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

Hidden Gem in Davis – Farmer’s Kitchen Cafe

The Farmer’s Kitchen Cafe, which is part of the Natural FoodWorks Store, is possibly the biggest hidden gem of a restaurant in Davis. They specialize in :

delicious, homemade bioregional foods, free of gluten and casein. Your food is made with locally grown and organic fruits and vegetables, free range meats and wild fish. No aluminum pans, no hydrogenated fats, no microwaved foods, no unnatural additives.

Although the service there can be a little slow, that is part of the point. This is not a fast food restaurant. It is fresh, in season, homemade, and usually organic or at least local. Last time I went I had the chicken noodle soup, which was, I have to say, even better than mom used to make. It has a nice simple clear broth, a smattering of flavorful veggies and chicken, and a good helping of clearly top of the line noodles. I also had an organic eggplant sandwich with pesto and feta cheese that was nearly perfect. The eggplant was creamy and intermixed with the pesto into a spread with no hint of the bad eggplant flavors one can get sometime. Plus, there is a great basket of miscellaneous crayons and toys that our daughter spent much of the time playing with.

This is one of my favorite places in Davis and definitely worth a visit, especially if you are into sustainable, organic or local foods. Check it out at 624 4th Street or at their website.

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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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Sea Urchin Genome and the Ridiculous Evolutionary Claims of Genome Researchers

All I can say is “AAAAARGH”

A sea urchin genome has been sequenced and there are some really interesting findings that have been reported based on analysis of the genome. For example, there appears to have been a large expansion of genes involved in the innate immune system in the species sequenced, Strongylocentrotus purpuratus.

All the good science aside, what most struck me were some of the ridiculous quotes attributed to some of the researchers in this project in stories and press releases. For example, in an article on MSNBC, George Weinstock says

“The sea urchin is surprisingly similar to humans,”
“Sea urchins don’t look any more like humans than fruit flies, but about 70 percent of sea urchin genes have a human counterpart whereas only about 40 percent of fruit fly genes do.”

Apparently, George was glossing over the reason this organism was chosen for sequencing in the first place. If you go to the NHGRIs web site you can get the white paper written that led to the selection of this species for sequencing. Perhaps the most important reason is that evolutionarily the sea urchin is closer to humans than fruit flies are. Therefore, it should only be a surprise to someone who does not know the evolutionary position of this species.

Perhaps even more appalling is the discussion of the apparent large number of genes for light sensory systems in this species. Again, Weinstock is quoted:

“There is not a lot of light at the bottom of the ocean, so it is not clear what they might be ‘seeing,'” Weinstock said. “This is certainly an area that will be studied intensively as a result of the genome project.”

I can only view this as some sort of joke. First of all, blind cavefish still have the genes for light perception even though they do not see. This is because it takes time for such genes to disappear. Second, apparently George has never really thought about where this species of sea urchin is found. It is found in the intertidal zone — hardly the dark depths of the ocean. I could go on and on but I will just get more annoyed. In this case, Weinstock has proven that many Genome Scientists are almost completely clueless about the organisms they are working on. Which is a shame. Becuase sea urchins are fascinating creatures and the fact that they are more closely related to humans than are most other invertebrates is one of the main reasons they have been a focus on so much research up until now. Oh well …

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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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Paramecium whining

I just got an announcement from Linda Sperling, announcing the publication of a paper on the Paramecium genome

Dear ciliate researcher,

We are pleased to announce that the Paramecium genome article is now available as an advanced online publication at the following address:

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05230.html

We thank all of you for your interest and support.

Jean Cohen and Linda Sperling

Linda Sperling
Centre de Génétique Moléculaire
CNRS
Avenue de la Terrasse
91198 Gif-sur-Yvette CEDEX
FRANCE

sperling@cgm.cnrs-gif.fr
+33 (0)1 69 82 32 09 (telephone)
+33 (0)1 69 82 31 50 (fax)
http://paramecium.cgm.cnrs-gif.fr/

She sent this to an email list for ciliate researchers. I am writing about this in my blog because a blog is where you are supposed to write things these days when you are pissed off. Why am I pissed off about this? Well, the Paramecium paper makes no mention whatsoever of our paper on the genome of a close relative of Paramecium (Tetrahymena thermohila for those interested) which was published in August. And they do not even explicitly mention the Tetrahymena genome project (even though they say they took our data and used it). I guess I am not too surprised since their paper is published in Nature, which recently seems to be taking many liberties with referencing things in Open Access journals (ours was in PLoS Biology).

