Toluu : The Tree of Life

The Tree of Life

Blog of Jonathan A. Eisen, evolutionary biologist, Open Access advocate, Professor at UC Davis and Academic Editor in Chief of PLoS Biology.

Ad for Genomics Faculty Position at UC DavisJanuary 6

Still getting back into things after being out sick ... here is an Ad for a job everyone should want ...

The UC Davis Genome Center integrates experimental and computational approaches to address key problems at the forefront of genomics. The Center is housed in a new research building with state-of-the-art computational and laboratory facilities and currently comprises 14 experimental and computational faculty. These faculty are developing an internationally recognized program in genomics and computational biology at Davis, building on and enhancing the unique strengths and unmatched breadth of the life sciences on the UC Davis campus.

The Genome Center invites applications for tenure-track faculty positions in all areas of genomics with emphasis on next-generation proteomics and statistical genomics involving animal, plant or microbial systems. Applicants interested in genomic approaches to human diseases and investigators employing large-scale, technology-driven approaches that complement existing strengths at UC Davis are particularly encouraged to apply. Candidates should be strongly motivated by the biological importance of their research and should value the opportunity to work in close collaboration with other groups and disciplines.

Candidates may be at any academic level. At the senior level, we invite applications from prominent scientists with distinguished records of research, teaching, and leadership in genomics. At the ju

What to do when your sick? Sickblogging (and a little bit about Adm. Dennis Blair)December 30 2008

Well, I have had some unpleasant winter bug that on top of everything my kids seems to have or at least have something similar. It has been fun at night here to say the least. I was hoping to get some work done over winter break especially since I was overwhelmed with teaching in the fall quarter. That is not happening. But in the few moments of peace here, I have looked for something to do --- and hey there is one thing I could do with only a little time. Blogging. And of course I am not alone in this. So here are some links to others on sickblogging:

And what have I to say today? Not much but here is a preview of things to come. I have a feeling that Obama is stalking me scientifically. Why? Well, I am one or two steps removed from a huge number of his appointees and I plan to write about them in th

Open Evolution Highlights - the Population Genetics of dN/dSDecember 16 2008

An interesting new paper in PLoS Genetics (PLoS Genetics: The Population Genetics of dN/dS) by Sergey Kryazhimskiy and Josh Plotkin that discusses the use of the widely used parameter dN/dS (in essence a measure of the ratio of non synonymous to synonymous substitutions in protein coding genes). This parameter is commonly used to estimate the type of selection that has occurred in a protein coding gene.

Here is their summary of their article:

Since the time of Darwin, biologists have worked to identify instances of evolutionary adaptation. At the molecular scale, it is understood that adaptation should induce more genetic changes at amino acid altering sites in the genome, compared to amino acid–preserving sites. The ratio of substitution rates at such sites, denoted dN/dS, is therefore commonly used to detect proteins undergoing adaptation. This test was originally developed for application to distantly diverged genetic sequences, the differences among which represent substitutions along independent evolutionary lineages. Nonetheless, the dN/dS statistics are also frequently applied to genetic sequences sampled from a single population, the differences among which represent transient polymorphisms, not substitutions. Here, we show that the behavior of the dN/dS statistic is very different in these two case

Obama indicates his clear support for science with Chu as Secretary of EnergyDecember 15 2008

Well, say what you will about Steve Chu, but the fact that Obama has nominated him to be the Secretary of Energy is only a good sign for science and society as far as I am concerned.

It is a good sign for science because it shows explicitly Obama's respect and support for science. Most recent Secretaries of Energy have been non scientists (the #s depends on whether you count an engineer as a scientist - I do - but some don't) and Bush (who I want to say is out previous president but we still have him for another month) does not believe in evidence in any way, let alone science.

It is a good sign for society because it is important for the president to understand and respect science. So - some may criticize Chu for some issues - but none of the criticisms I have seen really hit home with me. Sure, I would like a Biologist in their in the Cabinet, but Chu seems to actually understand that the biological diversity of the planet is under threat from global change and he wants to do something about it. I cannot really ask for much more from a Physicist/Administrator. For full disclosure - I have an Adjunct position at LAwrence Berkeley Lab where Chu just happens to be the Director. So maybe I am not completely objective, but anyway, I think this is a good day all around.

This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist an

Creative Commons- New Video and Fundraising CampaignDecember 13 2008

Everyone interested in Open Access and the open spread of information should check out the new video from the Creative Commons folks. This is being released as part of a fundraising campaign for Creative Commons and I recommend that people consider donating to this great organization. As a side note, the video was directed by Jesse Dylan, the director of the Emmy- award winning "Yes We Can" Barack Obama campaign video and features musical artist will.i.am from the Black Eyed Peas.

This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis..