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 jobs@plos.org 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 - mpatterson@plos.org. Principals only – email from recruiters will be ignored.

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.

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.

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.

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?

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.

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.

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 http://www2.eve.ucdavis.edu/jobs/. 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 (bashaneyfelt@ucdavis.edu). 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

All:

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:
http://www.sciencea2z.com/z_etomite/

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

• The Complete Genome Sequence of Yersinia pseudotuberculosis IP31758, the Causative Agent of Far East Scarlet-Like Fever Eppinger M, Rosovitz MJ, Fricke WF, Rasko DA, Kokorina G, et al. PLoS Genetics Vol. 3, No. 8, e142 doi:10.1371/journal.pgen.0030142

• Adaptive Evolution of Conserved Noncoding Elements in Mammals Kim SY, Pritchard JK PLoS Genetics Vol. 3, No. 9, e147 doi:10.1371/journal.pgen.0030147
• Gene Duplication and Adaptive Evolution of Digestive Proteases in Drosophila arizonae Female Reproductive Tracts Kelleher ES, Swanson WJ, Markow TA PLoS Genetics Vol. 3, No. 8, e148 doi:10.1371/journal.pgen.0030148
• Genome Analysis of Minibacterium massiliensis Highlights the Convergent Evolution of Water-Living Bacteria Audic S, Robert C, Campagna B, Parinello H, Claverie JM, et al. PLoS Genetics Vol. 3, No. 8, e138 doi:10.1371/journal.pgen.0030138
• Automated Protein Subfamily Identification and ClassificationBrown DP, Krishnamurthy N, Sjölander K Author Summary
• Deletion of Ultraconserved Elements Yields Viable Mice Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, et al. PLoS Biology Vol. 5, No. 9, e234 doi:10.1371/journal.pbio.0050234
• Cryptic Population Dynamics: Rapid Evolution Masks Trophic Interactions Yoshida T, Ellner SP, Jones LE, Bohannan BJM, Lenski RE, et al. PLoS Biology Vol. 5, No. 9, e235 doi:10.1371/journal.pbio.0050235
• Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single FilamentsPLoS Biology Vol. 5, No. 9, e230 doi:10.1371/journal.pbio.0050230

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.

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.

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
[PDF]

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

Breakouts:

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 Hernández 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]

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

Too eager for ethanol?

Just a quick one here along the lines of my biofools series. Anyone interested in biofuels should take a look at the LA Times Editorial from Aug 20 titles "Drunk on Ethanol" which discusses many of the negatives of growing corn for ethanol and of other aspects of the crop to ethanol pipeline. Also check out the letters to the editor following up on the piece (one of them by my sister, Lisa Coffman, Executive Director of the California Water Impact Network). My personal biggest concern is the environmental damage that could come from increased use of plants to produce ethanol. Such damage includes the conversion of rainforests into sugar cane plantations, the use of more and more pesticides and herbicides and fertilizers to go onto less useful land, and the excessive use of an already limited resource - water. Yes, if you do the calculations in certain ways, ethanol seems like a great idea. And it is certainly true that if we are going to make ethanol from crops we could do it more efficiently. But the way it is being done now - with corn sucking up water like their is not tomorrow we are heading down a bad path.

What would make more sense is to first make better use of all the wasted biomass from various agricultural systems and from solid waste. Lots of material is still being burned on farms for example (see pictures below of a fire near Davis --- these are going all the time, even on "spare the air" days). Sure - one can make lots of money from corn to fuel right now. But that does not make it the right thing to do when there are plenty of sources of biomass being wasted all around us. Lets hope that more of the biofuels projects work on converting leftovers not new crops.

Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes

Well, I have decided to start a new award. For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick - it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.

Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.

And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack Warren Werren and colleagues for their recent press release on their new study of lateral transfer in Wolbachia (plus it lets me plug their new study which is pretty ^$%# cool).

Basically, in their study (led by a past colleague of mine from TIGR, the brilliant up and coming Julie Dunning Hotopp) they showed that there have been multiple lateral transfers of DNA from Wolbachia (which are intracellular parasites that can infect germ cells) into invertebrates. Furthermore they showed that that the DNA transfered to the host genome is not completely transient and that in many cases it is passed on to future generations. This is interesting because it is the first report of strong evidence for such "stable" transfers from bacteria into multicellular species. Of course, one could say that this finding is not that surprising given that Wolbachia infect germ cells and given that DNA transfer from organellar genomes to nuclear genomes is quite common. But Wolbachia are not organelles and since it appears that their DNA can readily move into genomes of multicellular species, this opens up a new window into our understanding of gene transfer.

