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

Please – bash my latest paper – for the benefit of humanity

My lab has a new paper that just came out on the sequencing and analysis of the genome of a pretty cool (or hot actually) bacterium, Thermomicrobium roseum, which was isolated from a Toadstool Spring, an alkaline siliceous hotspring in Yellowstone National Park. This paper is from a grant we had when I was at TIGR as part of the “Assembling the Tree of Life” program at NSF. Our grant was focused on generating genome sequences from phyla of bacteria for which no genomes were available.

At the time this species was a representative of a phylum that had no genomes. After we started sequencing, the phylum was dissolved, but never mind that for now. We report what I think are some very interesting things in the paper. Among them:
  • We report the first example of a plasmid that encodes all the genes needed for chemotaxis including all the genes for making a flagellum. Given that they are on a plasmid this suggests that motility could be easily transfered between species.
  • We report experimental work and genome analysis that helps understand the novel membrane and cell wall structure in this species.
  • This is the first thermophile known to oxidize carbon monoxide
But I am not writing per se about the things I like about our paper. I am instead asking people out there to find things wrong with our paper. Why am I doing this? Because this paper is part of a broader experiment in publishing in that it is in PLoS One. And one of the main benefits of PLoS One is the features that allows commenting on publications. I personally believe such features are part of the future of scientific publication. But it is currently unclear just how effectively such commenting features are used (note Euan Addie is doing a survey about comments on PLoS One papers here).

So I am offering up my paper as a case study. If you comment and ask questions or make critiques, I will try to respond. And if you think something in our paper is wrong or weird, please say so. If you think something in our paper is supported by other work we do not cite, please say this too. If you have anything useful to say, please make comments.

How do you do this?

  • Go to the paper at the PLoS One Web Site.
  • In the upper right click on “Login” if you have an account or “Create account” if you do not.
  • Return to the paper once you are logged in
  • Find some part of the text you want to comment on
  • Highlight that text and click over on the right “Add a note” or “Make a comment”
  • Fire away.
——–
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.

——–

Harold Varmus on Science Friday

There was a very interesting interview on Science Friday last week.  The discussion was with Harold Varmus (see Science Friday Archives: Harold Varmus).
In the interview, Varmus discussed his new book, his role as an advisor to Obama, and some issues relating to Open Access.  I found his comments to be very interesting and insightful and it is worth listening to.  
——–
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.

——–

Pictures from Yolo Basin – Bitterns, Night Herons, Owl

Yolo Basin
——–
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.

——–

An ever more famous science blogger

Just a little one here. Pam Ronald, a professor and blogger here at Davis is featured on the home page of CNN.COM in a story about “Fighting Hunger with Flood-Tolerant Rice.” You can read about it at CNN or learn more about what Pam has been doing with rice from her blog or her book “Tomorrow’s Table” that she wrote with her husband.

——–
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.

——–

Nice little PLoS reference by Nicholas Kristof in the Times …

Just a quick one here. In an article in today’s Times, Nicholas Kristof writes about “Putting Torture Behind Us” and he has a little PLoS reference there …

“Granted, returning the base to Cuba may not be politically realistic. So here’s a fallback alternative: turn the base into a research center for tropical diseases.

This was proposed in a medical journal, PLoS Neglected Tropical Diseases, a year ago, and it makes more sense now than ever

In Latin America and the Caribbean, there are still more than half-a-million cases annually of dengue fever (which causes excruciating pain and sometimes death), nearly 50,000 new cases of leprosy and more than 700,000 cases of elephantiasis (which causes grotesque deformities). In addition, 50 million Latin Americans have hookworms inside them, often causing anemia and making it more difficult for children to concentrate in school.

Peter Hotez, the president of the Sabin Vaccine Institute at George Washington University and the editor of PLoS Neglected Tropical Diseases, says that an international center on Guantánamo could become a symbol of United States cooperation in the region.

Imagine if people around the world came to think of Guantánamo as a place where America led a battle against hookworms and leprosy. That would help us fight terrorism far more effectively than the prison at Guantánamo ever did..”

Hat tip to Chris Schelleng for pointing this out. The original PLoS NTD article by Peter Hotez is here.

——–
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.

——–

What’s better than brain doping? Cello Scrotum is what.

OK I have a lot to learn. I was (and still am) pretty proud of the April 1 prank I pulled off this year with many other bloggers announcing a fake crackdown on brain doping. But my joke is not even close to this one. A letter in a recent issue of BMJ has announced that the malady known as Cello Scrotum was in fact made up. Why did they make this up? In response to a publication about guitar nipple (for more on this see CNN and the Times Online). And now they have confessed only 35 years later.

