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  • richardmitnick 6:14 pm on December 15, 2017 Permalink | Reply
    Tags: Beth Shapiro, CALeDNA project, , eDNA-Environmental DNA, Erika Zavaleta, eSIE- Environmental DNA for Science Investigation and Education, Evolutionary Biology, Two UCSC biologists receive Howard Hughes Medical Institute Professor awards, UC Conservation Genomics Consortium,   

    From UCSC: “Two UCSC biologists receive Howard Hughes Medical Institute Professor awards” 

    UC Santa Cruz

    UC Santa Cruz

    December 13, 2017
    Tim Stephens
    stephens@ucsc.edu

    1
    Beth Shapiro (photo by C. Lagattuta)

    2
    Erika Zavaleta (photo by Matt Kroll)

    With funding from the Howard Hughes Medical Institute (HHMI), biologists at UC Santa Cruz will be using biodiversity surveys and field research to get more students engaged in science.

    Beth Shapiro and Erika Zavaleta, both professors of ecology and evolutionary biology, are among a select group of innovators in science education chosen this year for funding through the HHMI Professors Program.

    Zavaleta’s proposal won her a five-year, $1 million grant to create an inclusive and coordinated pathway that will engage students in ecology and conservation biology and support them all the way through to graduation. The program will provide increased access to research-based field courses and internships, along with sustained mentoring and a supportive community.

    “We have so many awesome field courses at UCSC, and I want to make sure they’re accessible to a full range of students and link them together into a pathway that will launch a diverse new generation of conservation leaders,” Zavaleta said.

    Environmental DNA

    Shapiro teamed up with Robert Wayne, a molecular ecologist at UCLA, to win a collaborative award of $1.5 million for a program to get large numbers of students involved in biodiversity surveys using environmental DNA. Environmental DNA (eDNA) is a highly sensitive molecular approach for cataloging biodiversity in any ecosystem by analyzing the DNA fragments found in soil and other environmental samples.

    “Environmental DNA is both a powerful tool for doing cutting-edge science and a great way to get people interested in science,” Shapiro said. “It’s fairly easy for a first experience, and yet the range of questions you can address is incredibly broad. It’s a gateway to all kinds of different science.”

    Shapiro and Wayne spearheaded the UC Conservation Genomics Consortium, which Wayne directs, and their HHMI project builds on the consortium’s work. Called Environmental DNA for Science Investigation and Education (eSIE), the three-tiered program starts with getting thousands of students involved in initial sampling efforts, either independently, with guidance from online instruction modules and mobile apps, or through organized sampling campaigns called “bioblitzes” at UC Natural Reserves and other sites throughout California. The consortium has been running bioblitzes through its CALeDNA project, and recruitment efforts are already under way to broaden the participation of students, including under-represented groups.

    “We want them to go out and have a positive first experience participating in actual field work and collecting samples and data that will be used by scientists, including themselves if they want to keep doing it,” Shapiro said.

    The second tier of the program will be a biodiversity course designed for both science majors and non-majors, using eDNA as a springboard for increasing science literacy and introducing students to some of the many ways science is relevant to important issues in society. Finally, the program includes funding to support students who want to do independent research projects with faculty mentors.

    Field courses

    Zavaleta’s program aims to build existing field research courses into a more coherent pathway that will guide students interested in ecology and conservation from their freshman or transfer year to graduation. Large introductory lecture courses required early in science majors are often blamed for attrition, and under-represented groups and disadvantaged students drop science majors at much higher rates than other students. Zavaleta said inquiry-based field courses and research opportunities provide experiences that can keep students engaged and inspired.

    “By combining the emotional rewards of nature and friendship, shared experience and co-creation, field courses provide the kind of experience that led many, including me, to careers in ecology and conservation biology,” she said. “They also create the kind of immersive experience that is so important to learning and is a big part of forming an understanding of the natural world.”