This of course does not mean that the DNA is anything but "junk" in terms of functions in the host genome. And this is where the adaptationomics comes in. One of the press releases associated with the paper has a bit of an outrageous adaptationomics claim that I would like to counter. In response to their finding of a nearly complete Wolbachia genome in the nuclear genome of a fly Warren Werren says

The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host.

And Dunning Hotopp in a Nature article says:

The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. "You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."

This notion that the DNA MUST have an beneficial function is pure adaptationomics. Consider the movement of DNA from organellar genomes into the nucleus. Such movement occurs at an incredibly high rate and the DNA seems to be maintained in the host genomes for millions of years. For example, when we were sequencing the Arabidospsis genome, we found at least one if not more whole copies of the mitochondrial genome embedded in the nuclear genome and we concluded this was likely a non adaptive event. That is, the mt DNA was not conferring some advantage on Arabidopsis plants. There is extensive work on what are called "numts" (nuclear mitochondrial DNA) in humans and other species that makes similar conclusions - the mtDNA in the nucleus is basically junk but it is maintained for long periods of time. Sure, occasionally, the DNA confers some selective advantage. But this is a very rare event and one cannot infer that some DNA is advantageous simply because it is present. This is especially the case for eukaryotes which are generally more able than bacteria to maintain DNA that confers little selective benefit.

So I would argue that WarrenWerren and colleagues appears to have fallen for the adaptationomics trap - they want to believe these Wolbachia DNA inserts confer some selective advantage. But there is no need to assume this simply because the DNA is there.

Anyway - as is the case more and more. Read the paper. Ignore the interviews and the press releases.

Calling for a Boycott of of AAP - Association of American Publishers

If you have not seen the wonderful news about the latest anti Open Access initiative called PRISM, well you should surf around the blogosphere a bit. PRISM is a group started by the AAP - the Association of American Publishers that - there is no nice way to put this - is a sad stage in the evolution of publishing. Basically, it is a Macarthy-Era ripoff where Open Access is the new evil that communism once was. And everything wrong with the world is in essence blamed on the Open Access movement. For more detail on PRISM, and what is wrong with it, including the pirates use of copyrighted material, see some of these links:

• Leah Arhibald's mumbo jumbo cartoon
• Steve Mount's bit on PRISM
• Boing Boings Discovery that PRISM was illicitly using copyrighted material on their website
• Peter Suber's got much more detail here
• Bora's great compilation of blogs about PRISM here
• Wired Science on PRISM
  
• The PISD spoof of PRISM (THIS is F*$&NG BRILLIANT)
• Steven Harnad on PRISM
  

I think academics and the public need to fight back against this attempt to mislead the public about the issues surrounding Open Access publishing. And one way to fight back is to recommend that the members of AAP drop out or request termination of the PRISM effort. So here is a list (see below for the full list) with links of the members of AAP. If you are involved or have connections to any of these groups, consider writing or calling them and suggesting they reconsider involvement in AAP. Look, for example at all the University presses. If they do not back out of PRISM we should consider launching a boycott of AAP members.

Full list of AAP from the AAP web site:

Absey & Company, Inc.

Academic Innovations

Academic Learning Company, LLC

Academy 123, Inc.

Academy of Management

Aequus Technologies Corporation

Al-Basheer Publications and Translations

Algora Publishing

American Academy of Pediatrics

American Academy Ophthamology

American Association of Cancer Research

American Association of Pharmaceutical Scientists

American Chemical Society

American Foundation for the Blind

American Geophysical Union

American Institute of Aeronautics and Astronautics

American Institute of Physics

American Mathematical Society

American Medical Association

American Psychiatric Publishing, Inc.

American Psychological Association

American Scholars Press, Inc.

American School of Classical Studies at Athens (The)

American Scientific Publishers

American Society of Clinical Oncology

Ames On-Demand

Apex CoVantage

Apex Learning, Inc.

Appalachian Trail Conference

Ardor Scribendi, Ltd.

ASIS International

Association for Computing Machinery (ACM, Inc.)

Association of Research Libraries

Athena Media, Inc.

Atypon Systems, Inc.

AV Book Publishers, Inc.

Avon Books/Harpercollins Publishers

Banta Company

Barnhardt & Ashe Publishing, Inc.

Barricade Books, Inc.

Baseline Development Group

Baydell & Brewer, Inc.

