product of splitting water in order to acquire electrons to be energized by light, this process led to dramatic changes in both the biological and geochemical processes on a planetary scale. Eventually, the continued accumulation of oxygen led to an oxidized surface, atmosphere, and ocean that persist to this day.</p> <p>Besides shedding light on a fundamental change in Earth’s climate, it is hoped that understanding the GOE will help scientists gain insight into the rise of eukaryotes — cellular organisms like us humans, in which genetic material is DNA in the form of chromosomes contained within a distinct nucleus. Eukaryotes require oxygen to produce sterols, an important part of their cell membranes. Furthermore, eukaryotes also contain mitochondria, organelles descended from ancient bacteria that use oxygen to generate energy using aerobic respiration.</p> <p>There are currently two schools of thought regarding how oxygen levels rose: The first proposes a small initial rise at the time of the GOE, with levels low but stable until increasing again around 600 million years ago, approaching modern levels. The second posits a more oscillatory rise with a greater increase immediately following the GOE, and then a subsequent crash, with levels only increasing again 600 million years ago.</p> <p>While geologists have been able to establish increasingly precise dates for the onset of the GOE through geochemical analyses, the ability to detect transient variations in oxygen levels following the GOE are less readily detected in the rock record. However, in the past couple of decades, it would be fair to say, science has experienced a "great genomics event" through which biologists, armed with the ability to sequence genes increasingly rapidly, now find themselves hard at work sequencing everything they can lay their hands on. And it turns out genomics may hold the answer to how oxygen continued to accumulate,</p> <p>Greg Fournier, an assistant professor of geobiology in the Department of Earth, Atmospheric and Planetary Sciences at MIT, is an expert in molecular phylogenetics, discovering the evolutionary histories of genes and genomes within microbial lineages across geological timescales.</p> <p>A particular current interest is the detection of events in the evolution of microbial metabolisms that likely align with global changes in Earth’s biogeochemical cycles, including oxygen.</p> <p>Molecular oxygen (O<sub>2</sub>) readily changes to an extremely reactive “free radical” form with an unpaired electron called superoxide, a chemical highly damaging to many biological systems. Many organisms are protected against superoxides by superoxide dismutase&nbsp;enzymes that convert superoxide to hydrogen peroxide, the first step in detoxifying this compound. It is present in most extant bacteria (i.e. ones that are alive today) but is assumed to have originally appeared in response to the increasingly oxygen rich environment of the GOE.</p> <p>Fournier is an expert in a process called <a href="" target="_blank">horizontal gene transfer</a>, or HGT. HGT is the exchange of genetic material between cellular organisms other than by regular “vertical” transmission of DNA from parent to offspring. He believes HGT evidence of oxygen-related genes like superoxide dismutase&nbsp;will enable him to distinguish between a steady and a fluctuating build-up.</p> <p>“If oxygen rose and remained steady we should see many such transfer events associated with superoxide dismutase,<em>”&nbsp;</em>Fournier explains. “If it rose and then fell back we would expect to see transfer events followed by the disappearance of the gene in different lineages, since the need to protect against oxygen would have ceased.”</p> <p>Because genetic data from old extinct lineages are not available, members of Fournier’s Lab use gene sequences sampled across modern organisms, building evolutionary trees known as phylogenies to explore how they relate to one another. By comparing these gene trees to the best guesses of how the microbial organisms are related, transfer events may be detected, and their relative timing inferred.</p> <p>Abigail Caron, a postdoc in the Fournier Group, uses a computer cluster housed at the&nbsp;<a href="">Massachusetts Green High Performance Computing Center</a> (MGHPCC) to run genetic analyses on different bacteria looking for instances of horizontal gene transfer, and mapping these events across many lineages.</p> <p>For only a small number of gene sequences, Caron can use a process called Ranger DTL (Rapid&nbsp;ANalysis of&nbsp;Gene Family&nbsp;Evolution using&nbsp;Reconciliation&nbsp;DTL) run on her laptop. But seeking to compare and integrate gene histories across upwards of 8,000 bacterial species, incorporating complex models of uncertainty within individual tree analyses, as she is attempting to do, is too intensive for any single computer. Having the MGHPCC cluster to work on allows her to run multiple analyses simultaneously across dozens of processors, making such high-resolution investigations into the history of these genes possible.</p> A bubble of oxygen emerges from a cyanobacterial mat growing in the lab.Photo: Tanja BosakResearch, Bacteria, Evolution, Genetics, EAPS, School of Science, Microbes Zika virus likely circulated in Americas long before its detection Analysis of largest collection of Zika genomes to date reveals trajectory and evolution of the virus. Wed, 24 May 2017 12:59:59 -0400 Broad Institute <p>The Zika virus circulated in many regions of the Americas for several months before cases of infection were detected, according to new data from an international research team from the Broad Institute of MIT and Harvard and several collaborating institutions.</p> <p>These findings, revealed today in <em>Nature</em> in a paper led by Pardis Sabeti of the Broad Institute and Harvard University, arise from an analysis of 174 Zika virus genomes — including the largest collection of new Zika virus genomes to date — sequenced from patient and mosquito samples collected in 11 affected countries and territories.</p> <p>The paper’s co-authors include Hayden Metsky, a graduate student in the Sabeti lab, MIT’s Department of Electrical Engineering, and the Computer Science and Artificial Intelligence Laboratory, who is one of the paper’s first authors; Lee Gehrke, the Hermann L.F. von Helmholtz Professor in MIT’s Institute for Medical Engineering and Science (IMES); and Irene Bosch, a research scientist at IMES.</p> <p>The genomic data allowed the research team to reconstruct for the first time the spread of the virus across South and Central America, the Caribbean, and into the southern United States.</p> <div class="cms-placeholder-content-video"></div> <p>In many of these regions, the virus circulated for months before local cases of infection were detected. Sabeti and colleagues’ analysis suggested that Zika was circulating in Brazil around February 2014, a year before that nation’s first confirmed infections were reported. Similarly, the virus appears to have arrived in Colombia, Honduras, Puerto Rico, and elsewhere in the Caribbean from 4.5 to 9 months before the first confirmed local infections, highlighting the importance of having sensitive and specific diagnostic tools early in an outbreak.</p> <p>These results appear only now, months after the peak of the outbreak, because sequencing Zika virus has proved to be challenging, particularly when done directly from patient samples. The difficulty arises because Zika virus is typically present at very low levels in patients and disappears quickly. As a result, very few Zika genomes had been generated prior to this study, leaving researchers with little basis for understanding how the virus is spreading and evolving.</p> <p>To address this lack of data, the team developed new laboratory and analytical methods for capturing robust Zika genomic data, and applied them to samples collected in partnership with collaborators in Brazil, Colombia, the Dominican Republic, Honduras, Jamaica, Puerto Rico, Massachusetts, and Florida to generate 110 new genomes for this study. The team combined those genomes with an additional 64 available in GenBank and in one of the study’s two companion papers, to carry out their analysis.</p> <p>“We knew it was important to understand the viral populations driving the epidemic, which motivated us to tackle the challenges of sequencing Zika,” says Metsky. “Because the data we generated capture the geographic diversity of the virus across the Americas, they provide an opportunity to trace how and when the virus spread. Our data and findings will also support development of more effective molecular diagnostic tests, as well as improved public health surveillance tools.”</p> <p>The work also highlights the importance of quickly creating trusted partnerships between researchers and across institutions and regions, and of sharing data openly during outbreaks.</p> <p>“This collaboration has been about each partner sharing their unique resources and expertise — samples, protocols, analyses, insights — to help understand and fight Zika,” says Thiago Moreno L. Souza, a study co-senior author and senior research scientist at Fundação Oswaldo Cruz in Rio de Janiero, Brazil. “Sharing the data widely for the same end goal was an obvious extension of that ethos.”</p> <p>The study was published together with two companion papers, one by Kristian Andersen from the Scripps Research Institute and colleagues examining Zika’s introduction into Florida, and the other by Oliver Pybus at Oxford University and colleagues examining the virus’s establishment and early spread within and beyond northeastern Brazil. All three teams committed to sharing data and ideas freely amongst themselves and to releasing their findings cooperatively and quickly.&nbsp;</p> <p>“Collectively our goal was to capture as complete a picture of the genetic underpinnings of the epidemic in the Americas as we could. Working together was critical to reaching that goal,” says study co-senior author Bronwyn MacInnis, associate director of malaria and viral genomics in the Broad’s Infectious Disease and Microbiome Program. “Instead of competing for publication, we wanted our papers to leverage each other and reflect our commitment to the greater good.”</p> <p>Zika remains a significant public health threat in affected countries and regions, highlighting the need for continued surveillance and research on the virus. According to MacInnis, the epidemic holds lessons about the role genomics can play in identifying and tracking emerging outbreaks early, before widespread infection occurs.</p> <p>“Genomics allowed us to reconstruct how the virus traveled and changed across the epidemic — which also means that genomics could have helped detect it much earlier,” she says. “We were way behind the curve on Zika. We need to be well ahead of the next emerging viral threat, and genomics can have a role in achieving this.”</p> <p>Support for this study was provided by Marc and Lynne Benioff, the National Institute of Allergy and Infectious Diseases, and other sources. Pardis Sabeti is an Investigator with the Howard Hughes Medical Institute.</p> <p>The work was and continues to be part of a collaboration across nations. Those currently involved include the following investigators, together with their teams and collaborators: Thiago Moreno L. Souza, Patrícia T. Bozza, Wim Degrave, et al. at Oswaldo Cruz Foundation in Brazil; Fernando Bozza at Oswaldo Cruz Foundation and D’or Institute in Brazil; Salim Mattar at the University of Córdoba in Colombia; Luis A. Villar Centeno at the Industrial University of Santander in Colombia; Ivette Lorenzana at the National Autonomous University of Honduras in Honduras; Joshua Anzinger at The University of the West Indies in Jamaica; Andrew Rambaut at the University of Edinburgh in the UK; Sharon Isern and Scott F. Michael at Florida Gulf Coast University; Sandra Smole at the Massachusetts Department of Health; Irene Bosch and Lee Gehrke at MIT; and Kristian Andersen at The Scripps Research Institute.</p> New research shows that the Zika virus circulated in many regions of the Americas for several months before cases of infection were detected. Courtesy of the Broad InstituteResearch, Broad Institute, School of Engineering, Electrical Engineering & Computer Science (eecs), Institute for Medical Engineering and Science (IMES), Biology, Disease, DNA, Medicine, Health sciences and technology, Evolution, Computer Science and Artificial Intelligence Laboratory (CSAIL) Entering the animal world In a history seminar, engineering students explore shifting ideas about animal intelligence and human uses of animals throughout the ages. Fri, 19 May 2017 16:05:01 -0400 Meg Murphy | School of Engineering <p>On a field trip, Harriet Ritvo and her MIT students went to look at preserved animals on public display, or stored as lab specimens, in collections housed at Harvard University. They encountered hundreds of species, some up close: touching the wings of a pickled bat, the silky fur of a mink, and the sharp claws of a lynx and a lion.</p> <p>Largely from the MIT School of Engineering, the students were part of a 14-person seminar on history and anthropology known as 21H.380 /21A.411/21H.980 (People and Other Animals). The class explores topics like how ideas about animal intelligence and agency have shifted over time, the human moral obligations to animals, and the limits imposed on the use of animals.</p> <p>Ritvo, the Arthur J. Conner Professor of History at MIT, and a pioneer in the field of animal-human cultural studies, divides the students’ explorations into units, including the history of hunting, the domestication of livestock, and the exploitation of animal labor.</p> <p>On this day’s outing, the aim was to “see how dead animals are displayed, and see behind-the-scenes how the displays are produced,” said Ritvo to her class. “We’ll see collections of dead specimens in various forms — stuffed, skins, skeletons.”</p> <p><strong>Fascinated by preservation</strong></p> <p>Zachary Bierstedt, an MIT senior in the Department of Aeronautics and Astronautics (AeroAstro), took a hands-on approach, jumping at the chance to handle the only mammal capable of sustained flight. &nbsp;</p> <p>“I am curious largely about what the preservation process actually does to the specimens,” said Bierstedt, as he lifted a bat, labelled <em>Phylbostomus hastatus panamensis</em> (great spear-nosed bat), from its jar. He spread its expansive wings. He ran a finger along the thick hair on its torso. “I was not expecting it to be so furry,” said Bierstedt.</p> <p>Access to the normally locked doors of labs and inventory within Harvard’s Museum of Comparative Zoology, was facilitated by Mark Omura, a curatorial staff member. He gathered students along a long metal table covered primarily in study skins and detailed the preservation process, explaining the systematic organization of the collection, one of the most extensive in the world.</p> <p>Moving to a cavernous storage room, he let students examine the additional specimen. Bierstedt lingered by a lion skin to feel its well-preserved claws.</p> <p>On another stop, MIT senior Alexa Garcia, a biological engineering major, took in the public displays in the Great Mammal Hall, a Victorian-era gallery in the Harvard Museum of Natural History.</p> <p>“We are learning to think about how people have related to other species over time,” said Garcia. She walked by glass cases holding a full-sized giraffe and camels. Hanging from the rafters were large skeletons of a sperm whale, a fin whale, and a right whale. “I find it very useful,” she added, perhaps all too aware of how new technologies developed at MIT, like gene editing, might alter our definition of natural life.</p> <p>MIT senior Veronica Padron, an AeroAstro major, stopped cold in front of some exhibits, snapping photographs. She zoomed in on a jellyfish in "Sea Creatures in Glass" — and then cried out as a hippo and a zebra rose into view as part of the Tropical Forest area.</p> <p>Asked about her experience in the class, Padron said: “In most engineering classes, you are told how things work. You apply principles. This class is more about interpreting meaning. We employ a different style of exploration and discussion. It balances us out.”</p> <p>The field trip wrapped up in the Glass Flowers Exhibit, a collection of models of more than 800 plant species. Students quickly handed Ritvo their final research papers before heading back to MIT. Watching them go, Ritvo said students in science and engineering benefit greatly from the lessons that humanities and social sciences offer. “Students learn a different way of understanding the world.”</p> <p><strong>Finding a voice</strong></p> <p>Students say that their reason for taking the course is more than just about knocking out a humanities requirement. “It’s really interesting to think about things from a different perspective,” said senior Matthew Nicolai. “We have to look through various subjectivities — the animal, the human — and contend with ethical issues. I don’t really think that way, so it’s intriguing.”</p> <p>He and Christian Argenti, both mechanical engineering majors, said they read the course description, and swiftly convinced two additional engineering students in their fraternity, Delta Kappa Epsilon, to take the course with them.</p> <p>In one class, they had delved into the ethical treatment of animals. A showing of the 1949 French documentary, "Le Sang des Bêtes" ("Blood of the Beasts"), featured the unvarnished butchering of horses, cattle, and sheep at a slaughterhouse.</p> <p>“There isn’t any attempt to make the killing ambiguous,” Ritvo said about the film. “What does it suggest about how things are perceived differently in different times and places?” Debate had ensued around their MIT seminar table as the scent of hyacinths drifted in from a nearby window overlooking the Charles.</p> <p>Marcus Urann, a junior studying mechanical engineering, appreciates such moments of dialogue. “You can get lost in the mix in engineering. We have large classes with hours of lectures. In this class, we meet weekly and discuss issues in depth,” he said. “It gives you a way to voice an opinion.”</p> Left to right: Matthew Nicolai, Dallace Francis, and Christian Argenti, MIT seniors in the Department of Mechanical Engineering and members of the fraternity Delta Kappa Epsom, took the MIT History seminar, People and Other Animals, together. Photo: Gretchen ErtlClasses and programs, History, Animals, Students, Undergraduate, Humanities, Evolution, History of science, SHASS, School of Engineering Darwin visits Wall Street Andrew Lo’s new book urges a rethink of financial markets, along evolutionary lines. Wed, 17 May 2017 23:59:59 -0400 Peter Dizikes | MIT News Office <p>If you have money in the stock market, then you are probably anticipating a profit over the long term — a rational expectation given that stocks have historically performed well. But when stocks plunge, even for one day, you may also feel some fear and want to dump all those stress-creating equities.</p> <p>There is a good reason for this: You’re human.</p> <p>And that means, to generalize, that you have both a rational side and some normal human emotions. To Andrew Lo, the Charles E. and Susan T. Harris Professor and director of the Laboratory for Financial Engineering at the MIT Sloan School of Management, accepting this basic point means we should also rethink some common ideas about how markets work.</p> <p>In economics and finance, after all, there is a long tradition of thinking about investors as profit-maximizing rational actors, while imagining that markets operate near a state of perfect efficiency. That sounds nice in theory. But evidence shows that this view is not sufficient for understanding the radical swings that market sentiment creates. &nbsp;</p> <p>“When you and I are making investment decisions independently, we’ll exhibit different behavior,” Lo says. Those varied decisions help keep markets stable, most of the time. “But when we all feel threatened at the same time, we’re likely to react in the same way. And if we all start selling stocks at once, we get a market crash and panic. Fear can overwhelm rationality.”</p> <p>Now Lo has written a new book about the subject, “<a href="">Adaptive Markets</a>,” published this month by Princeton University Press. In the book, he draws on insights from evolutionary theory, psychology, neuroscience, and artificial intelligence to paint a new picture of investors. Instead of regarding investors simply as either rational or irrational, Lo explains how their behavior may be “maladaptive” — unsuited to the rapidly changing environments that shifting markets present.&nbsp;&nbsp;</p> <p>In so doing, Lo would like to resolve the divergence between the realities of human behavior and the long-standing “efficient markets hypothesis” (EMH) of finance with his own “adaptive markets hypothesis,” to account for the dynamics of markets — and to provide new regulatory mechanisms to better ward off damaging crashes.</p> <p>“It takes a theory to beat a theory,” Lo quips, “and behavioralists haven’t yet put forward a theory of human behavior.”</p> <p><strong>Path-dependent</strong></p> <p>To get a grip on Lo’s thinking, briefly examine both sides of the EMH debate. On the one hand, markets do exhibit significant efficiencies. Do you own a mutual fund that tracks a major stock-market index? That’s because it is very hard for individual investors or fund managers to beat indexes over an extended period of time. On the other hand, based on what we know about market swings and investor behavior, it seems a stretch to think markets are always efficient.</p> <p>“The EMH is a very powerful theory that has added a great deal of value to investors, portfolio managers, and regulators,” Lo says. “I don’t want to be viewed as criticizing it. What I’m hoping to do is to expand its reach, by explaining under which conditions it’s likely to work well, and under which other conditions we require a different approach.”</p> <p>As Lo notes in the book, the EMH assumes that individuals always maximize their expected utility — they find the optimal way to spend and invest, all the time. Lo’s adaptive markets hypothesis relaxes this dictum on two counts. First, a successful investing adaptation doesn’t have to be the best of all possible adaptations — it just has to work fairly well at a given time.</p> <p>And second, Lo’s adaptive markets hypothesis does not hold that people will constantly be finding the best possible investments. Instead, as he writes in the book, “consumer behavior is highly path-dependent,” based on what has worked well in the past.</p> <p>Given those conditions, the market equivalent of natural selection weeds out poor investment strategies, Lo writes, and “ensures that consumer behavior is, while not necessarily optimal or ‘rational,’ good enough.” Not perfect, but decent.</p> <p>In this light, consider fund managers who do beat the big stock indexes for a while. In many cases, their successes are followed by years of poor performance. Why? Because they did not keep adapting to a changing investing environment. This familiar dynamic, Lo contends, is one reason we should drop the physics-inspired notions of the market as an efficient mechanism, and think of it in evolutionary terms.</p> <p>Or, as Lo writes in the book, “biology is a closer fit to economics than physics.” As the physicist Richard Feynman put it, “Imagine how much harder physics would be if electrons had feelings.”</p> <p><strong>Looking for policy impact</strong></p> <p>“Adaptive Markets” does not represent the first time Lo has put some of these ideas into print. It is the culmination of a long-term line of inquiry, and the most detailed, extended treatment he has given to the concept.</p> <p>The book is written for a general audience but has received a wide hearing in academia. Nobuhiro Kiyotaki, an economist at Princeton University, calls “Adaptive Markets” a “wonderful book” that “presents many valuable findings” and “is itself a manifestation of the important finding that rational thinking and emotion go together.”</p> <p>Lo says his hope for the book, however, is not just to change some minds among the public and other scholars, but to reach policymakers. Having served on multiple government advisory panels about regulation, Lo believes we need regulations that are more generally focused on limiting risk and large-scale crashes, rather than seeking to assess the legitimacy of umpteen new financial instruments.