    Zavaleta wants to lower the barriers that can keep some students from participating in field courses by offering scholarships to cover course fees and building more capacity and diversity among the faculty and graduate students who teach the courses. She also wants to increase opportunities for undergraduates to get research experience through paid internships. A new staff mentorship position will help students take advantage of opportunities such as scholarships and research internships and will provide guidance throughout the program. These efforts will be coordinated and funded through a new Center to Advance Mentored, Inquiry-based Opportunities (CAMINO).

    “The idea is to provide wraparound support and build a community for all kinds of students, so we avoid the situation where they get inspired by a great course and then fall of a cliff when they face the big lecture courses required before they can move on,” Zavaleta said. “It’s also important that we measure and communicate the outcomes of this effort so that we understand what works and can sustain it and scale it up.”

    The HHMI Professors Program began in 2002, and Manuel Ares, professor of molecular, cell, and developmental biology at UCSC, was among that first cohort of HHMI Professors. This year, out of 177 proposals, only 12 were chosen for funding. In addition to producing two of the funded proposals, UC Santa Cruz submitted four of the 26 finalist proposals that made it through the first two rounds of peer review.

    See the full article here .

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    UCO Lick Shane Telescope
    UCO Lick Shane Telescope interior
    Shane Telescope at UCO Lick Observatory, UCSC

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    Lick Automated Planet Finder telescope, Mount Hamilton, CA, USA

    UC Santa Cruz campus
    The University of California, Santa Cruz, opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

    UCSC is the home base for the Lick Observatory.

    Lick Observatory's Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building
    Lick Observatory’s Great Lick 91-centimeter (36-inch) telescope housed in the South (large) Dome of main building

    Search for extraterrestrial intelligence expands at Lick Observatory
    New instrument scans the sky for pulses of infrared light
    March 23, 2015
    By Hilary Lebow
    1
    The NIROSETI instrument saw first light on the Nickel 1-meter Telescope at Lick Observatory on March 15, 2015. (Photo by Laurie Hatch) UCSC Lick Nickel telescope

    Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at UC’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

    “Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at UC San Diego who led the development of the new instrument while at the University of Toronto’s Dunlap Institute for Astronomy & Astrophysics.

    Wright worked on an earlier SETI project at Lick Observatory as a UC Santa Cruz undergraduate, when she built an optical instrument designed by UC Berkeley researchers. The infrared project takes advantage of new technology not available for that first optical search.

    Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

    5
    UCSC alumna Shelley Wright, now an assistant professor of physics at UC San Diego, discusses the dichroic filter of the NIROSETI instrument. (Photo by Laurie Hatch)

    Frank Drake, professor emeritus of astronomy and astrophysics at UC Santa Cruz and director emeritus of the SETI Institute, said there are several additional advantages to a search in the infrared realm.

    “The signals are so strong that we only need a small telescope to receive them. Smaller telescopes can offer more observational time, and that is good because we need to search many stars for a chance of success,” said Drake.

    The only downside is that extraterrestrials would need to be transmitting their signals in our direction, Drake said, though he sees this as a positive side to that limitation. “If we get a signal from someone who’s aiming for us, it could mean there’s altruism in the universe. I like that idea. If they want to be friendly, that’s who we will find.”

    Scientists have searched the skies for radio signals for more than 50 years and expanded their search into the optical realm more than a decade ago. The idea of searching in the infrared is not a new one, but instruments capable of capturing pulses of infrared light only recently became available.

    “We had to wait,” Wright said. “I spent eight years waiting and watching as new technology emerged.”

    Now that technology has caught up, the search will extend to stars thousands of light years away, rather than just hundreds. NIROSETI, or Near-Infrared Optical Search for Extraterrestrial Intelligence, could also uncover new information about the physical universe.

    “This is the first time Earthlings have looked at the universe at infrared wavelengths with nanosecond time scales,” said Dan Werthimer, UC Berkeley SETI Project Director. “The instrument could discover new astrophysical phenomena, or perhaps answer the question of whether we are alone.”

    NIROSETI will also gather more information than previous optical detectors by recording levels of light over time so that patterns can be analyzed for potential signs of other civilizations.