What is most annoying about this whole thing is that Linda Sperling is on the Scientific Advisory Board of our project, and has been privy to all of our work from the inside and was I am sure fully aware of our paper being accepted long before theirs was. Common courtesy in science would have been for them to have made a reference to our paper in press or at least our project. But for whatever reason, they carefulyl crafter their words to make no mention of our work. Interestingly, here is the email I sent to the same ciliate list on August 29, 2006

For those interested, our paper on the Tetrahymena MAC genome has been published online at PLoS Biology

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040286

Jonathan Eisen

Strikingly, their paper was then accepted August 31, 2006. I hate to believe in conspiracies, but it seems just a little too coincidental that their was accepted just after ours was published. And yet still no mention of our work in their paper. Hmmm …

Fortunately, since our paper was in PLoS Biology, they cannot say “sorry – we did not have access to it.” Whatever they say, I can say clearly that Linda Sperling will not be invited to our next 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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Flu Evolution Revisited and Biology Direct’s Foray into Open Peer Review

Anyone interested in scientific publishing and/or the flu should check out a new paper in the journal Biology Direct. The paper suggests a new way of thinking about flu evolution. Whether you agree with the authors or not (I am still not sure), what is most interesting about this to me is that the reviews are posted online as are the authors responses. See the paper here and some stories about it here and here.

Biology Direct is an Open Access journal that is experimenting with the peer review system. Their experiment is quite intriguing in its methods. For details see here and here.
Basically, the author is charged with selecting reviewers and then getting the reviews. Then the paper can be published along with the reviews, whether they were positive or negative. The author can make changes based on the reviews or can choose not to. Thus someone could publish complete crap, but since the reviewers will be named publically, hopefully the reviews will indicatethat it is crap. The key to this is that the author has to select people from the Editorial Board that then select the reviewers. So as long as the Editorial Board is reasonable, the review process should be OK (note – I am on the Editorial Board although I have not been asked to do anything yet).

Do I like this system? I am not 100% sure. But I admire Eugene Koonin and colleagues for trying something different and giving the world an example of a possible way to get around the flaws of the current review system. Of course, to me, the most important thing is that the journal is Open Access, which means that anyone out there can get a fascinating look at peer review for free.

For example, people should really check out the paper and the reviewers comments and the authors responses. Or even better check out some other papers in the journal. It makes for a good read.

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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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Evolution and Politics

Scientists are acting up again. The New York Times reports that

75 science professors at Case Western Reserve University in Cleveland have signed a letter endorsing a candidate for the Ohio Board of Education.

This is great news if you ask me. Scientists seemed to be emboldened to play more of a role in politics. I think this is due to some of the recent pushes from anti-science coalitions, like the supporters of “intelligent design” as a scientific theory (which it is clearly not).

We desperately need more of this type of thing – with scientists speaking up. I do not want scientists to choose sides in truly political debates. And I hope scientists will avoid being too arrogant – such as when some suggest science can solve all the worlds woes. But when sound science is being ignored or belittled by politicians, scientists should speak up. The evolution debate is but one example. There are many more issues where sound science is being misused or ignored (e.g., global warming).

So – I recommend all scientists consider doing something to get involved. Lend your support to the folks in Ohio (e.g., Lawrence Krauss organized the group to write the letter). Or join an organization like SEFORA a new science based political action group. But just don’t sit on the side and say “scientists should not get involved.” If all scientists keep doing that, we are in deep trouble.

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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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The latest genomics buzz

The latest buzz in genomics is about the honeybee genome. The people working on this genome have really done a good job of organizing themselves (a sort of model social genomics network in a way). They have a veritable slew of papers coming out this week on various things about the genome and about honeybees that were learned by making use of the genome.

