Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Metagenomics Meeting July 11-13, 2007 UCSD

Fro those interested in metagenomics, a meeting will be held July 11-13 at UCSD with many of the major players in the field participating in some way (I am on the planning committee, so no bias here).

This meeting is connected to the new CAMERA Metagenomics Database run out of UCSD (as a Joint Venture with the Venter Institute). I am about to head down to the Scientific Advisory Board meeting for CAMERA. So I am asking anyone out there who is interested in metagenomics to check out CAMERA and let me know what you think. Right now I am I guess kind of an insider/outsider in CAMERA. I am supposed to have a subcontract to Davis to help integrate some phylogenetic tools into the database but alas the Davis office has been a bit lax shall we say about getting my subcontract set up. So until that is set up I guess I am a CAMERA advisor.

Anyway, if anyone has any useful opinions out there about CAMERA I will be happy to share them with those at the SAB meeting.

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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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Sanger Center Google Ads a little off

OK – this is a bit pithy, but I could not resist …

Dear Sanger Center. You might want to tell google to stop printing your ad that says

“Sanger PhD Programme – http://www.sanger.ac.uk – Fully funded 4 year studentships in genomics. Deadline 10th Dec 2006″

It seems to be a bit out of date.

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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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Looming Open Access

People out there who know me know I like to talk. A blog is a perfect outlet for someone who has opinions about just about everything. But my favorite thing about blogging these days is finding other blogs out there that say what I might have wanted to say in a much better and more elegant manner. And this is the case today for Carl Zimmer’s blog on “An Open Mouse.“

Zimmer, for those who are not familiar, is a science writer who also now has a good blog (called The Loom) but is probably best known for his articles in the New York Times and his books. (I have not read all of his books, but his Evolution book is quite good and I have Parasite Rex but alas have not read it yet).

Anyway, Zimmer in his new blog writes about how Open Access science makes his blog easy because he can use a figure from a PLoS paper (on mouse genetic interactions) and rather than sue him, PLoS simply encourages him. I could blather on and on about this (and in fact have – see here for example). But better to just read his words:

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it. In fact, I just did.

I certainly appreciate the importance of copyrights (as the owner of many for my articles and books), but in these situations, keeping information behind a thick wall starts to seem a bit crazy, like the loss of precious bodily fluids. Far from committing some sort of violation to the PLOS paper, I have actually just spread the word about it. A few readers may even go back to read the original. And it was so easy and straightforward for me to do so that I will be very reluctant to bother with anything else.

You go Carl. Welcome to the wonderful world of 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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Another way to support open access – call in to radio shows

So – I was driving today from Davis to Walnut Creek to attend the Joint Genome Institutes Scientific Advisory Council meeting (more on this hopefully later as I got lots of good advice from the SAC group which includes George Weinstock, Bruce Birren, Joe Ecker, Mark Adams, and Eric Mathur (who is perhaps the most energetic person I ever met)).

Anyway – on the drive over, I was listening to KQED’s Forum Show and they were doing a story on Avandia, the type II diabetes drug. A recent report on this drug indicates that taking it leads to a significant increase in very negative “side effects” like death. Most interesting and upsetting to me, the lead author of the new study said something to the effect of “our new study was limited significantly because we could not get access to the full results of the clinical trials on Avandia.” This is really stunning. Here is a drug making GSK billions of dollars and yet the clinical trial data that underlies the approval of this drug is not readily available for other people to look at. What is wrong with this picture? I though science was about building on prior results. If you can’t get the data, how exactly do you confirm what someone else did and how do you build on their results? Apparently, medicine does not follow the same procedures.

So I seethed while in the car. And then, I got stuck in a traffic jam (normally I take the train, but was unable to today). And at the same time, they announced the call in number. So I called — the first time I have ever even tried to call one of these shows. And on the second try it rang. And a man answered and asked for my first name and my question/comment. And then, I was on the air … asking about whether there were any attempts to make clinical trial data more readily available (OK, I knew there were attempts, but I was not sure of the details and they needed to be asked on the air anyway).

And if you want to know what I said, and what they said, well listen to the show (I am on at minute ~ 34).

Wed, May 23, 2007 — 9:00 AM
Avandia and Diabetes

Listen Listen (RealMedia stream)
Listen Download (MP3)
(Windows: right-click and choose “Save Target As.” Mac: hold Ctrl, click link, and choose “Save As.”)

And to add to the bonus of being on the air, Jim Bristow, Deputy Director of JGI, was, like me, a bit late to the SAC meeting at JGI. And he came up to me and asked if that was indeed me on the air while I was supposed to be at the meeting. To learn more about clinical trial access, see PLoS Clinical Trials.

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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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Is Nature going Open Access?

Nature and EMBO are together publishing “Molecular Systems Biology” and all basic research in this journal is Open Access. I am wondering why this has not gotten more press as it seems Nature is experimetning with OA models here. Nature has done some experimentation previously by making certian types of papers available freely (e.g., many genomics papers). But this is definitely one step beyond and they deserve massive kudos for it.

So if you are looking for a new OA journal to submit some systems biology related papers, you should try here. And maybe with a little effort, we can convince Nature it is worth doing for more of their journals.

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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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Thanks to Genome Technology

Just a quick thanks to Genome Technology for plugging my blog a few times. First, they ran a little thing about my Human Microbiome Meeting blog and now they have reported on the Seven Stones Blog (the blog for the new Nature journal Molecular Systems Biology) and my blog talking about the need for microbiologists to try and save the world.

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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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Calling all microbiologists – please help save the world

I read with dismay today news reports of the discovery that much of the Southern Oceans are saturated with CO2. This has happened much sooner than anyone anticipated and bodes very poorly for limiting the damaging effects of global warming. So I am starting a new call in my blog here

To all you microbiologists out there. Are you bored with what you are doing? Looking for something important and challenging to do? Sick of working on yet another human pathogen? Switch to working on a topic relating to limiting global warming and climate change (note if you want to learn more about global climate change check out the recent New Scientists article here which I found out about from the Davis Egghead Blog). Among the topics you could work on:

Any other suggestions for topics welcome.

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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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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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