Overselling genomics award #6: Quake/Helicos & the "democratization" of sequencing

For those interested in so-called "third generation" DNA sequencing systems, this week has had some buzz with the release of a publication in Nature Biotechnology reporting the sequencing and analysis of a human genome using a Helicos Heliscope sequencer. In this paper Stephen Quake and colleagues generated short read sequences from Quake's DNA using this machine and then analyzed them by comparing them to reference human genomes.

Certainly, what they did was cool. And the use of the Helicos equipment is a good thing for that company and it's development of single molecule sequencing. And given the "race" if you want to call it that for the $1000 genome, it is thus not surprising that this paper received a lot of coverage from all sorts of angles because they claim it involved the cheapest sequencing of a human genome yet achieved.

So first I want to commend Quake and Helicos for an important step in third generation sequencing. Quake mind you is one guy who is constantly inventing cool new techniques of great use in genomics and biology and he is always worth checking out.

But in this case, there are some aspects of what they claim they achieved here that are very off putting. In particular, I am concerned with the supposed "democratization of sequencing" that they think this project embodies (e.g., see some of the quotes in this). The basis for their concluding that democratization has happened here is that they believe this sequencing (of Quake's genome) was done at lower cost and with less effort than previous human genome sequencing efforts. To back this up they make a table (Supplemental Table 1) detailing estimates of these values for 8 human genome papers (the original Lander et al and Venter et al ones, as well as Watson's genome, etc) that is meant to represent some of this information).

In essence Quake et al are doing the following math (my formula, not theirs, but their discussions imply basically this)

D = B/(E*C)
Democratization factor (D) = # of bases sequenced (B) / (amount of effort (E) * cost (C))

That is, with more sequence, less effort, or less cost, the more democratized sequencing is. Sounds fine in some ways. Except when you look at the details.

For example consider the cost (C) of the sequencing. They report that the cost for the sequencing was < $50,000. But this number is misleading since, for example, they do not include any aspect of the cost of actually buying and setting up the machine. For more detail on the flaws in the cost calculation and for more detail on the whole story see Times Online and Dan Macarthur at Genetic Future and GenomeWeb).

However, more disconcerting to me is what they do with the rest of the implied calculation.

For example, they treat all the projects in essence as though they are equal in terms of total number of bases sequenced (B) because I guess after all, all were sequencing human genomes. But this is not fair since the depth of sequencing and the quality of sequencing varies between the projects and more recent projects, such as theirs, make use of the data from prior projects, which allows them to gather less data (e.g., in their paper here they assemble the genome by tiling the reads against reference genomes, thus allowing them to do lower coverage than would be required for denovo assemblies of genomes).

But even worse - the way they calculate effort required (E) is flabbergasting.

They seem to infer this in two ways. First, they make use of the number of runs of the machine that are required. They apparently used four runs while they claim that the use of second generation sequencing methods required many more runs. And many have been questioning this claim (e.g., see Chad Nusbaum's quotes in the GenomeWeb article).

It is the second way that they infer effort that is perhaps the most annoying. They infer this from number of authors on the papers describing the sequencing of these human genomes (e.g., In Supplemental Table 1 they say "number of authors" is "an estimate of labor.") And the big thing for Quake et al is that there are only three authors on their paper and dozens to hundreds on other human genome papers. Based on this lower number of authors they conclude that their work required less effort and discuss this as evidence for further democratization of sequencing.

Now suppose we gloss over that there is no way to infer amount of effort by number of authors (e.g., letters to the editor, which usually do not require a lot of effort, can sometimes have hundreds of authors while Origin of Species had but one author and was, shall we say, a lot of work). Even worse to me is that they are trying to compare their paper which is focused almost entirely on the technical aspects of the sequencing with other papers that spend much more effort on studying and discussing what the genomes might mean. For example the Venter/Celera and the public human genome papers are complex detailed volumes with analysis of everything you could think of. To compare the effort required to do this with the effort required to do what they did in the Quake paper which was pretty much assembly and analysis of SNPs is inappropriate and actually offensive.

Given the number of areas that they have oversold how their project has reduced effort and cost for sequencing a human genome and how this implies democratization, I am giving Quake and Helicos my coveted "Overselling genomics award". Again, not that what they did was not cool or interesting, but by overselling it, it detracts from everything they achieved.

New York Times Book Review Use of a "Tree of Life"

Funny use of a "Tree of Life" in the New York Times book review section from a few months ago (The New York Times:Natural Selections)

In this, they overlay onto a somewhat strange Tree of Life, the images used for various book publishers and what types of organisms they use. They say that this represents a fair amount of biodiversity, but really only because they draw the tree in a skewed manner. Basically, there are animals and plants in the logos and the way they draw the tree makes this look like it is a lot of biodiversity ... but really it is a small component compared to the whole tree of life. I also like that they put robots on the insect branch and they have mythology as a VERY deep branch in the tree.

New Open Access journal: ‘‘J. of Computational Biology and Bioinformatics Research‘‘

NOTE - NOT A FULLY OPEN ACCESS JOURNAL - COPYRIGHT MUST BE SIGNED OVER TO THE JOURNAL - THOUGH THEY DO USE A CC LICENSE

Journal of Computational Biology and Bioinformatics Research
www.academicjournals.org/JCBBR

Dear Colleague,

The Journal of Computational Biology and Bioinformatics Research (JCBBR)
is a multidisciplinary peer-reviewed journal published monthly by Academic
Journals (www.academicjournals.org/JCBBR). JCBBR is dedicated to
increasing the depth of research across all areas of this subject.

Editors and reviewers

JCBBR is seeking qualified researchers to join its editorial team as
editors, subeditors or reviewers. Kindly send your resume to
jcbbr.journal@gmail.com.

Call for Papers

JCBBR welcomes the submission of manuscripts that meet the general
criteria of significance and scientific excellence in this subject area,
and will publish:

• Original articles in basic and applied research
• Case studies
• Critical reviews, surveys, opinions, commentaries and essays

We invite you to submit your manuscript(s) to jcbbr.journal@gmail.com for
publication in the Maiden Issue (October 2009). Our objective is to inform
authors of the decision on their manuscript(s) within four weeks of
submission. Following acceptance, a paper will normally be published in
the next issue. Instruction for authors and other details are available on
our website; http://www.academicjournals.org/JCBBR/Instruction.htm

JCBBR is an Open Access Journal

One key request of researchers across the world is unrestricted access to
research publications. Open access gives a worldwide audience larger than
that of any subscription-based journal ad thus increases the visibility
and impact of published work. It also enhances indexing, retrieval power
and eliminates the need for permissions to reproduce and distribute
content. JCBBR is fully committed to the Open Access Initiative and will
provide free access to all articles as soon as they are published.

Best regards,

Oyo Excel
Editorial Assistant
Journal of Computational Biology and Bioinformatics Research(JCBBR)
E-mail: jcbbr.journal@gmail.com
www.academicjournals.org/JCBBR

Wanted - Bioinformatics Enginner to work on Metagenomics

A bioinformatics engineer position is available on a microbial metagenomics project called iSEEM (http://openwetware.org/wiki/ISEEM) under the direction of

Jonathan A. Eisen (UC Davis) http://128.120.136.15/mediawiki/index.php/Main_Page

Jessica L. Green (U Oregon) http://biology.uoregon.edu/people/green/

Katherine S. Pollard (Gladstone Institutes at UC San Francisco) http://docpollard.com

The engineer will work in an interdisciplinary research group of evolutionary biologists, ecologists, and statisticians. Applicants should have substantial experience with genome-scale bioinformatics, including comparative genomics, analysis of protein families, multiple sequence alignment, and phylogenetic analyses. Familiarity with SQL, Perl/Python, and standard bioinformatics tools are essential. Typical responsibilities for this position may include designing and managing an in-house MySQL database of metagenomic sequence data; running BLAST, HMMER, and AMPHORA on the Global Ocean Survey and other large metagenomic data sets; identifying OTUs (operational taxanomic units) based on 16S rRNA or proteins; writing Perl scripts to query databases, process data, or run simulations; distributing data, scripts, and information to project members on all three campuses. Strong project management skills are essential.

We will offer a generous salary and benefits commensurate with experience. The position is available immediately, and the initial appointment will be for one year. The engineer would ideally be located at UC Davis, although other arrangements will be considered.

TO APPLY: Applications should be submitted at

http://jobs.genomecenter.ucdavis.edu/start_app.php?job_id=78

and consist of (1) a cover letter describing your interest in the position, (2) the names and contact information for three references, (3) a curriculum vita (including publications). Applications will be reviewed upon receipt, until the position is filled.

A passionate call for a new war on cancer by James Watson

Sure, James Watson has been known, especially recently, to say some outrageous things. But here is something I think everyone, scientists and the public should read - an opinoin piece in the NY Times today by Watson ( Op-Ed Contributor - To Fight Cancer, Know the Enemy - NYTimes.com)

This piece is worth reading because it contains some critical ideas and wisdom which has been missing in discussions of the fight against cancer.

First, Watson discusses the critical importance of basic science and says that when he expressed this importance to the National Cancer Institute advisory board many years ago, he was eventually booted off.

Second, he discusses how we have only recently begun to understand the basic biology of cancer (he also mentions how the human genome project has helped in this). The genome project will, he says, allow for the determination of most/all of the major genetic changes that occur in cancer cells.

Third, he discusses some limitations of the FDA drug approval process that limit the ability to test combinations of drugs which Watson believes will be needed in the fight against cancer.

Fourth he suggests that the National Cancer Institute should help support small biotech companies in the development of new drugs since venture capital has dried up for such endeavors.

As usual, Watson would not be Watson if he did not say something potentially controversial. In this, the most controversial thing is probably how he discusses that the National Cancer Institute has become a "a largely rudderless ship in dire need of a bold captain who will settle only for total victory. " Now, I do not have any opinion about this since I have not followed NCI or its leadership. But it is certainly worth considering Watson's opinion here.

In the end, Watson says the time is now to reinvigorate the "War on Cancer." Despite misgivings about many things he has been up to recently, I found myself agreeing with almost everything he said in this piece. Again, definitely worth a read.

PLoS Medicine and NY Times open up can of worms regarding ghostwriting

Absolutely terrifying and intriguing story in the New York Times yesterday (Ghostwriters Paid by Wyeth Aided Its Drugs )

In the article Natasha Singer reports on how Wyeth commissioned the writing by a communication firm of a series of "draft" articles that were then published under the names of various medical professionals. It seems from the article that in some if not many cases the articles were in essence written by this company and then names of authors were placed on the papers which were then submitted to various journals and were published (they were generally review papers, and shockingly supported the use of Wyeth manufactured products).

The issues here are as always complex. But in the end, the articles did not disclose the role Wyeth played in paying for the writing of drafts and/or nearly complete forms of the papers and certainly should have. For more detail, read the Times article.

Interestingly, the documents that helped uncover the full details of the practice were obtained after a "a request in court from PLoS Medicine, a medical journal from the Public Library of Science, and The New York Times." For more detail on this see the PLoS Medicine blog here. Kudos to PLoS Medicine for getting involved in this and for pushing hard for more disclosure in medical publishing.

All I can say is the practice of ghostwriting medical and scientific articles should stop. Getting help with editing a paper is one thing. But putting your name on a paper conceived of and written by someone else is unacceptable.

Quick Post: Some free online children's books with sciency/dental themes at MelTells.Com

Just got pointed to this site by the author ... MelTells.Com has some online books for kids some of which have a sciency theme to them. All of them seem to have some dental connection, though not all in the same way. I have only looked at the bacteria one and it is not bad. Even though I have not looked at the others, since they are free, I am posting this bit here.

Also see review on ByteSizeBiology here

Can't get much worse than this: soaking my shorts before my 1st conference talk. Other bad experiences?

Well, I was talking with some people recently about someone who had a bad experience giving their first talk at a scientific conference. And so I said - you think that is bad - how about this? And I told them the story below. But before telling the story I am asking here for others to post comments about the worst thing that has happened to you during a talk at a scientific conference/meeting. Please fire away.

OK - so my talk. It was 1995. The SSE (Society of the Study of Evolution) meeting was in Montreal. And somehow I was going. I am not sure anymore how I ended up registering for the meeting. I do remember other evo-grad students who were or had been at Stanford like David Pollock, Joanna Mountain, maybe David Goldstein, maybe Sally Otto, Sarah Cohen, and a few others were going. And so I registered, got accepted to give a talk on the "Evolution of RecA" and made plane reservations to get to Montreal.

I arrived the night before my talk, found my dorm room on the McGill campus, and then went wandering around town for the Jazz Festival which was going on that night. After staying out pretty late, I got back to my room and had a bit of a panic attack when I looked at the schedule and found that the session in which I was talking started at 8:30 in the morning the next day and I did not have an alarm clock, nor was there one in my room. (I note, fortunately I was using real slides and could not spend the night modifying my talk in the way I do now with Keynote/PPT). Anyway - I pretty much knew I would sleep late without some work and so I made some notes with my room # and a plea to others to bang on my door if they could by 6:30 or 7 AM and I slipped these under the other doors in the hall. Fortunately in some ways, I barely slept b/c I was so scared of missing my first talk.

So at 6:30 AM or so I headed out to the conference area. I think I got some coffee and then headed to the room where my talk was to be. Nobody was even there so I wandered around for a bit and came back and the projectionist was there getting the room set up. When I said I was one of the speakers - he said "Are you planning on doing any side by side slides where you need two projectors?" Well, I had not thought of doing this, but now that he mentioned it, it sounded perfect b/c the main point of my talk was that the phylogenetic trees of RecA and rRNA were very similar to each other (see my 1995 J. Mol. Evol. paper on the topic here), supporting earlier suggestions by Lloyd and Sharp that RecA was a potentially useful phylogenetic marker. So I said "sure" and proceeded to load up two slide carousels for my talk. We checked them out and all looked good.

As the room started to fill up (I recall there were a lot of people interested in the "Molecular Evolution" session I was in) I decided to go grab a seat (in the far back on an aisle - I was a lurker even before blogging from meetings) and try to relax. I think I was the fourth talk and while speaker #3 (Michael Purugganan) was getting started I got nervous about the side by side slides so I went over to ask the projectionist if all was OK and he said it was. Alas, someone had grabbed my seat when I was up. I saw a table in the back back of the room with some misc. fliers on it so I went there to sit down for a few minutes and try to relax. And here was the trouble.

The table was also being used to hold some pitchers of water for people. And alas, someone had just spilled an entire pitcher of water on the table and I did not notice. I sat in the puddle. And there I was, in my tan shorts, now dripping wet. Minutes before my first talk. Looking like I had gotten a bit too nervous. Underwear showing through. As I desperately looked around to borrow a sweatshirt from someone to tie around my waist, the chair said "And our next speaker is Jonathan Eisen ...". Holy Crap. I was on.

So I went up there and I had thought to myself to crack a joke about just getting in from a swim. Or something. But as I still do, I entered another zone for my talk and forget everything but the talk. And so - there I was - dripping wet in my see through shorts - turning around and pointing to the screen talking about RecA as though all was fine.

Only when I was done with the talk did I re-remember that I was basically doing a "wet-shorts" contest for all in the audience. Yay. I can say truthfully that when I start to worry about things going wrong in talks, I remember this one and say "well, it could be worse ..."

Fwd: Sign-up now for Microbial Genomics & Metagenomics workshop September 14-18, 2009

Begin forwarded message:

Subject: Sign-up now for Microbial Genomics & Metagenomics workshop September 14-18, 2009

The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics September 14-18, 2009 in Walnut Creek, California. The workshop will include two days of intensive seminars and three days of hands-on tutorials. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research.

For more information, see:
http://www.jgi.doe.gov/meetings/mgm/index.html

Another scam pretending to be from Elsevier

Yet another scam pretending to be from elsevier

From: elsevier issues <elsjissues6@googlemail.com>
Date: July 23, 2009 5:28:22 AM PDT
To: undisclosed-recipients:;
Subject: Elsevier Scholarships

ELSEVIER JOURNALS - EUROPEAN CENTRAL BANK

European Central Bank- Elsevier Journals Initiative.

The European Central bank in collaboration with Elsevier Journals is seeking applications from students/ researchers for 10 European- Elsevier Scholarships in 2009.

The Scholarship programme was launched in 2003. It aims to promote high quality research on the structure, integration and performance of the European financial system. Each fellowship is endowed with a honorarium of €16,000 [Sixteen thousand Euros] which would be received by 10 students/ researchers on Merit.

To be amongst the fellows who can receive this honorarium:

· Send a research paper on your Major.

o The submitted paper will go through a screening process by our group of reviewers in your field. Manuscripts should be submitted in English and include a cover letter, and a comprehensive Resume.

Prospective authors should send their manuscript(s) in Microsoft Word or PDF format to elseviereuro@live.com and should Include a cover sheet containing corresponding Author(s) name, Paper Title, affiliation, phone, fax number, email address etc.

Kind Regards,

Gerald Rockfield.

Asst. Commercial Manager,

Elsevier- Eurobank Initiative,

United Kingdom.

Why endosymbionts rule - see #PLoS Genetics paper on origin of an alternative genetic code

Way way way cool new paper in PLoS Genetics from Nancy Moran's lab. The paper (Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont). The paper discusses the use of genome sequencing and proteomics (as well as a variety of bioinformatic analyses) of a bacterial symbiont (Hodgkinia) of cicadas.

And for those not in the know, this is an Open Access paper using a broad Creative Commons license (since it is in a PLoS journal) so anyone can reuse material from it as long as the source is cited. This image to the left is from their paper so I am citing the source here: McCutcheon JP, McDonald BR, Moran NA (2009) Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont. PLoS Genet 5(7): e1000565. doi:10.1371/journal.pgen.1000565

The study has some interesting things including:

• the genome of the symbiont has a much higher GC content than other small bacterial genomes for which the sequence is available
• the symbiont is member of the alpha proteobacterial group, which is somewhat unusual since most other insect endosymbionts that have been studied are from the gamma proteobacterial group and/or the bacteroidetes clade
• the UGA codon in this species is used to encode tryptophan and not as a stop codon

Taken together these things are very interesting since other species that have been found to have the UGA codon reassigned to code for an amino acid all have low genomic GC content. This correlation led people to conclude that the codon reassignment was directly related to the low GC content. However, the authors suggest here that the UGA reassignment in many species might be due to the genome reduction (loss of genes) seen in endosymbionts and not to low GC content.

Anyway the paper is worth a read ...


McCutcheon, J., McDonald, B., & Moran, N. (2009). Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont PLoS Genetics, 5 (7) DOI: 10.1371/journal.pgen.1000565

Ego Blogging of the Month: Thanks @SciAm for following selecting me as one of your "recommended" folks you follow on twitter

Another ego blog here. I am very honored that Scientific American listed me as one of the folks they follow on twitter (see Recommended: Science Folks We Follow on Twitter: Scientific American).

The tweeterers they list are:

• carlzimmer, science writer Carl Zimmer
• phylogenomics, evolutionary biologist Jonathan Eisen of the University of California, Davis
• seanmcarroll, theoretical physicist Sean Carroll of the California Institute of Technology
• RebeccaSkloot, science writer Rebecca Skloot
• Astro_Mike, NASA astronaut Mike Massimino
• BadAstronomer, astronomer and writer Phil Plait

Of course, I agree with them about me. I do follow Zimmer and Skloot already and will check out the others.

If you know nothing about twitter, I recommend checking it out. I think it has enormous potential as a tool in science communication (e.g., see this Bioscience article on science and twitter)

Worst new omics word award: diseasome (thx @steinsky @noahwilliamgray @mocost )

And the winner of the "worst new omics word award" is "diseasome."

Credit for pointing this one out goes to Noah Gray and MoCost on Twitter. See Mos first post here: Twitter / Mo: Diseasome project visualiz ...

And some follow up:

• Noah
• Joe Dunky
• Noah again

Amazingly, I missed this when the New York Times used it in a headline: "Mapping the Human 'Diseasome' - Interactive Graphic - NYTimes.com" and in many other reports (see Google search here).

What does diseasome actually mean? I do not know. And it does seem really unnecessary to me. And since I got blasted (justifiably) a bit by one of the people I gave my previous award to here is a clarification. I am not commenting here on the science behind the "diseasome" work. Just the word. And the word, I do not like.

Previous awards I have given:

• Worst New Omics Word Award: Museomics
• Worst new omics word award: ethomics

On Friendfeed:

Deep subseafloor microbiology talk at #UCDavis raises questions about the definition of life

Wildly interesting talk here at Davis yesterday by Bo Barker Jorgensen Prof. Dr. Bo Barker Jørgensen

He talked about deep subseafloor microbiology and how many/most of the microbes there grow VERY VERY slowly or not at all.

His talk was part of a series here on "Major Issues in Modern Biology Seminar Series" funded by the Tracy and Ruth Storer Lectureship in the Life Sciences endowment

He did a great job of presenting the evidence for and possibly against whether these organisms that live in the deep subseafloor are alive and whether or not they grow really slowly (with doubling times of hundreds of years). He refers to these organisms as the "starving majority" because their main challenge appears to be getting energy.

The way they do much of their work is to take cores (from ships) of the deep subseafloor and to then characterize the microbes in the cores. They have found, for example, high #s of microbes (mostly bacteria and archaea) as far as 1000m down in the cores.

Among the things he discussed were

• Paper by Whitman on estimating the number of prokaryotes (his word, not mine) in different places on the planet. This paper suggested most of the prokaryotes are in the subsurface (terrestrial and seafloor)
• Paper by him in Science reviewing the starving majority.
• Paper by Biddle et al on rRNA surveys of sedimentary subsurface that suggested that most of the microbes were archaea
• Paper by Schippers et al (on which Jorgensen is the sr. author) that used qPCR and suggested that most of the microbes were bacteria
  
• Paper by Biddle et al on metagenomics of subsurface microbes
  
• Paper by Lipp et al in 2008 that looked at membrane lipids to estimate the amount of cellular carbon in the deep subsurface.
  
• Various papers that suggest that radioactivity could be the indirect energy source fo these communities (note they are not proposing these are radiation-utilizaing microbes but rather that radiation can lead to the production of H2 which in turn is an energy source).
• Various papers that suggest that the archaea found in these environments are phylgoenetically very novel
• He did not mention it but he was a cuauthor on a cool PLOS Biology paper on giant bacteria.
  
• At the dinner he discussed briefly one of my favorite topics - nano wires and mentioned one of my favorite scientists - Yury Gorby who is studying these nanowires. Nanowires appear to be mechanisms by which microbes can move electrons around and scanege for electrons
  

Anyway - the talk gave me lots to think about in terms of slowly growing organisms and how to determine if something was living or not.

Strong Letter of Support for Katehi from group of UC Davis faculty

There was a strong letter of support for UC Davis' incoming chancellor Linda Katehi published in the Davis Enterprise yesterday. Alas, the enterprise is not available free online so unless you have a subscription you may not be able to read the whole thing. The letter is written by some big shot faculty on campus:

J. Clark Lagarias, professor of cellular and molecular biology
Walter S. Leal, professor and former chair of the department of entomology
Alan Hastings, professor of environmental science and policy
James R. Carey, professor of entomology
Judith S. Stern, professor of nutrition and internal medicine
Robert Rucker, emeritus professor of nutrition
Tilahun Yilma, professor of pathology, microbiology and immunology
Gabrielle Nevitt, professor of neurobiology, physiology and behavior
Chris Calvert, professor of animal science
Carl Keen, professor of nutrition and internal medicine
Charles H. Langley, professor of genetics
Bruce D. Hammock, distinguished professor of entomology

And in it they say "Katehi’s selection and appointment electrified us"

I agree.

And they also discuss the overblown reports that she may have been involved in some impropriety in admission of students at U. Illinois. I have already written about this here and I agree too. Now I am not saying the news should not report on these stories but I do wish the reports were clearer about how little evidence there is that she did anything untoward. In contrast, there is abundant evidence that she has enormous potential to help out UC Davis in trying times. So I too would like to welcome Katehi as they do.

Help request - how does one block some DNA from being PCR amplified?

Dear world:

We need help.  

We would like to use PCR amplification of rRNA genes to characterize rare bacteria in a sample where there are some very very dominant bacteria.  

The problem is that we do not know what those rare bacteria are and would like to use "universal" rRNA PCR primers to amplify the rRNA genes from these organisms. Such universal primers will also amplify the rRNA genes from the dominant organisms.  

If the rare organisms are, like, really rare, almost all the PCR products will be from the dominant organisms.  We would like to obtain sequence data for the rRNA genes from the rare organisms without sequencing 1000s of the known rRNA genes from the dominant organism.  How can we do this?  

I know of attempts to block PCR amplification of specific DNAs and also attempts to digest away PCR products or bind ones to a column to get rid of them.  But I do not know if any of these methods really work.  

Anyone out there know methods that work to do this?

Added - here are the responses on FriendFeed

The White House - Press Office - President Obama Announces Intent to Nominate Francis Collins as NIH Director

The White House - Press Office - President Obama Announces Intent to Nominate Francis Collins as NIH Director

Not much else to say here. Collins is being nominated to run NIH. I personally think Collins will be perfectly capable of running NIH. I have mixed fellings however about whether he is the best pick for the job. What do others think?

Much ado about nothing - sniffing around for scandal with new UC Davis chancellor and not finding any

Well, it seems that despite the attempts of California State Senator Leland Yee nobody has found anything of any interest in the background of the incoming chancellor of UC Davis Linda Katehi. The worst that has been dug up so far is an email that she forwarded while provost at U. Illinois that could be interpreted as applying subtle pressure to get a child of a well connected person admitted to the school (see New UC Davis leader denies wrongdoing in inquiries about student in previous job - Sacramento News - Local and Breaking Sacramento News | Sacramento Bee). I guess we will just have to wait and see but I personally really hate corruption and abuse of power and would not want anyone to be the UCD chancellor if they seemed to be part of something untoward. But so far, all I can see if Sen. Yee trying to get publicity for himself by throwing mud and really very little if any of the mud seems to stick. This crusade of his is starting to sound like some of the right wing "holier than thou" crusades of recent times. A bit to vocal when nothing much seems to be there

The end of Science? (Or, the danger of having a video camera at the beach with my brother)

Really sick of Bentham Open Spam

Once again, I am getting sick of getting email after email from various Bentham Open Journals like the one below.  This is basically a form of SPAM as they send these out to people no matter what the connection is to the journals field.  I like how they now emphasize that "Please note that submission of a manuscript is not a guarantee for acceptance for publication"

This likely has something to do with the recent controversy over a Bentham Open journal accepting a nonsense paper .

Just goes to show you that just as their are annoying commercial journals and annoying society journals, there certainly are annoying open access journals.  And many Bentham journals take the prize for being as annoying as they come.  Perhaps not all Bentham journals are like this, but I get spam-like email from dozens of them ... and do not get any from other Open Access journals.

Dr. J.A. Eisen

Institute for Genomic Research Rockville MD 20850

United States

Dear Dr. Eisen,

I am writing to you in my capacity as the Editor-in-Chief of Current Molecular Pharmacology, which is a cutting-edge peer-reviewed journal published by Bentham Science Publishers. Bentham Science publishes more than 300 print and open access journals.

Current Molecular Pharmacology is in its second volume and is indexed by all major indexing media includingChemical Abstracts, EMBASE, Genamics JournalSeek, Scopus, etc. The journal's homepage may be viewed athttp://www.currmolpharm.org

The journal invites contributions for both comprehensive review articles and guest edited issues in all areas of cellular and molecular pharmacology with a major emphasis on the mechanism of action of novel drugs under development, innovative pharmacological technologies, cell signaling, transduction pathway analysis, genomics, proteomics, and metabonomics applications to drug action.

It is a great pleasure to invite you to contribute to Current Molecular Pharmacology. If you wish to submit your work to the journal, then please provide us the title and an abstract (up to 250 words) of your article by email toeditorial@currmolpharm.org You may submit the full article.

Please note that submission of a manuscript is not a guarantee for acceptance for publication, as all manuscripts will be subjected to peer review. Each prospective first-named (corresponding) author will receive a limited number of free reprints and PDF of the paper.

Please could you also refer the journal to your colleagues and other contacts in the field, including your librarian, for promotional purposes. I look forward to hearing from you soon.

Yours sincerely,

Nouri Neamati,

Editor-in-Chief CMP

Here are some comments from FriendFeed

Nature Biotechnology is auditing me?

Just got this mail - it says "Important Audit Material Enclosed"

Turns out, it is a subscription notice from Nature Biotechnology (which I get for free).

Annoying, to say the least. I really wanted them to audit me.

Cool open source software of the month - mothur - for microbial ecology

Anyone interested in microbial ecology informatics should check out the "mothur" software (Main Page - mothur) from Pat Schloss at U. Mass. Schloss, who has developed a lot of great software tools inlcuding for example dotur and sons, is now developing an open source modular sofwate system for microbial ecology studies. And the name of it is mothur (get the theme?). Here is some more detail about mothur:

This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. As of version 1.2.0 we have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, and unifrac. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools. If you would like to contribute code to the project feel free to download the source code and make your own improvements. Alternatively, if you have an idea or a need, but lack the programming expertise, let us know and we'll add it to the queue of features we would like to add. Our current goal is to release a new iteration of the project monthly.

Anyway, thanks to my student Amber Hartman for pointing this out --- I will be perusing it but thought others should too. Hopefully, we can include some of the software from my lab such as AMPHORA, STAP, etc. into their code at some point.

Have money, would like to buy entrance to PhD program

Got this letter today.  Thought I would share, with some specifics removed.  I have never seen anything quite like this and I have gotten lots and lots of emails about jobs, positions, students, etc.

Subject: Application for Ph.D. studies Dear Prof.   Hope for your best.  I am working as lecturer, Department of XXXX, XXXX University, XXXX, Pakistan. I have completed my M.Phil (Biotechnology)  from XXXX University XXXXX, Pakistan (Thesis title something about microbe interactions with plants).  I have recently secured a fully funded scholarship for Ph.D studies (funding agency: Higher Education Commission, Islamabad, Pakistan).  This scholarship includes living expenses, university fees and travel expenses etc.  I wish to conduct my Ph.D studies at your esteemed university (in any area of biological sciences) .  I will highly appreciate if you kindly send me an acceptance letter for Ph,.D studies under your esteemed supervision,  so that I can proceed with my paper work with Higher Education commission, Islamabad.  Please also find attached herewith my brief CV.   Best regards   XXXXXX Lecturer Department of XXXX XXXX University, XXXX Pakistan

Here are some comments from FriendFeed

Another reason to publish as Open Access - libraries hurting big time financially and they will be cancelling many subscriptions

If you need any more incentive to publish a paper in an Open Access manner if you have a choice - here is one. If you publish in a closed access journal of some kind, it is likely fewer and fewer colleagues will be able to get your paper as libraries are hurting big time and will be canceling a lot of subscriptions. (e.g., see this page from UC Davis system Library Collections: A Forum - About the Libraries - University Library - UC Davis).

From Friendfeed

Who should have acess to publications supported by federal money? Well, everyone. See Federal Research Public Access Act

Well, this is good news. Here is some information on the Federal Research Public Access Act S. 1373 introduced by Sen. Lieberman and Sen. Cornyn (information is mostly from this site: Alliance for Taxpayer Access | Federal Research Public Access Act). This is really important as it will expand the accessibility of papers to agencies outside NIH (e.g., NSF are you listening, DOE are you listening). To help with this see Call to action: Tell Congress you support the Federal Research Public Access Act

Every federal agency with an annual extramural research budget of $100 million or more will implement a public access policy that is consistent with and advances the federal purpose of the respective agency. Each agency must:

• Require each researcher – funded totally or partially by the agency – to submit an electronic copy of the final manuscript that has been accepted for publication in a peer-reviewed journal.
• Ensure that the manuscript is preserved in a stable digital repository maintained by that agency or in another suitable repository that permits free public access, interoperability, and long-term preservation. Agencies have the flexibility to choose the best suitable location for their repository.
• Require that free, online access to each taxpayer-funded manuscript be available as soon as possible, and no later than six months after the article has been published in a peer-reviewed journal.

To whom this policy applies:

• Any researcher employed by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the work done for the funding agency in a peer-reviewed journal.
• Any researcher funded by a federal agency with an annual research budget exceeding $100 million who publishes an article based on the funded research in a peer-reviewed journal.

What is not covered by this legislation:

• The public access policy does not apply to laboratory notes, preliminary data analyses, author notes, phone logs, or other information used to produce the final manuscript.
• The policy does not apply to classified research. Research that results in works that generate revenue or royalties for the author (such as books), or patentable discoveries are exempt only to the extent necessary to protect copyright or a patent.

Also see below from the Congressional Record (and Hat Tip to Heather Joseph from SPARC for pointing all of this out).

From June 25 Congressional Record:          By Mr. LIEBERMAN (for himself and Mr. Cornyn):

S. 1373. A bill to provide for Federal agencies to develop public access policies relating to research conducted by employees of that agency; or from funds administered by that agency to the Committee on Homeland Security and Governmental Affairs

Mr. CORNYN. Mr. President, I rise to introduce the Federal Research Public Access Act. I am very pleased to be joined again by my good friend and colleague, Senator Joe Lieberman, who has remained dedicated to seeing this important legislation passed. This bipartisan bill is the same legislation we introduced in the 109th Congress. The purpose of this legislation is to ensure American taxpayers' dollars are spent wisely, which is even more important now in this time of fiscal tension.

To put things in perspective, the Federal Government spends upwards of $55 billion on investments for basic and applied research every year. There are approximately 11 departments/agencies that are the recipients of these investments, including: the National Institutes of Health, National Science Foundation, NASA, the Department of Energy, the Department of Defense, and the Department of Agriculture. These departments/agencies then distribute the taxpayers' money to fund research which is typically conducted by outside researchers working for universities, health care systems, and other groups.

While this research is undoubtedly necessary and is beneficial to America, it remains the case that not all Americans are capable of experiencing these benefits firsthand. Usually the results of the researchers are published in academic journals. Despite the fact that the research was paid for by Americans' tax dollars, most citizens are unable to attain timely access to the wealth of information that the research provides.

Some Federal agencies, most notably the NIH, have recognized this lack of availability and have proceeded to take positive steps in the right direction by requiring that those articles based on government- funded research be easily accessible to the public in a timely manner. I am proud to report that the NIH's public access policy has been a success over the past few years. By the NIH implementing a groundbreaking public access policy, there has been strong progress in making the NIH's federally funded research available to the public, and has helped to energize this debate.

Although this has surely been an encouraging and important step forward, Senator Lieberman and I believe there is more that can and must be done, as this is just a small part of the research funded by the Federal Government.

With that in mind, Senator Lieberman and I find it necessary to reintroduce the Federal Research Public Access Act that will build on and refine the work done by the NIH and require that the Federal Government's leading underwriters of research adopt meaningful public access policies. Our legislation provides a simple and practical solution to giving the public access to the research it funds.

Our bill will ask all Federal departments and agencies that invest $100 million or more annually in research to develop a public access policy. Our goal is to have the results of all government-funded research to be disseminated and made available to the largest possible audience. By speeding access to this research, we can help promote the advancement of science, accelerate the pace of new discoveries and innovations, and improve the lives and welfare of people at home and abroad.

Each policy that these departments and agencies develop will require that articles resulting from federal funding must be presented in some publicly accessible archive within six months of publication. In doing so, the American taxpayers will have guaranteed access to the latest research, ensuring that they do not have to pay for the same research twice--first to conduct it and then again to view the results.

This simple legislation will provide our government with an opportunity to better leverage our investment in research and in turn ensure a greater return on that investment. All Americans stand to benefit from this bill, including patients diagnosed with a disease who will have the ability to use the Internet to read the latest articles in their entirety concerning their prognosis, students who will be able to find full abundant research as they further their education, or researchers who will have their findings more broadly evaluated which will lead to further discovery and innovation.

While a comprehensive competitiveness agenda is still a work-in- progress, this legislation is good step forward. Providing public access to cutting-edge scientific information is one way we can encourage public interest in these fields and help accelerate the pace of discovery and innovation. In promoting this legislation, I hope to guarantee that students, researchers, and every American can access the published results of the research they funded.

Still hiring - despite budget issues

Recently I blogged about issues with the California budget possibly leading to major salary cuts/furloughs at UC campuses. Well, furloughs and salary cuts have been happening all around the country as many schools have had similar issues. But the good news is (1) if you are looking for a staff type position many people will have more money in their grants available since the people on the grants might get paid less and (2) many universities are not doing full faculty hiring freezes.

For example, the Center for Bioinformatics and Computational Biology - at U. Maryland is hiring faculty and post docs. UC Davis is continuing searches for faculty positions that are in progress (and we have some good candidates for people for the Genome Center). In evolution, a good place to look for job positings is Evoldir on the web or on Twitter.

And very shortly I will be posting ads for some bioinformatics related positions in my group - but have not finished writing the ads. Anyway - though the financial condition of many US Universities is less than ideal, those fields with a lot of government grant support seems to be doing OK.

Scientists getting antsy over possible salary reductions/furloughs at University of California

Just got this via email - a letter circulating at UC Santa Cruz about the possibility of furloughs/salary reductions at the University of California. Basically the issue is that UC is having some major financial trouble due mostly to getting less money from the state of California (due to California's financial problems). And the UC has circulated a memo saying that they are considering 4-8% pay cuts or furloughs that will reduce salary by 4-8% for ALL UC personnel.

This is a bit off putting to many since some personnel get their money from government grants not from the UC budget, but apparently to try and avoid inequality (which of course already exists) or to avoid hard decisions or for other reasons, UC is planning to have these cuts apply to everyone, even if that does not save UC money. I do find it strange that most of the people who work for/with me will get pay cuts which will lead to having extra $$ in my grants to spend. The extra weird thing is, if I cannot spend the money save from salary reductions, then UC loses money due to getting less indirect costs. I personally accept that the budget is in the toilet right now and UC needs to do some drastic things, but I am not sure if this across the board cut makes sense.

Anyway I thought the letter would be of interest to some.

We in the biomedical research community at the University of California, Santa Cruz are writing to express serious concerns about the salary budget cuts proposed as of 6/17/09. This letter represents the concerns of technicians, graduate students, postdoctoral scholars and fellows, research specialists, and project scientists in the departments of Molecular, Cell and Developmental Biology, Microbiology and Environmental Toxicology, Chemistry, Biomolecular Engineering, and Computer Engineering. We generally fall into the category of “staff”, and thus we understand that any staff salary cuts instituted in the future will affect all of us. However, it is important to understand that nearly all of us are paid by funds that do not come from the state of California, but rather from federal grants awarded by the National Institute of Health, the National Science Foundation, and grants awarded by many other public and private agencies. In many cases, the grant has been awarded to a Principal Investigator, and then is used by the Principal Investigator to pay us for our research work. In other cases, the grants are awarded directly to us to cover the salary necessary for our scientific training. So, as the majority of our salaries are not provided by the California state budget, a mandatory salary cut for our staff will not ease the University budget crisis, while it will indeed make our day-to-day living more difficult. Other effects of a mandatory reduction of our salaries are that: 1) This will actually reduce the amount of money the University receives in indirect costs from grants. 2) This will decrease the amount of income tax we pay to the state of California, further exacerbating the existing budget crisis. 3) The depletion of the funds coming into the University of California due to these salary cuts will make it increasingly difficult for the University to support its employees. 4) Lastly, the salary cut propos al may, in the longer-term, undermine confidence in the University of California system and lead talented people to move to states that are able and willing to support higher education and scientific research.

In summary, we strongly urge that no salary cut be instituted for University of California-affiliated personnel like ourselves whose salary is independent from the California state budget. Below you will find our signatures along with those of our supporting staff and Principal Investigators. Sincerely, The biomedical researchers of the University of California, Santa Cruz

See also

• Chronicle for Higher Education article
• Green Economics Blog
• Paul Thompson from UCLA wrote a letter to UC President Yudoff here

Plus here is a note from UC explaining their approach on reductions/furloughs:
Here is a communication from UC about the furloughs:

June 18, 2009

UC Furlough/Salary Reduction Plan Options – Questions & Answers
A summary of options for systemwide furloughs/salary reductions was sent to the UC
community on June 17, 2009. Following broad consultation, President Yudof intends to present
a specific option for approval to The Regents at their July 2009 meeting. To date, no decisions
have been made as to which option will be implemented. Below are answers to questions about
the proposals. Additional information will be added throughout this process as answers to other
questions become available and as the University approaches a decision on this issue.

Are these furloughs/salary reductions intended to be permanent?
No – the intent is for these actions to be temporary or short-term in nature, to help the University
through the current budget crisis. As indicated, the proposed duration for all three options is
August 1, 2009 through July 31, 2010 unless extended by the Regents.

Will furloughs/salary cuts apply to all employees, including faculty and represented
employees?
Yes. In order to ensure equity across the University, whichever option is chosen would apply to
all faculty and staff, except student employees. The Academic Senate has been closely involved
in consultation on these options. Implementation of the final plan is subject to collective
bargaining for represented employees. The President may recommend a hybrid Plan that
achieves the eight percent reduction in slightly different ways for the various employee groups.

If my salary is not supported by state funds, will I still have to take a furlough or salary cut?
Yes – participation is not based on the source of salary funds. Each of the options would apply to
UC employees whose salaries are funded by contracts and grants, clinical income and other
auxiliary activity, and general funds.

Will the proposed reductions apply to employees at the Lawrence Berkeley National
Laboratory?
The intent is for whatever option is selected to apply to all UC employees, including LBNL
employees. Since LBNL is funded by the Department of Energy (DOE), UC will comply with
all contractual obligations with the DOE.

W ill this be additive for the senior leaders who have already taken a five percent pay cut?
The senior UC officials who voluntarily agreed to have their salary reduced by five percent will
have their salaries reduced by a total of at least eight percent under these options.

How will the furlough/salary reduction impact vacation and sick leave accruals, UCRP service
credit and benefit calculations, and other benefits?
Under each option, the intent is to protect benefits and leave accruals to the extent possible. This
may not be possible in all situations. This issue continues to be evaluated and no final decisions
have been made yet. Approval from the Regents is required to protect UCRP benefits from being
impacted by a furlough/salary reduction plan.

I volunteered to participate in START to help the University manage the budget situation. Will
I have to take further reductions if a systemwide furlough or salary reduction is implemented?
How these options impact/relate to the START program is currently being analyzed. More
information on this issue is expected soon.

What’s the difference between the three options?
All three options are intended to achieve the same budgetary savings and have the same impact
on employee pay -- each option is closely equivalent to an eight percent pay reduction. Option I
is a straight pay reduction with no changes to work hours. Under Options II and III, employees
will be scheduled to work fewer days and a number of holidays will no longer be paid holidays.

In Options II and III, will I be able to schedule the unpaid day at a time that’s convenient for
me and my department, or will the days be pre-scheduled?
This is still being looked at. The unpaid days would include a combination of University
holidays and additional days, but the precise mix of holidays vs. additional days has not been
determined. The additional days may be pre-scheduled by the University in order to manage
critical operations, for example to ensure patient care at a medical center.

For unpaid days, can I "make up" for the lost salary by using my vacation leave, sick leave, or
compensatory time off?
No. The objective of these options is for the University to achieve budgetary savings. Accrued
vacation, paid time off (PTO), comp time and/or sick leave all are forms of paid time off and
thus may not be substituted for unpaid days.

Will furloughs or salary reductions affect the health of the UC retirement plan?
The potential impact of the options on the funding status of the UC retirement plan is being
analyzed by the Plan Actuary, and this will be taken into consideration as decisions are made.

also see Friendfeed comments

Now this is my kind of meeting

Just got to Asilomar conference center for a meeting organized by
CIFAR on integrated microbial diversity

It is my Kind of meeting in every way

1. On the coast
2. Few talks with lots of discussion and free time
3. Really diverse with runs and bacteria and archaea and viruses covered
4 not all about genomics (some meetings I go to are)
5. Did I say it is on the coast?
6 ford Doolittle is supposed to be here . He is one of my science heroes
7. The meeting is VERY small but still seems great
8 My family came (little Kids and wife)
And already felt welcome
9 I do not know many of the people
10 Elio Schaechter of Small Things Considered is giving a special talk

This is such a contrast to the big ASM meeting .. Which was fun in
ways and useful but overwhelming