There is an entire issue of Genome Research dedicated to studies of the honeybee (see the press release here) including papers on rates of evolution, circadian rhythms, chemical sensing, sex and death (of course), and even the royal jelly. If you don’t know what royal jelly is, do a google search for that. There is also an overview article in Nature and a genome report in Science. In total 170 researchers were involved in these papers.

Mind you, I am disappointed that these were not published in Open Access journals. And this is particularly sad given that the funding came from the NHGRI, the same group of sanctimonious individuals who kept talking about how the “public” human genome project was “open” in every way for the betterment of humanity. Unfortunately, what they mean by “open” even for the human genome project is a bit of a misnomer. They meant that people could look at the data immediately. But they restricted how people could use the data, despite their attempts to pretend otherwise. Consistent with this, the groups funded by the NHGRI generally do not publish their papers in Open Access journals. Shame shame shame.

OK, enough sniping. The honeybee is so fascinating biologically in so many ways that this genome sequence deserves a bit of extra attention. First, honeybees are social creatures. They have in fact been one of the key models in studying both the evolution of social behavior but also communication among organisms.

Another aspect of their biology that is very interesting is their genetic structure. Like other hymenoptera they have what is know as a haplodiploid life cycle with males being haploid (the result of unertilized eggs) and the females being diploid. This unusual genetics is another reason that honeybees and other hymenoptera have been studied extensively by biologists for many years. In fact, a great little bit of history about this is in a book on the history of studies of altruism from Princeton University press. One of Darwin’s biggest concerns in the origin of life related to the self sacrifical behavior, especially that in honeybee colonies. Apparently, honeybees were a topic of conversation among non scientists and the non reproductive worker castes were well known to the public. Darwin struggled quite a bit to come up with a good explanation that was consistent with natural selection for why some individuals would sacrifice their lives for others.

Dawrin actually cam up with a good logical explanation for this – that some individuals would sacrifice if they were related to others who would benefit. Bees and their relatives played a large part in studies that have revealed in much greater detail how altruism can evolve. They may not be as warm and fizzy as some other organisms being sequenced, but they certainly were a good pick for a genome sequencing project.

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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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Science Lobbying – The role of science in politics and vice versa – Scientists and Engineers for America

I listened to a very interesting Science Friday Podcast today (I listen to them on my bike rides to/from work here in Davis, CA, the most bike friendly town in which I have ever lived). This particular podcast had as one of the guests Susan F. Wood. Some people may remember that she resigned from a top job at the FDA over what she felt was politics getting in the way of good science.

Well, rather than disappear as some higher ups in the executive branch do after quitting, she has jumped into a whole new realm. She has helped start a group called Scientists and Engineers for America. Their aim is to help elect to office people

who respect evidence and understand the importance of using scientific and engineering advice in making public policy

from the NY Times article about this.

They have even created a “bill of rights” for scientists. Among the rights they include:

  1. Federal policy shall be made using the best available science and analysis both from within the government and from the rest of society.
  2. The federal government shall never intentionally publish false or misleading scientific information nor post such material on federal websites.
  3. Scientists conducting research or analysis with federal funding shall be free to discuss and publish the results of unclassified research after a reasonable period of review without fear of intimidation or adverse personnel action.
  4. Federal employees reporting what they believe to be manipulation of federal research and analysis for political or ideological reasons should be free to bring this information to the attention of the public and shall be protected from intimidation, retribution or adverse personnel action by effective enforcement of Whistle Blower laws.
  5. No scientists should fear reprisals or intimidation because of the results of their research.
  6. Appointments to federal scientific advisory committees shall be based on the candidate’s scientific qualifications, not political affiliation or ideology.
  7. The federal government shall not support any science education program that includes instruction in concepts that are derived from ideology and not science.
  8. While scientists may elect to withhold methods or studies that might be misused there shall be no federal prohibition on publication of basic research results. Decisions made about blocking the release of information about specific applied research and technologies for reasons of national security shall be the result of a transparent process. Classification decisions shall be made by trained professionals using a clear set of published criteria and there shall be a clear process for challenging decisions and a process for remedying mistakes and abuses of the classification system.

