Jonathan Eisen

BBB – Baseball, bioinformatics, and brothers

I know quite a few people in bioinformatics who are also pretty avid baseball fans. Ian Paulsen and I sneaked away from a conference to go see his beloved Padres last year get slaughtered in two playoff games. A resercher from Wash. U.’s Genome Center caught Mcgiure’s 70th home run a few years ago. An article in Bioinformatics even promotes a software package as being useful for viewing baseball stats.

I have tried to convince people there are connections between the two in the past. But the best article I have seen on this is, for better or worse, about my brother. What a scam he has pulled at Berkeley. He is teaching a course (with James Fraser) ostensibly about bioinformatics in some way. What is is really about? Baseball statistics. They are not even trying to pretend it is about bioinformatics. But they apparently hope that some of the stats rubs off enough that some students get into bioinformatics.

As an ex-baseball player I have some smpathy for their approach. Also, it was at a baseball game that my brother first convinced me that Open Access science was the way to go. But I think focusing on stats is the wrong way to use an interest in baseball to get an interest in biology. I think it would be better to get Drew Endy and his cohort into using one of their synthetic biology competitions to make some good new steroids. And then the stats course could be used to analyze the differences with and without the new drugs.

“I think this is a stunner,” Dr. Collins said. “This is like the seat of the soul of the genome.”

OK. I could not help myself with this one after I was sent the quote by Francis Collins in this New York Times Article. Dr. Collins, in relation to a new study that showed that one region of one human chromosome apparently plays roles in heart disease and diabetes, said

I think this is a stunner,” Dr. Collins said. “This is like the seat of the soul of the genome.”

Now, I have commented before about how Dr. Collins is doing a pretty good job about keeping his religious beliefs separate from his work. And since he is a strong supporter of evolutionary biology I like to give him the benefit of the doubt (I personally agree with him that there is no need for a conflict between evolutionary biology and non fundamentalist religious beliefs). But I think “the seat of the soul of the genome” is a bit much.

I frequently criticize researchers who observe something in the genome and immediately come up with an adaptive explanation for the observation. Such adaptationist, just so story responses, are common in molecular biology and many areas of biology and were written about extensively by Gould and Lewontin and others. But now I guess we have a new category of adaptationist-like explanations. Striking findings in a genome can now be called “just soul stories.”

National Academy of Sciences Elects New Members

Congratulations to all those elected to the National Academy of Sciences. I am attaching the press release from NAS below. Good to see a Davisite on there – Stephen Kowalczykowski, one of the undisputed kings of the study of the mechanisms of homologous recombination.

FOR IMMEDIATE RELEASE

72 New Members Chosen By Academy

WASHINGTON — The National Academy of Sciences today announced the election of 72 new members and 18 foreign associates from 12 countries in recognition of their distinguished and continuing achievements in original research.

The election was held this morning during the business session of the 144th annual meeting of the Academy. Those elected today bring the total number of active members to 2,025. Foreign associates are nonvoting members of the Academy, with citizenship outside the United States. Today’s election brings the total number of foreign associates to 387.

The National Academy of Sciences is a private organization of scientists and engineers dedicated to the furtherance of science and its use for the general welfare. It was established in 1863 by a congressional act of incorporation signed by Abraham Lincoln that calls on the Academy to act as an official adviser to the federal government, upon request, in any matter of science or technology.

Additional information about the Academy and its members is available online at http://www.nasonline.org.

Newly elected members and their affiliations at the time of election are:

ACUÑA, Mario H.; senior astrophysicist and project scientist, International Solar Terrestrial Physics Program, NASA Goddard Space Flight Center, Greenbelt, Md.

AGARD, David A.; investigator, Howard Hughes Medical Institute, and professor, department of biochemistry and biophysics, University of California, San Francisco

AMBROS, Victor R.; professor of genetics, Dartmouth Medical School, Hanover, N.H.

