Friday, September 28, 2007

Wanted: Brilliant Editor, Open Access Afficionado, Biology Background

I got this by email and figured I would post it here.

Senior Scientific Editor, PLoS Biology – based in San Francisco

The Public Library of Science (PLoS) seeks an experienced editor and manager to lead its flagship life science journal – PLoS Biology – in San Francisco. Since its launch in 2003, PLoS Biology has rapidly become established as both a high impact journal and a leader in the open-access publishing movement. This is a unique opportunity to develop a ground-breaking journal, and to shape a fundamental transition in scientific publishing.

The primary responsibilities of the job will be:

· Oversight of all editorial aspects of the journal, including peer review of research articles and commissioning of additional content. This includes fostering a collaborative decision-making process among in-house editors and the editorial board

· Management of the journal editorial staff

· Working with the PLoS leadership and the journal team to determine journal strategy within the context of our publishing portfolio and open-access goals

· Leading the further development of the journal specifically as we introduce web features that will allow greater user participation

· Attending scientific conferences and outreach to the scientific community, representing PLoS Biology and the broader aims of open access

Required experience and qualities:

· Extensive experience handling peer review of primary research

· Substantial management experience, and excellent communication skills

· Broad knowledge of the biological sciences, with a network of contacts in the scientific community

· Knowledge of and interest in the changing nature of scientific publishing, particularly in an online environment

· Strong commitment to open-access publishing

· Willingness to be flexible to accommodate time differences between our international offices

Application Procedure

PLoS offers competitive salaries, a creative and casual work environment as well as a full range of comprehensive benefits, including medical; dental and vision; life, LTD and STD coverage and a matching 401k program. If interested, please send resume and cover letter to and use “Managing Editor, PLoS Biology” as the subject of your email. Informal enquiries may be made by email to the Director of Publishing, Mark Patterson - Principals only – email from recruiters will be ignored.

Thursday, September 27, 2007

Another cool scientist video

Follow up on the "cool scientist" video posting from a few days ago. This one is about the research experience at sea.

Again, make sure the volume is on. And thanks to Jeff Hoffman for forwarding this .. he got it from Karla Heidelberg.

Please send/post more examples.

Tuesday, September 25, 2007

Symbionts have feelings too

The Onion, one of the key sources of all things wise and accurate in science is reporting on a sad story all too common among symbionts. They report:
After three rainy seasons together, a black rhinoceros and a parasite-eating tickbird are beginning to suspect that their symbiotic relationship has fallen into a rut, the couple reported Sunday.
And furthermore
"The rhino and tickbird may have evolved physiologically to meet each other's needs, but it's clear they haven't evolved emotionally," the elephant said. "They need to recognize that in order to go forward. The rhino's loud snorting is very alienating. And obviously the tickbird is projecting her own feelings of inadequacy when she criticizes the rhino for being a typical Diceros bicornis."
In other words - mutualisms are not the simple "You scratch my back, I'll scratch yours" they are presented to be. Symbionts have feelings too."

PS - Thanks to Sourav Chatterji in my lab for pointing out the Onion story.

Saturday, September 22, 2007

If only all scientists were this cool

OK - I admit I am a bit biased since I am starting to collaborate with her on metagenomics related projects, but everyone should check out the new YouTube Video from Jessica Green. Jessica just moved from U. C. Merced to U. Oregon and if you want to know what she works on, well check out the video. Oh and make sure the volume is on.

The funny thing is, I met one of the founders of YouTube (Chad Hurley) a few weeks ago, and I was telling him how I thought scientists were starting to use YouTube more frequently to actually communicate. But I did not have too many concrete examples to show him. So Chad ... you too should check out this video.

Thursday, September 20, 2007

Ego blogging -- what is your favorite self written blog entry or comment?

The Scientists is running a very informative discussion on people's favorite science blogs. There are some blogs there that I have never heard of that seem quite interesting as well as others I knew about and had forgotten. So it is a good place to look to see what people pick as their favorite.

But I think there is a more interesting question. What is your favorite blog entry that you have written in your own blog? Or, especially if you do not have a blog, what is your favorite comment you have written on someone else's blog? If you can't pick just one --- well do what they did on the Scientist site and pick a few.

My three favorites of my own blog entries:
  1. Why all medical professionals need to study evolution. I like this because I have been harping on it for years but never wrote about it or did anything about it.
  2. Top 10 Novel ways to contribute to the open access movement. I like this because it was one of my first serious moves to write about Open Access to scientific literature.
  3. Adaptationomics Award #1. This if high on my list because it represents both my obsession with adaptationism and my need to be snarky.
How about anyone else --- what are your favorite self-written blog entries?