BBC Motion Gallery

Beacon Group, The

Beacon Publishing Services

Berkery, Noyes & Co.

Berkshire Publishing Group, LLC

Black Dome Press Corp.

Blackwell Publishing

Bloomberg Press

Booklight, Inc.

Books International, Inc.

Booktech.com

British American Publishing

Brookings Institution (The)

Brown Publishing Network, Inc.

Cadmus Professional Communications

Cambridge University Press

Capitol Books

CAST

Castle Connolly Medical Ltd

Caxton Printers

CFA Institute

Children's Book Press

City Lights Books

Cold Spring Harbor Laboratory Press

Colorado Independent Publishers Association

Columbia University, DKV

Consumer Reports

Cornell Maritime Press

Cornell University Press

Council on Foreign Relations Press

Council on Library and Information Resources

Cover Publishing Co.

CQ Press

CrossRef

D2B Group, Inc.

Dana Press, The

Douglas & McIntyre

Eaglemont Press

Earthquake Engineering Research Institute

Educational Concepts

Element LLC

Elsevier Science Inc.

Emida International Publishers

Ernst & Young, LLP

F.A. Davis Company

Federation of American Societies for Experimental Biology

Feminist Press (The)

Focus Publishing/R. Pullins Company, Inc.

Fordham University Press

Fulcrum Publishing

Gallaudet University Press

Genesis Press, Inc. (The)

Gival Press, LLC

Globe Pequot Press, Inc.

Great River Technologies

Grolier Educational

Grove/Atlantic, Inc.

Grove's Dictionaries/Holtzbrinck

Hachette Book Group USA

Haiduk Press

Hammond, Inc.

Hampton-Brown Company, Inc. (The)

Hannacroix Creek Books, Inc.

Harcourt, Inc./Reed Elsevier

Harlequin Enterprises Ltd.

HarperCollins Publishers

Harvard Business School Press

Harvard University Press

Harvest House Publishers

Health Affairs/Project Hope

Hearst Book Group

Heinz Center (The)

Henry Holt & Co.

Hispanex, Inc.

Houghton Mifflin Co.

Howard University Press

Human Factors and Ergonomics Society

Hyperion

Impact Publishers, Inc.

Info Sys Technologies, Ltd.

Ingram Book Company

Institute for Electrical and Electronics Engineers, Inc. (IEEE)

Institute for International Economics

Institute for Scientific Information

Institute of Physics Publishing

Instrumentation, Systems, and Automation Society (The)

iUniverse

The Institute, Inc.

J. Paul Getty Trust Publications

James A. Rock & Company Publishers

John Wiley & Sons, Inc.

Johns Hopkins University Press (The)

Jordan Publishing House

Journal of Rehabilitation Research Development

Keene Publishing

Key Education Publishing Company LLC

KidBiz 3000

Kirchoff/Wohlberg, Inc.

Knovel.com

LAD Publishing Company

Lattice Press

League of American Poets

Leapfrog Enterprises Inc.

Learning.com

Liberty Fund, Inc.

Library of Congress Publishing Office (The)

Lidenmeyr Book Publishing Papers

Lippincott Williams $ Wilkins Journals

Literary Architects

Little Moose Press

Lousiana State University Press

Love Publishing Company

Luxury Travel Books

Lynne Rienner Publishers, Inc.

MacAdam/Cage Publishing Inc.

Mage Publishers, Inc.

Mark Logic Corporation

Market Data Retrieval

MarketingWorks, Inc.

Markus Wiener Publishers

Massachusetts Medical Society/New England Journal of Medicine

Math Teachers Press, Inc.

Mazer Corporation (The)

McGraw-Hill Companies (The)

Medical Group Management Association

Melville House Publishing

Meta Comet Systems

MG Taylor Corporation

Microsoft Corporation

Midland Information Resources

Minnesota Historical Society Press

MIT Press (The)

Modern Language Association of America

Momentum Books, LLC

Mondo Publishing

Mooring Field Books, Inc.

Morgan & Claypool Publishers

Morgana Press LLC

Moseley Associates, Inc.

Music Together, LLC

National Academy Press

National Computer Systems/Pearson

National Education Standards

National Geographic Society

National Learning Corp.

National Publishing Co.

National Science Teachers Association (NSTA)

Nature America

New England Journal of Medicine

New Press (The)

New York Botanical Garden (The)

New York University Press

Newmarket Press

Oak Knoll Press

Overlook Press (The)

Oxford University Press

P. H. Glatfelter Company

Pan American Health Organization

Pangaea

Paratex, LLC

Parmenides Publishing

Pearson Education

Pelican Publishing Co., Inc.