ANDERSON, David J.; investigator, Howard Hughes Medical Institute, and Roger W. Sperry Professor of Biology, California Institute of Technology, Pasadena

ATWATER, Brian F.; geologist, western earthquake hazards team, U.S. Geological Survey, and affiliate professor, department of earth and space sciences, University of Washington, Seattle

AWSCHALOM, David D.; professor of physics and of electrical and computer engineering, department of physics, University of California, Santa Barbara

BAKER, Tania A.; investigator, Howard Hughes Medical Institute, and E.C. Whitehead Professor Biology, Massachusetts Institute of Technology, Cambridge

BAWENDI, Moungi G.; professor of chemistry and Keck Professor of Energy, Massachusetts Institute of Technology, Cambridge

BELL, C. Gordon; senior researcher, Microsoft Bay Area Research Center, San Francisco

BELLUGI, Ursula; professor and director, Laboratory of Cognitive Neuroscience, Salk Institute for Biological Studies, La Jolla, Calif.

BLOCK, Steven M.; professor of applied physical and biological sciences, Stanford University, Stanford, Calif.

BRENNER, Michael B.; Theodore Bevier Bayles Professor of Medicine, Harvard Medical School, Boston

BRYANT, Robert L.; J.M. Kreps Professor, department of mathematics, Duke University, Durham, N.C.

CANFIELD, Donald E.; professor of ecology, Institute of Biology, and director, Nordic Center for Earth Evolution, University of Southern Denmark, Odense

CARROLL, Sean B.; investigator, Howard Hughes Medical Institute, and professor of molecular biology and genetics, University of Wisconsin, Madison

CLARK, Noel; professor, department of physics, University of Colorado, Boulder

COOK, Karen S.; Ray Lyman Wilbur Professor of Sociology, department of sociology, Stanford University, Stanford, Calif.

DANGL, Jeffrey L.; associate director, Carolina Center for Genome Sciences, and John N. Couch Distinguished Professor, University of North Carolina, Chapel Hill

DIXON, Richard A.; plant biology division director, The Samuel Roberts Noble Foundation, Ardmore, Okla.

DOONER, Hugo K.; professor, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway

DRAINE, Bruce T.; professor, department of astrophysical sciences, Princeton University, Princeton, N.J.

DRUKER, Brian J.; investigator, Howard Hughes Medical Institute, and JELD-WEN Chair of Leukemia Research, Oregon Health & Science University, Portland

DURRETT, Richard; professor, Cornell University, Ithaca, N.Y.

EDGAR, Robert S.; professor emeritus, University of California, Santa Cruz

EMANUEL, Kerry A.; Breene M. Kerr Professor, program in atmospheres, oceans, and climate, department of earth, atmospheric, and planetary sciences, Massachusetts Institute of Technology, Cambridge

EMR, Scott D.; investigator, Howard Hughes Medical Institute, and director, Institute of Cell and Molecular Biology, Cornell University, Ithaca, N.Y.

ESTELLE, Mark; Carlos O. Miller Professor of Developmental Biology, department of biology, Indiana University, Bloomington

ESTES, Mary K.; professor and Cullen Foundation Endowed Chair, department of molecular virology and microbiology, Baylor College of Medicine, Houston

FALKOWSKI, Paul G.; professor, Institute of Marine and Coastal Sciences and department of geological sciences, Rutgers, The State University of New Jersey, New Brunswick

FAYER, Michael D.; David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry, department of chemistry, Stanford University, Stanford, Calif.

FLEMING, Graham; Melvin Calvin Distinguished Professor of Chemistry, University of California, Berkeley

FRAKER, Pamela J.; professor of food science and human nutrition and distinguished professor of biochemistry, Michigan State University, East Lansing

GABRIELSE, Gerald; Leverett Professor of Physics, Harvard University, Cambridge, Mass.

GINSBURG, David; investigator, Howard Hughes Medical Institute, and James V. Neel Distinguished University Professor, University of Michigan Medical School, Ann Arbor

GOLDMAN, Allen M.; Institute of Technology Professor of Physics, and head, School of Physics and Astronomy, University of Minnesota, Minneapolis

GOTTLIEB, David; Ford Foundation Professor, Brown University, Providence, R.I.