    “Searching for intelligent life in the universe is both thrilling and somewhat unorthodox,” said Claire Max, director of UC Observatories and professor of astronomy and astrophysics at UC Santa Cruz. “Lick Observatory has already been the site of several previous SETI searches, so this is a very exciting addition to the current research taking place.”

    NIROSETI will be fully operational by early summer and will scan the skies several times a week on the Nickel 1-meter telescope at Lick Observatory, located on Mt. Hamilton east of San Jose.

    The NIROSETI team also includes Geoffrey Marcy and Andrew Siemion from UC Berkeley; Patrick Dorval, a Dunlap undergraduate, and Elliot Meyer, a Dunlap graduate student; and Richard Treffers of Starman Systems. Funding for the project comes from the generous support of Bill and Susan Bloomfield.

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  • richardmitnick 6:14 pm on November 13, 2017 Permalink | Reply
    Tags: , Collective computation is about how adaptive systems solve problems, Evolutionary Biology, Jessica Flack,   

    From Quanta: Women in STEM- “How Nature Solves Problems Through Computation” Evolutionary biologist Jessica Flack 

    Quanta Magazine
    Quanta Magazine

    1
    Jessica Flack, an evolutionary biologist at the Santa Fe Institute, studies how flocks of birds, networks of neurons, slime molds and other biological collectives jointly process information to arrive at group behaviors. Here, she contemplates an artwork at the institute, “The Lengua of Nahuatl,” by James Drake, that was inspired by a Feynman diagram. Gabriella Marks for Quanta Magazine.

    July 6, 2017 [Better late…]
    Joshua Sokol

    There are many patterns of collective behavior in biology that are easy to see because they occur along the familiar dimensions of space and time. Think of the murmuration of starlings. Or army ants that span gaps on the forest floor by linking their own bodies into bridges. Loose groups of shoaling fish that snap into tight schools when a predator shows up.

    Then there are less obvious patterns, like those that the evolutionary biologist Jessica Flack tries to understand. In 2006, her graduate work at Emory University showed how just a few formidable-looking fighters could stabilize an entire group of macaques by intervening in scuffles between weaker monkeys, who would submit with teeth-baring grins rather than risk a fight they thought they would lose. But when Flack removed some of the police, the whole group became fractured and chaotic.

    Like flocking or schooling, the policing behavior arises from individual interactions to produce a macroscopic effect on the entire ensemble. But it is subtler, perhaps harder to visualize and measure. Or, as Flack says of macaque society and many of the other systems she studies, “their metric space is a social coordinate space. It’s not Euclidean.”

    Flack is now a professor at the Santa Fe Institute, where she has spent all of her postgraduate career, except for a stint at the University of Wisconsin, Madison. Her “collective computation” group, C4, which she co-runs with her collaborator, David Krakauer, probes not just macaques but neurons, slime molds and the internet for the rules that underlie each model, as well as the general rules underlying them all.

    Flack describes her work as an investigation into three interlocking questions. She wants to understand how phenomenological rules in biology, which seem to work in aggregate, emerge from microscopic ground truths. She wants to understand how groups solve problems and come to decisions. And she wants to know how complex systems stay robust in the face of shocks, like the macaques with their own police force that acts as social glue.

    At its root, though, Flack’s focus is on information: specifically, on how groups of different, error-prone actors variously succeed and fail at processing information together. “When I look at biological systems, what I see is that they are collective,” she said. “They are all made up of interacting components with only partly overlapping interests, who are noisy information processors dealing with noisy signals.”

    Over the phone, by Skype and via email, Quanta Magazine caught up with Flack to ask about C4’s current projects, her own career path, and the overarching philosophy behind her work. An edited and condensed version of our conversations follows.
    How did you get into research on problem solving in nature, and how did you wind up at the Santa Fe Institute?

    I’ve always been interested in how nature solves problems and where patterns come from, and why everything seems so organized despite so many potential conflicts of interest. Those sorts of questions have been with me since I was really little.