</p> <p>The analogy Lo likes to make is that finance needs an equivalent of the National Transportation Safety Board, the federal agency that investigates the systemic causes of aviation accidents, among other things, and whose existence has helped engender a period of unprecedented air safety.</p> <p>Even in the run-up to the 2008 financial-sector crisis, Lo contends, the notorious bond markets trading securities backed by subprime mortgages, and their derivatives, were not deeply “irrational.” After all, those markets had winners as well as losers; the problems included the way the markets were constructed and the opportunity for firms to wildly increase their risks while seeking big payoffs.&nbsp;</p> <p>“It’s not so much that market prices were wrong, it’s that the policies and incentives were flawed,” Lo contends.</p> <p>That might generate some heated debate, but Lo says it is a discussion he welcomes.</p> <p>“We aren’t really getting traction arguing either for or against efficient markets,” Lo says. “So maybe it’s time for a new perspective.”</p> “Adaptive Markets,” by Andrew Lo, published by Princeton University Press Photo: Jason DorfmanBusiness and management, Economics, Behavior, Evolution, Behavioral economics, Finance, Government, Books and authors, Faculty, Research, Sloan School of Management Tracking the spread of bird flu Asian flu strains can enter North America through Alaska, study finds. Fri, 17 Mar 2017 14:30:00 -0400 Anne Trafton | MIT News Office <p>A new paper from an MIT-led team demonstrates that Alaska can offer a significant foothold for Asian flu viruses, enabling them to enter North America. The research also shows that the region serves as a fertile breeding ground for new flu strains.&nbsp;</p> <p>In 2014 and 2015, an outbreak of H5N8, H5N1, and H5N2 influenza affected poultry farms in North America, resulting in the culling of nearly 50 million chickens and turkeys. The new study finds that an epidemic flu strain, which originated in Southeast Asia, was most likely carried into Alaska by wild migratory birds. In Alaska, the viruses mingled with local flu strains and eventually evolved into the deadly strains that spread south to poultry farms in Washington, Oregon, and California.</p> <p>“We think there’s strong evidence that those viruses moved through the Bering strait through wild bird populations and began a process of evolution that ended up with them infecting poultry populations and becoming a big agricultural issue,” says Jonathan Runstadler, an assistant professor of biological engineering and comparative medicine at MIT and the senior author of the study.</p> <p>The paper’s lead author is MIT postdoc Nichola Hill. Researchers from the U.S. Geological Survey, the University of Alaska at Fairbanks, Vanderbilt University Medical Center, the J. Craig Venter Institute, the U.S. Department of Agriculture, and the University of California at Davis also contributed to the study.</p> <p><strong>Influenza migration</strong></p> <p>Influenza strains come in many subtypes, which are classified by the structure of two proteins (abbreviated H and N) found on the surface of their viral envelope. In 1997, an outbreak of H5N1 that began in birds infected 18 people in Hong Kong and killed six of them. The virus then re-emerged in southeast Asia in the early 2000s, killing many birds and causing small pockets of human disease.</p> <p>Since then, H5N1 and other H5 strains have continued to circulate in wild bird populations, raising concerns that bird flu could spread again into poultry or into humans. Part of Runstadler’s recent research has focused on trying to understand how these viruses evolve in wild bird populations, with a particular focus on Alaskan birds because many wild birds migrate from southeast Asia to Alaska.</p> <p>Alaska hosts huge flocks of migratory waterbirds, such as ducks, geese, and gulls, which fly north from both Asia and southern regions of North America. “Water birds spread virus easily, and a lot of these birds migrate intercontinentally. They make a great host for influenza viruses,” Hill says.</p> <p>This intermingling of birds gives flu viruses a chance to undergo a process called genetic reassortment, which allows them to develop new traits such as the ability to infect a different host. Flu viruses have eight genetic segments that are independent and unattached, and when two different viruses infect the same host, they can swap segments.</p> <p>“The virus then comes out of that cell with the mixture of the two viruses,” Runstadler says. “This reassortment seems to be a major mechanism by which the influenza virus can move between different hosts.”</p> <p>Runstadler and Hill have previously shown that reassortment occurs in wild birds in Alaska during the breeding season, and that the process occurs at an even greater frequency as the birds move south. This led them to hypothesize that Alaska could be the entry point for highly pathogenic H5 viruses from Asia, and that these viruses could diversify and spread south into the United States.</p> <p>The researchers got the chance to test this hypothesis after the U.S. poultry outbreak began in late 2014. The MIT team and another group from the University of Alaska at Fairbanks and the USGS had taken taken flu samples from wild birds in 2014 as part of a larger project on flu virus evolution. After the poultry outbreak began, the researchers went back to their samples to try to determine whether they were predecessors to the viruses that caused the poultry sickness.</p> <p>Analyzing these sequences and comparing them with viruses taken from birds infected at lower latitudes of North America revealed that the virus had come into Alaska from southeast Asia. Once the virus arrived in Alaska, it began swapping genes with less harmful flu viruses already present in the Alaskan wild bird population.</p> <p>“As the highly pathogenic H5 virus entered into North America, along the way it reassorted with locally circulating, less pathogenic strains from North American wild birds,” Hill says. “We’ve been able to understand the trajectory of how the virus moved in and reassorted by looking at the strains that these birds in Alaska were shedding.”</p> <p>This genetic reassortment allowed the flu strains to diversify in ways that made it easier for them to spread among the wild bird population and eventually infect poultry as the wild birds migrated south.</p> <p>“This data is very important to our understanding of flu evolution and shows the importance of timely sampling in surveillance,” says Ralph Tripp, a professor of infectious diseases at the University of Georgia’s College of Veterinary Medicine, who was not involved in the research.</p> <p><strong>“We don’t know enough”</strong></p> <p>The researchers say that the study highlights the need for surveillance of potentially dangerous flu strains that could enter through Alaska and spread south. Such strains could pose a threat to not only agricultural operations but also human heath, because viral reassortment can make it easier for the virus to spread among people.</p> <p>“I think it’s fair to say that the circulation of H5 viruses anywhere is cause for concern because of the fact that the influenza virus can do this reassortment,” Runstadler says. “If one of these viruses that was circulating in North America, or one of the ones still circulating in Asia, happened to be able to infect a person who is also sick with a seasonal H1N1 virus, you’d have some concern that those viruses would reassort and you might get a novel virus produced that is able to transmit between humans and could be a public health risk.”</p> <p>The researchers also plan to investigate how human activities, such as urbanization and agriculture in Alaska and elsewhere in North America might influence the flu virus’ ability to evolve and infect new hosts by changing the distribution and susceptibility of wild birds.</p> <p>“Humans have used and altered landscapes that provide food sources for populations of birds, and affected migration patterns,” Runstadler says. “We don’t know enough about influenza virus to say what’s really a risk and what’s not. That’s one reason why we do what we do, to try to figure that out better.”</p> A new paper from an MIT-led team demonstrates that Alaska can offer a significant foothold for Asian flu viruses, enabling them to enter North America. Research, Biological engineering, Division of Comparative Medicine, School of Engineering, Influenza, Disease, Evolution, Viruses, Genetics Study suggests complex life was present on Earth 2.33 billion years ago New estimate predates earliest fossil evidence by 800 million years. Mon, 06 Mar 2017 10:59:59 -0500 Jennifer Chu | MIT News Office <p>An exhaustive genetic analysis of modern-day organisms has revealed new insights into Earth’s earliest forms of complex life.</p> <p>The findings, reported by MIT earth scientists today in <em>Nature,</em> suggest that eukaryotes — the domain of life comprising animals, plants, and protists — were present on Earth as early as 2.33 billion years ago, right around the time when oxygen became a permanent fixture in the atmosphere.</p> <p>This new time-stamp for ancient life significantly predates the earliest sign of eukaryotes found in the fossil record —1.56 billion-year-old macroscopic fossils that scientists widely agree are the remains of multicellular algae-like organisms. &nbsp;</p> <p>The MIT researchers arrived at their estimate not by examining rocks for fossil evidence but by using a technique called “molecular clock analysis.” This approach involves first sifting through DNA databases to trace the evolution of particular gene sequences across hundreds of modern species. Then, using ages derived from the fossil animal and plant relatives, these sequences can be tied backward in time to the earliest point at which those sequences must have been expressed in ancestral eukaryotes.</p> <p>“We’ve again demonstrated the feasibility of using modern DNA to provide insights about early life,” says Roger Summons, professor of geobiology in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “We have no concrete records of early life. We have a few fossil microbes, which are often disputed, and some geochemical signals, but it’s not enough to reconstruct an informed history of life. What we’re saying is, you can look at what’s on the planet today, and you can tell something important about what the organisms’ ancient ancestors were doing.”</p> <p>The analysis was carried out by Summons and lead author David Gold, a former MIT postdoc who is currently at Caltech, along with Abigail Caron, a senior research support associate at MIT, and Gregory Fournier, the Cecil and Ida Green Career Development Assistant Professor in EAPS.</p> <p><strong>The oldest enzymes</strong></p> <p>The team focused its genetic search on DNA sequences that code for the biosynthesis of sterol, a class of molecules found in all eukaryotes that influences the characteristics and behavior of their cell membranes.</p> <p>“[Sterol] determines how a membrane changes shape and mediates behavior — for example, the ability to engulf a piece of food,” Summons says. “A single-celled eukaryote can engulf and digest its food, whereas most bacteria have to excrete enzymes to break something down before taking it in.”</p> <p>The group looked to trace the genetic evolution of the first two enzymes involved in sterol production: SQMO, or squalene monooxygenase, which inserts an atom of oxygen into squalene; and OSC, or oxidosqualene cyclase, which folds the oxidosqualene molecule up to form the classic four-ring configuration of a sterol, the best known example of which is cholesterol.</p> <p>The two enzymes represent the beginning steps in the biosynthesis of sterol, which over time has evolved to include many more enzymes that improve sterol function and effectivness. The researchers reasoned that if they could trace back the evolution of the enzymes in the first steps of sterol biosynthesis , they could then infer when some of the earliest eukaryotes were present on Earth.</p> <p><strong>Tracing a tree</strong></p> <p>The team looked for SQMO and OSC in the National Center for Biotechnology Information protein database, a vast compendium of genetic sequences for thousands of modern species, contributed by scientists all over the world. The researchers wrote algorithms to efficiently cull through the genetic data, looking for those species that expressed the DNA sequences coding for SQMO and OSC.</p> <p>Then, for each enzyme they drew up a phylogentic tree — a branching diagram showing the evolutionary relationship among those species expressing either SQMO or OSC. &nbsp;</p> <p>“When you plot the trees for both enzymes, you find they’re eerily similar,” Summons says. “To me, this was an astonishing fact: These histories of these two enzymes across the eukaryote tree, and also including some bacteria, look pretty close to identical. The genes always move together. It’s very rare to find one without the other right next to it.”</p> <p>In particular, the researchers noted two early points along both evolutionary trees, where it appeared that each enzyme was genetically transferred between eukaryotes and &nbsp;bacteria. These genetic jumps, known as horizontal gene transfers, mark the times when organisms shared these genes.</p> <p>To identify these points, the researchers performed a “molecular clock analysis,” a technique which measures time according to random changes in DNA, as these mutations occur at relatively constant rates. Summons and his colleagues used other algorithms based on the “topology,” or rate of genetic mutation, in each evolutionary tree.</p> <p>They calibrated the algorithm with data from known fossil records, including confirmed ages of certain species within each tree, including ancient corals, starfish, and algae. They then ran the algorithm — their molecular clock — backward in time to determine when the genes for sterol were transferred between bacteria and eukaryotes. Running the clock in subtly different ways, along with error propagations, gave dates that converged around one point, 2.3 billion years ago.</p> <p>“The age of eukaryotes has been argued for decades, and there are widely differing opinions,” Summons says. “We’re putting out this piece of evidence that we think is significant, that says we believe that sterol was being made at least 2.3 billion years ago, and that the earliest eukaryotes were here at least that long.”</p> <p><strong>Evolution, unraveled</strong></p> <p>In 2016, Summons’ group determined that another life-shifting event took place around 2.3 billion years ago: Oxygen became a permanent fixture in the Earth’s atmosphere, in what is now regarded as the Great Oxidation Event. Summons says the possibility that eukaryotes may have existed around the same time makes sense, as they would have required ample amounts of oxygen to synthesize sterols in order to maintain their cell membranes.&nbsp;</p> <p>Going forward, the team plans to trace the evolutionary history of enzymes further down in the sterol pathway — particularly those involved in synthesizing cholesterol — again by using modern genetic sequences to, as Summons puts it, “unravel its evolutionary story.”</p> <p>“People have known for many years that they can work out ancestries from DNA, including the ancestry of humanity,” Summons says. “We know a lot about the connections between Neanderthals, Denisovans, and other early groups of humans from pieces of DNA in bone. But that’s projecting back a couple million years. We’re projecting back 2.3 billion years. So we’re showing modern DNA can be used to understand key events in the history of life, billions of years ago.”</p> <p>This research was supported, in part, by the Simons Foundation, the Agouron Institute, and the National Science Foundation.</p> MIT earth scientists have found evidence that eukaryotes — the domain of life comprising animals, plants, and protists — were present on Earth as early as 2.33 billion years ago, right around the time when oxygen became a permanent fixture in the atmosphere. Bacteria, Microbes, Biology, DNA, EAPS, Evolution, Genetics, Chemistry, Research, School of Science New study sets oxygen-breathing limit for ocean’s hardiest organisms Bacteria can survive in marine environments that are almost completely starved of oxygen. Mon, 19 Dec 2016 00:00:02 -0500 Jennifer Chu | MIT News Office <p>Around the world, wide swaths of open ocean are nearly depleted of oxygen. Not quite dead zones, they are “oxygen minimum zones,” where a confluence of natural processes has led to extremely low concentrations of oxygen.</p> <p>Only the hardiest of organisms can survive in such severe conditions, and now MIT oceanographers have found that these tough little life-forms — mostly bacteria — have a surprisingly low limit to the amount of oxygen they need to breathe.</p> <p>In a paper published by the journal <em>Limnology and Oceanography</em>, the team reports that ocean bacteria can survive on oxygen concentrations as low as approximately 1 nanomolar per liter. To put this in perspective, that’s about 1/10,000th the minimum amount of oxygen that most small fish can tolerate and about 1/1,000th the level that scientists previously suspected for marine bacteria.</p> <p>The researchers have found that below this critical limit, microbes either die off or switch to less common, anaerobic forms of respiration, taking up nitrogen instead of oxygen to breathe.</p> <p>With climate change, the oceans are projected to undergo a widespread loss of oxygen, potentially increasing the spread of oxygen minimum zones around the world. The MIT team says that knowing the minimum oxygen requirements for ocean bacteria can help scientists better predict how future deoxygenation will change the ocean’s balance of nutrients and the marine ecosystems that depend on them.</p> <p>“There’s a question, as circulation and oxygen change in the ocean: Are these oxygen minimum zones going to shoal and become more shallow, and decrease the habitat for those fish near the surface?” says Emily Zakem, the paper’s lead author and a graduate student in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “Knowing this biological control on the process is really necessary to making those sorts of predictions.”</p> <p>Zakem’s co-author is EAPS Associate Professor Mick Follows.</p> <p><strong>How low does oxygen go?</strong></p> <p>Oxygen minimum zones, sometimes referred to as “shadow zones,” are typically found at depths of 200 to 1,000 meters. Interestingly, these oxygen-depleted regions are often located just below a layer of high oxygen fluxes and primary productivity, where fish swimming near the surface are in contact with the oxygen-rich atmosphere. Such areas generate a huge amount of organic matter that sinks to deeper layers of the ocean, where bacteria use oxygen — far less abundant than at the surface — to consume the detritus. Without a source to replenish the oxygen supply at such depths, these zones quickly become depleted.</p> <p>Other groups have recently measured oxygen concentrations in depleted zones using a highly sensitive instrument and observed, to their surprise, levels as low as a few nanomolar per liter — about 1/1,000th of what many others had previously measured — across hundreds of meters of deep ocean.</p> <p>Zakem and Follows sought to identify an explanation for such low oxygen concentrations, and looked to bacteria for the answer.</p> <p>“We’re trying to understand what controls big fluxes in the Earth system, like concentrations of carbon dioxide and oxygen, which set the parameters of life,” Zakem says. “Bacteria are among the organisms on Earth that are integral to setting large-scale nutrient distributions. So we came into this wanting to develop how we think of bacteria at the climate scale.”</p> <p><strong>Setting a limit</strong></p> <p>The researchers developed a simple model to simulate how a bacterial cell grows. They focused on particularly resourceful strains that can switch between aerobic, oxygen-breathing respiration, and anaerobic, nonoxygen-based respiration. Zakem and Follows assumed that when oxygen is present, such microbes should use oxygen to breathe, as they would expend less energy to do so. When oxygen concentrations dip below a certain level, bacteria should switch over to other forms of respiration, such as using nitrogen instead of oxygen to fuel their metabolic processes.</p> <p>The team used the model to identify the critical limit at which this switch occurs. If that critical oxygen concentration is the same as the lowest concentrations recently observed in the ocean, it would suggest that bacteria regulate the ocean’s lowest oxygen zones.</p> <p>To identify bacteria’s critical oxygen limit, the team included in its model several key parameters that regulate a bacterial population: the size of an individual bacterial cell; the temperature of the surrounding environment; and the turnover rate of the population, or the rate at which cells grow and die. They modeled a single bacterial cell’s oxygen intake with changing parameter values and found that, regardless of the varying conditions, bacteria’s critical limit for oxygen intake centered around vanishingly small values.</p> <p>“What’s interesting is, we found that across all this parameter space, the critical limit was always centered at about 1 to 10 nanomolar per liter,” Zakem says. “This is the minimum concentration for most of the realistic space you would see in the ocean. This is useful because we now think we have a good handle on how low oxygen gets in the ocean, and [we propose] that bacteria control that process.”</p> <p><strong>Ocean fertility</strong></p> <p>Looking forward, Zakem says the team’s simple bacterial model can be folded into global models of atmospheric and ocean circulation. This added nuance, she says, can help scientists better predict how changes to the world’s climate, such as widespread warming and ocean deoxygenation, may affect bacteria.</p> <p>While they are the smallest organisms, bacteria can potentially have global effects, Zakem says. For instance, as more bacteria switch over to anaerobic forms of respiration in deoxygenated zones, they may consume more nitrogen and give off as a byproduct nitrogen dioxide, which can be released back into the atmosphere as a potent greenhouse gas.</p> <p>“We can think of this switch in bacteria as setting the ocean’s fertility,” Zakem says. “When nitrogen is lost from the ocean, you’re losing accessible nutrients back into the atmosphere. To know how much denitrification and nitrogen dioxide flux will change in the future, we absolutely need to know what controls that switch from using oxygen to using nitrogen. In that regard, this work is very fundamental.”</p> <p>This research was supported, in part, by the Gordon and Betty Moore Foundation, the Simons Foundation, NASA, and the National Science Foundation.</p> MIT oceanographers have found that some small marine organisms — mostly bacteria — have a surprisingly low limit to the amount of oxygen they need to breathe.Image: MIT NewsBacteria, EAPS, Environment, Evolution, Global Warming, Greenhouse gases, Oceanography and ocean engineering, Research, School of Science, Climate change, Microbes, Climate &quot;Song of the Human&quot;: An origin story New work by composer Pete M. Wyer draws inspiration from MIT linguistic scholar Shigeru Miyagawa&#039;s hypothesis on the origins of human language. Tue, 13 Dec 2016 12:20:00 -0500 School of Humanities, Arts, and Social Sciences <p>History gives us a long, rich account of scholarly and scientific knowledge influencing artists — and artistic works in turn affecting the reception of ideas and scientific developments. This migration of ideas and flow of influence, back and forth, from one discipline to another can be extremely fruitful.</p> <p>In the 16th century, for example, the work of Copernicus, "De revolutionibus," captivated William Shakespeare, whose plays are replete with references to the new astronomy. In the same century, the anatomist Andreas Vesalius enlisted the best draftsmen from Titian’s studio to create "De humanis corporis fabrica," a book that had incalculable influence on both medical science and artistic practice, outpacing other similar texts in its impact, largely because of the masterful illustrations and superb printing.