Penguin Putnam, Inc.

Pennsylvania State University Press (The)

People's Publishing Group

Peter Li Education Group

Posterity Press, Inc.

Pillsbury Winthrop Shaw Pittman, LLP

Posterity Press, Inc.

Princeton University Press

ProQuest Information

Pub Smarts, LLC

Publish America, Inc.

Publisher's Group Incorporated

Publishing House Research

Publishing Illuminations

Publishing Works

Quarasan Group, Inc. (The)

R R Donnelley

R.R. Bowker

Rainbow Books, Inc.

Rand

Random House, Inc.

Ray of Light Publishing Company, Inc.

Reader's Digest Association

ReadHowYouWant.com

Recording for the Blind and Dyslexic

Red Rock Press

Reed Reference Publishing

Resolve Corporation

Resources for the Future/RFF Press

Rockefeller University Press

Rosetta Solutions, Inc.

Rowland Reading Foundation

Saferock USA, LLC

Sagaponack Books

Sage Publications, Inc.

Scholastic, Inc.

Scholatic Testing Services, Inc.

Scientific American/St. Martin's College Publishing Group

Sea Hawk Publishing

Seven Locks Press

SGI-USA

Sheridan House, Inc.

Simon & Schuster

Six Red Marbles LLC

Soft Skull Press

Springer Publishing Co.

Springer-Verlag New York, Inc.

St. Martin's Press

Stanford University Press

Stoeger Publishing

Swan Isle Press

Teachers College Press

Thames & Hudson, Inc.

Thieme New York

Thomson Learning

Tichenor Publishing

Tighe Publishing Services, Inc.

Too Far

Tribune Education

Tupelo Press

Turtle Books

The University of Hawaii Press

UAHC Press

University of California Press

University of Chicago Press

University of Illinois Press

University of Tennessee Press

University of Texas Press

University Press of Kentucky

van Tulleken Company (The)

Vantage Press, Inc.

Veronis, Suhler & Associated, Inc.

Victory Productions, Inc.

Virginia Museum of Fine Arts

Viz Media, LLC

Von Hoffmann Corporation

Walford Press

Wesleyan University Press

Western Economic Association

White Rhino Press

Whitston Publishing Company, Inc.

Wiggin and Dana LLP

William Morrow & Co., Inc./HarperCollins Publishers

Willow Creek Press, Inc.

Wooster Book Company

Words & Numbers.com

Workman Publishing

World Bank Group

Worth Publishing, Inc.

Xerox Corporation

Yale University Press

PRISM - Partnership for Research Integrity in Science and Medicine - Seems like a spoof but it is real, and sad

I just came across this web site for something called the "Partnership for Research Integrity in Science and Medicine." I looked through it an thought - this must be a spoof. A good April 1 joke about the dinosaurs of the publishing industry. The reason it seems like a joke is well, the stuff there is so incredibly inane as to make one laugh. In essence the whole site is an anti Open Access site. They are against Open Access to publications it seems because Open Access does things like

• "undermines the peer review process." Yes that's right. If an article is freely available for all to read, that must mean that peer review has been compromised. Nevermind that openness in other areas (e.g., politics, law, etc) is well established to promote critical review (anyone heard of freedom of the press). But apparently in science, openness is bad.
• "opens the door to scientific censorship". Yup. Making publications freely available apparently means that you will stifle communication. Again, the logic here is completely silly - how on earth is openness connected to censorship?
• "undermining the reasonable protections of copyright holders." Yup, the publishers of scientific articles, who do not deserve the copyright to articles in the first place, are now saying that because they have stolen the copyright from many scientists, now we should defend them because they have the copyright. Kind of like saying that someone who steals some money should not give it back because of finders keepers rules.
  

I could go on and on about the silly stuff there ... but lets just say that everything on the site seems like a spoof. But alas, it is not. PRISM is for real. It is the last gasp of a dying breed - publishers who refuse to do what is the right thing for science and society. Yes, I understand there are some issues with Open Access that still need to be solved. But this McCarthy like tone of PRISM - basically equating openness with evil and godlessness is ridiculous. I think this is a sad day for the people behind PRISM - the AAP (Association of American Publishers). I am sure they have done some good things over the years. This is certainly not one of them and a good sign that anyone out there with any common sense who might be involved in AAP should get out or fight for change within the institution.

For more on Prism see

• Open Reading Frame
• Peter Suber

Anyone else having gmail spam filtering issues?