    At Cornell, I was taking evolutionary biology classes, but none of the material really addressed these questions. I would spend a lot of time in Mann Library, which was where all the good biology books were. So I would sit on the floor in the dusty, dimly lit stacks with this pile of books around me. And in that way I discovered that there was a community of people working on these questions in evolutionary biology that I found more interesting.

    They weren’t in the mainstream. One of the main places that turned out to be home to a lot of these people was the Santa Fe Institute. This was in the early to mid-’90s. I emailed the Santa Fe Institute and I requested something like 40 working papers. I was being a really annoying undergraduate. And someone mailed them to me! They actually snail-mailed me 40 of these papers, and I was thrilled, and I read them all.

    Now that you’ve ended up there, can you break down what your C4 research group means by “collective computation”?

    Collective computation is about how adaptive systems solve problems. All systems are about extracting energy and doing work, and physical systems in particular are about that. When you move to adaptive systems, you’ve got the additional influence of information processing, which we think allows a system to extract energy more efficiently even though it has to expend a little extra energy to do the information processing. Components of adaptive systems look out at the world, and they try to discover the regularities. It’s a noisy process.

    Unlike in computer science where you have a program you have written, which has to produce a desired output, in adaptive systems this is a process that is being refined over evolutionary or learning time. The system produces an output, and it might be a good output for the environment or it might not. And then over time it hopefully gets better and better.

    What we are doing at C4 is taking messy, conceptually challenging problems and turning them into something rigorous. We’re very philosophically oriented, but we’re also very quantitative, particularly in thinking about how nature can overcome subjectivity in information processing through collective computation. We really think the answer to these questions requires combining insights from statistical physics, theoretical computer science, information theory, evolutionary biology and cognitive science.

    The human brain contains roughly 86 billion neurons, making our brains the ultimate collectives. Every decision we make can be thought of as the outcome of a neural collective computation. In the case of our study, which was lead by my colleague Bryan Daniels, the data we analyzed were collected during an experiment by Bill Newsome’s group at Stanford from macaques who had to decide whether a group of dots moving across a screen was traveling left or right. Data on neural firing patterns were recorded while the monkey was performing this task. We found that as the monkey initially processes the data, a few single neurons have strong opinions about what the decision should be. But this is not enough: If we want to anticipate what the monkey will decide, we have to poll many neurons to get a good prediction of the monkey’s decision. Then, as the decision point approaches, this pattern shifts. The neurons start to agree, and eventually each one on its own is maximally predictive.

    We have this principle of collective computation that seems to involve these two phases. The neurons go out and semi-independently collect information about the noisy input, and that’s like neural crowdsourcing. Then they come together and come to some consensus about what the decision should be. And this principle of information accumulation and consensus applies to some monkey societies also. The monkeys figure out sort of semi-independently who is capable of winning fights, and then they consolidate this information by exchanging special signals. The network of these signals then encodes how much consensus there is in the group about any one individual’s capacity to use force in fights.
    I noticed that another recent paper uses the same macaque data set you produced during your graduate work at the Yerkes National Primate Research Center in Lawrenceville, Georgia. What did you find when you returned to thinking about this system?

    We wanted to understand how social systems or other biological systems go from state A to state B. How a group of fish goes from shoaling to schooling, or how a social system goes from having a few super-powerful animals to a setup where there is less inequality. One mechanism known to facilitate switching between different states like this is for the system to sit near what’s called a critical or tipping point. We set out to find a way to measure, in biologically meaningful terms, how far a system sits from the critical point. Could we come up with units that mechanistically make sense?

    We were interested in whether we could induce the monkey society we were studying to change from its status quo of many small fights and a few large ones to having many large fights. We observed that fights in this monkey group range in size from two to 30 or so individuals, with small fights common and large fights very rare. By simulating the society using data we had collected on fight-joining decisions, we found that we could measure the number of monkeys whose propensity to join fights would have to increase to move the system closer to the critical point.