I confess to being a little worried that they may become too partisan and to be effective I think they should try to be as non partisan as possible (although there is no doubt that the current administration has violated more of the items in their bill of rights than probably any previous administration). Neverthless, this sounds like a great idea and hopefully they can help increase the use of science in decision making.

To sign up go to http://www.sefora.org/

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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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Genomics Education Bus

I just got back from the new version of the old GSAC meeting. It is now called GME or Genomes, Medicine and the Environment (or, as we like to call it – stuff Craig Venter is interested in these days). The meeting is organized by the Venter Institute and this year was one of the better versions of this meeting. There were some really interesting talks in a few topic areas (I will try and post some details about these later). But to me, the most interesting part was seeing the Venter genomics education bus (part of their Genomics Discovery program) on tour. They use this bus to go around to high schools and other places to do some genomics education.

Just before coming to the meeting, the bus apparently rolled into New Orleans (see Wired news story here). Lots of people like to complain about Venter and his style, but whatever you may think of him, I think this bus is a great idea. We desperately need more people who do science making an effort to interact with and educate people about scientific research. And since this bus is outfitten with lab equipment and various genome-related toys, it can go into a neighborhood without the best science labs and help introduce students to the fun and excitement of modern science.

Note – the photo was taken by me at the GME meeting in Hilton Head, SC. In the photo are Lisa McDonald, Jennifer Colvin, and (I think) Darryl Bronson.

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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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Harvard Crimson changes its mind – supports PLoS One

Well, the folks at the Harvard Crimson have apparently changed their mind. In a new Editorial, two writers from the Crimson discuss PLoS One and open peer review. Unlike the previous Crimson editorial (see my blogs about it here and here), the two writers of this one now come out clearly in support of the PLoS One idea as well as some PLoS ideals.

For example, the liken the battle between Open Access and Closed Access publishing to the battle over democracy

Democracy has reached a new frontier, and we’re not talking about the Berlin Wall. It’s a new decade and a new millennium, and yet another wall is crumbling—this time, not between countries, but in the domain of scientific research.

Perhaps most importantly, they end the editorial with

Initiatives such as PLoS ONE will help promote free and unfettered scientific study, supplementing and revolutionizing an oligarchic academic process. It is both ignorant and regressive to reject this democratization.

Although they did not address the previous highly ignorant editorial in their own newspaper, Yifei Chen and Patrick Jean Baptiste deserve kudos for a well written, well thought out editorial on a key topic for the whole endeavor of science.

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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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World’s Smallest Genome of a Cellular Organism?

ResearchBlogging.org

A one page paper in Science reports on what I think is one of the most exciting findings in microbial genomics in years. The reports describes the sequencing and analysis of the genome of a bacterial endosymbiont of an aphid. This bacteria, known as Carsonella, has a TINY genome – only 160 kbp in length. This is ~ 3 fold smaller than the previously known smallest genome – that of Nanoarchaeum equitans which has a genome of 490 kbp.

I think almost certainly this symbiont should be considered an organelle. It is missing many cellular functions found even in the most reduced symbionts. Thus in essence it may not be the smallest genome of a cellular organism. But who cares how we define it. If it is a new organelle – that is amazing. If it is a tiny cellular genome – that is amazing too.

One thing that strikes me as strange is the fact that the paper is only one page long. It contains so little detail on what was done and what was found in the genome that the story is woefully incomplete. This I would guess is somehow related to a rush to publish but also likely due to it being published in Science, which has severe page restrictions.

This paper has been getting ENORMOUS press coverage for valid reasons. But I agree with Craig Venter (see the New Scientist article) that this genome is not of much relevance to efforts to create a “minimal” genome. This is because the ideal minimal genome is one that can support independent life. Carsonella, is far from independent and thus represents a really wild evolutionary story, but nothing of much relevance to minimal genome studies.

Some related links:

Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H., Moran, N., & Hattori, M. (2006). The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella Science, 314 (5797), 267-267 DOI: 10.1126/science.1134196

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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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