Human evolution prize - Congrats to Spencer Wells

Kyung M. Song in the Seattle Times reports that Spencer Wells has won a relatively unknown but quite lucrative prize ($100,000) for his work on the human Genographic Project (see this article in the New York Times by Amy Harmon for more information on this project)

I love the lead in to the story
"Nearly half of all Americans reject the theory of evolution, with many believing instead that humans were created by a higher power. But for more than a decade, a little-known nonprofit based in Bellevue has promoted scientific research into the evolution of the human genome — and dispensed money to spread the knowledge."
Apparently the "Foundation For the Future" is big on human evolution having awarded their Kistler Prize (named after the Foundations founder Walter Kistler) to the likes of Richard Dawkins, E O. Wilson, etc. Congratulations to Spencer, who I still owe for giving me some excellent advice (when I was an undergraduate and he was a graduate student) about people to work for in graduate school (which I ignored, but it was still excellent advice).

Enough about Spencer --- The Times reports that
the foundation wields its $25 million endowment to support an array of scientific endeavors, awarding prizes for books, documentaries and teaching.
Hey - what about for blogs?

Wednesday, September 19, 2007

Biotechnology SPAM getting worse and worse

I simply cannot hold off any longer. I posted on Biotech. SPAM and backed off after getting some really really hostile email and comments. But here we go again.

In the last few months I have gotten so much biotech SPAM and last week I did something that added to the deluge. I got my email from where I used to work (The Institute for Genomic Research, also known as TIGR) forwarded to my current account. I still am doing projects with TIGR (well, TIGR technically does not exist anymore - it is now part of the J. Craig Venter Institute also known as the JVCI) so they have been kind enough to let me keep getting my email from there at least until my projects with them are over.

The problem with this is that many biotech. companies latch onto email addresses associated with TIGR/JCVI like, well, leeches. And they never seem to let go. And if you combine my TIGR, gmail, and Davis accounts, I get a lot of unsolicited email advertisements from biotech companies. I get so much that I am now going to fight back, again, by posting names of organizations that send biotech-related such unsolicited advertisements.

Here are some of the recent scofflaws in my inbox:
  • Malaysian Genomics Resource Centre. #1 Worst offender. I have unsubscribed from their email lists 100s of times and still keep getting their inane ads for various services. It is entirely possible they do useful stuff. But by the amount of SPAM they send out, I would doubt it.
  • EZBiolab - many emails from them.
  • Beckman Coullter - I have unsubscribed from their lists before but every once in a while get back on them
  • NIH - they seem to give out email addresses way too freely.
  • Drug Discovery News - can't seem to get off their lists
  • Invitrogen (I have unsubscribed many times but keep getting new things from them).
  • Infocast Inc
  • VWR
  • qPCR news
  • Campbell Alliance
Please feel free to chime in with other examples. I am sure I am not the only person getting these.

Tuesday, September 18, 2007

Evolution for Goodness Sake

Generally, I like the articles Nick Wade writes for the New York Times on science. In fact, I like them so much that I used his work as a template for my April 1 joke about Craig Venter sequencing his own microbiome. But I cannot help but feel that he really punted a bit in his article today entitled "Is ‘Do Unto Others’ Written Into Our Genes? " The article is mostly about new work by Jonathan Haidt, who has written about "evolutionary views of morality"

I will skip for now discussing my opinions on the meat of the article Haidt's work. But what irked me about Wade's article was the beginning. The article opens with
"Where do moral rules come from? From reason, some philosophers say. From God, say believers. Seldom considered is a source now being advocated by some biologists, that of evolution.

At first glance, natural selection and the survival of the fittest may seem to reward only the most selfish values. But for animals that live in groups, selfishness must be strictly curbed or there will be no advantage to social living. Could the behaviors evolved by social animals to make societies work be the foundation from which human morality evolved?"

I have two problems with this lead in. First, it implies that altruism and related behaviors evolved "to make societies work." This of course is not accurate. Yes, their existence allows societies to work, but they did not evolve to make societies work. Evolution does not have a drive to make societies work. It is a subtle distinction perhaps but an important one.