    In this system, it takes about three to five individuals to push the system over the edge. We also found that individuals vary in how much their behavior influences the system. If big contributors become more likely to join fights, the system moves toward the critical point where it is very sensitive, meaning a small perturbation can knock it over into this all-fight state. And while we didn’t study this in the paper, we speculate that the all-fight state, which means the system is going to change dramatically, might be useful. It might be something you want to do, to move toward the critical point and completely reconfigure the group if the environment is changing from known to unknown.

    The macaques served as the model system for asking these questions, but we hope the approach that we developed can be applied to lots of other different kinds of data.


    VIDEO: Jessica Flack describes the special challenges of applying collective computation to the understanding of complex biological systems. Gabriella Marks for Quanta Magazine.

    Human society also seems a little chaotic recently. Are you ever tempted to apply this kind of thinking in that direction?

    Absolutely. With the help of some friends in finance and economics, we are moving a little bit into financial markets in our research. I think that’s an amazing model system for asking these kinds of collective computation questions. My next meeting today is about how to apply our criticality approach, coupled to new machine-learning results that are able to find phases of matter for physical systems, to either political data or market data. Our goals are to address whether there is evidence for phase transitions or critical phenomena in financial data and to understand the behavioral processes that might move markets closer to critical points.
    Now that you can follow up on these kinds of questions to your heart’s content, what would you say if you could visit yourself back at Cornell, in the stacks of the library?

    Jorge Luis Borges is one of my favorite writers, and he wrote something along the lines of “the worst labyrinth is not that intricate form that can trap us forever, but a single and precise straight line.” My path is not a straight line. It has been a quite interesting, labyrinthine path, and I guess I would say not to be afraid of that. You don’t know what you’re going to need, what tools or concepts you’re going to need. The thing is to read broadly and always keep learning.
    Can you talk a bit about what it’s like to start with a table of raw data and pull these sorts of grand patterns out of it? Is there a single eureka moment, or just a slow realization?

    Typically what happens is, we have some ideas, and our group discusses them, and then over months or years in our group meetings we sort of hash out these issues. We are ok with slow, thoughtful science. We tend to work on problems that are a little bit on the edge of science, and what we are doing is formalizing them. A lot of the discussion is: “What is the core problem, how do we simplify, what are the right measurements, what are the right variables, what is the right way to represent this problem mathematically?” It’s always a combination of the data, these discussions, and the math on the board that leads us to a representation of the problem that gives us traction.

    We have this argument at the Santa Fe Institute a lot. Some people will say, “Well, at the end of the day it’s all math.” And I just don’t believe that. I believe that science sits at the intersection of these three things — the data, the discussions and the math. It is that triangulation — that’s what science is. And true understanding, if there is such a thing, comes only when we can do the translation between these three ways of representing the world.

    See the full article here .

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    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

     
  • richardmitnick 11:39 am on September 16, 2014 Permalink | Reply
    Tags: , Evolutionary Biology, ,   

    From M.I.T.: “Neuroscientists identify key role of language gene” 


    MIT News

    September 15, 2014
    Anne Trafton | MIT News Office

    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.

    image

    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.

    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.

    “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.

    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 Proceedings of the National Academy of Sciences 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.

    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.

    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.

    Pääbo, who is also an author of the new PNAS 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.

    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.

    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.

    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.

    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.

    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.”

    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.

    See the full article here.

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  • richardmitnick 1:54 pm on September 11, 2014 Permalink | Reply
    Tags: , Evolutionary Biology,   

    From Quanta: “Evolution’s Random Paths Lead to One Place” 

    Quanta Magazine
    Quanta Magazine

    September 11, 2014
    Emily Singer

    In his fourth-floor lab at Harvard University, Michael Desai has created hundreds of identical worlds in order to watch evolution at work. Each of his meticulously controlled environments is home to a separate strain of baker’s yeast. Every 12 hours, Desai’s robot assistants pluck out the fastest-growing yeast in each world — selecting the fittest to live on — and discard the rest. Desai then monitors the strains as they evolve over the course of 500 generations. His experiment, which other scientists say is unprecedented in scale, seeks to gain insight into a question that has long bedeviled biologists: If we could start the world over again, would life evolve the same way?