And I must say – God Bless Pubmed Central. Because here is the original very brief letter which I am posting below:

——–
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.

——–

Benefits of Open Access: enabling musical interpretations of human genomics …

Not this is one of the most creative uses of open access science publications I have seen in a while. The video is from a paper by Dan Falush and colleagues that was in PLoS Genetics. Listen/see how the music changes with the genetics/migration of humans.

So I guess given some of my recent posts, we must ask what should we call this? Musicomics (which has a following but most of the use of the term seems to refer to music and comics together, although I did find one site with a reference that is about genomics) or genomusic (most of which seems to refer to people named Geno making music). Maybe, maybe, we just should say it is “nameless” but nice.

Anyway — a nice use of open access — the material from the PLoS Genetics paper is under a broad Creative Commons license and thus this type of use is allowed (and the source is attributed in the YouTube notes). Not sure about the exact details of the origins of the music for the video, but Dan Falush has hinted to me that it was some spontaneous contribution by a band in LA.

——–
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.

——–

Obama’s Science Team Big on Evolution

Much has been written and will be written about how Obama is taking science seriously.  To me, one great sign of this is that not only is evolution OK to talk about now, but – gasp – many of his science team actually have worked on evolution.   For example:

  • Eric Lander, part of Obama’s council of advisors on science and technology, has written many papers either directly or indirectly about evolution. 
  • Harold Varmus also on this Council, has written about evolution of viruses (e.g. here),
  •  Jane Lubchenco is an ecologist who in much of her work has an evolutionary ecology angle
Even John Holdren, who is more of a physicist and as far as I can tell has not written explicitly about evolution recently certainly discussed it in some of his earlier publications with Paul Ehrlich.  
So – not only is science in general and life science in particular on the upswing.  But evolution is too.  Maybe this is why Darwin endorsed Obama so many months back. 
——–
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.

——–

The Bush Administration IS NOT and WAS NOT anti-science

So much has been written about the supposed anti-science stance of the Bush administration (see for example Chris Mooney, AFP, many Nobel laureates, etc  and even me).  But I have been obsessing about this in my head for some time now.  And I think it misses the point.  Bush and his administration have not really been anti-science.  There I said it.  Ready to smack me over the head?

Before you do that.  Wait.  What I think Bush is is even more insidious.  He is anti-evidence.  Or, in other words, he does not believe science should be used to discover things but instead simply as a means to an end.  Sound familiar?  This was his approach to weapons, torture, Guantanamo, gathering intelligence about US citizens, and so on.   All these things were justified because evidence and objectively testing multiple possibilities was not really needed – we knew the answer and just had to back it up with something consistent with the theory.  In essence, everything he did titled against evidence in all sorts of areas.  
So – even though he was not anti-science per se.  The anti-evidence attitude hit scientists really hard.  Science is NOT about just trying to get to an end.  It is also about discovery.  And thus I look forward to a president who believes science is a way to discover things about the world that we do not already know.
——–
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.

——–

You could call it symbiomics (but please do not)… but whatever name you use, this is $^@#&* so cool.

Once again, Nancy Moran’s lab has knocked the scientific wind out of me with a cool paper. This seems to happen every 6 months or so (and I hope my paper with her lab a few years ago knocked the wind out of some others). And this new one, even though it is in a non OA journal which I usually avoid writing about here, is so cool, I just had to say something. So, if you are interested in a brilliant study of “The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria” see the recent Science paper by Moran, Heather McLaughlin and Rotem Sorek. Here are some key lines that summarize some of what they did:

We documented the dynamics of symbiont genome evolution by sequencing seven strains of Buchnera aphidicola from pea aphid hosts….

….A. pisum is native to Eurasia, but has been introduced worldwide. It was first detected in North America in the 1870s (11). We sequenced the genomes of seven Buchnera-Ap strains descended from two colonizers of North America (and hence diverging up to 135 years ago), including two strains diverging in the laboratory for 7.5 years. Solexa sequencing was combined with verification by Sanger sequencing (12), to determine genomic sequences of these seven strains (Table 1)….

…Our estimated mutation rate for base changes was unexpectedly high: more than 10 times the previous estimates of mutation rate calculated on the basis of silent site divergences in both Buchnera and free-living bacteria…

…Our model predicts that the initial step leading to genome reduction is a shift in nucleotide composition toward higher A+T content….

Alas, I am really busy right now finishing some grants and papers or I would try to write more, especially since some may not be able to get this paper.  Note for you conflict of interest aficionados –  much of the sequencing for this project was done at the Joint Genome Institute where I have an Adjunct appointment.

——–
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.

——–