Second, and more important to me, the introduction could be interpreted as implying that the evolution of altruism itself is not well studied and/or is being debated. This does not appear to be what Wade means (when he says "
Could the behaviors evolved by social animals to make societies work" he means in part, "Given that altruism and other social behaviors evolve ...").

However, in discussions I have had with many people about this article they thought Wade was saying the evolution of altruism itself is under debate. If many people are coming away from Wade's article with this impression that is too bad since the evolution of altruism is well studied (there is a great book on this topic called "The Altruism Equation" by Lee Alan Dugatkin - a good blog about the book is one by Jason Rosenhouse here).

The evolution of altruism is one of my recent pet peeves since it was treated so poorly by Francis Collins in his recent book "The Language of God." In his book, which has some good discussion of how science and religion should be considered separate areas of study, Collins says that since evolution has been unable to explain altruism, therefore God must exist. This not only contradicts his own discussion in the book on how one should not use a "God is in the gaps argument" as evidence for religious beliefs , but it is simply wrong - evolutionary theory can explain altruism (see the Dugatkin book for more detail).

Note I am not saying anything here about whether I think God or gods exist. I personally believe religion and science can and should be separate fields. But certainly, one cannot use misleading references to non-existent gaps in evolutionary biology as evidence for the existence of one's own personal view of God/gods.

So - to sum up a way to long blog --- altruism can be explained by evolutionary biology and if people say otherwise (i.e., Collins) or could be interpreted as implying otherwise even if they do not mean to (i.e., Wade), don't believe it.

Saturday, September 15, 2007

Faculty Position in Quantitative Phylogenetics/Comparative Methods in the Section of Evolution and Ecology at U. C. Davis

To all evolutionary biologists or people working on phylogenetics/comparative methods. There is a faculty position available in the Section of Evolution and Ecology at U. C. Davis. U. C. Davis was ranked #1 in the country for graduate programs in Evolution and Ecology in 2006. It is a great school with lots of cool stuff going on in evolution and ecology as well as all aspects of the life sciences. The posting is below:

Quantitative Phylogenetics/Comparative Methods

Quantitative Phylogenetics/Comparative Methods, UNIVERSITY OF CALIFORNIA, DAVIS -- The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Section of Evolution and Ecology at the ASSISTANT PROFESSOR level. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields. Candidates should have a strong record of research applying phylogenetics to problems in evolution and/or ecology. We will give particular attention to applicants who are both developing and applying quantitative phylogenetic methods. The successful candidate will be expected to teach in the section's undergraduate program and the graduate program of the Population Biology Graduate Group. Applicants should submit materials online at These should include: curriculum vita, description of current and projected research, summary of teaching interests and experience, and up to five publications. Applicants should also arrange to have three referees submit supporting letters online at the above website. Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by October 15, 2007, to assure full consideration. Administrative contact: Barbara Shaneyfelt ( Faculty contacts: Bradley Shaffer and Peter Wainwright. The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.

An Anti Anti-Evolution Petition to reclassify non-science books from science categories in bookstores and libraries

Just got forwarded this email that I thought would be worth posting

The graduate students at my institution (Portland State) have created an online petition
to reclassify non-science books from science categories in bookstores
and libraries. To quote from the first paragraph of their petition:

"As scientists, we feel strongly that categorizing Intelligent Design
("ID") as science is both inappropriate and misleading. Local bookstores
and libraries unintentionally exacerbate this misleading categorization
when they shelve ID books and legitimate science texts in the same
section . Our goal is to convince the U.S. Library of Congress to
re-classify ID books into sections other than the science section."

If this is something about which you feel strongly (or even are
lukewarm!), I urge you to support their petition. Check URL:

Saturday, September 08, 2007

Quick bite - Recent interesting evolution papers in PLoS Journals

There have been a slew of interesting evolution papers recently in PLoS journals. Here are some

RNA based metagenomics - bee CCD study suggests a way to survey all microbes at once

After being reprimanded justifiably by one of the authors of the recent paper on bee colony collapse disorder (for a blog I posted and then removed) I have come to realize they used a very interesting approach to metagenomics that I have not seen used extensively before.

Their paper can be found here.

Here is the problem they were faced with - how to survey an sample for ALL the microbes present including both viruses and cellular microbes. The challenge to this is that some viruses have RNA genomes and thus if one simply extracts DNA and sequences it one will not sample any of the RNA viruses. One approach to such a challenge would be to isolate RNA and make cDNA and sequence to sample the RNA viruses. And then to separately isolate DNA and then sequence it either directly (using shotgun sequencing) or indirectly by first amplifying genes with PCR.