    md
    Michael Desai, a biologist at Harvard University, uses statistical methods to study basic questions in evolution.
    Sergey Kryazhimskiy

    Many biologists argue that it would not, that chance mutations early in the evolutionary journey of a species will profoundly influence its fate. “If you replay the tape of life, you might have one initial mutation that takes you in a totally different direction,” Desai said, paraphrasing an idea first put forth by the biologist Stephen Jay Gould in the 1980s.

    yeast
    Different strains of yeast grown under identical conditions develop different mutations but ultimately arrive at similar evolutionary endpoints.

    Desai’s yeast cells call this belief into question. According to results published in Science in June, all of Desai’s yeast varieties arrived at roughly the same evolutionary endpoint (as measured by their ability to grow under specific lab conditions) regardless of which precise genetic path each strain took. It’s as if 100 New York City taxis agreed to take separate highways in a race to the Pacific Ocean, and 50 hours later they all converged at the Santa Monica pier.

    The findings also suggest a disconnect between evolution at the genetic level and at the level of the whole organism. Genetic mutations occur mostly at random, yet the sum of these aimless changes somehow creates a predictable pattern. The distinction could prove valuable, as much genetics research has focused on the impact of mutations in individual genes. For example, researchers often ask how a single mutation might affect a microbe’s tolerance for toxins, or a human’s risk for a disease. But if Desai’s findings hold true in other organisms, they could suggest that it’s equally important to examine how large numbers of individual genetic changes work in concert over time.

    “There’s a kind of tension in evolutionary biology between thinking about individual genes and the potential for evolution to change the whole organism,” said Michael Travisano, a biologist at the University of Minnesota. “All of biology has been focused on the importance of individual genes for the last 30 years, but the big take-home message of this study is that’s not necessarily important.”

    yeast
    Yeast on Plates
    Sergey Kryazhimskiy

    To efficiently analyze many strains of yeast simultaneously, scientists grow them on plates like this one, which has 96 individual wells.

    The key strength in Desai’s experiment is its unprecedented size, which has been described by others in the field as “audacious.” The experiment’s design is rooted in its creator’s background; Desai trained as a physicist, and from the time he launched his lab four years ago, he applied a statistical perspective to biology. He devised ways to use robots to precisely manipulate hundreds of lines of yeast so that he could run large-scale evolutionary experiments in a quantitative way. Scientists have long studied the genetic evolution of microbes, but until recently, it was possible to examine only a few strains at a time. Desai’s team, in contrast, analyzed 640 lines of yeast that had all evolved from a single parent cell. The approach allowed the team to statistically analyze evolution.

    “This is the physicist’s approach to evolution, stripping down everything to the simplest possible conditions,” said Joshua Plotkin, an evolutionary biologist at the University of Pennsylvania who was not involved in the research but has worked with one of the authors. “They could partition how much of evolution is attributable to chance, how much to the starting point, and how much to measurement noise.”

    man
    Fluid-handling robots like this one make it possible to study hundreds of lines of yeast over many generations.
    Courtesy of Sergey Kryazhimskiy

    Desai’s plan was to track the yeast strains as they grew under identical conditions and then compare their final fitness levels, which were determined by how quickly they grew in comparison to their original ancestral strain. The team employed specially designed robot arms to transfer yeast colonies to a new home every 12 hours. The colonies that had grown the most in that period advanced to the next round, and the process repeated for 500 generations. Sergey Kryazhimskiy, a postdoctoral researcher in Desai’s lab, sometimes spent the night in the lab, analyzing the fitness of each of the 640 strains at three different points in time. The researchers could then compare how much fitness varied among strains, and find out whether a strain’s initial capabilities affected its final standing. They also sequenced the genomes of 104 of the strains to figure out whether early mutations changed the ultimate performance.