GRONENBORN, Angela M.; professor of pharmacology, and director, Structural Biology Program, University of Pittsburgh, Pittsburgh

HILDEBRAND, John G.; Regents Professor and professor of neurobiology, biochemistry and molecular biophysics, entomology, and molecular and cellular biology, and director, Arizona Research Laboratories Division of Neurobiology, University of Arizona, Tucson

HOBBS, Helen H.; investigator, Howard Hughes Medical Institute, and director, McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas

HOUSE, James S.; Angus Campbell Collegiate Professor of Sociology and Survey Research, Institute for Social Research, University of Michigan, Ann Arbor

JOHNSON, William L.; Ruben and Donna Mettler Professor of Materials Science, Engineering, and Applied Science, California Institute of Technology, Pasadena

JOHNSON-LAIRD, Philip N.; Stuart Professor of Psychology, department of psychology, Princeton University, Princeton, N.J.

KIESSLING, Laura L.; professor of chemistry and biochemistry, University of Wisconsin, Madison

KOWALCZYKOWSKI, Stephen C.; distinguished professor of microbiology and of molecular and cellular biology, and director, Center for Genetics and Development, University of California, Davis

LAITIN, David; James T. Watkins IV and Elise V. Watkins Professor of Political Science, department of political science, Stanford University, Stanford, Calif.

LIBCHABER, Albert J.; professor of physics, The Rockefeller University, New York City

LOVEJOY, Claude Owen; university professor, Kent State University, Kent, Ohio

MARDER, Eve E.; professor of neuroscience, department of biology, Brandeis University, Waltham, Mass.

McMULLEN, Curtis T.; professor, Harvard University, Cambridge, Mass.

MICALI, Silvio; professor, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge

MILLER, Christopher; investigator, Howard Hughes Medical Institute, and professor, Brandeis University, Waltham, Mass.

MOERNER, William E.; Harry S. Mosher Professor, Stanford University, Stanford, Calif.

MORGAN, M. Granger; university professor and head, department of engineering and public policy, Carnegie Mellon University, Pittsburgh

OLSON, Peter L.; professor of geophysical fluid dynamics, Johns Hopkins University, Baltimore

PACALA, Stephen W.; Frederick D. Petrie Professor, department of ecology and evolutionary biology, Princeton University, Princeton, N.J.

PLOG, Stephen; Commonwealth Professor, department of anthropology, University of Virginia, Charlottesville

PLOTT, Charles R.; Edward S. Harkness Professor of Economics and Political Science, division of humanities and social sciences, California Institute of Technology, Pasadena

RICHMOND, Timothy J.; professor, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zurich, Switzerland

SCHILLER, Peter H.; professor, Massachusetts Institute of Technology, Cambridge

SCHRAMM, Vern L.; professor and chair, department of biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, N.Y.

SEIDMAN, Jonathan G.; Henrietta B. and Frederick H. Bugher Professor of Cardiovascular Genetics, Harvard Medical School, Boston

SHULMAN, Gerald I.; investigator, Howard Hughes Medical Institute, and professor of medicine and cellular and molecular physiology, Yale University School of Medicine, New Haven, Conn.

SPENCER, Charles S.; curator of anthropology, and chair, division of anthropology, American Museum of Natural History, New York City

SPERGEL, David N.; professor, department of astrophysical sciences, Princeton University, Princeton, N.J.

SREENIVASAN, Katepalli R.; Martin Professor of Engineering and distinguished university professor, University of Maryland, College Park

STARK, Harold M.; professor of mathematics, University of California, San Diego

TABIN, Clifford J.; professor, department of genetics, Harvard Medical School, Boston

WELLEMS, Thomas E.; chief, laboratory of malaria and vector research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.

WILL, Clifford M.; James S. McDonnell Professor of Physics, Washington University, St. Louis

WISE, Mark B.; John A. McCone Professor of High Energy Physics, California Institute of Technology, Pasadena

YOKOYAMA, Wayne M.; investigator, Howard Hughes Medical Institute, and Sam and Audrey Lowe Levin Professor of Medicine and of Pathology, Washington University School of Medicine, St. Louis

YOUNG, Michael W.; vice president of academic affairs and Richard and Jeanne Fisher Professor, The Rockefeller University, New York City

Newly elected foreign associates, their affiliations at the time of election, and their country of citizenship are:

ASKONAS, Brigitte A.; visiting professor, Imperial College of Science, Technology, and Medicine, London (United Kingdom)

CIECHANOVER, Aaron J.; distinguished professor, faculty of medicine, Technion, Haifa (Israel)

DELIGNE, Pierre; professor, Institute for Advanced Study, Princeton, N.J. (Belgium)

