Sunday, October 07, 2007

Undercooked meat does not kill people, E. coli O157:H7 does

Which would you prefer? A clean meat supply, where the meat you eat is generally free of nasty pathogenic bacteria? Or a meat supply that has to be irradiated and cooked in order to make it safe?

Check out the article in Newsweek for a sort of discussion of this issue relating to the E. coli O157:H7 strain found in ground beef recently, and more frequently all the time.

Why is E. coli O157:H7 in ground beef in the first place? The answer to this depends on at what point in the life cycle of the meat processing you want to track the E. coli to. Meat processors would like to say it just comes from a little bit of "contamination" during making ground beef. But the real question to me is, why is there so much E. coli O157:H7 around for it to contaminate the ground beef? Well, I like the explanations of Michael Pollan and Eric Schlosser given in the Newsweek article:

Schlosser says
we have a systemic problem here starting in the feedlots, spreading in the slaughterhouses, and winding up in the ground beef at plants that make frozen patties. Putting Topps out of business isn't going to solve that fundamental problem.”
Pollan says
This particular bug was not a problem before the industrialization of the meat supply,” says Michael Pollan, an investigative journalist and food writer. “It’s an adaptation to the feedlot diet [which is composed of corn, ethanol byproducts and other grain feed]. Animals who get a proper diet and are outside eating grass don’t get much of it. Even if you give the animals fresh hay in the last days of their lives, the E. coli burden drops 80 percent. But it would just screw up the workings of the [industry]. The other way [to reduce risk] is to slow down the lines, if you could butcher with more care.”
A meat industry consultant counters this by saying
When you pack people together in cities, diseases pass between them easier. If you’re living in the plains with five miles between households, you’re less likely to get sick. I think it’s the nature of the world. The reality is if you cook the meat you’ll never have a problem. I eat beef a lot and I may get indigestion from time to time, but I don’t get sick. No one will ever get sick if you fully cook the meat. This isn’t rocket science.
Not the most ringing endorsement in the first place (is indigestion supposed to be a good thing?). But Pollan wraps up my feeling on this:
if there is indeed manure in the meat, however microscopic, you’re still eating cooked manure.
So - yes, getting cheap meat will require us to industrialize the process somewhat. But do we really want the meat to be as cheap as possible? I do not think so. I think quality of the environment, quality of the meat, and reducing the spread of nasty pathogens should also be part of the equation. I am not going to start eating raw meat, but just because you can kill the bacteria in contaminated meat does not mean I want to eat it.

Saturday, October 06, 2007

Hilary Clinton on Science and Evolution

The New York Times has an article on Hilary Clinton's science agenda. She discussed space exploration, global warming, stem cells, and evolution. On evolution she says

“I believe in evolution, and I am shocked at some of the things that people in public life have been saying,” Mrs. Clinton said in the interview. “I believe that our founders had faith in reason and they also had faith in God, and one of our gifts from God is the ability to reason.”

“I am grateful that I have the ability to look at dinosaur bones and draw my own conclusions,” she added, saying, too, that antibiotic-resistant bacteria is evidence that “evolution is going on as we speak.”

I think candidates statements on evolution and a nearly perfect test of whether they will really support science or not if they were to be elected. Those candidates that say they do not believe in evolution and/or that they support teaching ID in science classes are unquestionably more likely to not treat science in general very well. And though I could quibble with Clinton's quote (antibiotic resistant bacteria are not per se evidence of evolution --- it is the spread of antibiotic resistance and the rapid origin of new forms of resistance that are due to evolution). But she has the general issue correct. Good to see some of the politicians are not sucking up too much to the anti-science crowds.



Wanted - Entomologist to Work for New York Yankees

Bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs bugs

They are in the news. Yesterday at the Yankees-Indians game in Cleveland, bugs came out in full force. Basically, a swarm of bugs came out in the 8th inning and helped annoy and distract the Yankees pitcher, who then gave up the tying run in the game, which the Yankees went on to lose. Apparently it was a swarm of midges. Whatever it was, expect the value of an entomology PhD to go skyrocketing as Steinbrenner will have to hire a whole team of them.

In addition, the bug puns came out in full force too

Friday, October 05, 2007

The Economist on the power of Evolution

Evolution gets some great props in a new article in the Economist. Specifically they are talking about using "natural selection" as a computation tool in design. I think the article speaks for itself so people should check it out. Some of the quotes I like in particular are:

The inventor’s trial-and-error approach can be automated by software that mimics natural selection
AND
“I HAVE not failed. I have just found 10,000 ways that won’t work.” So said Thomas Edison, the prolific inventor, speaking of his laborious attempts to perfect the incandescent light bulb.
AND
As in biology, most mutations are worse than the original. But a few are better, and these are used to create the next generation.
AND
A century and a half after Darwin suggested natural selection as the mechanism of evolution, engineers have proved him right once again.

Thursday, October 04, 2007

Where math, biology and the bay area meet


A quick posting here on a meeting coming up in the Bay Area. I went and talked at it last year and it was quite rewarding.