    Previous studies have indicated that small changes early in the evolutionary journey can lead to big differences later on, an idea known as historical contingency. Long-term evolution studies in E. coli bacteria, for example, found that the microbes can sometimes evolve to eat a new type of food, but that such substantial changes only happen when certain enabling mutations happen first. These early mutations don’t have a big effect on their own, but they lay the necessary groundwork for later mutations that do.

    Diminishing Returns

    Desai’s study isn’t the first to suggest that the law of diminishing returns applies to evolution. A famous decades-long experiment from Richard Lenski’s lab at Michigan State University, which has tracked E. coli for thousands of generations, found that fitness converged over time. But because of limitations in genomics technology in the 1990s, that study didn’t identify the mutations underlying those changes. “The 36 populations we had then would have been much more expensive to sequence than the hundred they did here,” said Michael Travisano of the University of Minnesota, who worked on the Michigan State study.

    More recently, two papers published in Science in 2011 mixed and matched a handful of beneficial mutations in different types of bacteria. When the researchers engineered those mutations into different strains of bacteria, they found that the fitter strains enjoyed a smaller benefit. Desai’s study examined a much broader combination of possible mutations, showing that the rule is much more general.

    But because of the small scale of such studies, it wasn’t clear to Desai whether these cases were the exception or the rule. “Do you typically get big differences in evolutionary potential that arise in the natural course of evolution, or for the most part is evolution predictable?” he said. “To answer this we needed the large scale of our experiment.”

    As in previous studies, Desai found that early mutations influence future evolution, shaping the path the yeast takes. But in Desai’s experiment, that path didn’t affect the final destination. “This particular kind of contingency actually makes fitness evolution more predictable, not less,” Desai said.

    Desai found that just as a single trip to the gym benefits a couch potato more than an athlete, microbes that started off growing slowly gained a lot more from beneficial mutations than their fitter counterparts that shot out of the gate. “If you lag behind at the beginning because of bad luck, you’ll tend to do better in the future,” Desai said. He compares this phenomenon to the economic principle of diminishing returns — after a certain point, each added unit of effort helps less and less.

    Scientists don’t know why all genetic roads in yeast seem to arrive at the same endpoint, a question that Desai and others in the field find particularly intriguing. The yeast developed mutations in many different genes, and scientists found no obvious link among them, so it’s unclear how these genes interact in the cell, if they do at all. “Perhaps there is another layer of metabolism that no one has a handle on,” said Vaughn Cooper, a biologist at the University of New Hampshire who was not involved in the study.

    It’s also not yet clear whether Desai’s carefully controlled results are applicable to more complex organisms or to the chaotic real world, where both the organism and its environment are constantly changing. “In the real world, organisms get good at different things, partitioning the environment,” Travisano said. He predicts that populations within those ecological niches would still be subject to diminishing returns, particularly as they undergo adaptation. But it remains an open question, he said.

    Nevertheless, there are hints that complex organisms can also quickly evolve to become more alike. A study published in May analyzed groups of genetically distinct fruit flies as they adapted to a new environment. Despite traveling along different evolutionary trajectories, the groups developed similarities in attributes such as fecundity and body size after just 22 generations. “I think many people think about one gene for one trait, a deterministic way of evolution solving problems,” said David Reznick, a biologist at the University of California, Riverside. “This says that’s not true; you can evolve to be better suited to the environment in many ways.”

    See the full article here.

    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

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  • richardmitnick 3:13 pm on August 19, 2014 Permalink | Reply
    Tags: , , Evolutionary Biology   

    From Astrobiology: “New home for an ‘evolutionary misfit’” 

    Astrobiology Magazine

    Astrobiology Magazine

    Aug 19, 2014
    No Writer Credit
    Source: University of Cambridge

    Worm-like creature with legs and spikes finds its place in the evolutionary tree of life

    One of the most bizarre-looking fossils ever found – a worm-like creature with legs, spikes and a head difficult to distinguish from its tail – has found its place in the evolutionary Tree of Life, definitively linking it with a group of modern animals for the first time.

    thing
    Fossil Hallucigenia sparsa from the Burgess Shale. Credit: M. R. Smith / Smithsonian Institute

    The animal, known as Hallucigenia due to its otherworldly appearance, had been considered an ‘evolutionary misfit’ as it was not clear how it related to modern animal groups. Researchers from the University of Cambridge have discovered an important link with modern velvet worms, also known as onychophorans, a relatively small group of worm-like animals that live in tropical forests. The results are published in the advance online edition of the journal Nature.