</p> <p><strong>Migration of ideas</strong></p> <p>A contemporary example of the influences between scholarship and art is “Song of the Human,” a new musical work using birdsong, human voices, and found sound, for which British composer Pete M. Wyer drew on the research and hypotheses of Shigeru Miyagawa, a professor of linguistics in the MIT Department of Linguistics and Philosophy.</p> <div class="cms-placeholder-content-video"></div> <p>Hypotheses — which represent unfinished business for scientists — have often proven to be fertile ground for artists, and for Wyer, Miyagawa’s ideas about the origins of human language, occupy a borderland where reason, imagination, science, and philosophy meet. While developing “Song of the Human,” Wyer read extensively from Miyagawa’s research, in particular his Integration Hypothesis, which builds upon Darwin’s observation that “the sounds uttered by birds offer in several respects the nearest analogy to language.”</p> <p>The 18-channel sonic installation and live choral performance that comprise “Song of the Human” — which premiered in October in the Winter Garden of the World Financial Center in New York — is now introducing Miyagawa’s ideas to communities beyond the academy.&nbsp; &nbsp;</p> <p><strong>How we speak in music</strong></p> <p>In brief, Miyagawa’s hypothesis suggests that there are two layers in all human languages: a "lexical" layer (words), and an "expressive" layer (grammar), which closely resembles birdsong, and that these two layers merged between 50,000 and 80,000 years ago to form human language. In 2010, he published a monograph on syntax across many languages, "Why Agree? Why Move?" (MIT Press), a formal linguistic study of the two layers of language from the prism of what’s called the "duality of semantics."</p> <p>While writing this book, Miyagawa was struck by how fundamentally different these two systems are and began researching correlates to both the lexical and expressive layers in nonhuman species. He found a counterpart for the lexical layer in the alarm calls system used by primates, wherein distinct calls correspond to outside stimuli.</p> <p>Finding a correlate for the expressive layer was elusive, however, until one day, he recalls, “I was sitting with some graduate students who were teaching children to play Japanese chess, shogi. When one graduate student from MIT Brain and Cognitive Sciences sat next to me, I asked about his research. He was researching songbirds and explained how they create patterns without meaning.</p> <p>“And I said, ‘Ah!’ and asked him for a reading list. Everything was completely serendipitous.” In 2013, Miyagawa published his findings in "Frontiers in Psychology," in a co-authored paper, "The emergence of hierarchical structure in human language."</p> <p>Meanwhile, in England that same year, Wyer chanced to overhear a couple on a train arguing in a language he does not speak. While he could not understand their words, he nevertheless understood the essence of their conversation — an experience that illuminated “something we easily forget: that we speak in music.”</p> <p>Wyer wrote an article about the event for "Broad Street Review" in which he likened speech to birdsong. At that time, he had also observed that, after feeding mealworms to a robin in his garden, “The robin sang a little thank-you song, followed by a very soft song, which I initially thought to be sub-song. I was struck by how close the contours of the song were to human babbling. I also noticed how birds borrow melodies from each other, and humans do that in speech too. We take speech-melodies from people we like perhaps for the same reason, to make ourselves more attractive. This all led me to googling "speech" and "birdsong," and I soon discovered an article about Professor Miyagawa’s hypothesis on the BBC website.”</p> <p><strong>Almost a new species</strong></p> <p>Discovering Miyagawa’s hypothesis was “validating and inspiring,” Wyer says. “While I had made a connection between speaking voice and birdsong, I was conscious that I was approaching everything as an artist, not a scientist. As a musician and composer, it makes perfect sense that our speech developed from birdsong. I can’t think of another creature in the animal kingdom that has that variety of pitch, tone, dynamic and structure. The discovery of the Integration Hypothesis, however, gave me a whole new view — it was no longer a personal comparison that was somewhat interesting, it was a scientific exploration. It deepened my own analysis and approach: I wouldn't have made ‘Song of the Human’ without it.”<br /> <br /> Wyer wrote to Miyagawa to tell him he was composing a piece that dealt with human language and birdsong. Miyagawa recalls the letter: “He said the musical composition was inspired by my research. He read everything I wrote about it, which is not easy because there’s a lot of technical stuff in these articles. And he would write to ask me to clarify what I meant by certain things. He was really committed to understanding my research.”</p> <p>But it was not just the linguistic hypothesis that captivated Wyer: “What attracts me to Miyagawa’s idea is the whole philosophical principle underlying it. We use pitch, rhythm, tone and dynamic, musical elements, as part of our speech, and when we remove words and listen&nbsp;only to that music, we almost do encounter a new species. I find that a hopeful encounter. In this wordless song we get a glimpse of our inner nature. We can hear love, fear, playfulness, and other states of mind and emotion, but nationality, religion, race, gender disappear. Whatever we find in this song, we find in all people — the song of the human."<br /> <br /> The New York premiere of “Song of the Human” included a 40-minute choral score performed by The Crossing choir, with an immersive soundscape comprised of the dawn chorus — a term for birds’ singing in the early morning, particularly in mating season. Wyer recorded the dawn chorus simultaneously at 16 locations in woods in Cornwall, Suffolk, and London in order to play back a vivid, immersive re-creation of nature's morning symphony. For the Winter Garden installation, Wyer also used multiple, independent speakers and software to move prerecorded sounds, such as wind and rain, throughout the space. By physically dispersing the sound, Wyer created an individualized experience in which each person can walk within the soundscape.<br /> &nbsp;<br /> <strong>A way to interact with the world</strong></p> <p>In his “Song of the Human” compositions, Wyer emphasizes “what we share in music when we abandon words, and the connections we can rediscover when we move past the labels we attach to ourselves and others.” Miyagawa’s work likewise causes us to think of the universality of language in evolutionary terms. It is not just a random cultural construct, but is based in part on capacities humans share with other species.</p> <p>After attending the premiere, Miyagawa observed, “What I understood, and appreciated, about what Pete did is this: He literally pulled off that idea that if you take language and drop all the words, what you have is a system with which you can communicate, but without specific lexical meaning. Instead, you communicate intent and emotions. That’s what the expressive system is. That's what gets you in contact with the world. Some would disagree, but I think that’s what the expressive system does — it gives us a way to interact with the world.”</p> <p>“Song of the Human” will be performed in the Messums Wiltshire Gallery and Arts Centre in Tisbury, Wiltshire, England from February to March 2017.<br /> &nbsp;</p> <h5><em>Story prepared by MIT SHASS Communications<br /> Writing and Editorial team: Sharon Lacey, Emily Hiestand, Kathryn O'Neill</em><br /> &nbsp;</h5> <h4></h4> "Song of the Human" made its world premiere at the Winter Garden in New York City. Discovering MIT Professor Shigeru Miyagawa’s research on birdsong was “validating and inspiring,” creator Pete Wyer says. Arts, Faculty, Linguistics, Music, Evolution, Behavior, SHASS 3Q: Historian Harriet Ritvo on what it means to be &quot;wild&quot; Scientists, social scientists, and humanists heed the call of the wild at MIT workshop. Fri, 04 Nov 2016 17:50:01 -0400 School of Humanities, Arts, and Social Sciences <p><em>What does "wild" mean?<strong> </strong>Scientists, social scientists, and humanists tackled this question during "Call of the Wild," a workshop convened at MIT by Harriet Ritvo, the Arthur J. Conner Professor of History at MIT, and Sally Shuttleworth, professor of English literature at Oxford University. The event was sponsored by MIT International Science and Technology Initiatives (MISTI), a program of the MIT School of Humanities, Arts and Social Sciences, and co-sponsored by Constructing Scientific Communities, a project based at Oxford and supported by the United Kingdom Arts and Humanities Research Council.</em></p> <p><em>In opening remarks, Ritvo observed that the term “wild” is receiving renewed attention from academics and popular authors alike. Even those who are critical of the term employ it frequently, she said, also noting that most of us are uncertain of the word's conceptual parameters.</em></p> <p><em>Thus, Ritvo explained, a major goal of the workshop was to "tease apart" this ambiguous "multivalent term." In doing so, presentations spanned disciplines from biology to anthropology, astrophysics, and literature, exploring topics such as "Wildness in the Microbial World," "Bewilderness," "Drawing Boundaries around the Wild," and "Domesticating the Wave." For a full account of all the conference discussions, read the <a href="" target="_blank">Call of the Wild Workshop Report</a>, prepared by Alison Laurence, a PhD candidate in the MIT doctoral program in History, Anthropology, and Science, Technology, and Society (HASTS)</em></p> <p><em>Ritvo, who teaches courses in British history, environmental history, the history of human-animal relations, and the history of natural history, is the author of four books, among them "<a href="" target="_blank">The Animal Estate</a>," recently named as one of the 100 most significant books published by Harvard University Press. She shared her thoughts recently about the concept "wild" with SHASS Communications.</em></p> <p><strong>Q</strong>: How can we tell whether or not something is "wild"?</p> <p><strong>A: </strong>This was the question that provided the underlying structure for the workshop, and there are no definitive answers — this is one reason that the workshop was so interesting.</p> <p>"Wild" is a very powerful category now, as it has been for many centuries. The emotional or ethical response to this power, however, has recently altered. That is to say, for most of history, to call something "wild" was to express disapproval, but the term has become sufficiently positive for the Shaw's supermarket chain to brand its "organic" product line as "Wild Harvest," described on its website as "created, flavored, and colored by nature." As wildness has come to seem less threatening and more threatened, people have come to like it better.</p> <p>Even when people agree about whether wildness is good or bad, they have often disagreed about exactly what it is, and about whether an individual organism or group of organisms or even an environment should be described as wild. Sometimes this divergence reflects shifting historical contexts (or lack of historical context). For example, the landscape of the English Lake District has often been characterized as wild, although it is the creation of many generations of sheep and shepherds. Similarly, the first European settlers to arrive in New England perceived the fruitful open woodlands as wild since they were unable to recognize the subtle yet productive management techniques of the people already living there.</p> <p>Sometimes the definition of "wild" reflects the lenses provided by disciplines. The workshop included participants representing the range of academic disciplines, from literary studies to astrophysics. Presentations focused on animals, plants, microorganisms, as well as the metaphoric extension of wildness to such entities as waves. They explored the reactions of non-specialists as well as of scientists and scholars.</p> <p>Unsurprisingly, it turns out that deciding whether a fungus is wild or domesticated is a very different process than making an analogous discrimination with regard to a cat. And cheese makers think differently about the wildness of the fungi that transform their milk than do truffle growers about the fungi that they attempt to coax from unpredictably recalcitrant trees. House cats may seem wilder to specialists in animal behavior than they do to historians or pet owners (or the reverse, depending on the cat).</p> <p><strong>Q</strong>: Do these alternative understandings of wildness have practical consequences?</p> <p><strong>A: </strong>The stakes involved in receiving — or being denied — designation as "wild" can be very high. Sometimes the rewards are merely economic (for the designators, not those designated). For example, the aesthetic cachet of wildness has inspired the development of domestic cat breeds that include small wild cats among their relatively distant forebears; thus the Savannah cat has the African serval in its family tree. Such breeds are much more expensive than breeds with no claims to exotic extraction or cats of no particular breed.</p> <p>But often being recognized as "wild" has farther-reaching consequences, especially in the realms of environmental conservation and species protection. It is much easier to garner political and financial support for the preservation of a landscape if it is described as "wild" or "virgin" or "pristine," even though most such claims are vulnerable to challenge. This is one reason that the national park movement in the United States and many other places (although not in Europe) began by trying to erase the signs of previous human occupation.</p> <p>Twenty years ago, the environmental historian William Cronon argued against this absolute understanding of "wilderness" in a <a href="" target="_blank">well-known essay</a> that has remained surprisingly controversial.</p> <p>Individual species can also be held to very demanding standards of purity. If their descent is suspected to include significant miscegenation, they can be rejected as candidates for protection or reintroduction. For example, the designation of the red wolf as an endangered species has been entangled with the question of whether it is a pure species or a hybrid of the gray wolf and the coyote.</p> <p>Similar discussions have swirled around "rewilding" projects — that is, both attempts to re-create vanished (preindustrial and preagricultural) landscapes, such as the Buffalo Commons proposed to replace the most arid portions of the Great Plains, and attempts to resurrect the extinct species that inhabited them, such as the aurochs, the ancestor of all extant domesticated cattle that once roamed the forests of Europe. Needless to say, such attempts raise a variety of political issues, as well as environmental and economic ones.</p> <p><strong>Q</strong>: Are such terms as "invasive species" useful in light of the broad spectrum of biological change that occurs continuously, with or without human engagement?</p> <p><strong>A: </strong>Perhaps because being recognized as wild can have such significant consequences, various gatekeeping designations have emerged. That is to say, people have tried to erect barriers to restrict the designation of wildness to animals or other organisms found worthy. In addition to demonstrating unsullied descent, protected species need to be perceived as indigenous or native. This requirement reflects the relative brevity of human historical imagination — or the sense that "wild" or "natural" ecosystems are somehow static — in either case, a reluctance to recognize that all terrestrial and marine environments have experienced radical change.</p> <p>The term "invasive" also tends to obscure the extent to which humans bear responsibility for the intrusive presence of such organisms. Thus the Australian brushtail possum is persecuted as invasive in New Zealand, where it was introduced over a century and a half ago in an attempt to establish a fur industry. The lionfish that have become common in the Caribbean were brought to Florida to stock home aquariums; like Japanese knotweed, many plants now targeted for extirpation were introduced to adorn home gardens. Other so-called invasions, such as those of purple loosestrife and zebra mussels, occurred as unintended side effects of global trade.</p> <p>On the other hand, not being sufficiently or conventionally domesticated can also put organisms at risk. Thus animals who lapse from their domesticated condition can be castigated as "feral" — as, occasionally, can be humans who lapse from their civilized condition. In Australia, the sense of "feral" has shifted to overlap significantly with "invasive," so that the Department of the Environment and Energy includes cane toads and red foxes in that category, along with cats, pigs, and camels who have slipped their chains.</p> <p>It is interesting that although humans are occasionally willing to castigate each other as "feral" or "wild," we are seldom inclined to characterize our species as "invasive."</p> <h5><em>Interview prepared by MIT SHASS Communications<br /> Editorial team: Emily Hiestand and Kathryn O'Neill</em><br /> <br /> &nbsp;</h5> The term “wild,” is receiving renewed attention from academics and popular authors alike. MIT historian Harriet Ritvo notes that even those who are critical of the term employ it frequently, and that most of us remain uncertain of the word's conceptual parameters.Photo collage: SHASS Communications Biology, Evolution, History, History of science, Humanities, Environment, Faculty, 3 Questions, Social sciences, Animals, SHASS, MISTI Retracing the origins of a massive, multi-ring crater Scientists reconstruct first hours after a giant impact created one of the largest craters on the moon. Thu, 27 Oct 2016 14:00:00 -0400 Jennifer Chu | MIT News Office <p>Scientists from MIT and elsewhere have reconstructed the extreme collision that created one of the moon’s largest craters, 3.8 billion years ago. The team has retraced the moon’s dramatic response in the first hours following the massive impact, and identified the processes by which large, multi-ring basins can form in the aftermath of such events.</p> <p>The findings, published today in two papers in the journal <em>Science</em>, may shed light on how giant impacts shaped the evolution of the moon, and even life on Earth, shortly after the planets formed.</p> <p>The team’s results pertain to the moon’s Orientale basin, an expansive, bull’s eye-shaped depression on the southwestern edge of the moon, just barely visible from Earth. The basin is surrounded by three concentric rings of rock, the largest one stretching 580 miles across — about three times as wide as the state of Massachusetts. Until now, it’s been unclear how such massive, multi-ring basins materialized.</p> <p>Using data collected by NASA’s Gravity Recovery and Interior Laboratory (GRAIL) mission, the researchers determined that the 3.8-billion-year-old basin was created by a huge impactor that punched an initial, transient crater into the lunar surface, measuring up to 285 miles in diameter — about as wide as the state of New York.</p> <p>This impact, the researchers calculated, sent at least 816,000 cubic miles of pulverized lunar crust flying out from the impact site — an amount equivalent to 135 times the combined volume of the Great Lakes.</p> <p>The ejected material, which the team modeled in computer simulations, rose up like a tidal wave, then crashed down to the lunar surface, creating giant faults through the entire crust and forming two concentric walls of rock on the surface, each rising several kilometers high. Most of the action, according to simulations, occurred over just a couple of hours.&nbsp;&nbsp;</p> <p>If such massive, violent impacts were pummeling the moon, they must have been doing the same, if not more, to the Earth, says Maria Zuber, vice president for research and the E.A. Griswold Professor of Geophysics at MIT.</p> <p>“What’s interesting is, this was during the time when the first life forms were starting to emerge on the Earth,” says Zuber, who is the principal investigator for GRAIL and lead author on one of the <em>Science </em>papers. “These very large impacts probably came in, sterilizing the surface, and goodness knows how many times nascent life may have started and stopped and had to start again. It’s just amazing how catastrophic these impacts were.”</p> <p><img alt="" src="/sites/" style="width: 595px; height: 430px;" /></p> <p><span style="font-size:9px;">Above is the most realistic animation of the Orientale crater collapse and ring formation. Colors denote temperature, from hot, red crustal material to cooler material, in blue. Over a little more than 2 hours, the animation shows the moon’s initially cool surface as it responds to a very large impact. Instantly, the energy from the collision heats up the material closest to the impact, and the crust surges more than 100 km above the lunar surface, before crashing back down. The pulverized material oscillates back and forth for 2 hours before settling into the pattern of the present-day basin. (Courtesy of the researchers. Animation has been sped up.)</span></p> <p><strong>Flying low</strong></p> <p>The team’s results are based on gravity field measurements taken by GRAIL’s twin spacecraft, which orbited the moon from January to mid-December in 2012. In the waning days of the mission, the GRAIL probes were programmed to fly over the Orientale basin, dropping their altitude to just 1.2 miles above the basin’s rings — even lower than the altitude at which commercial jets fly over the Earth. Flying so close to the ground, the probes were able to take measurements of the basin’s gravity field at high spatial resolution, providing scientists with a precise map of the moon’s interior mass distribution.</p> <p>Zuber, who directed the mission and led the planning of the probes’ route, notes that the Orientale basin is the best-preserved large impact basin on the moon, having undergone very little transformation since it first formed. For this reason, the basin is considered a relatively pristine example of what the moon and the Earth experienced during a period in which the solar system was dominated by large, catastrophic impacts.</p> <p>“The interesting thing is, if you look up at the moon, you see all these craters, and Earth used to look like that — it went through a very similar bombardment history,” Zuber says. “In trying to reconstruct the extreme environmental conditions that existed during this period of time, we have a clearer window into the past through studying basins on the moon, because the record of those impacts isn’t preserved on the Earth.”</p> <p><strong>Measured impact</strong></p> <p>In one of two papers in <em>Science</em>, Zuber and her colleagues analyzed GRAIL’s gravity field measurements and were able to solve a key mystery, namely, the size and location of the basin’s transient crater, which is the initial depression created when an asteroid blasts material out from the lunar surface. In smaller impacts, the transient crater is largely preserved. But in very large collisions, the transient crater collapses due to loss of strength in the target crust, erasing any hint of the impactor’s size.</p> <p>In the case of the Orientale basin, many scientists had thought that one of its three rings might represent the transient crater. But the new measurements of the basin’s gravity field show that the transient crater may have been somewhere between the two inner rings, spanning around 200 to 300 miles across. From the size of the transient crater, the team estimated that the initial impact blasted away about 816,000 cubic miles of lunar crust. The gravity signal also showed that two huge faults exist beneath the basin’s two outer rings.</p> <p>“One of the really exciting results in this paper is, the outer two basin rings correspond to massive faults,” Zuber says. “And we were able to detect that these faults appear to have penetrated entirely through the crust and into the mantle, which is quite something.”