Category: Misc.

Another education use of Open Access publications

I was reminded of another important use of Open Access publications last week when I gave a talk at Chico State University. Chico St. is one of the California State Universities (I guess it’s formal name is California State University, Chico). The people in the Biology Department there invited me to give a talk (I think this was because of the press coverage of my PLoS Biology paper on the symbionts of the glassy winged sharpshooter – a pest of great concern throughout California since it transmits Pierce’s Disease in grapes).

I had a great visit and a nice drive to and from Chico. I met with lots of faculty doing interesting stuff. And after my talk we went to a local pub with some faculty and students. I had opened up my talk discussing the benefits of Open Access publication and how it was just as important as databases like Genbank (In fact, I think it is a good idea to discuss the importance of OA in scientific presentations in general – spreading the word). And much of our conversation at the pub centered on Open Access.

The most interesting thing I found out was that for one of the journal club/discussion courses that they have there, they only use papers from OA journals like PLoS journals. There were two major reasons for this. (1) As a woefully underfunded university (note – read this Arnold), they do not have funds for their libraries to subscribe to a diversity of journals and (2) using OA publications means they can post all the publications or links to them on a web site for students and do not have to make them closed access / password protected to prevent illicit sharing of non Open publications.

So – another benefit of Open Access publishing. Easing access even o major universities in the US, and making it easier to use research papers as part of course readers and course web sites.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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California Metagenomics Meeting presentations available online

For those interested in metagenomics, the presentations from a metagenomics meetings that was held at the Moore Foundation HQ are now available online.

I wrote about the meeting previously in my blog.

The speakers were Eric Allen (UCSD-SIO), Doug Bartlett (UCSD-SIO), Weizhong Li (UCSD), Victor Markowitz (JGI), Jonathan Eisen (UCD), Victoria Orphan (Caltech), Adam Martiny (UCI), Jessica Green (UCM), Kimmen Sjolander (UCB), and Steven Brenner (UCB). All Powerpoint presentations are available in PDF format.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Darwin and Conservatives

The New York Times is reporting that Darwin (and by Darwin, they mean evolution by natural selection) is getting more and more support within the conservative community in the US.

Basically there appear to be two camps emerging. The anti-science group (not what they called them in the Times article but that is what they are) who cannot reconcile Darwinism (or many other scientific tenets) with their religious beliefs. And on the other side are conservatives who not only accept evolution by natural selection as a fact, but embrace it as supporting many of their conservative ideals. This second pro-evolution conservative clade includes fundamentalist types who, like Francis Collins, believe that evolution by natural selection is indirectly the hand of God. The pro-evolution clade also includes political and social conservatives, who are not particularly religiously conservative.

I found the article fascinating in many ways because finally philosophical conservatives are taking a stand against the religious right. For example:

“I do indeed believe conservatives need Charles Darwin,” said Larry Arnhart, a professor of political science at Northern Illinois University in DeKalb, who has spearheaded the cause. “The intellectual vitality of conservatism in the 21st century will depend on the success of conservatives in appealing to advances in the biology of human nature as confirming conservative thought.”

Also — from the article

What both sides do agree on is that conservatives who have shied away from these debates should speak up. Mr. Arnhart said that having been so badly burned by social Darwinism, many conservatives today did not want “to get involved in these moral and political debates, and I think that’s evasive.”

Yet getting involved is more important than ever, after “the disaster” of “President Bush’s compassionate conservatism,” he said, because the only hope for Republicans is a “fusion of libertarianism and traditionalism, and Darwinian nature supports that conservative fusion.”

So I say to all you social or political conservatives who think that anti-evolution talk is not necessary and potentially damaging, come out come out wherever you are. The time is now for evolutionary biologists to embrace these conservatives. Not because they agree or disagree with their politics. But because evolutionary biology does not itself make ANY moral judgements nor force one to make any political decisions. It is science. Just as quantum physics does not support the right or the left, evolutionary science is apolitical. That is not to say that evolutionary science cannot be used to inform political and social and moral decisions. It is just that evolutionary science is not about those things. It is about studying the way the world works.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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open access hits the elections

Well, nice to see OA in the political arena. Obama is asking that the video from the Presidential Debates be released without copyright so that it can be freely blogged, etc.

See the SF-GATE article here.

Obama is quoted as saying

“Rather than restricting the product of those debates, we should instead make sure that our democracy and citizens have the chance to benefit from them in all the ways that technology makes possible.”

I could not agree more. Now if only that were the case for all scientific research.

Thanks to Melinda Simmons for pointing this out

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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“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.”

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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