GRANT, Peter R.; professor, Princeton University, Princeton, N.J. (United Kingdom)

IIJIMA, Sumio; professor, department of materials science and engineering, Meijo University, Nagoya (Japan)

ITO, Masao; director, RIKEN Brain Science Institute, Saitama (Japan)

IZQUIERDO, Ivan A.; professor of medicine and head, Memory Center, Institute of Biomedical Research, Pontifical Catholic University of Rio Grande, Porto Alegre (Brazil)

KINGMAN, John; director, Isaac Newton Institute for Mathematical Sciences, University of Cambridge, Cambridge, England (United Kingdom)

LI, Aizhen; Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai (People’s Republic of China)

LORDKIPANIZDE, David O.; director, Georgian National Museum, Georgian National Academy of Sciences, Tblisi (Georgia)

MARASAS, Walter F.O.; director, Programme on Mycotoxins and Experimental Carcinogenesis Unit, Medical Research Council, Tygerberg (South Africa)

PINGALI, Prabhu L.; director, division of agricultural and development economics, United Nations Food and Agricultural Organization, Rome (India)

SALAS, Margarita; research professor, Severo Ochoa Center for Molecular Biology, Autonomous

University of Madrid, Madrid (Spain)

SEEBACH, Dieter; professor of chemistry emeritus, laboratory of organic chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland (Germany)

TAKEICHI, Masatoshi; director, Center for Developmental Biology, RIKEN, Kobe (Japan)

WHITE, Simon D.M.; director, Max Planck Institute for Astrophysics, Garching, Germany (United Kingdom)

WOODMAN, Ronald F.; executive president, Geophysical Institute of Peru, Mayorazgo (Peru)

ZHANG, Qifa; professor and director, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan (People’s Republic of China)

Nice plea for Open Access in Harvard Crimson

An opinion piece in the Harvard Crimson (student newspaper) by GREGORY N. PRICE and ELIZABETH M. STARK pleas for students to lend more support to the Open Access movement. It is a well thought out piece and worth a look. I particuarly like the proposal for students to make their senior theses available somehow and for students to write letters to Congress supporting OA.

Fair Use and Open Access

Really interesting blog, with a collection of other information is available from Coturnix at Science Blogs. Basically the discussion revolves around the use of figures from non Open Access publications. She writes:

My esteemed colleague here at scienceblogs, Shelley Batts of the Retrospectacle blog, did what we all do all the time – what is one of the primary role of science blogs: compared what a scientific paper says to what the press releases and media say about the paper. It was a paper widely reported by the press about the potential health effects of drinks like daikiri. Shelley wrote in her post that the paper is fine, but that the media coverage is faulty (what’s new?). In order to demonstrate what the paper really says, she, as we often do, reprinted a table and one panel of a figure from the paper in her post.

The blog has lots of links to other blogs about this issue. My favorite line:

The old model will crumble and the dinosaurs can choose to adapt or go extinct.

My sentiments exactly. You go get ’em.

PS Thanks to Karl Mogel at the Innoculated Mind for pointing this out.

More on the Human Microbiome Program Workshop – Day1

As a follow up to my previous blog I am posting some additional information here about the NIH Roadmap Human Microbiome Project Workshop, which was held in Bethesda, MD.

The general outline of the meeting was as follows:

Sunday Night

Introduction

Welcome by Francis Collins (NHGRI), Hugh Auchincloss (NIAID) and Griffin Rodgers (NIDDK)

Comments by Gary Schoolnik

Overview of the NAS report on metagenomics by Jim Tiedje

Overview of the NIH Roadmap program by Francis Collins

Introductory talks on human microbiome

Jeff Gordon

David Relman

Gary Huffnagle

Jo Handelsman

Monday AM

Technological issues

Elaine Mardis

Jill Banfield

Deirdre Meldrum

Bioinformatics issues

Lior Pachter

Rolf Apweiler

Peer Bork

ELSI Issues Pilar Ossorio

Lunch
Monday PM – Breakout sessions and discussion

Group 1 – Reference microbiome (Claire Fraser and Martin Blaser)
Group 2 – Changes in microbiome and human health (Rita Colwell and Martin Rosenberg)
Group 3 – Enabling technologies (Bruce Birren and Mary Lidstrom)
Group 4 – Bioinformatics tools (Ewan Birney and Owen White)
Group 5 – Ethical legal and social issues (Midred Cho)