</p> <p><strong>Making a bull’s-eye</strong></p> <p>In the second paper, led by Brandon Johnson, a former MIT postdoc in Zuber’s group and now an assistant professor at Brown University, the team created a computer simulation to reconstruct the first hours following the initial impact that created the Orientale basin. The team ran the simulation multiple times, with varying conditions, until the final basin and its concentric rings matched the observations made by GRAIL.</p> <p>Based on these simulations, the team estimated that the basin was carved out by a 40-mile-wide object that collided with the moon at about 9 miles per second, or 32,400 miles per hour. The impact pulverized the underlying crust, and the propagation and subsequent unloading of the shockwave caused material to rise up, then crash back down, sloshing back and forth in a wave-like fashion for the next two hours. The material eventually settled back to the surface in the pattern of the basin’s two outermost rings, each rising several kilometers high. This entire process obliterated any trace of the initial crater.</p> <p>The simulations showed that the basin’s innermost ring was formed by a different process. While smaller impacts can cause material in a crater to flow inward, forming a mound in the middle, Orientale’s central mound was so large that it was unstable. The material eventually collapsed, forming the basin’s innermost ring.</p> <p>“Ultimately, what this tells us is that the early history of the planets, at the time life was developing on Earth, was an extraordinarily hostile environment,” Zuber says. “There were extreme, energetic events that produced remarkably difficult environmental conditions. Maybe that’s why life is as tenacious as it is, because life forms somehow developed in the time subsequent to these catastrophic events. They were tough little buggers.”</p> <p>This research was supported by the NASA Discovery Program. The papers’ authors from MIT include David Smith, Katarina Miljković, and Jason Soderblom.</p> This image shows free-air gravitational anomalies and a shaded topographic relief of the Moon’s 930-km-diameter Orientale impact basin. Red corresponds to mass excesses and blue to mass deficits relative to a reference value. This gravitational field model, based on measurements acquired from the NASA GRAIL mission, shows the detailed structure of the central basin depression that is filled with dense mare basalts, as well as the rings that formed due to gravitational collapse of the initial crater cavity shortly after the impact.Image: Ernest Wright/NASA/GSFC Scientific Visualization StudioEAPS, NASA, Moon, Planetary science, Research, Satellites, Earth and atmospheric sciences, Geology, Evolution, School of Science, Space, astronomy and planetary science Gregory Stephanopoulos receives Samson Prize for Innovation in Alternative Fuels Metabolic engineering pioneer recognized for his work in the engineering of microbes for biofuels production. Wed, 19 Oct 2016 12:35:01 -0400 Melanie Miller Kaufman | Department of Chemical Engineering <p>Gregory Stephanopoulos, the Willard Henry Dow Professor of Chemical Engineering and Biotechnology at MIT, has been selected to receive the Eric and Sheila Samson Prime Minister's Prize for Innovation in Alternative Fuels for Transportation.</p> <p>Awarded by the prime minister of the state of Israel and totaling $1 million, the Samson Prize is the world's largest monetary prize awarded in the field of alternative fuels. Stephanopoulos shares the honor with Mercouri G. Kanatzidis of Northwestern University. The two researchers are being honored for “their innovative scientific and technological contributions that have the potential to lead to the development of alternative fuels for transportation, replacing the fast depleting fossil fuels which are the major fuels used nowadays in transportation.”</p> <p>Stephanopoulos was recognized “for his pioneering work in the field of metabolic engineering which contributed in a major way to the progress in the engineering of microbes for biofuels production.” The prize citation reads:</p> <p>“Prof. Gregory Stephanopoulos is a pioneer in the field of metabolic engineering and made seminal contributions to the engineering of microbes for biofuels production. He authored the first report on the targeting and engineering of mitochondria as a favorable component for production of biofuels and introduced the concept of global Transcriptional Machinery Engineering (gTME) for improving multigene microbial phenotypes. Of specific relevance are his achievements on xylose isomerase overexpression along with the engineering of the pentose phosphate pathway that enables rapid xylose utilization and ethanol production by Saccharomyces Cerevisiae (a species of yeast). He has also developed several strategies for the conversion of natural gas (methane) to liquid fuel with much higher energy density.”</p> <p>Stephanopoulos's current research focuses on metabolic engineering and its applications to the production of fuels, biochemicals and specialty chemicals, as well as mammalian cell physiology as it pertains to diabetes and metabolism. He has co-authored or edited five books — including co-authoring the first textbook on metabolic engineering — and some 300 papers, and he holds 25 patents. Stephanopoulos is presently the editor-in-chief of the journal <em>Metabolic Engineering;</em> he also serves on the editorial boards of seven scientific journals. He has been recognized with many awards and honors, including the Founders Award from the American Institute of Chemical Engineers (AIChE), the M.J. Johnson Award of the American Chemical Society, the Merck Award in Metabolic Engineering, and election to the National Academy of Engineering. In 2014, he was the recipient of the Walker Award from AIChE and currently serves as the organization’s president.</p> <p>Stephanopoulos received his BS from the National Technical University of Athens, in Greece; his MS from the University of Florida; and his PhD from the University of Minnesota. He is presently directing a research group of approximately 25 researchers who work on applications of metabolic engineering for the production of fuels and chemicals.</p> <p>Kanatzidis and Stephanopoulos were selected by a committee of international experts, who submitted their recommendation to a board of trustees, headed by former Technion president, Professor Yitzhak Apeloig. This is the fourth time the Samson Prize has been awarded by the prime minister's office — the Ministry of Science, Technology and Space — and Keren Hayesod, the official fundraising organization for Israel.</p> <p>The prize ceremony will take place during the Fuel Choices Conference in Tel Aviv on Nov. 2.</p> MIT Professor Gregory StephanopoulosPhoto: Webb ChappellAwards, honors and fellowships, Faculty, Chemical engineering, School of Engineering, Bioengineering and biotechnology, Energy, Microbes, Evolution, Greenhouse gases, Alternative energy, Biofuels MIT researchers prove fast microbial evolutionary bursts exist Study reveals closely related microbes can diversify rapidly via horizontal gene transfer. Thu, 22 Sep 2016 12:10:19 -0400 Marilyn Siderwicz | Department of Civil and Environmental Engineering <p>There are more than a dozen species of finch that evolved on the Galapagos Islands, each identified by beak shape and size. Some have strong beaks to crack nuts while others have long, fine beaks to grasp larvae with surgical precision. All of the finches evolved from a common ancestor in a very short period of time, an evolutionary process known as adaptive radiation.</p> <p>Although this burst of adaptive radiation is common for animals and plants, it has remained elusive and difficult to document in microbes in the wild — until now.</p> <p>A new study published today in the journal <em>Nature Communications</em> and led by researchers from the MIT Department of Civil and Environmental Engineering (CEE) shows that adaptive radiation does exist in microbes. The discovery could portend new applications that create more economical and renewable biofuels, or innovate biomedical chemicals and products.&nbsp;</p> <p>“Many people doubted it should be possible in contemporary environments since microbes have co-evolved with ecosystems on the planet for billions of years, so that most ecological opportunities might have been taken advantage of,” says CEE Professor Martin Polz. “We demonstrated adaptive radiations do happen, and that they can lead to a rapid diversification of a single species into multiple, differentially adapted species.”</p> <p>Lead authors working under the supervision of Polz and Eric Alm, a professor in CEE and the MIT Department of Biological Engineering, included graduate student Philip Arevalo, former postdoc Jan-Hendrik Hehemann, and postdoc Manoshi Datta, all of CEE. Other contributors included current and former CEE postdocs Christopher H. Corzett, Andreas Henschel and former CEE graduate student Sarah P. Preheim; Sonia Timberlake of the Department of Biological Engineering; and Xiaoqian Yu of the MIT Department of Biology.</p> <p><strong>Microbial adaptation</strong></p> <p>“We were able to reveal the evolution of different ways the bacteria consume alginate, an important carbohydrate from kelp,” says Hehemann, who sought a postdoc appointment within MIT’s Department of Civil and Environmental Engineering precisely to explore this question of how microbes adapt to different resource use.</p> <p>Hehemann, now a group leader at the Max Planck Institute for Marine Microbiology in Germany, is a biochemist by training as well as a structural biologist. He found that closely related populations of bacteria had very different sets of enzymes, suggesting they had different feeding strategies. Like the beaks of Darwin’s finches, these enzymes allow the bacteria to most efficiently consume a narrow set of resources derived from kelp.</p> <p>“Microbial diversity is so vast, which is why it remains a major challenge to understand how they all fit into this world. However, our work shows that resources might be partitioned at much finer scales than we previously thought,” he says, adding: “This may be part of the puzzle why there are so many microbial species.”</p> <p>Datta helped bridge Hehemann’s lab work with Arevalo’s computation analysis, which fit well with her background in microbiology and specialization in computational biology.</p> <p>“One of the unique and powerful aspects of this project is that we were able to generate a hypothesis by looking at bacterial genomic data, test their metabolic capabilities in the lab, and then go back to the genomes to see how these traits evolved,” she says.</p> <p><strong>Gene transfers</strong></p> <p>Researchers have been able to sequence bacterial genome for the last two decades, but now the process has become routine as costs and analysis time have dropped significantly — from years and millions of dollars to perform to now under $100 and just a few hours.</p> <p>Arevalo explains that the team looked at hundreds of Vibrionaceae strains whose full genomes were genetically sequenced: “What I was doing was computational — finding how the microbes adapted to different forms on the algae, and then looking at the history of these microbial genes.”</p> <p>Through this analysis, the researchers found that horizontal gene transfer, not point mutation, was the primary diversification driver. Horizontal gene transfer is a process by which an organism receives genetic material from a source other than its parent (e.g., from neighboring cells or the surrounding environment). In principle, this could occur through numerous mechanisms, and can transfer genes among organisms that are not closely related.</p> <p>“It’s very common to have gene duplication in bacteria, presumably to be able to synthesize a particular enzyme faster,” Polz explains. “This research shows, however, that these bacteria duplicate not just one copy in the same genome, but instead acquire a new copy of the same functional gene by horizontal gene transfer from one microorganism to another. This differentiation tells us how selection in the environment works to create different types of organisms that either work together when degrading a substrate or compete when seeking nourishment.”</p> <p>Polz adds that some “pioneer” microbes partially degrade the algae substrate by releasing enzymes to make it more soluble, and then other bacteria come in and degrade it more.</p> <p>“It takes a village,” he says.</p> <p>“This paper is part of the exemplary series of studies in microbial evolutionary diversification which put the Alm and Polz labs miles ahead of their competitors,” says Professor W. Ford Doolittle, an evolutionary microbiologist at Dalhousie University in Canada who was not involved in the research. “Particularly intriguing is that it is gene transfer, not duplication, that is the operative process, reinforcing our appreciation of bacterial communities as&nbsp;highly interactive&nbsp;at the genetic — as well as the metabolic — level.”</p> Manoshi Datta, a postdoc in the Department of Civil and Environmental Engineering, pipettes bacterial samples in the lab.Photo: Marilyn SiderwiczResearch, Civil and environmental engineering, Biology, Biological engineering, Microbes, Bacteria, Evolution, Ocean science, School of Engineering, School of Science A mutual breakdown Species relationships devolve from jointly beneficial to competitive in benign environments. Wed, 24 Aug 2016 14:00:00 -0400 Jennifer Chu | MIT News Office <p>Nature abounds with examples of mutualistic relationships. Think of bees pollinating flowers whose nectar nourishes the bees, or clownfish that fight off predators of anemones that in turn provide habitats for the clownfish. Each species benefits the other, and together their chances of survival are better than if they lived apart.</p> <p>Now scientists at MIT have found that such mutualistic relationships aren’t always set in stone. Depending on environmental conditions, once-simpatico species can become competitors, and in extreme cases, one species can even drive the other to complete extinction.</p> <p>Studying two similar strains of yeast, the researchers found that this deterioration in relations is marked by multiple transitions in the species’ degree of codependence. What’s more, such mutualistic relations tend to break down in more “benign” environments, such as nutrient-rich conditions, in which each species isn’t required to rely solely on the other to survive.</p> <p>The researchers have published their results today in the journal <em>PLOS Biology.</em> The team is led by Jeff Gore, the Latham Family Career Development Associate Professor of Physics at MIT, and includes Tim Hoek, who performed most of the experiments as a research intern in MIT’s Physics of Living Systems group; Eugene Yurtsev, Tommaso Biancalani, and Jinghui Liu of the same group; and Kevin Axelrod of Harvard University.</p> <p><strong>Breaking down relations</strong></p> <p>In laboratory experiments, Gore and his colleagues studied the interactions between normally mutualistic strains of yeast that cross-feed, each producing a needed amino acid for the other.</p> <p>The researchers supplied gradually increasing amounts of nutrients to the yeast and observed population changes in strains grown both together and apart. They found that in nutrient-poor conditions, both strains did better together than they did alone, forming more mutualistic relationships in which each strain depended heavily on the other. The opposite was true in conditions with more plentiful nutrients: The strains seemed to do worse together, with one dominating strain that grew in size while the other dwindled and eventually collapsed.</p> <p>Interestingly, as the amount of nutrients gradually increased, the relationship between the strains, originally mutualistic, transitioned through multiple phases before devolving into competition, and even extinction of one partner. With just a small amount of extra added nutrients, the strains established an “obligate mutualism,” in which they were obliged to co-exist in order to survive. With more nutrients, a “facultative mutualism” took hold, in which the two strains could survive on their own but did better together. With even more nutrients, this relationship gave way to “parasitism,” in which one strain thrived while the other’s population plummeted.</p> <p>Finally, when the researchers added the highest concentration of nutrients to the strains, they observed that the yeast’s previously mutualistic relationship completely broke down: The strains were both worse off growing together, with one strain outcompeting the other for nutrients, eventually driving the weaker strain to extinction.</p> <p>“What’s amazing is, often when we talk about these interactions between species, we say, ‘Oh, a clownfish and an anemone is mutualism, whereas a lion and an antelope is predator-prey.’ We talk about these species having fixed interactions,” Gore says. “Whereas here we see these strains go through all these different regimes, just by changing one knob.”</p> <p><strong>A “niche overlap”</strong></p> <p>From their experiments, the researchers developed a simple model to predict the type of mutualistic relationship that would develop between the two strains, given how their populations changed over time.</p> <p>“In mutualism, we see that first, the abundances of each species become equal, 50-50, and then the overall size of the populations reach equilibrium, whereas in the competitive regime it’s the other way around,” Gore explains. “So we can determine which regime of interaction the species are in, based on the dynamics of the species.”</p> <p>However, there may be a limit to the extent to which a mutualistic relationship can break down. The researchers note that the two strains of yeast they studied were genetically very similar, and had very similar resource requirements, feeding off similar nutrients to stay alive. This “niche overlap” may predispose a genetically close pair of species to completely break from each other in benign, nutrient-rich conditions, and instead compete for the same resources.</p> <p>Mutualistic pairs such as clownfish and anemones, or, similarly, ants and acacia trees, may be sufficiently different in their nutritional requirements that they would likely not end up in complete collapse.</p> <p>“We think the degree of niche overlap will influence how far along the mutualism-parasitism spectrum you would go, when the environment becomes benign,” Gore says.</p> <p>Ultimately, the group’s results may help scientists better understand the ways in which interactions in nature can change with a changing environment.</p> <p>“There’s a general idea that more challenging environments favor mutualistic type interactions,” Gore says. “These experiments provide further support for the idea that mutualisms will often break down or become more competitive in more benign environments. Which is something that people have seen some evidence for in natural populations, but this is a nice context in which we can see it happening in a very direct way.”</p> <p>This research was supported, in part, by the Allen Distinguished Investigator Program and an NIH New Innovator Award.</p> Clownfish fight off predators of anemones that in turn provide habitats for the clownfish, an example of mutualism. But mutualistic relationships aren’t always set in stone; depending on environmental conditions, once-simpatico species can become competitors.Biology, Biological engineering, Evolution, Ecology, Animals, Materials Processing Center, Microbes, Physics, Research, School of Science, National Institutes of Health (NIH) Microbial engineering technique could reduce contamination in biofermentation plants Approach could lower cost and eliminate need for antibiotics during biofuel production. Thu, 04 Aug 2016 13:59:59 -0400 Helen Knight | MIT News correspondent <p>The cost and environmental impact of producing liquid biofuels and biochemicals as alternatives to petroleum-based products could be significantly reduced, thanks to a new metabolic engineering technique.</p> <p>Liquid biofuels are increasingly used around the world, either as a direct “drop-in” replacement for gasoline, or as an additive that helps reduce carbon emissions.</p> <p>The fuels and chemicals are often produced using microbes to convert sugars from corn, sugar cane, or cellulosic plant mass into products such as ethanol and other chemicals, by fermentation. However, this process can be expensive, and developers have struggled to cost-effectively ramp up production of advanced biofuels to large-scale manufacturing levels.</p> <p>One particular problem facing producers is the contamination of fermentation vessels with other, unwanted microbes. These invaders can outcompete the producer microbes for nutrients, reducing yield and productivity.</p> <p>Ethanol is known to be toxic to most microorganisms other than the yeast used to produce it, <em>Saccharomyces cerevisiae</em>, naturally preventing contamination of the fermentation process. However, this is not the case for the more advanced biofuels and biochemicals under development.</p> <p>To kill off invading microbes, companies must instead use either steam sterilization, which requires fermentation vessels to be built from expensive stainless steels, or costly antibiotics. Exposing large numbers of bacteria to these drugs encourages the appearance of tolerant bacterial strains, which can contribute to the growing global problem of antibiotic resistance.</p> <p>Now, in a paper published today in the journal <em>Science</em>, researchers at MIT and the Cambridge startup Novogy describe a new technique that gives producer microbes the upper hand against unwanted invaders, eliminating the need for such expensive and potentially harmful sterilization methods.</p> <p>The researchers engineered microbes, such as <em>Escherichia coli</em>, with the ability to extract nitrogen and phosphorous — two vital nutrients needed for growth — from unconventional sources that could be added to the fermentation vessels, according to Gregory Stephanopoulos, the Willard Henry Dow Professor of Chemical Engineering and Biotechnology at MIT, and Joe Shaw, senior director of research and development at Novogy, who led the research.</p> <p>What’s more, because the engineered strains only possess this advantage when they are fed these unconventional chemicals, the chances of them escaping and growing in an uncontrolled manner outside of the plant in a natural environment are extremely low.</p> <p>“We created microbes that can utilize some xenobiotic compounds that contain nitrogen, such as melamine,” Stephanopoulos says. Melamine is a xenobiotic, or artificial, chemical that contains 67 percent nitrogen by weight.</p> <p>Conventional biofermentation refineries typically use ammonium to supply microbes with a source of nitrogen. But contaminating organisms, such as <em>Lactobacilli</em>, can also extract nitrogen from ammonium, allowing them to grow and compete with the producer microorganisms.</p> <p>In contrast, these organisms do not have the genetic pathways needed to utilize melamine as a nitrogen source, says Stephanopoulos.</p> <p>“They need that special pathway to be able to utilize melamine, and if they don’t have it they cannot incorporate nitrogen, so they cannot grow,” he says.</p> <p>The researchers engineered <em>E. coli </em>with a synthetic six-step pathway that allows it to express enzymes needed to convert melamine to ammonia and carbon dioxide, in a strategy they have dubbed ROBUST (Robust Operation By Utilization of Substrate Technology).</p> <p>When they experimented with a mixed culture of the engineered <em>E. coli</em> strain and a naturally occurring strain, they found the engineered type rapidly outcompeted the control, when fed on melamine.</p> <p>They then investigated engineering the yeast <em>Saccharomyces cerevisiae </em>to express a gene that allowed it to convert the nitrile-containing chemical cyanamide into urea, from which it could obtain nitrogen.</p> <p>The engineered strain was then able to grow with cyanamide as its only nitrogen source.</p> <p>Finally, the researchers engineered both <em>S. cerevisiae </em>and the yeast <em>Yarrowia lipolytica </em>to use potassium phosphite as a source of phosphorous.</p> <p>Like the engineered <em>E. coli</em> strain, both the engineered yeasts were able to outcompete naturally occurring strains when fed on these chemicals.</p> <p>“So by engineering the strains to make them capable of utilizing these unconventional sources of phosphorous and nitrogen, we give them an advantage that allows them to outcompete any other microbes that may invade the fermenter without sterilization,” Stephanopoulos says.