Over the last week I have had a sudden increase in missing email messages, both from me and to me. Only by luck did I figure out that at least the missing incoming messages are being placed into the spam folder by gmail, which I run all my messages through since in the past their spam filter has been phenomenal.

The incoming messages included diverse messages - some with the word "FWD" in the subject line but some appearing as normal as can be.

Anyone else out there experiencing a sudden increase in missing email?

Save the Bay Delta

Just a quick one here. I am appalled by some of the discussions of water resources out here in the Central Valley in California. I know there is a long history here relating to the allocation of water but we are risking destroying an incredible ecosystem in the Bay Delta by dishing out water rights like they are candy (not to mention the pollution, pesticides, antibiotics and other crap (literally) we allow to flow into the Delta. So here is a plug for a petition being circulated relating to one of the latest US Bureau of Reclamation activities in this area.

Overselling Genomics Award #2

Well, all I can say is "Aaaaargh" again. So I am awarding my second overselling genomics award to a Press Release from U. Florida entitled "Conquest of land began in shark genome" relating to a paper in PLoS One on shark development . The press release centers on a reported finding that

Using molecular markers to study the formation of skeletal cartilage in embryos of the spotted catshark, UF scientists isolated and tracked the activity of Hox genes, a group of genes that control how and where body parts develop in all animals, including people.

Now admittedly, this is not genomics here - but the press release just had to use genomics in the title so my automated google search for "genome" and "evolution" picked it up. So - why do they get the overselling award? Read more in the press release:

The finding shows what was thought to be a relatively recent evolutionary innovation existed eons earlier than previously believed, shedding light on how life on Earth developed and potentially providing insight for scientists seeking ways to cure human birth defects, which affect about 150,000 infants annually in the United States.

Yes that is right, this genome-ish gene expression study in sharks is going to help cure human birth defects (note the paper in PLoS One seems entirely reasonable ... this is another case of press releases being disconnected from the science - and is another reason to support OA publications because here you can actually all go and read the paper and ignore the press release).

In addition, the press release says

“We’ve uncovered a surprising degree of genetic complexity in place at an early point in the evolution of appendages,” said developmental biologist Martin Cohn, Ph.D., an associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. “Genetic processes were not simple in early aquatic vertebrates only to become more complex as the animals adapted to terrestrial living. They were complex from the outset. Some major evolutionary innovations, like digits at the end of limbs, may have been achieved by prolonging the activity of a genetic program that existed in a common ancestor of sharks and bony fishes.”

Now I accept that the specific details of Hox gene expression here might have been surprising but what friggin evolution textbook are these people reading if they are surprised that there is not a chain of life going from less complex to the pinnacle of complexity in humans? Hopefully not mine.

SciFoo Camp - The End and New Beginnings

Well, I am finally getting around to writing about the last day of SciFoo camp (see here for my other blogs on the topic).

For Day 3, I got up early, packed up my bag, and then polished up my presentation for a session on "The Human Microbiome." This was particularly difficult for me since I do not really at this time work on the human microbiome much (although I want to). But I figured, of all the things microbial I know about, this would be the one that would be most fun to talk about to scifooers and would catalyze the most interest. So I searched around for slides and figures and ideas on the web for a while and then said "WTF - I can do a chalk talk if I need to" and I headed downstairs to the lobby in the hopes of getting over to Googleplex and enjoying the last bits of scifoo.

There was quite a crowd in the lobby and I ended up talking to a few other evolutionary biologists which was good and then finally got a bus ride over to camp. At Google, I had a bit of breakfast and then went inside to sit at a table to do the last bits of preparation for my talk. If I had been at a normal conference I would have simply skipped the first two sessions to prepare for my talk at 11:30 (the last session of the meeting). But I said this would be silly and decided to go to a session at 9:30. My choices were:

Golem: Data Mining for Materials (and Non-Programmers): sketching information systems (Andrew Walkingshaw) --AND-- Searching the Edges of the Web

Novel Biofuels, smart materials in energy production, the energy mix in the short term.

