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

Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria

Was browsing Twitter and I saw one post that caught my eye. @MicrobeWorld, which by the way, rocks, wrote

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water http://bitly.com/15l9mR

This caught my eye because, well, I study radiation resistance some of the time and the “old as dirt” statement seemed weird.

The article being referred to was in the Columbus Dispatch (The Columbus Dispatch : Tricking toxins) and it was about some interesting work on Shewanella by Brian Lower and others from Ohio State. The work involves using one particular species of Shewanella for bioremediation of radiative waste. The problem however is in the lead in to the article. This is painful to me. It says

A microbe that is as old as dirt could one day help keep radioactive metals out of our drinking water.

Shewanella oneidensis bacteria have existed for billions of years, thriving even when the Earth’s atmosphere lacked oxygen.

This is just so so so wrong. Shewanella oneidensis is one species of a large group in the genus Shewanella which itself is part of one subgroup (the gamma group) of the Phylum Proteobacteria (I note I helped analyze the genome sequence of this species a few years ago – see paper here). While it is possible (though not certain) that the Phylum Proteobacteria was established billions of years ago, it is certain that Shewanella oneidensis did not exist at that time. Perhaps this species has been around for tens of millions of years but certainly not billions. This would be like saying “Humans have been around for hundreds of millions of years” simply because animals have been around for that long. In the context of humans the statement is clearly absurd. It is in fact equally absurd in the context of bacteria. And for this, the Columbus Dispatch is getting my third Twisted Tree of Life Award.

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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 Science Stimulus Spam

Updated —

Getting even more Science Stimulus Spam from a company called Metabolon. I have gone back and forth about whether to post text of such messages. Originally I posted the full text here.. After the comment from Cariaso I have decided to remove some of the text but to leave some to giver the gist of the spam.

“Research using metabolomics, the global profiling of biochemicals, was a common topic in the recent NIH Challenge Grant request. Metabolon, the leading provider of metabolomics services, is supporting many of these grant submissions by providing free quotes and a description of services and deliverables.”

“Please visit” XXXX (deleting their link) “to submit a brief overview of your study and Metabolon will provide a free quote for services which can be included in your proposal.”

Metabolon self promotional text here.

More self promotional text here.

“Please visit” XXX “to submit your study now.”

“We look forward to working with you.

The Metabolon Team”

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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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A Postdoctoral research position in Antarctic Metagenomics and Microbial Ecology

Here is an ad for a post doc that is to work on a joint project between my lab and that of Craig Cary.

POST-DOC ANNOUNCEMENT

A Postdoctoral research position in Antarctic Metagenomics and Microbial Ecology

A Royal Society Marsden Funded project “Life at the extreme: resolving the genetic basis of microbial endemism in the super-heated soils of Mt. Erebus, Antarctica” is available at the University of Waikato, Hamilton, New Zealand.

Project description

Tramway Ridge geothermal site on Mt. Erebus, an active volcano in Antarctica, is the most geographically isolated geothermal site on earth providing an excellent system for studies of microbial speciation, biogeography, and evolution of thermal adaptation. A recent preliminary genetic survey of the Tramway Ridge microflora revealed an unprecedented diversity of extremely novel microbes only distantly related to any known bacteria [Soo et al., (2009). Environ. Microbiol. 11 (3), 715-728]. Most of these loose affiliations are with organisms identified from deep-subsurface systems suggesting the Tramway Ridge community may be archaic and of a sub-surface origin. A group dominates the community that to date has no known cultured or environmental representative. The successful candidate will employ cutting-edge high throughput DNA sequencing and bioinformatics to acquire and decipher the genetic capabilities and structure of entire microbial community at Tramway Ridge. A combination of these advanced genetic methods coupled with culture dependant approaches will be used to analyse the Tramway Ridge microflora and other Antarctic geothermal sites to address questions focused on endemism, biogeography, evolution, and adaptation.

The project is in collaboration with Dr. Jonathan Eisen, U.C. Davis Genome Center.

Required qualifications

We are looking for a highly motivated postdoctoral scientist with and interest in Antarctic microbiology and experience in metagenomics, microbial ecology, cultivation of microorganisms, and bioinformatics. The successful candidate will drive his/her own project within the context of the project and be actively involved with practical guidance of an MSc student. The University is especially interested in candidates who can contribute to the diversity and excellence of the academic community through research and service.

The position is full time with a salary of NZ$ $56,164 to $68,060 depending on experience. The initial appointment is for 1-year on this multiyear project; continuation beyond will be based on performance. Applicants should submit a CV, a statement of research interests, and the names of three referees to caryc@udel.edu or caryc@waikato.ac.nz. The position is available immediately and will remain open until filled.

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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 Stimulus Spam II – Double Yuck

And another science stimulus spam, this one from Perkin Elmer

PerkinElmer self promotional statement deleted to not help them distribute it.

“As you know, the American Recovery & Reinvestment Act of 2009 (ARRA) is providing large opportunities for grant funding through the NIH.