</p> <p>The microbes were tested successfully on a variety of biomass feedstocks, including corn mash, cellulosic hydrolysate, and sugar cane, where they demonstrated no loss of productivity when compared to naturally occurring strains.</p> <p>The paper provides a novel approach to allow companies to select for their productive microbes and select against contaminants, according to Jeff Lievense, a senior engineering fellow at the San Diego-based biotechnology company Genomatica who was not involved in the research.</p> <p>“In theory you could operate a fermentation plant with much less expensive equipment and lower associated operating costs,” Lievense says. “I would say you could cut the capital and capital-related costs [of fermentation] in half, and for very large-volume chemicals, that kind of saving is very significant,” he says.</p> <p>The ROBUST strategy is now ready for industrial evaluation, Shaw says. The technique was developed with Novogy researchers, who have tested the engineered strains at laboratory scale and trials with 1,000-liter fermentation vessels, and with Felix Lam of the MIT Whitehead Institute for Biomedical Research, who led the cellulosic hydrosylate testing.</p> <p>Novogy now hopes to use the technology in its own advanced biofuel and biochemical production, and is also interested in licensing it for use by other manufacturers, Shaw says.</p> The ability to ferment low-cost feedstocks under nonsterile conditions may enable new classes of biochemicals and biofuels, such as microbial oil produced by the yeast Yarrowia lipolytica (shown here, oil in lipid bodies is stained green and cells walls stained blue).Image: Novogy, Inc.Research, School of Engineering, Chemical engineering, Alternative energy, Bioengineering and biotechnology, Energy, Greenhouse gases, Climate change, Evolution, Microbes Microbiome genes on the move Largest metagenomic view of the developing world uncovers “mobile genes” that reveal how culture shapes the human microbiome. Thu, 14 Jul 2016 13:00:00 -0400 Lisa Girard | Broad Institute <p>The word “culture” typically refers to a group’s shared heritage — such as its customs, cuisine, music, and language — that connects people in unique ways. But what if culture extended to a population’s microbiome, the collection of microorganisms that live on and within the human body?</p> <p>Scientists are learning that the state of the microbiome can have an impact on human health, with the risk for everything from autoimmune disease to certain cancers being linked to the diversity and wellbeing of the trillions of microbes living in and on the body. In work published in this week’s <em>Nature</em>, Eric Alm and Ilana Brito from MIT and the Broad Institute of MIT and Harvard and their colleagues took a deep look at the microbiomes in developing world populations to study how culture can influence their makeup.</p> <p>They uncovered an interesting role for “mobile genes” — genetic material that moves between organisms by a process called horizontal gene transfer — in shaping culturally distinct microbiomes in developing world populations. These mobile genes are useful for highlighting key genes in microbial genomes that help individuals adapt to their environment.</p> <p><strong>Isolated populations provide a clear lens</strong></p> <p>In 2008, the Human Microbiome Project (HMP) of the National Institutes of Health began an effort to survey the human microbiome on a large scale, by gathering samples (such as skin swabs, saliva samples, and stool) from hundreds of healthy North Americans, primarily those living in urban areas. They sequenced the microbes in those samples with the goal of understanding how they influence health and disease, and produced an unprecedented look at the diversity of the healthy human microbiome.</p> <p>The human race, however, is more diverse than urban-dwelling North Americans. To understand how the microbiome of a population from the developing world might compare to the HMP dataset, Brito traveled quite far from urban North America, venturing all the way to the South Pacific islands of Fiji, where many of the country’s native villagers live in remote, isolated communities. “I wanted to track microorganisms that move from place to place, and I thought the best place for doing this was where all contacts are local contacts who use local water and food,” explains Brito, a postdoc in the lab of Eric Alm, an institute member at the Broad Institute, professor of biological engineering at MIT, and co-director of the MIT Center for Microbiome and Therapeutics. &nbsp;“In contrast, in big cities, we come into contact with a lot of different people, eat food from around the world, and use lots of hygiene products and antibiotics which can prevent the transmission of even endogenous microbes.”</p> <p>The villages Brito studied were on the second-largest island in Fiji, but they were still fairly remote, with about 100-150 people living in each village. While the HMP had been limited in the amount of information it collected about its participants, Brito conducted a thorough survey of the villagers she met. She mapped out people’s family trees and social networks, noted what medications they took, and recorded the GPS coordinates of their homes and drinking water supplies. In addition to sampling the individuals’ microbiomes, she sampled their water, identified who touched livestock, and took samples from those livestock. Brito captured not only the human microbiome, but also the reservoirs of microbes in the community. The project’s name, the Fiji COmmunity Microbiome Project (FijiCOMP), reflects this holistic approach.</p> <p><strong>Metagenomic data reveals layers of stories</strong></p> <p>While much of the earlier microbiome research used a method known as 16S ribosomal subunit sequencing to identify microbial species in a population, that approach tells little about the rest of their genomes. Brito’s goal was instead to do metagenomic sequencing, a more comprehensive way to look at microbial genomes that allows for more granular, strain-level distinctions. “There are layers of stories that can be missed just looking at the 16S profiles,” says Brito.</p> <p>When Brito arrived home from Fiji with more than 1,000 samples in hand, she and Alm joined forces with Broad’s microbial sequencing group and, with the support of Broad along with funding from the National Human Genome Research Institute, were able to do metagenomic sequencing on over 500 of the samples. This was a game-changer for the researchers, moving them from having very little data to building the largest data set of this type and the only one of its kind on a developing world population. So massive was the influx of data that the researchers had to develop a new way to assemble and analyze the information.</p> <p><strong>Mobile genes identify welcome genomic additions</strong></p> <p>Data in hand, Brito and Alm could now dig in. In particular, they were looking for mobile genes, genetic elements that have been shared among species and that likely perform some crucial or survival-promoting function. “If you look at a microbial genome with 5,000 genes in it, which ones are particularly important?” Alm asks. “Probably not all 5,000 genes. Most of them are probably either housekeeping genes that every bacterium has or some random selfish gene. But if you go into an environment and see a particular gene being transferred to many different species, to every bug in this environment, which is maybe rich in tetracycline, [and if this is a] tetracycline resistance gene, then you’re like, aha! Then it’s likely that gene is one … of the 5,000 genes that’s super important.”</p> <p>Brito and Alm scoured their data for signs of horizontal gene transfer — the process by which mobile genes move among species — and in collaboration with researchers at Sandia National Laboratory and Broad core institute member Paul Blainey, they used microbial single-cell sequencing to create a new set of reference genomes to compare with the metagenomic data and identify mobile genes. To pinpoint gene transfer events, they took a cue from earlier work in Alm’s lab.</p> <p>“In 2011, we created the first map of who was sharing genes with whom,” says Alm. “We downloaded all of the microbial genomes in Genbank and looked for identical stretches of DNA that were surprisingly present in two totally different species.” Between microbes that diverged evolutionarily hundreds of millions of years ago, it is expected that their sequences would have diverged over the years and there would be a lot of sequence differences. But, if large stretches of DNA are identical between two very different organisms, they reasoned, it strongly suggested that the DNA was horizontally transferred.</p> <p>What Alm found in this earlier work was that two bacteria of different species were more likely to share a gene if they came from essentially the same site on the human body, for example, both from different spots in the mouth, than if they came from different sites — one from the mouth and one from the gut. So while this data showed that geography was not particularly indicative for sharing genes, perhaps due to lack of geographic coverage, what about in the developing world? What about people in these relatively isolated Fijian villages?</p> <p>In this new study, Brito and the team looked at the gene transfer events, not only for the Fijian samples but also those from the Human Microbiome Project, to understand how the local environment influences the microbiome. What emerged from the data was that among the Fijian samples it was actually possible to identify particular functional genes selected for within particular populations, which meant the genes were culturally important.</p> <p>One big difference between participants in the FijiCOMP study and the HMP is diet. For example, the Fijian diet is rich in local fare such as cassava, coconut, and regional seafood. Looking at families of digestive enzymes called glycoside hydrolases, particular family members useful for digesting particular foods were transferred as mobile genes within groups of people that eat those foods. Here, looking at mobile genes allowed the researchers to more directly assess the impact of environmental factors such as diet rather than the impact of which species were present.</p> <p>“While 16S sequencing can identify which species are present and let us make associations between particular species and disease, what the mobile genes tell us is that even if we know the species, there seem to be culturally important genes that are crossing species boundaries that don’t show up in the 16S data,” says Alm. “So if we want to fully understand the public health impact of the microbiome overall, we need to not only track the species, but also the genes of interest. Combining single-cell and metagenomic analysis provides a powerful way to do it.”</p> <p>This research was supported by the Fiji Ministry of Health, National Human Genome Research Institute, Center for Environmental Health at MIT, Center for Microbiome Informatics and Therapeutics at MIT, Wildlife Conservation Society and the Earth Institute at Columbia University, Broad Institute of MIT and Harvard, Burroughs Welcome Fund, the National Institute of Dental and Craniofacial Research, and the United States Department of Energy.</p> MIT and Broad Institute postdoc Ilana Brito sampled not only the human microbiome in the remote villages in Fiji she studied, but also the reservoirs of microbes in the community.Courtesy of Broad CommunicationsResearch, Bacteria, Biology, Broad Institute, Developing countries, Evolution, Genetics, Microbes, Microbiology, Biological engineering, Health, School of Engineering Study pinpoints timing of oxygen’s first appearance in Earth’s atmosphere Beginning 2.33 billion years ago, atmospheric oxygen built up in just 10 million years. Fri, 13 May 2016 13:59:59 -0400 Jennifer Chu | MIT News Office <p>Today, 21 percent of the air we breathe is made up of molecular oxygen. But this gas was not always in such ample, life-sustaining supply, and in fact was largely absent from the atmosphere for the first 2 billion years of Earth’s history. When, then, did oxygen first accumulate in the atmosphere?</p> <p>MIT scientists now have an answer. In a paper appearing today in <em>Science Advances</em>, the team reports that the Earth’s atmosphere experienced the first significant, irreversible influx of oxygen as early as 2.33 billion years ago. This period marks the start of the Great Oxygenation Event, which was followed by further increases later in Earth’s history. &nbsp;</p> <p>The scientists have also determined that this initial rise in atmospheric oxygen, although small, took place within just 1 to 10 million years and set off a cascade of events that would ultimately lead to the advent of multicellular life.</p> <p>“It’s the start of a very long interval that culminated in complex life,” says Roger Summons, senior author of the paper and professor in the Department of Earth, Atmospheric, and Planetary Sciences (EAPS) at MIT. “It took another roughly 1.7 billion years for animals similar to those we have today to evolve. But the presence of molecular oxygen in the ocean and the atmosphere means that organisms that respire oxygen could thrive.”</p> <p>Summons’ MIT co-authors include lead author and postdoc Genming Luo, as well as EAPS Associate Professor Shuhei Ono and graduate student David Wang. Professors Nicolas Beukes from the University of Johannesburg, in South Africa, and Shucheng Xie from the China University of Geosciences are the other co-authors.</p> <p><strong>Whiffs in the air</strong></p> <p>For the most part, scientists agree that oxygen, though lacking in the atmosphere, was likely brewing in the oceans as a byproduct of cyanobacterial photosynthesis as early as 3 billion years ago. However, as Summons puts it, oxygen in the ancient ocean “would have instantly been sucked up” by hungry microbes, ferrous iron, and other sinks, keeping it from escaping into the atmosphere.</p> <p>“There may have been earlier, and temporary, ‘whiffs’ of oxygen in the atmosphere, but their abundances and durations are not currently measurable,” Summons says.</p> <p>That changed with the Great Oxygenation Event (GOE), a period that scientists believe marked the beginning of oxygen’s permanent presence in the atmosphere. Previous estimates have placed the start of the GOE at around 2.3 billion years ago, though with uncertainties of tens to hundreds of millions of years.</p> <p>“The dating of this event has been rather imprecise until now,” Summons says.</p> <p><strong>A transition, pinned</strong></p> <p>To get a more precise timing for the GOE, Luo first analyzed rocks from around this period, looking for a particular sulfur isotope pattern. When volcanoes erupt, they emit sulfur gases, which, when exposed to the sun’s ultraviolet radiation, can fractionate chemically and isotopically. The pattern of isotopes generated in this process depends on whether or not oxygen was present above a certain threshold.</p> <p>Luo looked to pinpoint a major transition in a particular sulfur isotope pattern called mass-independent fraction of sulfur isotopes (S-MIF), in order to determine when oxygen first appeared in the Earth’s atmosphere. To do this, he first looked through sediment cores collected by Ono on a previous expedition to South Africa.</p> <p>“Genming is a very tenacious and thorough guy,” Summons says. “He found rocks from deep in the core had S-MIF, and rocks shallow in the core had no S-MIF, but he didn’t have anything in between. So he went back to South Africa.”</p> <p>There, he was able to sample from the rest of the sediment core and two others nearby, and determined that the S-MIF transition — marking the permanent passing of the oxygen threshold — occurred 2.33 billion years ago, plus or minus 7 million years, a much smaller uncertainty compared with previous estimates.</p> <p><strong>Getting a “decent hold”</strong></p> <p>The team also discovered a large fractionation of the isotope sulfur-34, indicating a spike in marine sulfate levels around this same time. Such sulfate would have been produced from the reaction between atmospheric oxygen with sulfide minerals in rocks on land, and sulfur dioxide from volcanoes. This sulfate was then used by ocean-dwelling, sulfate-respiring bacteria to generate a particular pattern of sulfur-34 in subsequent sediment layers that were dated between 1 and 10 million years after the S-MIF transition.</p> <p>The results suggest that the initial buildup of oxygen in the atmosphere was relatively rapid. Since its first appearance 2.33 billion years ago, oxygen accumulated in high enough concentrations to have a weathering effect on rocks just 10 million years later. This weathering process, however, would have leached more sulfate and certain metals into waterways and ultimately, the oceans. Summons points out that it would be quite some time before the Earth system would reach another stable state, by the burial of organic carbon, and exceed the higher oxygen thresholds needed to encourage further biological evolution.</p> <p>“Complex life couldn’t really get a decent hold on the planet until oxygen was prevalent in the deep ocean,” Summons says. “And that took a long, long time. But this is the first step in a cascade of processes.”</p> <p>Timothy Lyons, professor of biogeochemistry at the University of California, Riverside, says the group’s timeline for oxygen’s rise “is a major contribution toward a refined understanding of the co-evolution of Earth’s early life and environments.”</p> <p>“There are hints from past research of early transient accumulation of oxygen in the atmosphere and surface oceans before the loss of S-MIF, but the irreversible loss of this signal from the geologic record is now taken as the smoking gun for what we call the Great Oxidation Event—when appreciable levels of oxygen became a permanent feature in our atmosphere,” says Lyons, who did not contribute to the research. “The authors have done the community a great service by refining the timing of this event.”</p> <p>Now that the team has constrained the timing of the GOE, Summons hopes others will apply the new dates to determine a cause, or mechanism, for the event. One hypothesis that the team hopes to explore is the connection between oxygen’s sudden and rapid appearance, and Snowball Earth, the period in which Earth’s continents and oceans were largely ice-covered. Now, thanks to the improved precision in geochronology, which Summons largely credits to EAPS Professor Samuel Bowring, scientists can start to nail down the mechanisms behind major events in Earth’s history, with more precise dates.</p> <p>“It’s Sam’s insistence about this whole issue about ‘no dates, no rates’ that I think encourages people to focus on getting better data on the timing and duration of geological events,” Summons says.</p> <p>“Because the other big question is, why do we have 21 percent oxygen in the Earth’s atmosphere that’s stable? That’s remarkable. And we need to understand that.”</p> <p>This research was funded by the Simons Foundation with additional support from NASA, the Chinese National Natural Science Foundation, and the National Science Foundation.</p> MIT scientists say that the Great Oxygenation Event (GOE), a period that scientists believe marked the beginning of oxygen’s permanent presence in the atmosphere, started as early as 2.33 billion years ago. Biology, School of Science, Climate, Climate change, EAPS, Earth and atmospheric sciences, Environment, Evolution, Geology, Microbes, Planetary science, Research, NASA, National Science Foundation (NSF) Code of the humans New book by Noam Chomsky and Robert Berwick explores how people acquired unique language skills. Tue, 01 Mar 2016 00:00:00 -0500 Peter Dizikes | MIT News Office <p>For many years, researchers tried to teach other kinds of animals some human language. Chimps, dolphins, gorillas — it didn’t seem to matter which animals they tried. Few experiments were regarded as success stories.</p> <p>Small children, however, learn whichever language they are taught, and abundant evidence points toward the universality of human language. Platoons of linguists have detailed strong syntactical similarities among the world’s tongues. And biologists have begun to identify some of the genes involved in the development of speech and possibly language.</p> <p>“Human language is a generative system that determines an infinite set of possible semantic objects,” says Noam Chomsky, Institute Professor and Professor of Linguistics Emeritus at MIT.</p> <p>“People don’t realize how uniform the human population is,” adds Robert C. Berwick, a computer scientist at the Laboratory for Information and Decision Systems at MIT. “We’re all very alike as humans, and this language capacity is incredibly uniform. If you take a baby from Southern Africa and put it in Beijing, they’ll speak Chinese.”</p> <p>Now Berwick and Chomsky have collaborated on a new book on the topic, “<a href="">Why Only Us?</a>,” published on March 1 by the MIT Press, which explores the grand riddles of human language — what makes it unique, as well as where, when, why, and how humans acquired a distinctive, language capacity of nonpareil sophistication.&nbsp;</p> <p><strong>Out of Blombos?</strong></p> <p>The questions of when and where human language emerged are probably the simplest to grapple with. Like some other scholars, Berwick and Chomsky think the emergence of symbolic behavior is a guidepost indicating when human language developed. The Blombos cave artifacts in South Africa, comprising engravings and beads that are 80,000 years old, are a possible landmark. Modern humans arose about 200,000 years ago, so the development of our language capacity most likely falls in between those two points in time. Still, Chomsky notes how “thin the empirical record is” on this count.</p> <p>Precisely what evolved, Berwick and Chomsky contend, is what Chomsky calls “Merge:” the human cognitive capacity to take any two things that we now recognize as sentence elements, and combine them into a new, more complex, hierarchically structured phrase.</p> <p>“In its simplest terms, the Merge operation is just set formation,” the authors write. But if it sounds simple, this operation is precisely what allows human language to be infinite; there is absolutely no limit on the number of sentences we can form.</p> <p>There are some other things that mark human language as distinct, so far as we know — for instance, our statements do not have to make reference to the external world. But the unbounded nature of language appears crucial at all times.</p> <p>If so, how did such a powerful capability emerge in people? Berwick and Chomsky suggest it resulted from not a giant evolutionary leap but a modest evolutionary step that turned out to be very useful.</p> <p>“What we’re arguing is that there was probably a very small change which had large effects,” Chomsky says. In the book as well, the authors suggest our language capacity was “the result of a minor mutation” in genomic terms that had far-reaching changes in our capacities.</p> <p>“Evolution has [often] assembled lots of other parts that enable a whole host of other behaviors that you didn’t have before,” Berwick observes. “It [the language capacity] is standard in that kind of picture. It’s fully compatible with what a Darwinian might have thought.”</p> <p>He adds: “We’re getting more and more of an understanding of the genomic basis for some of these traits, but it’s extremely challenging to work out.”</p> <p><strong>The real leap: intentional, conceptual thoughts</strong></p> <p>The hardest question to answer, it seems, is why humans should have a uniquely unbounded language. Or, to put it another way, what purpose did language play that made it a useful trait in evolutionary terms?</p> <p>Berwick and Chomsky, following decades of work and theorizing by Chomsky, do not believe that language evolved primarily as a form of communication. Rather, it is an offshoot of the development of our cognitive capacities — an “inner mental tool,” as they write, at the interface of intentional thought and the ability to think conceptually.</p> <p>In this sense, “Merge would be just like any other ‘internal’ trait that boosted selective advantage,” they write, something that would be helpful in planning, making inferences, and other basic capacities.</p> <p>That said, Berwick and Chomsky readily acknowledge they do not possess a full hypothesis explaining how people developed the capacity for having those abstract conceptual thoughts in the first place.</p> <p>“There is no explanation of where those come from,” Berwick says. &nbsp;</p> <p>“The nature of elementary human concepts, such as table or chair, is unknown, and what’s striking about them is that they’re radically different than anything in the animal world,” Chomsky says. “It’s very different from other animals.”</p> <p>“Why Only Us” has received advance praise from other scholars. Martin Nowak, a professor of mathematics and biology at Harvard University, calls it “captivating and a must for everyone interested in evolution and humans.”</p> <p>And Berwick and Chomsky note that they hope to inspire further research, potentially integrating neuroscience to a growing extent, in addition to proposing answers to these scientific mysteries.</p> <p>Or, as they write, “a vast array of language phenomena remain unexplained and even barely examined, but the picture sketched here seems to us the most plausible one we have, and one that offers many opportunities for fruitful research and inquiry.”</p> “Why Only Us: Language and Evolution” (MIT Press), by Robert C. Berwick (top left) and Noam Chomsky (bottom left)Research, Linguistics, Language, Evolution, Electrical Engineering & Computer Science (eecs), Books and authors, SHASS, School of Engineering, Laboratory for Information and Decision Systems (LIDS) Title for ‘Earth’s first animal’ likely goes to simple sea creature Sponges may be source of molecular fossils that significantly predate Cambrian explosion. Mon, 22 Feb 2016 15:00:00 -0500 Jennifer Chu | MIT News Office <p>The first animal to appear on Earth was very likely the simple sea sponge.</p> <p>New genetic analyses led by MIT researchers confirm that sea sponges are the source of a curious molecule found in rocks that are 640 million years old. These rocks significantly predate the Cambrian explosion — the period in which most animal groups took over the planet, 540 million years ago — suggesting that sea sponges may have been the first animals to inhabit the Earth.</p> <p>“We brought together paleontological and genetic evidence to make a pretty strong case that this really is a molecular fossil of sponges,” says David Gold, a postdoc in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “This is some of the oldest evidence for animal life.”</p> <p>The results are published today in the <em>Proceedings of the National Academy of Sciences</em>. Gold is the lead author on the paper, along with senior author and EAPS Professor Roger Summons.</p> <div class="cms-placeholder-content-video"></div> <p><strong>Ancient molecular clues</strong></p> <p>Paleontologists have unearthed an extraordinary number of fossils from the period starting around 540 million years ago. Based on the fossil record, some scientists have argued that contemporary animal groups essentially “exploded” onto Earth, very quickly morphing from single-celled organisms to complex multicellular animals in a relatively short geological time span. However, the fossils that are known from before the Cambrian explosion are peculiar in many respects, making it extremely difficult to determine which type of animal was the first to the evolutionary line.</p> <p>Summons’ lab has been looking for the answer in molecular fossils — trace amounts of molecules that have survived in ancient rocks long after the rest of an animal has decayed away.</p> <p>“There’s a feeling that animals should be much older than the Cambrian, because a lot of animals are showing up at the same time, but fossil evidence for animals before that has been contentious,” Gold says. “So people are interested in the idea that some of these biomarkers and chemicals, molecules left behind, might help resolve these debates.”</p> <p>In particular, he and his colleagues have focused on 24-isopropylcholestane, or 24-ipc for short — a lipid molecule, or sterol, that is a modified version of cholesterol. In 1994, Summons was part of a team, led by Mark McCaffrey PhD ’90, that first found 24-ipc, in unusually high amounts, in Cambrian and slightly older rocks. They speculated that sponges or their ancestors might be the source.</p> <p>In 2009, a team led by University of California at Riverside Professor Gordon Love, then a postdoc in Summons’ lab, did the first detailed study of rocks in Oman. The researchers confirmed the presence of 24-ipc in 640-million-year-old rock samples, potentially representing the oldest evidence for animal life. That work utilized high precision uranium-lead dating techniques developed by EAPS Professor Samuel Bowring.</p> <p>“This research topic has a 20-plus-year history intimately connected to MIT scientists,” Summons notes. “Now, in 2016 David Gold has been able to apply his skills and the new tools of the genomic era, to add a further layer of evidence supporting the ‘sponge biomarker hypothesis.’”</p> <p><strong>Growing an evolutionary tree</strong></p> <p>It’s known that some modern sea sponges and certain types of algae produce 24-ipc today, but which organism was around to make the molecule 640 million years ago? To answer this question, Summons and Gold sought to first identify the gene responsible for making 24-ipc, then find the organisms that carry this gene, and finally trace when the gene evolved in those organisms.</p> <p>The team looked through the genomes of about 30 different organisms, including plants, fungi, algae, and sea sponges, to see what kinds of sterols each organism produces and to identify the genes associated with those sterols.</p> <p>“What we found was this really interesting pattern across most of eukaryotic life,” Gold says.</p> <p>By comparing genomes, they identified a single gene, sterol methyltransferase, or SMT, responsible for producing certain kinds of sterols depending on the number of copies of the gene an organism carries. The researchers found that sea sponge and algae species that produce 24-ipc have an extra copy of SMT when compared with their close relatives.</p> <p>The researchers compared the copies to determine how they were all related and when each copy of the gene first appeared. They then mapped the relationships onto an evolutionary tree and used evidence from the fossil record to determine when each SMT gene duplication occurred.</p> <p>No matter how they manipulated the timing of the evolutionary tree, the researchers found that sea sponges evolved the extra copy of SMT much earlier than algae, and they did so around 640 million years ago — the same time period in which 24-ipc was found in rocks.</p> <p>Their results provide strong evidence that sea sponges appeared on Earth 640 million years ago, much earlier than any other animal life form.</p> <p>“This brings up all these new questions: What did these organisms look like? What was the environment like? And why is there this big gap in the fossil record?” Gold says. “This goes to show how much we still don’t know about early animal life, how many discoveries there are left, and how useful, when done properly, these molecular fossils can be to help fill in those gaps.”</p> <p>This research is supported, in part, by the Agouron Institute and the NASA Astrobiology Institute.</p> Biology, Evolution, Earth and atmospheric sciences, Environment, Genetics, Research, School of Science, EAPS, NASA Kevin Esvelt to join the MIT Media Lab Fri, 04 Dec 2015 13:03:56 -0500 MIT Media Lab <p>Kevin Esvelt, a Harvard University biologist who is merging some of the newest techniques in molecular biology with ecological engineering, will be joining the MIT Media Lab as assistant professor of media arts and sciences in January 2016. He will lead a new <a href="" target="_blank">Sculpting Evolution</a> research group at the lab.</p> <p>Esvelt’s research focuses on evolutionary approaches to the engineering of ecosystems ranging from the microbial to the global. His discoveries offer new ways to control vector-borne and parasitic diseases, as well as agricultural pests and environmentally damaging invasive species. Because his work could be used to impact the shared environment, he emphasizes the importance of safeguards, transparency, and community-responsive science.</p> <p>During his graduate and post-graduate work at Harvard, Esvelt wove many different areas of science into novel approaches to ecological engineering. As a Technology Development Fellow at Harvard’s Wyss Institute, he collaborated closely with researchers in Professor George Church’s <a href="">laboratory</a>. Most recently, he described how to use the <a href="">CRISPR</a> gene-editing system to create gene drive elements that could be used to alter the traits of wild populations, and demonstrated safeguards for their use. Previously, working in the laboratory of Professor David Liu, he invented phage-assisted continuous evolution (PACE), a synthetic microbial ecosystem for rapidly evolving biomolecules.</p> <p>"Having Kevin join the Media Lab is a major coup for us," says Media Lab Director <a href="">Joi Ito</a>. “He is one of the key researchers working on the CRISPR gene drive, and an important voice in the very difficult conversation around the use of technologies that can permanently alter entire species. Almost more important than the science are the meta questions of who makes these decisions, and how can we forecast the consequences?”</p> <p>Esvelt received his bachelor’s degrees in biology and chemistry from Harvey Mudd College and a PhD in biochemistry from Harvard University. He is a winner of the Harold M. Weintraub Award, the Hertz Foundation Thesis Prize, and the National Institutes of Health K99.</p> Kevin EsveltFaculty, Biological engineering, Biology, Ecology, Media Lab, CRISPR, Evolution, School of Architecture and Planning The rapid rise of human language New paper suggests people quickly started speaking in a now-familiar form. Mon, 30 Mar 2015 23:59:59 -0400 Peter Dizikes | MIT News Office <p>At some point, probably 50,000 to 100,000 years ago, humans began talking to one another in a uniquely complex form. It is easy to imagine this epochal change as cavemen grunting, or hunter-gatherers mumbling and pointing. But in a new paper, an MIT linguist contends that human language likely developed quite rapidly into a sophisticated system: Instead of mumbles and grunts, people deployed syntax and structures resembling the ones we use today.</p> <p>“The hierarchical complexity found in present-day language is likely to have been present in human language since its emergence,” says Shigeru Miyagawa, Professor of Linguistics and the Kochi Prefecture-John Manjiro Professor in Japanese Language and Culture at MIT, and a co-author of the new paper on the subject.</p> <p>To be clear, this is not a universally accepted claim: Many scholars believe that humans first started using a kind of “proto-language” — a rudimentary, primitive kind of communication with only a gradual development of words and syntax. But Miyagawa thinks this is not the case. Single words, he believes, bear traces of syntax showing that they must be descended from an older, syntax-laden system, rather than from simple, primal utterances.</p> <p>“Since we can find syntax within words, there is no reason to consider them as ‘linguistic fossils’ of a prior, presyntax stage,” Miyagawa adds.</p> <p>Miyagawa has an alternate hypothesis about what created human language: Humans alone, as he has asserted in papers published in recent years, have combined an “expressive” layer of language, as seen in birdsong, with a “lexical” layer, as seen in monkeys who utter isolated sounds with real-world meaning, such as alarm calls. Miyagawa’s “integration hypothesis” holds that whatever first caused them, these layers of language blended quickly and successfully.</p> <p><strong>Word to the wise</strong></p> <p>Miyagawa’s paper is published this month in the peer-reviewed journal <em>Frontiers in Psychology.</em> Vitor A. Nobrega of the University of Sao Paulo co-authored the paper.</p> <p>In the paper, Nobrega and Miyagawa write that a single word can be “internally complex, often as complex as an entire phrase,” making it less likely that words we use today are descended from a presyntax mode of speech.</p> <p>To see a straightforward example of this in English, take “nationalization,” Miyagawa suggests. It starts with “nation,” a noun; adds “-al” to create an adjective; adds “-iz(a)” to form a verb; and ends with “-tion,” to form another noun, albeit with a new meaning.</p> <p>“Hierarchical structure is present not only in single words, but also in compounds, which, contrary to the claims of some, are not the structureless fossilized form of a prior stage,” Miyagawa says.</p> <p>In their paper, Nobrega and Miyagawa hold that the same analysis applies to words in Romance languages that have been described elsewhere as remnants of formless proto-languages. In Italian, “porta asciuga-mani” — literally “carry dry-hands,” but today colloquially meaning “towel holder” — is one such case, they contend, where a compound derived from old words has a clear internal structure. (In this case, “dry hands” is a complement to the verb.)</p> <p>Miyagawa’s integration hypothesis is connected intellectually to the work of other MIT scholars, such as Noam Chomsky, who have contended that human languages are universally connected and derive from our capacity for using syntax. In forming, this school of thought holds, languages have blended expressive and lexical layers through a system Chomsky has called “Merge.”</p> <p>“Once Merge has applied integrating these two layers, we have essentially all the features of a full-fledged human language,” Miyagawa says.</p> <p>Scholars think the integration hypothesis could generate a productive set of research questions. Andrea Moro, a professor of linguistics at the Institute for Advanced Study in Pavia, Italy, who edited the paper, calls it a “very interesting” critique of the idea that human language developed gradually.</p> <p>However, Moro suggests there is an “intuitive difference” between cases where words assemble to form either a compound word or a sentence. He believes it is possible that studies of the concept of “symmetry-breaking,” a potentially distinctive part of sentence formation, “may offer new empirical data to test the hypothesis and shed light on the birth of human language.”</p> Image: Jose-Luis Olivares/MITResearch, SHASS, Linguistics, Language, Evolution Evolutionary approaches to big-data problems Una-May O&#039;Reilly applies machine learning and evolutionary algorithms to tackle some of the world&#039;s biggest big-data challenges. Wed, 14 Jan 2015 14:51:01 -0500 Eric Brown | MIT Industrial Liaison Program <p>The <a href="" target="_blank">AnyScale Learning For All (ALFA) Group</a> at <a href="" target="blank">MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL)</a> aims to solve the most challenging big-data problems — questions that go beyond the scope of typical analytics. ALFA applies the latest machine learning and evolutionary computing concepts to target very complex problems that involve high dimensionality.</p> <p>“People have data coming at them from so many different channels these days,” says ALFA director Una-May O’Reilly, a principal research scientist at CSAIL. “We’re helping them connect and link the data between those channels.”</p> <p>The ALFA Group has taken on challenges ranging from laying out wind farms to studying and categorizing the beats in blood pressure data in order to predict drops and spikes. The group is also analyzing huge volumes of recorded click data to predict MOOC-learning behavior, and is even helping the IRS protect against costly tax-evasion schemes.</p> <p>ALFA prefers the challenge of working with raw data that comes directly from the source. It then investigates the data with a variety of techniques, most of which involve scalable machine learning and evolutionary computing algorithms.</p> <p>“Machine learning is very useful for retrospectively looking back at the data to help you predict the future,” says O’Reilly. “Evolutionary computation can be used in the same way, and it’s particularly well suited to large-scale problems with very high dimensions.”</p> <p>In the past, machine learning was challenged by the lack of sufficient data to infer predictive models or classification labels, says O'Reilly. “Now we have too much data, so we have scalable machine learning to try to process a vast quantity of data exemplars,” she says. “We also need to improve machine learning’s capability to cope with the additional variables that come with extremely high dimensional problems.”</p> <p>O’Reilly has a particular interest in ALFA’s other major tool: evolutionary computing. “Taking ideas from evolution, like population-based adaptation and genetic inheritance, and bringing them into computational models is really effective,” she says. “In engineering, we often use evolutionary algorithms like covariance-matrix adaptation or discrete-valued algorithms for optimization. Also, one can parallelize evolutionary algorithms almost embarrassingly easily, which allows it to handle a lot of the latest data-knowledge discovery problems.”</p> <p>Within the evolutionary field, O’Reilly is especially interested in genetic programming, or as she defines it, “the evolution of programs.” “We distribute the genetic programming algorithms over many nodes and then factor the data across the nodes,” she explains. “We take all the independent solutions we can compute in parallel and bring them together. We then eliminate the weaker ones and collectively fuse the stronger ones to create an ensemble. We’ve shown that ensemble based models are more accurate than a single model based on all the data.”</p> <p><strong>Laying out wind farms</strong><br /> <br /> One of ALFA’s most successful projects has been in developing algorithms to help design wind farms. The problem is marked by very high dimensionality, especially when hundreds of turbines are involved, says O’Reilly.</p> <p>“One can see great efficiency gains in optimizing the placement of turbines, but it’s a really complex problem,” she says. “First, there are the parameters of the turbine itself: its energy gain, its height, and its proximity cone. You must find out how much wind is required for the site and then acquire the finer detailed information about where the wind is coming from and in what quantities. You have to factor in the topographical conditions of the land and the way the wind sweeps through it.”</p> <p>The most difficult variable is the wake effect of one turbine on the turbines behind it, says O’Reilly. “We have to do very complex flow modeling to be able to calculate the loss behind each turbine.”</p> <p>ALFA discovered how to apply parallelized evolutionary algorithms that could scale up for wind farms of a thousand plus turbines. “We were able to scale to lay out turbines on a bigger scale than anyone had ever done before,” says O’Reilly.</p> <p>More recently, ALFA has been building a generative template for site design. “Now, we’re using evolutionary concepts to develop a program that can lay out any set of turbines on any site,” she says. “We’re building a design process rather than the site design itself.”</p> <p><strong>GigaBEATS: Making sense of blood pressure data</strong><br /> <br /> Many of the same evolutionary and machine-learning concepts used to lay out a wind farm can also be applied to gleaning insights from clinical data. ALFA is attempting to elicit useful information from the growing volume of physiological data collected from medical sensors. The data include measurement of everything from sleep patterns to ECG and blood pressure.</p> <p>“It’s hard for clinicians to understand such a high volume of data,” says O’Reilly. “We’re interested in taking signal-level information and combining it with machine learning to make better predictions.”</p> <p>Researchers tend to collect a small amount of data from a small sample, and do a study that takes over 18 months, says O’Reilly. “We want to take that 18 months and reduce it to hours,” she says.</p> <p>ALFA is working on a project called GigaBEATS that extracts knowledge from very large sets of physiological data. Initially, the project has studied blood-pressure data taken from thousands of patients in critical care units.</p> <p>“We are examining the microscopic characteristics of every beat,” says O’Reilly. “Eventually, we will aggregate those characteristics in terms of historical segments that allow us to predict blood pressure spikes.”</p> <p>The ALFA group has created a database called BeatDB that collects not only the beats of the waveforms, but “a set of properties or features of every beat,” says O’Reilly. BeatDB has already stored a billion blood pressure beat features from more than 5,000 patients.</p> <p>“For every beat we describe a time-series set of morphological features,” explains O’Reilly. “Once we establish a solid set of fundamental data about the signals, we can provide technology as services on top of that, allowing new beats to be added and processed.”</p> <p>Because BeatDB enables beats to be aggregated into segments, physicians can better decide how much history is needed to make a prediction. “To predict a blood pressure drop 15 minutes ahead, you might need hours of patient data,” says O’Reilly. “Because the BeatDB data is organized, and leverages machine learning algorithms, physicians don’t have to compute this over and over again. They can experiment with how much data and lead time is required, and then check the accuracy of their models.”</p> <p>Recently, O’Reilly has begun to use the technology to explore ECG data. “We’re hoping to look at data that might be collected in context of the quantified self,” says O’Reilly, referring to the emerging practice of wearing fitness bracelets to track one’s internal data.</p> <p>“More and more people are instrumenting themselves by wearing a Fitbit that tells them whether they’re tired or how well they sleep,” says O’Reilly. “Interpreting all these bodily signals is similar to the GigaBEATS project. A BeatDB-like database and cloud-based facility could be set up around these signals to help interpret them.”</p> Una-May O'ReillyDavid SellaBig data, Algorithms, Evolution, Wind, Massive open online courses (MOOCs), Computer science and technology, Electrical Engineering & Computer Science (eecs), School of Engineering, Faculty, Profile, Research, Computer Science and Artificial Intelligence Laboratory (CSAIL) Neuroscientists identify key role of language gene Mutation that arose long ago may be key to humans’ unique ability to produce and understand speech. Mon, 15 Sep 2014 15:00:00 -0400 Anne Trafton | MIT News Office <p>Neuroscientists have found that a gene mutation that arose more than half a million years ago may be key to humans’ unique ability to produce and understand speech.</p> <p>Researchers from MIT and several European universities have shown that the human version of a gene called Foxp2 makes it easier to transform new experiences into routine procedures. When they engineered mice to express humanized Foxp2, the mice learned to run a maze much more quickly than normal mice.</p> <p>The findings suggest that Foxp2 may help humans with a key component of learning language — transforming experiences, such as hearing the word “glass” when we are shown a glass of water, into a nearly automatic association of that word with objects that look and function like glasses, says Ann Graybiel, an MIT Institute Professor, member of MIT’s McGovern Institute for Brain Research, and a senior author of the study.</p> <p>“This really is an important brick in the wall saying that the form of the gene that allowed us to speak may have something to do with a special kind of learning, which takes us from having to make conscious associations in order to act to a nearly automatic-pilot way of acting based on the cues around us,” Graybiel says.</p> <p>Wolfgang Enard, a professor of anthropology and human genetics at Ludwig-Maximilians University in Germany, is also a senior author of the study, which appears in the <em>Proceedings of the National Academy of Sciences</em> this week. The paper’s lead authors are Christiane Schreiweis, a former visiting graduate student at MIT, and Ulrich Bornschein of the Max Planck Institute for Evolutionary Anthropology in Germany.