Looking forward to the week

----------------------------------

Note added after the fact -

 Here are my tweets about the meeting (mostly mine) some by Rosie Alegado

rosiealegado Listening to Jonathan Eisen at #CIFAR talk about a genomic encyclopedia for bacteria & archaea. 2 days ago from Tweetie phylogenomics Huge % of talks at #CIFAR make use of Venter Sargasso or GOS metagenomic data 2 days ago from TwitterFon phylogenomics I am next at #CIFAR talking about a phylogeny driven genomic encyclopedia of bacteria and archaea 2 days ago from TwitterFon phylogenomics The one and only WF Doolittle is talking at #CIFAR about Thermotogales and lateral transfer 2 days ago from TwitterFon phylogenomics Rebecca Rundell is talking at #CIFAR about the amazing diversity of "meiofauna" (not big nor tiny) in marine samples 2 days ago from TwitterFon phylogenomics Nicole King at #CIFAR is talking about using choanoflagellate genomics/experiments to study the origins of multicellularity in animals 2 days ago from TwitterFon phylogenomics Barry Leadbetter at #CIFAR is using modelling/microscopy to study how choanoflagellates (single celled animal relatives) move/assemble 2 days ago from TwitterFon nthmost #ff @phylogenomics is live-tweeting some very interesting stuff from #CIFAR (Canadian Institute for Advanced Research): http://bit.ly/Eei6X 2 days ago from TweetDeck phylogenomics Michael Worobey at #CIFAR is telling how phylogenetics of archival samples helps resolve questions about the history of HIV movement 2 days ago from TwitterFon phylogenomics Michael Worobey at #CiFAR just told the story of how the brilliant WD Hamilton died after their trip to Africa to get chimp SIV samples 2 days ago from TwitterFon phylogenomics Michael Worobey who does fantastic "open science" flu work is talking at #CIFAR about HIV and swine flu origins 2 days ago from TwitterFon MicrobeWorld @phylogenomics Is there a site for this #CIFAR event? 2 days ago from web phylogenomics Relman at #CIFAR outlines benefits from microbes in gut: vitamins, digestion, infection protection, developmnt, immune training, etc 2 days ago from TwitterFon phylogenomics David Relman at #CIFAR is talking about humans as an ecological collective with microbes as an extension/component of self 2 days ago from TwitterFon CigarRadio @NetworkCacher Thanks, glad you enjoyed tghe show. #cigars #cifar #dogwatch 3 days ago from TweetDeck domonicmongello RT @phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - genomics .. http://bit.ly/AYVEJ 3 days ago from twitterfeed aeroculus RT @phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - genomics ecology geography - GenGIS 3 days ago from web phylogenomics Rob Beiko at #CIFAR is talking re: geospatial visualization of microbial diversity - merging of genomics, ecology and geography - GenGIS 3 days ago from TwitterFon phylogenomics Rebeeca Case is taking at #CIFAR about how marine algae also suffer from bleaching like coral 3 days ago from TwitterFon rosiealegado Listening to Kevin Carpenter #CIFAR. Learned a new word: ectosymbiont. 3 days ago from Tweetie phylogenomics Kevin Carpenter at #CIFAR is talking about and showing aamazing picture of microbes that live in termite and cockroach guts 3 days ago from TwitterFon phylogenomics Jan Janouskovec talking at #CIFAR about alveolate plastids "assessing the evidence" & how # of membranes are useful to know 4 days ago from TwitterFon phylogenomics Adrian Reyes-Prieto at #CIFAR is talking about plastid and chromatophore evolution 4 days ago from TwitterFon pathoadaptation @phylogenomics #CIFAR exactly the kind of meeting I need to get back to going to...must work harder to get out of my government 'hole'. 4 days ago from Tweetie phylogenomics Andrew Roger at #CIFAR is talking about the origin and evolution of mitochondria and related organelles 4 days ago from TwitterFon phylogenomics Joel Dacks at #CIFAR is talking about evolution of eukaryotic membrane traffiicking & how it is about "more than just eating" 4 days ago from TwitterFon JATetro @phylogenomics Will there be a proceedings or at least a review of the meeting? #CIFAR 4 days ago from Seesmic Desktop phylogenomics Tom Cavalier-Smith at #CIFAR is one of the few people who can really mix molecar phylogenetics and function/morphology for microbial euks 4 days ago from TwitterFon phylogenomics Listening to THE Tom Cavalier-Smith talking about eukaryotic evolution at #CIFAR - I don't always agree with him but he still rocks 4 days ago from TwitterFon phylogenomics Yan Boucher at #CIFAR is talking about "the life aquatic - vibrio an their mobile gene pool" - looking at lateral transfer & recombination 4 days ago from TwitterFon matthewherper RT @phylogenomics Alex Worden at #CIFAR communities of microbes are not a black box "physiology is not a bulk or an average property" 4 days ago from web matthewherper RT @phylogenomicsAlex Worden at #CIFAR communities of microbes are not a black box "physiology is not a bulk or an average property" 4 days ago from web phylogenomics Alex Worden at #CIFAR says we cannot treat communities of microbes as a black box "physiology is not a bulk or an average property" 4 days ago from TwitterFon phylogenomics Listening to Andrew Allen talk about phylogenomics, transposins, and gene transfer in diatoms at #CIFAR 4 days ago from TwitterFon phylogenomics Hearing Robert Morris from UW talking about proteomic studies of functions of bacterioplankton in Atlantic ocean at #CIFAR 4 days ago from TwitterFon phylogenomics Hearing Jennifer Foster discuss diatom bacterial symbioses and nitrogen fixation in oceans at #CIFAR microbial diversity meeting

Jonathan Losos wins E O Wilson award

Just got this in email

Harvard Biologist Jonathan Losos to Receive 2009 E. O. Wilson Naturalist
Award

The American Society of Naturalists is pleased to announce that Dr.
Jonathan B. Losos of Harvard University has been selected to receive
the 2009 E. O. Wilson Naturalist Award. The award, established in
recognition of Professor Wilson's lifetime contributions to ecology
and evolutionary biology, is given each year to a scholar who has made
significant contributions to the knowledge of a particular ecosystem
or group of organisms.

Dr. Losos is the Monique and Philip Lehner Professor for the Study of
Latin America, and Curator of Herpetology, Museum of Comparative
Zoology, Harvard University. His work with anole lizards in the West
Indies has contributed fundamentally to our understanding of the roles
of natural selection, competition, and niche evolution in shaping
assemblages of Anolis species.

Through the pioneering application of molecular phylogenetics and
comparative methods, he has thoroughly characterized the historical
biogeography and evolutionary radiation of anoles in the Caribbean,
including the roles of historical contingency and reiterated adaptive
evolution. His work on ecomorphology established early on the
relationship between morphology and ecologically relevant aspects of
behavioral performance, providing a foundation for work on
morphological evolution in the group. His experimental work with Tom
Schoener has demonstrated rapid selective impacts of introduced
predators, altered competition, and, by chance, hurricanes on Anolis
populations on tiny islands.

His work culminated this year in the publication of a major book on
the biology and adaptive radiation of the genus Anolis.

As Editor of The American Naturalist from 2002 to 2006, Dr. Losos
encouraged the publication of natural history observations in the
context of major issues in ecology and evolutionary biology.

"His enthusiasm as a colleague and mentor has inspired a generation of
biologists," said Dr. Robert Rickfels, a professor at University of
Missouri-St. Louis and chair of the award committee. "Dr. Losos's work
epitomizes the integration of natural history into scientific
investigation at the highest level."

The E. O. Wilson Naturalist Award was established in 1987, the year of
Professor Wilson's retirement from Harvard University. An appropriate
work of art and an honorarium of $2,000 will be presented to Dr. Losos
at the annual meeting of the American Society of Naturalists in June.

http://www.oeb.harvard.edu/faculty/losos/