NIH Challenge Grants in Health and Science Research (RC1)
Recovery Act Limited Competition: High-End Instrumentation Grant Program (S10)
Recovery Act Limited Competition: Biomedical Research Core Centers to Enhance Research Resources (P30)
View More NIH Grant Funding Opportunities
PerkinElmer is here to assist you. “

More self promotional text deleted.

More yuck.

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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 Stimulus Spam – Yuck

Just got this email from Sequenom

“NIH Challenge Grants

As part of the American Recovery and Reinvestment Act of 2009, the NIH invites Challenge Grant (RC1) applications from domestic institutions/organizations proposing research on Challenge Topics that address specific scientific and health research challenges in biomedical and behaviorial research that will benefit from significant two-year jumpstart funds.

Challenge Areas, defined by the NIH, focus on specific knowlege gaps, scientific opportunities, new technologies, data generation, or research methods that would benefit from an influx of funds to quickly advance the area in significant ways. The research in these areas should have a high impact in biomedical, behavioral science and/or public health.

We are here for you!”

Sequenom self promotional text here deleted to not aid them in distribution.

I mean, Sequenom might do some cool things but yuck. SSS. Science stimulus spam.

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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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Congrats to Phil Bourne who beat out me and some others to win the Ben Franklin Award.

Congrats to Phil Bourne for winning the “Ben Franklin Award.” (Bio-IT World) I was honored to be one of the nominees, but if I had had a vote, I would have voted for him. He has been relentless as an Open Access advocate as well as as a bioinformatician.

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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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Yet Another Reason Davis Should Be Selected for the Bicycling Hall of Fame

Davis is just an incredible bike town.  There is good reason it is one of two finalists for being the host city of the Bicycling Hall of Fame.  And here is one example of why it should win — the bike paths and bike lanes around town make this city great for commuting on ones bike.  Here are some pictures I took yesterday of my favorite bike ride to work.  It is a little bit out of the way but it is worth it.  About 7 or so miles total each way and it only has ~ 4 road crossings and one short stretch of a few hundred yards on a bike lane – and the rest is on off road bike paths.  

http://picasaweb.google.com/s/c/bin/slideshow.swf

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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 Evolution Particle?

The New York Times is reporting that the Large Hadron Collider was not actually shut down over the winter but was actually apparently looking into the possibility that a new particle is particularly mutagenic.   It seems that when they fired up the accelerator, they found that some particles with unusual affinity for DNA were created.  So, no black hole but particles that could shape evolution.  Seems like the ID people will be all over this one — maybe this is the guiding hand they have been looking for?

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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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HHMI early career scientists

HHMI has announced a new list of anointed ones (HHMI News: HHMI Gives 50 Early Career Scientists a Jump on Their Next Big Idea).

A few comments.

First, it is really really surprising that they are so low on females here (41 men, 9 women by my count). Given that this is for early career scientists and that women have on average sometime more challenges in the early career than men, it would have been nice to see this the other way around.

That being said, they did pick some good people in this list (shocking, I know). Here are a few I want to highlight as they are related to things I tend to write about here:

Rob Knight, at U. Colorado at Boulder who has been developing computational methods to study microbial diversity and has developed lots of cool methods.
Harmit Malik, FHCRC, who does some great stuff on genome evolution.
Michael Laub, MIT who works on Caulobacter development.
Martin Cohn, U. Florida who has done some very cool work on evolution of development in vertebrates.
Neil Hunter UC Davis. UCD’s first HHMI awardee. And a good one to pick. He does some cool work on recombination.
Molly Przeworski, U. Chicago, who works on population genetics on a genome-wide scale.
Aviv Regev, Broad Institute, who has done some interesting work on regulatory networks.

I love the idea of finding people not projects. Too bad there is not more of this type of thing from Federal Agencies. We would probably save money in the long run — review people once every few years and give them some money to do work. Not that competitive grant programs should be eliminated, but funding people more would reduce the # of grant proposals and panels and would probably save $$ in the long run by allowing people to focus on doing work.

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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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Sean Eddy in PLoS Biology on Open Revolution

Interesting article by Sean Eddy on “Open Education” in PLoS Biology on March 24. (see PLoS Biology – Open Revolution). The article is (mostly) a review of “Opening Up Education” a book from MIT Press.

For those not in the now, Sean is a big supporter and proponent of Open Science and is now at the HHMI’s Janelia Farm Campus. In addition to developing some smashing software and doing cool science, Sean was instrumental in my conversion to supporting Open Science so I pay attention to what he says. And there is some interesting material in this pub. The ending sums up a lot of what is in there:

More attention must be paid to the fact that someone still needs to spend time painstakingly developing artful ways to make difficult concepts understandable—to teach!—and that it will take even more time (thus money) to render these hard-won ideas using multimedia web technology compared with writing textbooks. Success hinges on the adoption of open licensing by the professionals who make digital educational resources, and on finding ways to finance their work.

Basically, Sean is saying the Open Education is great in concept but that many Open Education resources need work for them to be effective. And that work can take a lot of money. So we need to find ways to get more money into the development of Open Education materials.

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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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