They chose a different approach - to isolate RNA and make cDNA and then sequence it. In doing this they in fact do get a sample of both RNA viruses AND cellular organisms. For cellular organisms, since most of the RNA in a cell is ribosomal RNA they get a sample of that organisms rRNA which can be used to say what type of organisms are present. Thus in one fell swoop they in essence sample ALL the microbes present in a sample. I had blogged about this and criticized them because they did not explain in the paper or in the press releases all of this logic, but one of the authors set me straight so I deleted my blog. Then I started thinking about it and realized that this seemed to be a relatively novel approach to metagenomics.

Now - I am not sure if this method is quantitative or exactly how robust it is, but it does provide an alternative to rRNA PCR (which has all the biases of PCR) and also provides an alternative to separately sequencing RNA and DNA from a sample. Certainly many have used RNA to cDNA and then sequencing to survey RNA viruses before. But usually they do this in material in which the cellular organisms have been first removed so that one does not get overwhelmed by the RNA from those organisms. But here, they used the power of massively high throughput sequencing and turned this "problem" of getting RNA from cellular organisms on its head and used it to sample RNA viruses and cellular organisms at the same time.

I do not know if this has been done before --- maybe other out there know of examples. But whether or not it has been done before, it is an important approach that should be considered in metagenomic surveys and it also suggests that ANYONE doing metagenomic surveys of microbes might want to purify RNA and save it form samples even if one is going to first focus on DNA.

Retraction - I was buzzing off about bees before my time

Recently I wrote a post about the recent study on bees associated with colony collapse disorder. After receiving a well thought out email from one of the authors on the study I have decided to retract my blog and apologize to the authors of the bee study. I rushed out my blog without really considering the evidence and the data very carefully and accept that I screwed this one up big time. The study is much more complex and comprehensive that I led people to believe. In part this was due to lack of detail in the actual manuscript but alas most of the fault lies with me - in not trying to contact the authors for more detail before mouthing off.

So I am giving myself a new award - the genomic jerk award. Hopefully there will be no more recipients.

Monday, September 03, 2007

Quality Genomic Reporting Award - Seeking Nominations

Well, Genome Technology magazine got on my case for being a bit too snarky with my "awards" saying
If Jonathan Eisen Offers You an Award, You Probably Want to Decline
Fair enough. I can be both passive aggressive and just plain aggressive about my opinions on how things should be done out there. And yes I have ended up focusing frequently on the negative (which is the case for both the awards I have begun dishing out here - the Adaptationomics Award and the Overselling Genomics Award). Plus, my giving out the latest award has taken away a bit from what should be an enormous positive vibe for the latest Wolbachia paper by Julie Dunning Hotopp and Jack Werren and colleagues, which is a spectacular piece of science.

So I have decided to try and be positive (occasionally) and have created a new award to give out - the Quality Genomic Reporting Award.

This award will be given to news articles (or blogs occasionally) written for the general public (e.g., in newspapers or news magazines) that do a good job of covering a scientific study involving genomic data.

At first, I wanted to give the award to HENRY FOUNTAIN for his article in the NY Times on September 4, 2007 entitled: "When Bacteria Transfer Genes to Invertebrates and Spread From There." This would have been ironic since this story is about the same scientific study that led me to give out the first Adaptationomics Award a few days ago (also see Larry Moran's discussion on his Sandwalk blog and Evolgen's).

I confess, when I saw the NY Times had an article in this Tuesday's Science Times about this Wolbachia story, I expected to find the same stuff that I went after in the Adaptationomics award and I was expecting an easy blog topic. But on first glance, Fountain seemed to do a pretty good job. For example he reports:
The researchers looked for Wolbachia genes in the genomes of more than 24 invertebrates, including wasps and nematodes, and found it in 8.
Thus providing a level of detail normally missing from genomic reporting. In addition, he does a good job of setting up the story:
But lateral gene transfer between bacteria and multicellular organisms has been assumed to be exceedingly rare, for the reason that most cells in a higher organism are somatic; their genetic material does not get passed on.
Alas though the story is good, it does contain some bits I am not keen on. For example, he reports that
This genome-within-a-genome involves Wolbachia pipientis, a bacterial parasite that is one of the most prevalent in the world, infecting close to three-quarters of all invertebrate species, typically in the reproductive cells
This is a bit misleading. The statement that Wolbachia infect 3/4 of all inverts is not really accurate. It would be better to say "some researchers estimate that Wolbachia infects up to 3/4 of all inverts." The research that I know of on Wolbachia prevalence in different species has focused on surveys of insects and arthropods (which are only a subset of invertebrates). And these studies have given conflicting results with some showing 20% of species surveyed being infected and others showing up to 70%.