Wrap up

Overall, I found the Sunday night talks very useful to set the stage. The introductory talks by the representatives from NHGRI, NIAID, and NIDDK clearly indicated that NIH as well as others consider the human microbiome an incredibly important research area. Then Jim Tiedje gave a nice overview of the recent NAS report on metagenomics (which was about metagenomics in general, not specifically for the human microbiome). The main points of the report are basically: microbes rule the world, metagenomics is a very powerful tool in studying them, and there is a need for a more coordinated effort among funding agencies to push metagenomics as a tool and a field. (My only complaint about Tiedje’s presentation was he kept using the term “higher organisms” for those multicellular species with nuclei. But otherwise, he did a good job of concicely summarizing the report and the benefits as well as challenges of metagenomics).

Francis Collins then gave an overview of the NIH Roadmap Program. The Roadmap was started in ~2003 as an initaitive to identify projects that would need coordination across multiple NIH agencies. These projects should meet certain characteristics: truly transforming, require all NIH, must need incubator scape, and the outcome should produce material into the public domain. Collins then discussed how, from among hundreds of suggestions, the Human Microbiome was picked as one of five topic areas for in depth consideration for the new round of Roadmap competition. Thus the point of this workshop was to discuss this in more detail and help provide material and ideas for the full consideration of an HMP program.

I should note, I found one thing disappointing in the introduction which was a response to my question concerning whether this project would be limited only to studies of humans or would allow for studies of model systems that inform human work. The answer was basically that this would likely be limited to humans. I think this is a big mistake. The human genome project came to the realization that comparative studies with other species were critical to understanding and interpreting studies of the human genome. The same will be true of the human microbiome program.

Jeff Gordon then gave an overview of human microbiome studies, and focused on what are the key questions that need to be answered. Among the key questions: Do we share a core set of microbes? How should we view differences in microbes between people and over time? How do we relate communities of microbes to health and disease? How should we sample microbial communities to characterize them? What determines robustness of microbial communities in people?

To start to answer these and other questions, he suggested that we have three tiers of data collection: (1) deep draft assemblies of microbial communities and reference genomes, (2) reference microbiome work (deep characterization of individuals including information about the familiy history and genetics) (3) 16s surveys of communities (a global human microbial diversity survey). I basically liked all of his ideas. He did talk about work in model organisms too. His work has shown just how important this is … and I think as I said above it needs to be emphasized more in the HMP.

David Relman, from Stanford, then talked about patterns in human microbial diversity. He talked about some of the challenges in such studies as well as results of his and others work. He discussed many interesting aspects of the diversity of samples, and the shapes of diversity. Some of the patterns he emphasized were that history plays a role in the diversity, that archaea generally seem to have limited presence, that diversity is uneven and complex.

Then Gary Huffnagle discussed in more detail the interaction of microbes with the host immune system. And Jo Handelsman discussed what she calls functional metagenomics, which involves focusing on the functions of genes found in the environment on top of examining the phylogenetic diversity of communities. Unfortauntely, I did not take extensive notes for these two talks so do not have much to base my comments on here. In addition, I confess, the fact that the room in which the meeting was held was incredibly crowded and boiling hot, and the fact that I had flown in from California earlier in the day, made taking notes challenging at this point. However, that did not stop me from going out afterwards for a beer with Julian Parkhill, Ewan Birney, Owen White, and Jacques Ravel. The worst part of going out for the beer – I grew up in Bethesda but I made multiple wrong turns in the two blocks to the brew pub. I am sure from now on Julian and Ewan will never trust my directions. Fortunately, the fact that the pub had the RedSox pummeling the Yankees on TV made up for my direction problems.

I will post more about the second day soon.

Jonathan Badger on another reason not to publish in non Open Access journals

Jonathan Badger on his blog has a good little blurb about how he cannot examine a recent piece of research because his institution does not have a subscription to the journal. So the authors lose a reader becuase they published in a non OA journal. Worth a little read for microbiologists since many may not have access to the journal Geology where the paper was published. But the paper was about a fossil that may have been of a fungus.

A human microbiome program?

