Tag: Evolution

Amazing post-doc fellowship opportunity: Center for population biology at #UCDavis

No bias here — but this really is an incredible post doc opportunity in population biology here at U. C. Davis. See below:



EFFECTIVE: December 7, 2009
DEADLINE: January 20, 2010
POSTDOCTORAL FELLOW IN POPULATION BIOLOGY–The Center for Population Biology at UC Davis invites applications for a Postdoctoral Fellowship in Population Biology, broadly defined to include ecology, phylogenetics, comparative biology, population genetics, and evolution. We particularly encourage applications from candidates that have recently completed, or will soon complete, their PhD. The position is for TWO YEARS, subject to review after one year, and can begin as early as 1 July 2010. It has an annual salary of $38,000 plus benefits, and $6,000 per annum in research support. The Fellow will be a fully participating member in the Center for Population Biology and will be expected to have an independent research program that bridges the interests of two or more CPB research groups. We strongly encourage candidates to contact appropriate faculty sponsors before applying. We also ask that each Fellow teach a multi-day workshop, discussion or lecture series that is of broad interest to the community of population biologists at UC Davis; faculty sponsors or the Director of CPB, Jay Stachowicz, can provide additional input on this aspect of the fellowship. For samples of past workshop abstracts and more information about UC Davis programs in population biology, see http://cpb.ucdavis.edu/jobs.htm.
ONLINE APPLICATION: Interested candidates should submit a cover letter, CV, a short (1-2 page) description of research accomplishments, a short (1-2
page) description of proposed research including potential faculty mentors, a brief description of their proposed workshop/minicourse, and copies of two publications at http://www2.eve.ucdavis.edu/jobs/ all as PDFs. We require 3 letters of recommendation. The referees you list in the online application will receive an automatic notification from our system instructing them how to directly upload letters to our website. Refer to the on-line instructions for further information. For full consideration, applications should be received by January 20. 2010. The University of California is an affirmative action/equal opportunity employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences. E-mail questions to gradcoordinator@ucdavis.edu.
DEADLINE: January 20, 2010
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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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My favorite evolution stuff 2. Charles Darwin Tobacco Card




In honor of Charlie D. I am posting one of my favorite Darwin items.  I got this from Ebay years ago.  It is a Darwin card – about 3 x 5 cm.  From Ogden’s Cigarettes, much like baseball cards.


Also see my previous “Favorite Darwin thing” – a post card from 1900 or so. 
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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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Biologists rally to sequence ‘neglected’ microbes : Nature News

UPDATE: Our paper on this topic is out and there has been a bit of news here and there about it (e.g., NyTimes).  For more see

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Nice little story in Nature News about the need to sequence “neglected” microbes.

Biologists rally to sequence ‘neglected’ microbes : Nature News

Quotes me and a few others. Love the fact that it quotes Steven Giovannoni in support of this notion:

“The broad brush strokes of microbial diversity are not adequately represented in that first thousand,” says Stephen Giovannoni, a microbiologist at Oregon State University in Corvallis. “It’s absolutely important that we sequence more.”

I like this because Steve gave me enormous grief about this project at a conference last year. Though I argued with him and disagreed with him, his critiques helped guide much of our work on this project that helped make our paper on the work (which is in press) much better. Glad he generally is now in support of this type of project, though not sure what he thinks about our work in this area …

Here are some of my quotes:

“There’s no doubt to us that filling in the branches of the tree is going to be useful to lots of scientific studies that use genomic data,” says Eisen. “There have been four billion years of evolution and we can really benefit from having some of that information in our databases.”

All these new genomes should improve researchers’ understanding of the evolution, physiology and metabolic capacity of microbes, says Eisen. They will also help match DNA sequences to their proper species from large-scale, high-throughput metagenomic studies from environmental samples, and ultimately contribute in the fields of synthetic biology and genetic engineering.

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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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Adopt a GEBA genome program for education – from the DOE/JGI

The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “adopt” bacterial genomes, such as those sequenced as part of the “Genomic Encyclopedia of Bacteria and Archaea” (GEBA project), for analysis. This “Adopt a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.

For more information, and to apply for the November 2, 2009 deadline, see:
http://www.jgi.doe.gov/education/genomeannotation.html

For more on the GEBA project, which I am coordinating, see a video of a talk I gave about it at the JGI User meeting. Slides from that talk are on slideshare here.

Data fro the GEBA project is available at a dedicated IMG site here.

http://www.scivee.tv/flash/embedCast.swf

A much much much older talk, from when we just started the project is here:

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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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3rd Annual Western Evolutionary Biology Meeting 12/5/09 at Berkeley

The 3rd Annual Western Evolutionary Biology Meeting will be at UC Berkeley. This is a meeting of the UC Network for Experimental Research on Evolution (NERE), attendees from the UC campuses will be present, other evolutionary biologists, researchers, teachers and writers are encouraged to participate as well.

When: Sat. 5 December FREE registration – deadline, 29 October 2009 Submit Abstracts – deadline 16 October 2009 – or present a poster

Where: On the UCB Campus in VLSB, see website for details NOMINATE: Western Evolutionary Biologist of the Year by 9 Oct. 2009

See website for details. Open to Researchers, Teachers, Writers.
REGISTER at http://www.lifesci.ucsb.edu/nere-web/

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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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Got phylogeny?

For an obsessed evolutionary biologist, it is always good to see “Need phylogeny” on the blackboard while sitting through a faculty 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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New Web Resource on Evolution … EvolverZone

Looks like T. Ryan Gregory, who writes the GenoMicron blog has evolved … he has released a new web resource on evolution – Evolver Zone. Clearly still a work in progress, it has some good collections of links to videos, journals, books and other materials about evolution. Worth checking out.

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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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Francis Collins Launches Biologos – a strange re-working of theistic evolution

Biologos.  All I can say is, well, I am just really baffled by the whole thing. I am all for trying to have discussions about science and religion. But I do not think the two topics are really compatible in the sense of merging them together. Science (and medicine) should be about, well, science. And religion can be about whatever it wants to be. And when we can get religious and scientific leaders together to talk about the implications of each area on the other and on the world, fine too.  But merging the two together into one hybrid such as Christian Science and Creation Science?  Not for me.
Thus it is with some horror that I have been browsing the web site for Francis Collins’ new The BioLogos Mission | The BioLogos Foundation (f0r some other discussions of it see e.g., Larry Moran’s discussion here, and PZ Myers here and Time Magazine here and US News here). BioLogos appears to be Collins attempt to promote a slight variant of “theistic evolution” which he has been discussing for years and is also in his recent book.
And whatever you may think of theistic evolution, the Biologos version of it is just icky in many ways in my mind. For example, the site has many many links and pointers to books authored by the members of the Foundation (e.g., the front page says “Among other resources, this website posts responses to many of the questions received by Collins, Giberson, and Falk since the publication of their books, including: The Language of God; Saving Darwin; and Coming to Peace With Science.”) There are also other links to this page with ads for their books. Not that there is anything wrong with selling ones books, but to have a foundation whose purpose seems in a large part to promote one’s books really seems distasteful. 
And the details of Collins attempt to merge science and religion into a version of theistic evolution are really unclean.  Basically, he is trying to argue that on the one hand science and religion are completely separate activities (I support this) but at the same time argues that God can intervene in the setting up of natural laws and in providing some guidance here and there in order to, for example, produce human beings in his image.  
The web site repeats some things from Collins book that are equally illogical – such as saying that altruism can be explained by science (and even specifically saying that science is the way to explain the natural world) but then turning around and saying that science cannot explain extreme forms of altruism (and therefore implying that actually, the natural world cannot be explained by science).  Which is it?  Is science for the natural world or not?
What one wants to believe in terms of faith/religion is a highly personal issue.  But trying to both say that science and religion are completely separate but also that they are not is just completely illogical.  
UPDATE: See also:

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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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Should evolutionary biologists "debate" creationists/ID advocates?

Last week I received an email also sent to a group of other local evolutionary biologists asking if one of us would be willing to participate in a “debate” with a creationist who was coming in to town to give some sort of talk.  The email said, among other things:

… we have a creationist (who holds to the 6-literal day creation and young earth 6,000 year position), (name deleted), coming on our campus challenging someone to debate him. 

And, well, I ignored the email as did the others apparently.  Then we all got a second email a few days later:

Dear Professors, 

The Creationist side is offering $300 for accepting the challenge! And another $250,000 to anyone presenting any empirical evidence for macro evolution! 

Why has this offer been out there for years? Where are the experts??? Where is the evidence?? How is  this possible?

If you are convinced that Darwin was right, if you accept it, if you teach it to students, as a career, then WHY DO YOU REFUSE TO DEBATE?!

You betray the students that look up to you!! Come on, Creationist don’t bite!

Sorry for this sarcastic tone, but it doesn’t make sense. If you teach it in class you must be the first ones defending it.

We have a philosophy graduate wanting to debate, no science professors yet, especially Biology and Anthropology.

Please respond to this email asap!

Clearly, they people organizing this were trying to get someone to do the debate.  But this strategy just convinced me that debating creationists was an absurdly silly thing.  So I wrote back:

The issue is pretty simple to me.  There is nothing really to debate.  Creationism is not science.  It is a religion driven position that pretends (and does so poorly) to be about science.  I for one have perfectly pleasant interactions with many creationists and I understand their beliefs at least at some level.  But just as I would not encourage physicists to debate with those who deny gravity, and just as I would not encourage chemists to debate with those who claim the periodic table is invented, I think it is inappropriate to evolutionary biologists to “debate” with creationists in this type of setting.  Discussing creationism – fine.  Discussing criticism of evolutionary hypotheses – fine.  Having a reasonable panel discussion of science and religion – fine.  Meeting with creationists to discuss their ideas about evolution – ok too.  But engaging in a “debate” and thus even for a second implying that creationism stands on the same ground as evolution – completely ludicrous.  
Sincerely
Jonathan Eisen

Alas, the people doing the inviting were not particularly impressed with my answer:

You Sir, are a COWARD.
If it is so easy in your mind to refute Creationist’s arguments, why don’t you do it publically? FOR MONEY?! 
Your words do nothing to change the standing offer of $250,000 for evidence of Macro-Evolution. How about Actions, not Words only?

By denying there is a challenge, and at the same time refusing to accept the challenge you tell us that you’re unable to defend your position.
We know why you are fine with a panel discussion: because there is no Looser or Winner, you are afraid to loose, that is the real reason behind your rhetoric.

your answer is a nonanswer

Try again.

I guess they did not get my point.  But anyway – I am asking readers out there – what do you think one should do?  Should one debate creationists/ID supporters?  

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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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