</p> <p>All animal species communicate with each other, but humans have a unique ability to generate and comprehend language. Foxp2 is one of several genes that scientists believe may have contributed to the development of these linguistic skills. The gene was first identified in a group of family members who had severe difficulties in speaking and understanding speech, and who were found to carry a mutated version of the Foxp2 gene.</p> <p>In 2009, Svante Pääbo, director of the Max Planck Institute for Evolutionary Anthropology, and his team engineered mice to express the human form of the Foxp2 gene, which encodes a protein that differs from the mouse version by only two amino acids. His team found that these mice had longer dendrites — the slender extensions that neurons use to communicate with each other — in the striatum, a part of the brain implicated in habit formation. They were also better at forming new synapses, or connections between neurons.</p> <p>Pääbo, who is also an author of the new <em>PNAS</em> paper, and Enard enlisted Graybiel, an expert in the striatum, to help study the behavioral effects of replacing Foxp2. They found that the mice with humanized Foxp2 were better at learning to run a T-shaped maze, in which the mice must decide whether to turn left or right at a T-shaped junction, based on the texture of the maze floor, to earn a food reward.</p> <p>The first phase of this type of learning requires using declarative memory, or memory for events and places. Over time, these memory cues become embedded as habits and are encoded through procedural memory — the type of memory necessary for routine tasks, such as driving to work every day or hitting a tennis forehand after thousands of practice strokes.</p> <p>Using another type of maze called a cross-maze, Schreiweis and her MIT colleagues were able to test the mice’s ability in each of type of memory alone, as well as the interaction of the two types. They found that the mice with humanized Foxp2 performed the same as normal mice when just one type of memory was needed, but their performance was superior when the learning task required them to convert declarative memories into habitual routines. The key finding was therefore that the humanized Foxp2 gene makes it easier to turn mindful actions into behavioral routines.</p> <p>The protein produced by Foxp2 is a transcription factor, meaning that it turns other genes on and off. In this study, the researchers found that Foxp2 appears to turn on genes involved in the regulation of synaptic connections between neurons. They also found enhanced dopamine activity in a part of the striatum that is involved in forming procedures. In addition, the neurons of some striatal regions could be turned off for longer periods in response to prolonged activation — a phenomenon known as long-term depression, which is necessary for learning new tasks and forming memories.</p> <p>Together, these changes help to “tune” the brain differently to adapt it to speech and language acquisition, the researchers believe. They are now further investigating how Foxp2 may interact with other genes to produce its effects on learning and language.</p> <p>This study “provides new ways to think about the evolution of Foxp2 function in the brain,” says Genevieve Konopka, an assistant professor of neuroscience at the University of Texas Southwestern Medical Center who was not involved in the research. “It suggests that human Foxp2 facilitates learning that has been conducive for the emergence of speech and language in humans. The observed differences in dopamine levels and long-term depression in a region-specific manner are also striking and begin to provide mechanistic details of how the molecular evolution of one gene might lead to alterations in behavior.”</p> <p>The research was funded by the Nancy Lurie Marks Family Foundation, the Simons Foundation Autism Research Initiative, the National Institutes of Health, the Wellcome Trust, the Fondation pour la Recherche Médicale, and the Max Planck Society.</p> Brain and cognitive sciences, Language, Learning, Memory, McGovern Institute, School of Science, Research, Evolution, Biology Wrinkles in time Researchers say that ripples in ancient rock may be signs of early life. Fri, 12 Sep 2014 00:00:04 -0400 Jennifer Chu | MIT News Office <p>Take a walk along any sandy shoreline, and you’re bound to see a rippled pattern along the seafloor, formed by the ebb and flow of the ocean’s waves.</p> <p>Geologists have long observed similar impressions — in miniature — embedded within ancient rock. These tiny, millimeter-wide wrinkles have puzzled scientists for decades: They don’t appear in any modern environment, but seem to be abundant much earlier in Earth’s history, particularly following mass extinctions.</p> <p>Now MIT researchers have identified a mechanism by which such ancient wrinkles may have formed. Based on this mechanism, they posit that such fossilized features may be a vestige of microbial presence —&nbsp;in other words, where there are wrinkles, there must have been life.</p> <p>“You have about 3 billion years of Earth’s history where everything was microbial. The wrinkle structures were present, but don’t seem to have been all that common,” says Tanja Bosak, the Alfred Henry and Jean Morrison Hayes Career Development Associate Professor in MIT’s Department of Earth, Atmospheric and Planetary Sciences. “But it seems they become really abundant at the time when early animals were around. Knowing the mechanism of these features gives us a better sense of the environmental pressures these early animals were experiencing.”</p> <p>Bosak and her colleagues have published their study, led by postdoc Giulio Mariotti, in the journal<em> Nature Geoscience.&nbsp;</em>Co-authors include Taylor Perron, an associate professor of geology at MIT, and Sara Pruss, an associate professor of geosciences at Smith College.</p> <p><strong>Sedimentary footprints</strong></p> <p>Ancient sedimentary wrinkles can be found in rocks up to 575 million years old — from a time when the earliest animals may have arisen — in places such as Australia, Africa, and Canada.</p> <p>“Some of them look like wave ripples, and others look like raindrop impressions,” Mariotti says. “They’re shapes that remain in the sediment, like the footprint of a dinosaur.”</p> <p>Researchers have put forth multiple theories for how these shapes may have arisen. Some believe that ocean waves may have created such patterns, while others think the answer may lie in ancient sea foam.</p> <p>But the prevailing theory involves the presence of microbes: In a post-extinction world, microbial mats likely took over the seafloor in wide, leathery patches that were tough enough to withstand the overlying flow. As these mats were destroyed, they left small, lightweight microbial aggregates that shifted the underlying sand, creating wavelike patterns that were later preserved in sediment.</p> <div class="cms-placeholder-content-video"></div> <p><strong>A fragmentary sweet spot</strong></p> <p>To test this last theory, Mariotti attempted to recreate the wrinkled patterns by growing microbial mats in custom-built wave tanks, partially filled with sand. To track his progress, he set up a camera to take time-lapse images of the tank. His initial results were successful — although, he admits, accidental.</p> <p>“I reproduced something that looked like wrinkle structures, although at first it wasn’t on purpose,” Mariotti says.</p> <p>In his first attempts to seed a tank with microbes, Mariotti obtained fragments of microbial mats from another wave tank in which microbes were growing at a moderate rate. After a few days, he spotted tiny, millimeter-wide ripples in the sand. Looking back at the time-lapse images, he discovered the mechanism: Fragments of microbial mats were rolling along the surface and, within a few hours, rearranging sediments to create wavelike patterns in the sand.</p> <p>Mariotti followed up on the observation with more controlled experiments with various wave conditions and microbial fragments, confirming that fragments, and not whole microbes, were forming the wrinkled features in the sediment.</p> <p>The results led the group to raise another question: What might have created such microbial fragments? Bosak says the likely answer is the early appearance of small animals, which may have grazed on microbial mats, ripping them into fragments in the process.</p> <p>“What we’re suggesting is that there may be some sort of sweet spot: You can’t have too many animals feeding, because then you lose microbial mats completely, but you need enough to produce these fragments,” Bosak says. “And that sweet spot could occur after a large marine extinction event.”</p> <p>Mariotti says the mechanism he’s identified may shed light on the environmental conditions early animals faced as they tried to gain a foothold following an extinction event. For example, early animals may have thrived in protected environments such as shallow lagoons, where microbial fragments might best create wrinkled patterns.</p> <p>“You need an environment where there’s not much energy, but still some wave motion, and close enough to the photic zone where you have light, so that microbial mats can grow,” Mariotti says. “Our finding may change how we see early animals.”</p> <p>David Bottjer, a professor of earth sciences at the University of Southern California, says knowing the mechanism by which these wrinkle structures formed is important not just for understanding life on Earth, but life on other planets as well.</p> <p>“It has been suggested that if a Martian rover was scanning sedimentary rocks that had been deposited underwater, and it saw wrinkle structures, that this could mean that there was microbial life present when the rocks were deposited,” says Bottjer, who was not involved in the work. “This study provides experimental evidence that, indeed, microbial fragments derived from microbial mats would be necessary to produce wrinkle structures. So, as a ‘biomarker’ indicating that microbial life would have existed on Mars, this strengthens the case for wrinkle structures, if they are found.”</p> <p>This research was partially supported by NASA and the National Science Foundation.</p> Fossils, Geology, History, Early Earth, Evolution, EAPS, Earth and atmospheric sciences, earth, Origins of life, Mass extinction, School of Science Rise of the dinosaurs New evidence raises questions about when dinosaurs evolved in North America. Tue, 12 Aug 2014 00:00:02 -0400 Jennifer Chu | MIT News Office <p>The Jurassic and Cretaceous periods were the golden age of dinosaurs, during which the prehistoric giants roamed the Earth for nearly 135 million years. Paleontologists have unearthed numerous fossils from these periods, suggesting that dinosaurs were abundant throughout the world. But where and when dinosaurs first came into existence has been difficult to ascertain.</p> <p>Fossils discovered in Argentina suggest that the first dinosaurs may have appeared in South America during the Late Triassic, about 230 million years ago — a period when today’s continents were fused in a single landmass called Pangaea. Previously discovered fossils in North America have prompted speculation that dinosaurs didn’t appear there until about 212 million years ago — significantly later than in South America. Scientists have devised multiple theories to explain dinosaurs’ delayed appearance in North America, citing environmental factors or a vast desert barrier.</p> <p>But scientists at MIT now have a bone to pick with such theories: They precisely dated the rocks in which the earliest dinosaur fossils were discovered in the southwestern United States, and found that dinosaurs appeared there as early as 223 million years ago. What’s more, they demonstrated that these earliest dinosaurs coexisted with close nondinosaur relatives, as well as significantly more evolved dinosaurs, for more than 12 million years. To add to the mystery, they identified a 16-million-year gap, older than the dinosaur-bearing rocks, where there is either no trace of any vertebrates, including dinosaurs, in the rock record, or the corresponding rocks have eroded.</p> <p>“Right below that horizon where we find the earliest dinosaurs, there is a long gap in the fossil and rock records across the sedimentary basin,” says Jahan Ramezani, a research scientist in MIT’s Department of Earth, Atmospheric and Planetary Sciences. “If the record is not there, it doesn’t mean the dinosaurs didn’t exist. It means that either no fossils were preserved, or we haven’t found them. That tells us the theory that dinosaurs simply started in South America and spread all over the world has no firm basis.”</p> <p>Ramezani details the results of his geochronological analysis in the <em>American Journal of Science</em>. The study’s co-authors are Sam Bowring, the Robert R. Shrock Professor of Geology at MIT, and David Fastovsky, professor of geosciences at the University of Rhode Island.</p> <p><strong>The isotope chronometer</strong></p> <p>The most complete record of early dinosaur evolution can be found in Argentina, where layers of sedimentary rock preserve a distinct evolutionary progression: During the Late Triassic period, preceding the Jurassic, dinosaur “precursors” first appeared, followed by animals that began to exhibit dinosaur-like characteristics, and then advanced, or fully evolved, dinosaurs. Each animal group is found in a distinct rock formation, with very little overlap, revealing a general evolutionary history.</p> <p>In comparison, the dinosaur record in North America is a bit muddier. The most abundant fossils from the Late Triassic period have been discovered in layers of rock called the Chinle Formation, which occupies portions of Arizona, New Mexico, Utah, and Colorado, and is best exposed in Petrified Forest National Park. Scientists had previously dated isolated beds of this formation, and determined the earliest dinosaur-like animals, discovered in New Mexico, appeared by 212 million years ago.</p> <p>Ramezani and Bowring sought to more precisely date the entire formation, including levels in which the earliest dinosaur fossils have been found. The team took samples from exposed layers of sedimentary rock that were derived, in large part, from volcanic debris in various sections of the Chinle Formation. In the lab, the researchers pulverized the rocks and isolated individual microscopic grains of zircon — a uranium-bearing mineral that forms in magma shortly prior to volcanic eruptions. From the moment zircon crystallizes, the decay of uranium to lead begins in the mineral and, as Ramezani explains it, “the chronometer starts.” Researchers can measure the ratio of uranium to lead isotopes to determine the age of the zircon, and, inferentially, the rock in which it was found.</p> <div class="cms-placeholder-content-slideshow"></div> <p><strong>A unique but incomplete record</strong></p> <p>The team analyzed individual grains of zircon, and created a precise map of ages for each sedimentary interval of the Chinle Formation. Ramezani found, based on rock ages, that the fossils found in New Mexico are, in fact, not the earliest dinosaurs in North America. Instead, it appears that fossils found in Arizona are older, discovered in rocks as old as 223 million years.</p> <p>In this North American mix, the early relatives of dinosaurs apparently coexisted with more evolved dinosaurs for more than 12 million years, according to Ramezani’s analysis.</p> <p>“In South America, there is very little overlap,” Ramezani says. “But in North America, we see this unique interval when these groups were coexisting. You could think of it as Neanderthals coexisting with modern humans.”</p> <p>While fascinating to think about, Ramezani says this period does not shed much light on when the very first dinosaurs appeared in North America.</p> <p>“The fact that our record starts with advanced forms tells us there was a prior history,” Ramezani says. “It’s not just that advanced dinosaurs suddenly appeared 223 million years ago. There must have been prior evolution in North America — we just haven’t identified any earlier dinosaurs yet.”</p> <p>He says the answer to when dinosaurs first appeared in North America may lie in a 16-million-year gap, in the lower Chinle Formation and beneath it, which bears no fossils, dinosaurian or otherwise. The absence of any fossils is unremarkable; Ramezani notes that fossil preservation is “an exceptional process, requiring exceptional circumstances.” Dinosaurs may well have first appeared during this period; if they left any fossil evidence, it may have since been erased.</p> <p>“Every study like this is a step forward, to try to reconstruct the past,” Ramezani says. “Dinosaurs really rose to the top of the pyramid. What made them so successful, and what were the evolutionary advantages they developed so as to dominate terrestrial ecosystems? It all goes back to their beginning, to the Late Triassic when they just started to appear.”</p> <p>The new dates provide a framework against which other theories of dinosaur evolution may be tested, says Raymond Rogers, a professor of geology at Macalester College in Saint Paul, Minn., who was not involved in this work.</p> <p>“This is the kind of careful work that needs to be done before evolutionary hypotheses that relate to the origination and diversification of the dinosaurs can be addressed,” Rogers says. “This gap in the Chinle fossil record makes comparing the North American and South American dinosaur records problematic. Existing hypotheses that relate to the timing of dinosaur evolution in North and South America arguably need to be reconsidered in light of this new study.”</p> <p>This research was supported by funding from the National Science Foundation.</p> Dinosaurs, Geology, paleontology, Evolution, Research, Earth and atmospheric sciences, School of Science Did Neanderthals eat their vegetables? MIT study provides first direct evidence of plants in the Neanderthal diet. Wed, 25 Jun 2014 17:00:00 -0400 Jennifer Chu | MIT News Office <p>The popular conception of the Neanderthal as a club-wielding carnivore is, well, rather primitive, according to a new study conducted at MIT. Instead, our prehistoric cousin may have had a more varied diet that, while heavy on meat, also included plant tissues, such as tubers and nuts.</p> <p>Scientists from MIT and the University of La Laguna in Spain have identified human fecal remains from El Salt, a known site of Neanderthal occupation in southern Spain that dates back 50,000 years. The researchers analyzed each sample for metabolized versions of animal-derived cholesterol, as well as phytosterol, a cholesterol-like compound found in plants. While all samples contained signs of meat consumption, two samples showed traces of plants — the first direct evidence that Neanderthals may have enjoyed an omnivorous diet.</p> <p>“We have passed through different phases in our interpretation of Neanderthals,” says Ainara Sistiaga, a graduate student at the University of La Laguna who led the analysis as a visiting student at MIT. She and her colleagues have published their study in the journal <em>PLoS ONE.</em></p> <p>“It’s important to understand all aspects of why humanity has come to dominate the planet the way it does,” adds co-author Roger Summons, a professor of geobiology in MIT’s Department of Earth, Atmospheric and Planetary Sciences. “A lot of that has to do with improved nutrition over time.”</p> <p><strong>Unearthing a prehistoric meal</strong></p> <p>While scientists have attempted to reconstruct the Neanderthal diet, much of the evidence has been inconclusive. For example, researchers have analyzed bone fragments for carbon and nitrogen isotopes — signs that Neanderthals may have consumed certain prey, such as pigs versus cows. But such isotopic data only differentiate between protein sources — underestimating plant intake, and thereby depicting the Neanderthal as exclusively carnivorous</p> <p>Other researchers recently identified plant microfossils trapped in Neanderthal teeth — a finding that suggests the species may have led a more complex lifestyle, harvesting and cooking a variety of plants in addition to hunting prey. But Sistiaga says it is also possible that Neanderthals didn’t eat plants directly, but consumed them through the stomach contents of their prey, leaving traces of plants in their teeth.</p> <p>Equally likely, she says, is another scenario: “Sometimes in prehistoric societies, they used their teeth as tools, biting plants, among other things. We can’t assume they were actually eating the plants based on finding microfossils in their teeth.”</p> <p><strong>Signs in the soil</strong></p> <p>For a more direct approach, Sistiaga looked for fecal remains in El Salt, an excavation site in Alicante, Spain, where remnants of multiple Neanderthal occupations have been unearthed. Sistiaga and her colleagues dug out small samples of soil from different layers, and then worked with Summons to analyze the samples at MIT.</p> <p>In the lab, Sistiaga ground the soil into a powder, then used multiple solvents to extract any organic matter from the sediment. Next, she looked for certain biomarkers in the organic residue that would signal whether the fecal remains were of human origin.</p> <p>Specifically, Sistiaga looked for signs of coprostanol, a lipid formed when the gut metabolizes cholesterol. As humans are able to break down more cholesterol than any other mammal, Sistiaga looked for a certain peak level of coprostanol that would indicate the sample came from a human.</p> <p>She and Summons then used the same geochemical techniques to determine the proportions of coprostanol — an animal-derived compound — to 5B-stigmastanol, a substance derived from the breakdown of phytosterol derived from plants.</p> <p>Each sample contained mostly coprostanol — evidence of a largely meat-based diet. However, two samples also held biomarkers of plants, which Sistiaga says may indicate a rather significant plant intake. As she explains it, gram for gram, there is more cholesterol in meat than there is phytosterol in plants — so it would take a significant plant intake to produce even a small amount of metabolized phytosterol.</p> <p>In other words, while Neanderthals had a mostly meat-based diet, they may have also consumed a fairly regular portion of plants, such as tubers, berries, and nuts.</p> <p>“We believe Neanderthals probably ate what was available in different situations, seasons, and climates,” Sistiaga says.</p> <p>Richard Wrangham, a professor of biological anthropology at Harvard University, says that since no isotopic signatures have yet been found for plants that might be eaten by Neandertals, determining whether Neanderthals consumed plants “has been entirely a matter of guesswork until recently.”</p> <p>“These lovely new data on fecal sterols confirm what many people have been increasingly thinking, which is that something is wrong with the inference that Neanderthals were 100 percent carnivores,” says Wrangham, who was not involved in the research. “The Sistiaga data are a wonderful new source for challenging conventional wisdom. In the end it would not be surprising to find that Neanderthals show little difference from sapiens in their diet composition.”</p> <p>Sistiaga, Summons, and their colleagues plan to use similar geochemical biomarker techniques, coupled with micromorphological analysis, to analyze soil samples in Olduvai Gorge, Tanzania — a 1.8-million-year-old site where some of the earliest evidence of human ancestry have been discovered.</p> <p>“We’re working in a micro context,” Sistiaga says. “Until now, people have carried out residue analysis on pots, tools, and other objects, but 90 percent of archaeology is sediment. We’re opening a new window to the information that is enclosed in Paleolithic soil and sediment.”</p> paleontology, Geochemistry, Evolution, Neanderthals, Human, Earth and atmospheric sciences, Ecology, Research, School of Science From contemporary syntax to human language’s deep origins New paper amplifies hypothesis that human language builds on birdsong and speech forms of other primates. Wed, 11 Jun 2014 00:00:01 -0400 Peter Dizikes | MIT News Office <p>On the island of Java, in Indonesia, the silvery gibbon, an endangered primate, lives in the rainforests. In a behavior that’s unusual for a primate, the silvery gibbon sings: It can vocalize long, complicated songs, using 14 different note types, that signal territory and send messages to potential mates and family.