Genome Voyeurism -- Let's poke through Jim Watson's genome

International polar year, an opportunity to... (Dave Carlson)

Simplifying citation linking (Dan Chudnov)

Would You Upload? (Melanie Swan)

Future health care delivery and transport models: When "science" is not enough, benefit of new research vehicles (Berman and Neelagaru)

Reforming Patent Systems, patent informatics and innovation

5 mins on your favorite science website / tell us your dream science web tool (Richard Akerman)

How to Celebrate Darwin in 2009 (Phil Campeck)

Innovation is Not Pointless...But It's So 20th Century (Bingham)

And again, the choosing was brutal. Though I really wanted to go to Lincoln Steins Genome Voyeurism session, I followed my rule of going to things I did not know a lot about and went to the session on the International Polar Year. This was one of those sessions in a giant room and I expected a huge crowd. Instead, there were about seven people. But boy did the others miss something brilliant. Dave Carlson not only told us about the whole IPY project but proceeded to tell us about how their project was completely Open Science. That is, everyone involved was required to post their data on the web for anyone to use. OK - well apparently they are allowed to publish in non Open Access journals, which seems counter to their whole philosophy, but their openness about data is brilliant (Note - I just found out from a Google search that a childhood friend of mine, Thomas Nylen, is participating in the IPY project -- see this blog here for some of what Tom has been up to).

Unfortunately, I missed the next session due to my computer having issues and me freaking out about whether it would work for my presentation at 11:30. The choices for the session I skipped were:

Incorporating science into social networks (Josh Koarer and Jon Durant) Assessing the risks of tech innovation, ethics of synthetic bio. Do we have any choice? (Caruso) Tree of Life: Fractal Data Problem (Sereno) Provenance analytics: illuminating science trails. Future of scientific publications, dynamic and evolving papers. (Juliana Freire) Planetary Defense Against Asteroids (Pete Worden)

Science Blogging

Towards an open source science learning collaboratory (Ted Kahn Design Worlds)

Opening the scientific literature: OpenLibrary, Google Scholar (Aaron Swartz)

21st century medicine: electronic medical records, privacy, and data mining (Erez L. and Kevin F.)

Then it was time for the final session. And I was up -- the Human Microbiome. Here is what I was up against

Social limits of scientific knowledge - can too much information impede science? (Dalton Convoy)

Culture of Fear: Scientific Communication and Young Scientists (Alex Palazzo, Andrew Walkingshaw)

Towards DataWiki (Hugh Rienhoff, Alan Littleford)

Do systems organize themselves to produce entropy at the maximum rate? (Ralph Lorenz)

Science on the Stage, "science-in-theatre" (Djerassi)

Human Microbiome, microbes in and on us (Jonathan Eisen)

Science fiction: what is it for? (Henry Gee)

It would have been funny if I had gone to someone elses session and skipped mine, but I am glad I did not as actually quite a few people showed up to mine. I started by saying I had a presentation but would prefer if people just asked questions along the way. And the great part was - did they ever. This included some by Freeman Dyson - kind of cool to have the guru asking me questions about microbial colonization of babies. Finally, after I had spent too much time on background - Drew Endy said something to the effect of "Lets get to the technically hard stuff" and I briefly discussed using genome sequencing to study microbes that live in and on humans. And then - we just had to stop.

I decided to linger for the wrap up session after lunch so I had lunch, made some phone calls, and then we had a wrap up which was mostly an open mike for comments and this ended up being a bit too much of "It was great" and not enough of "How could we make it better." But hey - it was great so I guess I understand. I went around saying thanks to the Google team and the Nature and O'Reilly folks and then moseyed on to the train back to Davis.

Some brief notes about the end and the new beginnings:

• I got lots of ideas for new projects and new things to do from this meeting as with the last one.
• Over the next few weeks I will be posting about some of the other things I saw there and discussing why/how they are interesting.
• I think this "un-conference" style would be really good to emulate for other gatherings. Not sure how to pull it off though.
• I know I will get in trouble from some of my Open Access colleagues, but I definitely came away from the meeting being really impressed with some of the things Nature Publishing group is doing. They really seem to be trying to move into the Web 2.0 area for science communication with Nature Preceedings, and the Nature Network and Scintilla and Connotea and Podcasts and of course Scifoo. Sure there were probably too many people from Nature at Scifoo, but hey, they were sponsoring it so why shouldn't they send them? Here's hoping that they continue to experiment with Open forums and Open material and that they change to OA for all their publications as a way to bring in more people to their Web services. And lets hope other publishers, especially truly open ones build similar resources for the community.
  
• Thanks to Timo Hannay, Tim O'Reilly, and all the folks at Google, Nature, and O'Reilly for organizing this and inviting me.

Some interesting scifoo collections and follow up discussions:

• Nature network discussion of Open Science
• Alex Palazzo's discussion of Open Science
• Nature.Com's SciFoo compilation
• Lexical SciFoo Campfire
• Timo Hannay's overview