But this is a minor quibble. And I was still getting ready to give Fountain the award. But then it ends the article with a quote by Jack Werren that fits into the Adaptationomics paradigm for the award I gave a few days ago:
“It’s happening frequently enough,” he added, “that it’s inevitably going to be leading to the evolution of new genes.”
Sure Werren might be right. And, in case people thought I was saying otherwise - he is more than welcome to state his opinion about things and give his insight even when evidence is not there. That is after all part of what makes science fun and interesting. And I should make clear, this is NOT meant to disparage the science in the Wolbachia paper. But when a scientist makes such a statement, it would be good for reporters to at least say specifically the speaker is predicting something that is not yet known. That is, just try to clarify what was supported by evidence and what was more of a jump.

So alas - this article is not going to get my Quality Genomic Reporting Award, even though overall it is pretty good. But pretty good is not good enough. So if anyone out there has good candidates for the award, let me know and I will keep looking too.

Saturday, September 01, 2007

Metagenomics 2007 presentations available

For those interested in metagenomics, the Metagenomics 2007 meeting (also see Konrad's blog) has posted video and pdf's of most of the presentations. You can get everything at the CAMERA web site here. I have posted links and titles below:

Larry Smarr
[video] [PDF]

Masahira Hattori, Tokyo University/RIKEN
Length: 56:30 [video] [PDF]

Paul Gilna, UCSD
Length: 5:55 [video]

Jed Fuhrman, University of Southern California
Length: 1:04:01 [video] [PDF]

Dawn Field, Oxford Centre for Ecology and Hydrology
Length: 27:05 [video] [PDF]

Janet Jansson, Swedish Univ of Agricultural Sciences

James M. Tiedje, Michigan State University
Length: 27:09 [video] [PDF]


Medical Metagenomics
Human Biology
Chair: Trevor G. Marshall, Autoimmunity Research Foundation
Speaker: Peter J. Turnbaough, Washington University
Length: 49:32 [video] [PDF]

Computational Metagenomics
Ontology and Standardization
Chair: Jonathan Eisen UC Davis
Length: 44:18 [video]

Discovering opportunity for Bioenergy
Chair: Phil Hugenholtz, JGI
Speaker: Yuri Gorby, JCVI
Length: 50:45 [video] [PDF]

Modeling the natural world
Chair: Trina McMahon, Univ. of Wisconsin-Madison
Speaker: Patrick Schloss, UMass Amherst
Length: 1:00:36 [video] [PDF]

Evolution and population
Chair: Francisco Rodriguez-Valera, Universidad Miguel Hern√°ndez in Alicante
Length: 1:00:36 [video]

John Wooley, UCSD (Moderator); various speakers
Length: 40:47 [video]

Metagenomic analyses of corals
Forest Rohwer, San Diego State University
Length: 21:15 [video] [PDF]

Population structure of microbial communities in the world's oceans
Mitchell Sogin, Marine Biological Lab, Woods Hole
Length: 41:20 [video] [PDF]

Structural metagenomics: Lessons from the first experimentally characterized GOS proteins
Adam Godzik, Burnham Institute
Length: 46:35 [video]

Detailed view of the architecture and implementation of a metagenomics server
Philip Papadopoulos, UC San Diego/SDSC
Length: 24:27 [video] [PDF

Metagenome sequence data management and analysis
Victor M. Markowitz, Lawrence Berkeley National Lab
Length: 34:25 [video] [PDF]

Developing a software workbench for marine ecological genomics
Frank Oliver Gloeckner, Max Planck Institute for Marine Microbiology
Length: 32:39 [video] [PDF]

The Metagenomics RAST server: Automated analysis of Sanger and 454-type metagenomes
Folker Meyer, Argonne National Laboratory
Length: 17:00 [video] [PDF]

Technologies for metagenomics selection and sequencing
Gautam Dantas, Harvard University
Length: 33:30 [video] [PDF]

Micro-Mar: A database for dynamic representation of marine microbial diversity
Ravindra Pushker, University College Dublin
Length: 32:00 [video]

Kayo Arima, UC San Diego
Length: 2:16 [video]

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