I am currently attending a workshop sponsored by NIH in which the participants are discussing whether there should be a Human Microbiome Project, and if so, what that should mean.

First, what is generally meant by the “Microbiome.” In essence the humn microbiome is the sum collection of all the microbes found in or on people. The human microbiome has become an important research field because the microbes that live in and among us play critical roles in human disease and health. An important aspect of this is the idea that microbes can be and are beneficial. For example, in the gut the normal microbes help with digestion and nutrient absorption as well as protect from infection. In addition, a variety of diseases (e.g., IBD, Krohns) seem likely to be caused by disruption in the normal microbial flora. In general, it seems likely that other ailments, like autoimmune diseases, allergies, etc will be found to have a connection to disruptions in the beneficial microbes that live among us.

Because of the importance of beneficial / commensal microbes in human biology, there have been growing efforts to characterize the microbes in various body locations – gut, mouth, lungs, skin, etc. But the efforts so far have simply given a tantalizing taste of how interesting and important these microbes are. So here comes this meeting. Organized by NIH (specifically, Francis Collins at NHGRI), this workshop is geared to discuss the possibility that studies of the human microbiome will be included in the next list of “NIH Roadmap” programs. More on the NIH Roadmap some other time.

Basically, the general idea is – do we need an big scale, organized program to tackle the human microbiome.? To get us in the mood, we had talks by many of the pioneers/leaders in the field (e.g., David Relman, Jeff Gordon, Jim Tiedje) as well as discussion of the NIH Roadmap program. I personally did not need any convincing but it was good to hear some of the ideas presented. In the end, I think there is no doubt that a large scale Human Microbiome Program is needed and would be very beneficial.

One of the reasons that an organized effort is needed is that studies of the human micribome are difficult. Reasons for this include:

1. Many of the microbes in the human system have not, and maybe cannot, be grown in isolation in the lab

2. The key features of the microbiome are determined by by populations of microbes and thus even if a representative of a species could be grown in the lab, it would not represent all the diversity in the population.

3. The best way to sample the populations is via “metagenomic” sequencing which involves isolating DNA and sequencing it directly without culturing.

4. Many of the important sites contain hundreds of species each with significant variation within species.

5. There likely will be ENORMOUS variation in and among people. Within a person, there will be variation over time as well as great variation in different sites. On top of that there will be great variation between people.

Given these and other complications, it seems a no brainer there is a need for a coordinated project to gather background information about the human microbiome that would then be useful to researchers, much like the human genome was useful to many researchers. So what would such a project do? Here are some possibilities

1. Sequence many “reference genomes.” By reference genomes here I mean genomes of cultured isolates that are closely related to organisms known in various human locations.

2. Do metagenomic sequencing of a variety of human mcirobiome samples.

3. Conduct large scale human microbiome diversity studies. This could involve rRNA PCR surveys as well as some amount of genome sequencing.

4. Develop the computational tools needed to analyze the massive amounts of data that will come out.

5. Encourage the development of new methods to aid in studies of the microbiome.

So today I guess we will be discussing what specific things are needed in more detail. But again, even though I do not really work on human microbiome projects much, I think it is pretty clear that the time is right for a Human Microbiome Program. And importantly, the methods and tools and discoveries that could come from this will be of use in all studies of microbes in the environment.

That’s all I have for now … will try to write more later.

From bad to good – how a parasite became a mutualist

Just saw this very cool paper in PLoS Biology on Wolbachia that appear to have converted from parasites to mutualists. Wolbachia are among my favorite organisms. They are intracellular bacteria that have been found to infect a wide diversity of invertebrate species. In many cases, the Wolbachia have male specific detrimental effects (I like to call the WMDs – Wolbachia of male destruction). In other cases (e.g., in filiarial nematodes), Wolbachia appear to be beneficial.

I had heard about the work in the new paper from one of the authors Michael Turelli, who was one of the main people to convince me to move to Davis. In this study, the authors returned to examine a population of Drosophila simulans that Turelli had studied some 20 years ago. In the previous studies Turelli and colleagues had found a “classic case” of Wolbachia infection spreading in nature. When they returned to study the population and did a suite of experiments, they found that the Wolbachia had acquired fecundity increasing mutations, making them mutualistic.