The Biology and Mathematics in the Bay Area (BaMBA) meeting is a forum for discussions of concepts, issues, and methods by leading researchers in the applications of mathematics, statistics, and computer science in modern biology.

The goal of the meeting is to encourage dialog between researchers and students from different disciplines in an atmosphere intended to promote the exchange of ideas and viewpoints. BaMBA is a one-day annual event that takes place in the San Francisco Bay Area. The first meeting was hosted by San Francisco State University, the second by the Mathematical Sciences Research Institute and BaMBA III will take place at San Jose State University on November 10, 2007.

Attendance is open to everyone but we expect the majority of the participants from the Bay Area universities (Stanford University, UC Berkeley, UC Santa Cruz, UC San Francisco, San Jose State University, San Francisco State University, University of Santa Clara, and etc). In 2006, BaMBA II attracted around 120 participants.

Mark your calendars:

Saturday, November 10,
from 9 to 5pm.
Eng 189 (San Jose State University)

More information including free
resgistration can be found at www.cs.sjsu.edu/~bamba3.

Tuesday, October 02, 2007

PLoS One Commentary Expansion and Metagenomics of Warm Waters

ResearchBlogging.org

People interested in metagenomics and/or marine microbiology should check out a recent paper in PLoS One on Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat.

In this paper, the authors use metagenomic sequencing to study microbes from 3000m depth int he Mediterranean. The most interesting thing about this paper is that the water at this depth is much warmer than water from similar depths that have been previously studied by metagenomics. The authors do some comparative metagenomic analysis and conclude that temperature of the water is more important than depth in determining the suite of organisms and genes that are present in the water. This is a preliminary result but does being to show the potential power of comparative metagenomic analyses.

The other thing people might want to check out is the Commentary on this article. I have been trying to get people in my lab to layer their comments and annotations onto this article as a test of the new PLoS One system. So far a few people in the lab have added comments as have I and more are coming. Others should add comments too. This commenting system is one of the nice new features of PLoS One in my mind, although it is still in beta testing. One thing I am still trying to work out is the trackback system ...


Martín-Cuadrado, A., López-García, P., Alba, J., Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G., & Rodríguez-Valera, F. (2007). Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat PLoS ONE, 2 (9) DOI: 10.1371/journal.pone.0000914

Wanna help run a major University - apply for this job

U. C. Davis, where I am a faculty, is recruiting nominations and applications for "PROVOST AND EXECUTIVE VICE CHANCELLOR." So if you are itching for something new out there, and think you have what it takes, consider applying.

Oh, and hopefully, from my point of view, you will be more supportive of Open Access publishing than our interim Provost and Executive Vice Chancellor, Barbara Horwitz (see here and here for more on her position on Open Access).

Let me state first, that I realize that Open Access is not the only important thing in the world and that there are many kinds of OA and furthermore that some people may generally support OA but may be worried about how to get there (e.g., see Timo Hannay's discussion of some of his concerns about doing full OA here ).

And Dr. Horwitz has done some quite good things in other aspects of her job. But her more recent foray into the OA debate was so icky, so misleading, that I am really hoping she does not become full time provost and furthermore that whomever does has a different take on the whole thing.

What was it that raised my ire? Well, she was directly involved in what could be considered a bit of a test run of the ideas behind PRISM, the much panned "coalition" against open access. I wrote about the PRISM-esque test run by Horwitz and colleagues here. In summary, she and a group of other anti-OA advocates wrote a letter stating their PRISM-esque objections to the OA movement. For example here is one of their PRISM-esque quotes

"The free posting of unedited author manuscripts by government agencies threatens the integrity of the scientific record, potentially undermines the publisher peer review process, and is not a smart use of funds that could be better used for research."
Ooh you say --- a letter --- what's the big deal. Well, the ten people who wrote the letter wrote it as individuals, but then a PRISM-esque anti OA group wrote a press release wherein they referred to the people who wrote the letters as "University Officials" which they were (all were deans, provosts, etc) and how University Officials were against OA. This was clearly done to give the impression that the Universities themselves were against OA, which was not true. And this misleading presentation was clearly done in collaboration with the letter writers. So Horwitz and crowd allowed the fact that they were University officials to be used to mislead people into thinking that their opinions were POSITIONS of the university.

Horwitz is welcome to her opinions and I agree with Timo Hannay that we need a fair and measured debate about OA (although I think he goes overboard in dinging people for being a bit agressive in their blog commentaries about it --- this is after all what makes blogs a bit fun). But let's not abuse our positions of authority and responsibility within the University to mislead about our positions. And just because we have a pleasant debate does not mean I will support an anti OA advocate to help run UC Davis, not that I have much say in the matter.

But given that U. C. Davis is strong and getting stronger in the sciences means that one key aspect of the recruitment of a new Provost and Executive Vice Chancellor should be how they stand on scientific publishing.

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 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.

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 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/

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
[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]

Friday, August 31, 2007

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.


Thursday, August 30, 2007

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.

Tuesday, August 28, 2007

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:

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

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