    The affinity of Hallucigenia and other contemporary ‘legged worms’, collectively known as lobopodians, has been very controversial, as a lack of clear characteristics linking them to each other or to modern animals has made it difficult to determine their evolutionary home.

    What is more, early interpretations of Hallucigenia, which was first identified in the 1970s, placed it both backwards and upside-down. The spines along the creature’s back were originally thought to be legs, its legs were thought to be tentacles along its back, and its head was mistaken for its tail.

    thin
    This is a reconstruction of the Burgess Shale animal Hallucigenia sparsa. Credit: Elyssa Rider

    Hallucigenia lived approximately 505 million years ago during the Cambrian Explosion, a period of rapid evolution when most major animal groups first appear in the fossil record. These particular fossils come from the Burgess Shale in Canada’s Rocky Mountains, one of the richest Cambrian fossil deposits in the world.

    Looking like something from science fiction, Hallucigenia had a row of rigid spines along its back, and seven or eight pairs of legs ending in claws. The animals were between five and 35 millimetres in length, and lived on the floor of the Cambrian oceans.

    A new study of the creature’s claws revealed an organisation very close to those of modern velvet worms, where layers of cuticle (a hard substance similar to fingernails) are stacked one inside the other, like Russian nesting dolls. The same nesting structure can also be seen in the jaws of velvet worms, which are no more than legs modified for chewing.

    “It’s often thought that modern animal groups arose fully formed during the Cambrian Explosion,” said Dr Martin Smith of the University’s Department of Earth Sciences, the paper’s lead author. “But evolution is a gradual process: today’s complex anatomies emerged step by step, one feature at a time. By deciphering ‘in-between’ fossils like Hallucigenia, we can determine how different animal groups built up their modern body plans.”

    While Hallucigenia had been suspected to be an ancestor of velvet worms, definitive characteristics linking them together had been hard to come by, and their claws had never been studied in detail. Through analysing both the prehistoric and living creatures, the researchers found that claws were the connection joining them together. Cambrian fossils continue to produce new information on origins of complex animals, and the use of high-end imaging techniques and data on living organisms further allows researchers to untangle the enigmatic evolution of earliest creatures.

    “An exciting outcome of this study is that it turns our current understanding of the evolutionary tree of arthropods – the group including spiders, insects and crustaceans – upside down,” said Dr Javier Ortega-Hernandez, the paper’s co-author. “Most gene-based studies suggest that arthropods and velvet worms are closely related to each other; however, our results indicate that arthropods are actually closer to water bears, or tardigrades, a group of hardy microscopic animals best known for being able to survive the vacuum of space and sub-zero temperatures – leaving velvet worms as distant cousins.”

    “The peculiar claws of Hallucigenia are a smoking gun that solve a long and heated debate in evolutionary biology, and may even help to decipher other problematic Cambrian critters,” said Dr Smith.

    See the full article here.
    Astrobiology Magazine is a NASA-sponsored online popular science magazine. Our stories profile the latest and most exciting news across the wide and interdisciplinary field of astrobiology — the study of life in the universe. In addition to original content, Astrobiology Magazine also runs content from non-NASA sources in order to provide our readers with a broad knowledge of developments in astrobiology, and from institutions both nationally and internationally. Publication of press-releases or other out-sourced content does not signify endorsement or affiliation of any kind.
    Established in the year 2000, Astrobiology Magazine now has a vast archive of stories covering a broad array of topics.

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