Though they have not yet figured out what mutations occurred, it seems that a little genome sequencing might help them. Just a little selfish plug there, since I led the first project to sequence a Wolbachia genome and would love to do some more …

For more information, see Weeks AR, Turelli M, Harcombe WR, Reynolds KT, Hoffmann AA (2007) From Parasite to Mutualist: Rapid Evolution of Wolbachia in Natural Populations of Drosophila. PLoS Biol 5(5): e114 doi:10.1371/journal.pbio.0050114.

Weeks, A., Turelli, M., Harcombe, W., Reynolds, K., & Hoffmann, A. (2007). From Parasite to Mutualist: Rapid Evolution of Wolbachia in Natural Populations of Drosophila PLoS Biology, 5 (5) DOI: 10.1371/journal.pbio.0050114

Wu, M., Sun, L., Vamathevan, J., Riegler, M., Deboy, R., Brownlie, J., McGraw, E., Martin, W., Esser, C., Ahmadinejad, N., Wiegand, C., Madupu, R., Beanan, M., Brinkac, L., Daugherty, S., Durkin, A., Kolonay, J., Nelson, W., Mohamoud, Y., Lee, P., Berry, K., Young, M., Utterback, T., Weidman, J., Nierman, W., Paulsen, I., Nelson, K., Tettelin, H., O’Neill, S., & Eisen, J. (2004). Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements PLoS Biology, 2 (3) DOI: 10.1371/journal.pbio.0020069

What can Justin Timerblake tell us about evolution?

I read with fascination an article in the New York Times magazine this weekend on Pop Culture entitled “Is Justin Timberlake a Product of Cumulative Advantage?” No, I was not fascinated by the Timerlake part. But what was interesting was Duncan Watt’s argument that it is very difficult to predict the success or failure of entities in pop culture. He presented a model that is summarized as “The cumulative advantage:”

The reason is that when people tend to like what other people like, differences in popularity are subject to what is called “cumulative advantage,” or the “rich get richer” effect. This means that if one object happens to be slightly more popular than another at just the right point, it will tend to become more popular still

He then described an experiment they performed that was published in Science last year where

more than 14,000 participants registered at our Web site, Music Lab (www.musiclab.columbia.edu), and were asked to listen to, rate and, if they chose, download songs by bands they had never heard of. Some of the participants saw only the names of the songs and bands, while others also saw how many times the songs had been downloaded by previous participants. This second group — in what we called the “social influence” condition — was further split into eight parallel “worlds” such that participants could see the prior downloads of people only in their own world. We didn’t manipulate any of these rankings — all the artists in all the worlds started out identically, with zero downloads — but because the different worlds were kept separate, they subsequently evolved independently of one another.

They used this set up to test among two different possibilities.

First, if people know what they like regardless of what they think other people like, the most successful songs should draw about the same amount of the total market share in both the independent and social-influence conditions — that is, hits shouldn’t be any bigger just because the people downloading them know what other people downloaded. And second, the very same songs — the “best” ones — should become hits in all social-influence worlds. What we found, however, was exactly the opposite. In all the social-influence worlds, the most popular songs were much more popular (and the least popular songs were less popular) than in the independent condition. At the same time, however, the particular songs that became hits were different in different worlds, just as cumulative-advantage theory would predict. Introducing social influence into human decision making, in other words, didn’t just make the hits bigger; it also made them more unpredictable.

Why you may ask am I so fascinated by this? Well, what he described is mathematically and conceptually identical to Luria and Delbruck’s fluctuation test (see my earlier blog about L & D), where they were testing the origin of mutants. Luria and Delbruck designed a test where they grew E. coli from the same starting point in different culture tubes. Then they exposed these tubes to selective pressures. If the number of mutants in the tubes were basically the same, this would mean that the mutants arose in response to the selection. If the number of mutants were vastly different (somehting they called a jackpot pattern) this would mean the mutants arose in the growth of the bacteria in the tubes prior to selection.

In the entertainment experiment, the different music “worlds” are the equivalent to the different test tubes. And the preferences of people are the equivalent of the selection. Their result in the music experiment was the jackpot pattern – the same thing seen by Luria and Delbruck. For Luria and Delbruck this meant selection did not guide mutation. For the music, this means the personal preference for the music has less influence than the random history of which music was picked early on.

So – thank you Justin for a modern lesson in evolution.

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