</p> <p>Far from being a mere curiosity, the silvery gibbon may hold clues to the development of language in humans. In <a href="">a newly published paper</a>, two MIT professors assert that by re-examining contemporary human language, we can see indications of how human communication could have evolved from the systems underlying the older communication modes of birds and other primates.</p> <p>From birds, the researchers say, we derived the melodic part of our language, and from other primates, the pragmatic, content-carrying parts of speech. Sometime within the last 100,000 years, those capacities fused into roughly the form of human language that we know today.</p> <p>But how? Other animals, it appears, have finite sets of things they can express; human language is unique in allowing for an infinite set of new meanings. What allowed unbounded human language to evolve from bounded language systems?</p> <p>“How did human language arise? It’s far enough in the past that we can’t just go back and figure it out directly,” says linguist Shigeru Miyagawa, the Kochi-Manjiro Professor of Japanese Language and Culture at MIT. “The best we can do is come up with a theory that is broadly compatible with what we know about human language and other similar systems in nature.”</p> <p>Specifically, Miyagawa and his co-authors think that some apparently infinite qualities of modern human language, when reanalyzed, actually display the finite qualities of languages of other animals — meaning that human communication is more similar to that of other animals than we generally realized.</p> <p>“Yes, human language is unique, but if you take it apart in the right way, the two parts we identify are in fact of a finite state,” Miyagawa says. “Those two components have antecedents in the animal world. According to our hypothesis, they came together uniquely in human language.”</p> <p><strong>Introducing the ‘integration hypothesis’</strong></p> <p>The current paper, “The Integration Hypothesis of Human Language Evolution and the Nature of Contemporary Languages,” is published this week in <em>Frontiers in Psychology</em>. The authors are Miyagawa; Robert Berwick, a professor of computational linguistics and computer science and engineering in MIT’s Laboratory for Information and Decision Systems; and Shiro Ojima and Kazuo Okanoya, scholars at the University of Tokyo.</p> <p>The paper’s conclusions build on past work by Miyagawa, which holds that human language consists of two distinct layers: the expressive layer, which relates to the mutable structure of sentences, and the lexical layer, where the core content of a sentence resides. That idea, in turn, is based on previous work by linguistics scholars including Noam Chomsky, Kenneth Hale, and Samuel Jay Keyser.</p> <p>The expressive layer and lexical layer have antecedents, the researchers believe, in the languages of birds and other mammals, respectively. For instance, in another paper published last year, Miyagawa, Berwick, and Okanoya presented a broader case for the connection between the expressive layer of human language and birdsong, including similarities in melody and range of beat patterns.</p> <p>Birds, however, have a limited number of melodies they can sing or recombine, and nonhuman primates have a limited number of sounds they make with particular meanings. That would seem to present a challenge to the idea that human language could have derived from those modes of communication, given the seemingly infinite expression possibilities of humans.</p> <p>But the researchers think certain parts of human language actually reveal finite-state operations that may be linked to our ancestral past. Consider a linguistic phenomenon known as “discontiguous word formation,” which involve sequences formed using the prefix “anti,” such as “antimissile missile,” or “anti-antimissile missile missile,” and so on. Some linguists have argued that this kind of construction reveals the infinite nature of human language, since the term “antimissile” can continually be embedded in the middle of the phrase.</p> <p>However, as the researchers state in the new paper, “This is not the correct analysis.” The word “antimissile” is actually a modifier, meaning that as the phrase grows larger, “each successive expansion forms via strict adjacency.” That means the construction consists of discrete units of language. In this case and others, Miyagawa says, humans use “finite-state” components to build out their communications.</p> <p>The complexity of such language formations, Berwick observes, “doesn’t occur in birdsong, and doesn’t occur anywhere else, as far as we can tell, in the rest of the animal kingdom.” Indeed, he adds, “As we find more evidence that other animals don’t seem to posses this kind of system, it bolsters our case for saying these two elements were brought together in humans.”</p> <p><strong>An inherent capacity</strong></p> <p>To be sure, the researchers acknowledge, their hypothesis is a work in progress. After all, Charles Darwin and others have explored the connection between birdsong and human language. Now, Miyagawa says, the researchers think that “the relationship is between birdsong and the expression system,” with the lexical component of language having come from primates. Indeed, as the paper notes, the most recent common ancestor between birds and humans appears to have existed about 300 million years ago, so there would almost have to be an indirect connection via older primates — even possibly the silvery gibbon.</p> <p>As Berwick notes, researchers are still exploring how these two modes could have merged in humans, but the general concept of new functions developing from existing building blocks is a familiar one in evolution.</p> <p>“You have these two pieces,” Berwick says. “You put them together and something novel emerges. We can’t go back with a time machine and see what happened, but we think that’s the basic story we’re seeing with language.”</p> <p>Andrea Moro, a linguist at the Institute for Advanced Study IUSS, in Pavia, Italy, says the current paper provides a useful way of thinking about how human language may be a synthesis of other communication forms.</p> <p>“It must be the case that this integration or synthesis [developed] from some evolutionary and functional processes that are still beyond our understanding,” says Moro, who edited the article. “The authors of the paper, though, provide an extremely interesting clue at the formal level.”</p> <p>Indeed, Moro adds, he thinks the researchers are “essentially correct” about the existence of finite elements in human language, adding, “Interestingly, many of them involve the morphological level — that is, the level of composition of words from morphemes, rather than the sentence level.”</p> <p>Miyagawa acknowledges that research and discussion in the field will continue, but says he hopes colleagues will engage with the integration hypothesis.</p> <p>“It’s worthy of being considered, and then potentially challenged,” Miyagawa says.</p> Illustration: Christine Daniloff/MITLinguistics, Electrical Engineering & Computer Science (eecs), Laboratory for Information and Decision Systems (LIDS), Faculty, Research, Evolution, Biology Yeast studies suggest alternative cancer approach Biophysicist Jeff Gore and collaborators urge applying lessons from yeast colony collapse to tumor growth. Fri, 02 May 2014 14:30:00 -0400 Denis Paiste | Materials Processing Center <p>Yeast populations exposed to a sudden environmental shock can be driven to extinction, MIT researchers have shown. Could this principle also apply to human cancer cells? Possibly, argue researchers from MIT, Boston University, and Memorial Sloan-Kettering Cancer Center in a Perspectives article published online on April 17 by&nbsp;Nature Reviews Cancer&nbsp;and appearing in the May 2014 print edition.</p> <p>Tools from ecology and evolution are bringing about new ways to think about cancer and new pathways for fighting its development and spread. These tools include population dynamics, evolutionary game theory, frequency dependent selection and critical slowing down, genetic drift, and spatial diversity.</p> <p>In the article, co-authors&nbsp;Kirill Korolev, assistant professor of physics at Boston University,&nbsp;Joao B. Xavier, computational biologist at Memorial Sloan-Kettering Cancer Center, in New York, and <a href="">Jeff Gore</a>, Latham Family Career Development Assistant Professor of Physics at MIT, suggest that evidence from natural population extinctions and from theoretical and empirical studies points to new ways of guiding drug delivery by identifying the threshold population size for cancer cells to form a tumor.</p> <p>"By thinking about cancer cells as an endangered species, cancer vulnerabilities become more apparent," the authors say in their abstract.</p> <p>Just as fish swim in schools to avoid predators, it may be that cancer cells cooperate and that they must reach a certain threshold population before they can form a tumor. A number below that threshold may lead to extinction of those cells.</p> <p>Researchers at Princeton, University of California-San Francisco, and the Salk Institute argued similarly in a&nbsp;May 2011 Perspectives&nbsp;article in Nature Reviews Cancer that bacterial populations, which have much in common with human cancer tumors, could serve as a biological model for scientific studies of adaptation and evolution.</p> <p>The new Perspectives piece grew out of work at the&nbsp;<a href="">Gore Laboratory</a> at MIT, where lead author Korolev previously served as a Pappalardo Postdoctoral Fellow. In nature, an organism may thrive at an intermediate population size but fail when that population grows too small. This phenomenon, called a strong Allee effect, has been observed in laboratory cell cultures, where it is hard for an individual cancer cell to grow by itself in isolation unless the media is conditioned by secretions from other cells, the authors note. Similarly, small groups of cancer cells that spread from their original site may stay dormant for a long time. Allee effects might open several new mechanisms for cancer treatment, such as drugs that reduce the number of cells below the threshold for survival or raise the threshold for tumor formation by interfering with cooperative growth among cancer cells. "A radically new approach to therapy would be to focus on the size of the threshold, rather than on the population size," the authors suggest.</p> <p>The fact that some cancers return after treatment seems to contradict this argument, or at least point to an alternative route for tumor formation. Since&nbsp;cancer&nbsp;is typically a collection of a variety of mutated cells rather than a single deformed line, recurrence could indicate either that some cells remained after treatment that had weak or absent Allee effects or that some left-over cancer cells continued to mutate during remission, becoming more potent tumor formers.</p> <p>One hope from the new approach is that identifying and targeting Allee effects could block the spread of cancer from the primary site. "Even a modest increase in the size of the growth threshold can yield a marked reduction in the probability of successful metastasis being formed," the authors wrote. For existing tumors, traditional cancer treatments would still be needed at the primary site, but that treatment "would push the primary tumor below the critical population size and lead to a rapid population 'meltdown.' Here, again, high growth thresholds could be beneficial, because they make it harder for new mutations to rescue the population."</p> <p>Complex interactions between prostate cancer cells, for example, and the body's macrophages (white blood cells) and stromal cells (connective tissue) can change the body's natural environment, creating a new ecology that favors tumor formation. Targeting not only the cancer cells but also the altered blood cells or tissue cells could create a new route to stop the spread of the cancer. The drug clodronate, for example, is used to block the spread of breast cancer to the bone. "As mutations tend to vary across patients, whereas stromal cells do not, therapies that target the stroma may have wider applicability than therapies that target somatic mutations," the authors wrote. (Somatic mutations are ones that are not inherited.) Other researchers have applied evolutionary game theory models to explore cancer spread in multiple myeloma, a cancer affecting specialized white blood cells called plasma.</p> <p>Because of their genetic diversity, several variant cancer cell lines, each adapted to carry out different functions, could exist simultaneously as a small proportion of the overall tumor population. For example, some cancer cells could carry lower rates of natural cell death (apoptosis), while others add the ability to recruit blood vessels. Such interdependency of related but differently adapted cells raises the possibility of additional strategies to fight the cancer, such as attacking the weakest cell line needed to support the tumor or increasing the interdependencies of different cell lines, making it harder for them to spread and form remote tumors.</p> <p><a href="">Previous research</a> by Gore and&nbsp;Alvaro Sanchez, a former MIT postdoctoral associate who is now a&nbsp;junior fellow at the Rowland Institute of Science at Harvard University, demonstrated that a mixed population of “cooperators” and “cheaters” in yeast responded to stress by altering the mix of cooperators and cheaters. Given sufficient time, the population evolved to reach a new stable state, but a sudden stress caused the population to collapse. If cancer cells behave in a similar way, this suggests that time is the enemy in terms of controlling cancer, and that a sudden shock will have the best results against it. Thus, cancer should be "hit hard," the new article proposes.</p> <p>Robert Austin, professor of physics at Princeton University, says of the Nature Cancer Reviews piece, “I think this perspective is interesting, but maybe needs to look more carefully at some of the experiments that already exist that would indicate that things are not as simple or optimistic as you might hope.” In a truly complex ecology, Austin says, there is always a place for a mutant to slowly grow and increase fitness. In a September 2011 <em>Science</em>&nbsp;<a href="">paper</a>, with lead author Qiucen Zhang, Austin and colleagues developed a complex ecology to accelerate the evolution of drug resistance in bacteria. “The problem is, that experiment showed that even with only 100 bacteria in the initial inoculation, the eventual emergence of drug resistance was inevitable,” he says.</p> <p>Korolev also previously studied the role of tumor cells known as&nbsp;<a href="">"passenger" cells</a>&nbsp;in the MIT lab of Leonid Mirny, associate professor of health sciences and technology and physics in the Harvard-MIT Division of Health Sciences and Technology. As a mutation-driven asexual evolutionary process, cancer may follow the same evolutionary dynamics as viruses and bacteria. One possible consequence of such a process is that small tumors produce mutations that are less able to reproduce themselves and shrink, while large tumors produce more self-sustaining mutations, called drivers, and grow. "The critical population size, which controls the ability of the tumor to adapt, depends on evolutionary parameters of the cancer," Gore and colleagues argue. That opens pathways to interfere with the evolutionary dynamics of the cancer. "Mutation rates can be increased by adding a mutagen or by inhibiting DNA repair machinery."</p> <p>Animal tests to measure threshold size may be possible by targeting a tumor with pulsed application of a drug and studying the response. If tests show that a large attack shrinks the tumor and leads to remission while a smaller attack at first shrinks the tumor but then lets it rebound, that split response would indicate a potential Allee threshold and prescribe a minimum level for effective drug dosage.</p> <p>"When replica experiments are possible, a direct way to ascertain a growth threshold is to measure how the probability of remission depends on the initial size of the tumor," they say. "Given the complexity of cancer, it would be remarkable if such simple techniques can succeed at identifying thresholds in cancer dynamics. Nevertheless, their success in natural populations suggests that some potentially cancer-specific indicators of thresholds can be identified and deployed in laboratory-based research and in the clinic."</p> <p>Like expansions of wild animal populations, tumor growth shows spatial diversity, with similar mutations clustering to the exclusion of other variants. The segregation is helped along by genetic drift, which is random fluctuations in the number of successive generations from a cancer cell line, and it might be limited by nutrient control. Studies by other researchers have shown that such genetic variety in tumors can produce faster cancer cell evolution and lead to more aggressive cells. These findings suggest that inclusion of evolutionary and ecological factors in cancer drug development is an important next step, Gore and colleagues offer in their opinion piece.</p> <p>"The authors did a great job in summarizing a difficult topic and weaving together many different threads of research," says Dr.&nbsp;Robert A. Gatenby, chair of radiology at the Moffitt Cancer Center in Tampa, Fla. "It is likely that evolution represents the first principles of cancer, but it is important to recognize that cancer also has an ecology that causes spatial and temporal heterogeneity, which strongly affects therapeutic outcome. While the conceptual model of cancer as evolution is at least 50 years old, the full implications of this paradigm in cancer treatment and prevention are only now being realized. The biggest challenge now is moving from theory to practice and using evolutionary principles in cancer therapy."</p> <p>Korolev, Xavier, and Gore suggest two techniques to address evolutionary dynamics and cancer cell line evolution in tumors: lineage tracing, which has been used to identify cancer stem cells, and methylation patterns of non-expressed genes. "It remains to be seen if lineage tracing, spatially resolved sequencing or other experimental techniques can fully characterize evolutionary and ecological dynamics within the tumor, thereby opening up possibilities for accurate modeling of tumor evolution and new treatment strategies," they say.</p> <p>Gore's work is supported by an NIH New Innovator Award and an NSF CAREER Award. Gore is also a Pew Scholar, Allen Distinguished Investigator, and Sloan Research Fellow. Xavier's work is supported by grants from the National Cancer Institute and the National Institutes of Health.</p> Collaborators, Jeff Gore (left) of MIT and Kirill Korolev of Boston University discuss joint research into range expansions. They suggest applying ecological and evolutionary lessons from dynamics of microbial populations to treating human cancers in a paper co-authored with Joao B. Xavier of the Memorial Sloan-Kettering Cancer Center. Photo: Denis PaisteFaculty, Cancer, Population, Ecology, Evolution, Tumors Ocean microbes display remarkable genetic diversity One species, a few drops of seawater, hundreds of coexisting subpopulations. Thu, 24 Apr 2014 14:00:00 -0400 Denise Brehm | Civil and Environmental Engineering <p>The smallest, most abundant marine microbe, Prochlorococcus<em>,</em> is a photosynthetic bacteria species essential to the marine ecosystem. An estimated billion billion billion of the single-cell creatures live in the oceans, forming the base of the marine food chain and occupying a range of ecological niches based on temperature, light and chemical preferences, and interactions with other species. But the full extent and characteristics of diversity within this single species remains a puzzle.&nbsp;</p> <p>To probe this question, scientists in MIT’s Department of Civil and Environmental Engineering (CEE) recently performed a cell-by-cell genomic analysis on a wild population of Prochlorococcus living in a milliliter — less than a quarter teaspoon — of ocean water, and found hundreds of distinct genetic subpopulations<em>. </em></p> <p>Each subpopulation in those few drops of water is characterized by a set of core gene alleles linked to a few flexible genes — a combination the MIT scientists call the “genomic backbone” — that endows the subpopulation with a finely tuned suitability for a particular ecological niche. Diversity also exists within the backbone subpopulations; most individual cells in the samples they studied carried at least one set of flexible genes not found in any other cell in its subpopulation.</p> <p>Sallie Chisholm, the Lee and Geraldine Martin Professor of Environmental Studies in CEE and in MIT’s Department of Biology; former CEE postdoc Nadav Kashtan; and co-authors published a paper on this work in the April 25 issue of <em>Science</em>.</p> <p>The researchers estimate that the subpopulations diverged at least a few million years ago. The backbone is an older, more slowly evolving component of the genome, while the flexible genes reside in areas of the genome where gene exchange is relatively frequent, facilitating more rapid evolution.</p> <p>The study also revealed that the relative abundance of the backbone subpopulations changes with the seasons at the study site, near Bermuda, adding strength to the argument that each subpopulation is finely tuned for optimal growth under different conditions.</p> <p>“The sheer enormity of diversity that must be in the octillion Prochlorococcus cells living in the seas is daunting to consider,” Chisholm says. “It creates a robust and stable population in the face of environmental instability.”</p> <div class="cms-placeholder-content-slideshow"></div> <p>Ocean turbulence also plays a role in the evolution and diversity of Prochlorococcus: A fluid mechanics model predicts that in typical ocean flow, just-divided daughter cells drift rapidly, placing them centimeters apart from one another in minutes, tens of meters apart in an hour, and kilometers apart in a week’s time.</p> <p>“The interesting question is, ‘Why does such a diverse set of subpopulations exist?’” Kashtan says. “The huge population size of Prochlorococcus suggests that this remarkable diversity and the way it is organized is not random, but is a masterpiece product of natural selection.”</p> <p>Chisholm and Kashtan say the evolutionary and ecological distinction among the subpopulations is probably common in other wild, free-living (not attached to particles or other organisms) bacteria species with large populations and highly mixed habitats.</p> <p>“This is perhaps the most sophisticated and thorough study yet to be published on the fine-scale genetic diversification of an environmental microbial species, and it correctly, I think, predicts that amazingly diverse populations may be maintained over astonishingly long times,” says Ford Doolittle, a member of the biochemistry and molecular biology faculty at Dalhousie University who was not involved in the research. “If microbiologists persist in believing in ‘species,’ they will likely have to drastically revise upward their estimates of&nbsp;how many such things there are. What we will probably be arguing about for a long time is what processes or forces other than selection might be responsible for such stable diversity, and, unless we find such processes, how something so seemingly well mixed as the ocean can offer up so many different tiny selective regimes.”</p> <p>“This study may be setting a record for progress made in microbiology by analyzing just three drops of seawater,” says Ramunas Stepanauskas of the Bigelow Laboratory for Ocean Sciences in Boothbay, Maine, who worked on the genomic analysis.</p> <p>Other co-authors are Sara Roggensack, Sébastien Rodrigue, Jessie Thompson, Steven Biller, Allison Coe, Huiming Ding, Roman Stocker, and Michael Follows of MIT; Pekka Marttinen of the Helsinki Institute for Information Technology; and Rex Malmstrom of the Department of Energy’s Joint Genome Institute.</p> <p>The work was supported by the National Science Foundation (NSF) Division of Environmental Biology, the NSF Biological Oceanography Section, the NSF Center for Microbial Oceanography Research and Education (C-MORE), the U.S. Department of Energy’s Genomics Science Program, and the Gordon and Betty Moore Foundation Marine Microbiology Initiative.</p> Biology, Microbes, Bacteria, Genetics, Evolution, Ocean science, Civil and environmental engineering