Venter on Colbert

Craig Venter was on Colbert last night, talking mostly about synthetic biology and using microbes to make various things (e.g., energy). Colbert kept trying to egg him on in various areas, but Craig played the straight man again (like the last time he was on Colbert) through most of it. Although I should note, Craig seemed much more relaxed this time.

Wanted - Good Microbiologist/Molecular Geneticist for UC Davis Section on Microbiology

Continuing on my trend of posting UC Davis Jobs of Relevance to my Blog. Here is a new posting:

ASSISTANT PROFESSORS
MICROBIOLOGY AND MOLECULAR GENETICS

The Section of Microbiology, College of Biological Sciences, University of California, Davis, invites applications for two tenure-track positions at the level of Assistant Professor. This is a broadly based search for candidates working on bacterial, archaeal or eukaryotic systems (microbial and non-microbial). Candidates must have an outstanding record of achievement in research and will be expected to develop a strong, externally funded, research program in microbiology and/or molecular genetics. Successful candidates will be expected to participate in normal undergraduate and graduate teaching responsibilities. Department faculty members use microbial and non-microbial systems to study diverse research subjects ranging from environmental microbiology and bacterial gene regulation to single molecule studies of protein-DNA interaction and transcriptional control in mammalian cells. See http://microbiology.ucdavis.edu/ugfaculty.htm for descriptions of faculty research. Due to limits on laboratory space availability, one of the two positions must commence on or after January 1, 2009. Applicants should submit (1) a curriculum vitae, (2) a statement of current and proposed research, (3) copies of no more than two key publications, (4) a statement of teaching interests, and (5) arrange to have at least three letters of recommendation submitted. Applications will only be accepted online at http://microbiology.ucdavis.edu/. Please see the website for details.
While applications will be reviewed until the positions are filled, only applications completed by November 16, 2007 can be assured of full consideration. 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 a respect for differences.

Ten Things I Love About Cold Spring Harbor Laboratory

I know. They have gotten a bit of negative publicity recently. But CSHL is a great place. Here are some reasons.

1. Dolan DNA Learning Center. A pioneer in many aspects of biotechnology and genomics education.
   
2. Banbury Center. Just on the other side of the harbor from the main lab. The Banbury Campus is a truly spectacular place to hang out. I would know. I must have gone there a dozen times while working on my textbook. It has great places to walk to, like down a big hill to a secluded beach. And it is always peaceful and pleasant.
   
   View Larger Map
3. The main campus. Also a very pleasant place to hang out. Not quite as nice maybe as Banbury, but still very peaceful and conducive to science.
4. Meetings and Courses. They have quite a collection of well known meetings and courses. Personally, I have a place near and dear to my heart for the main Genomes meeting, which I used to go to often. It was the place where I first talked about "Phylogenomics" as a means to predict gene function and this was how I got my first taste of the lab.
   
5. Books from CSHL Press Of course I am a bit biased since they just published my evolution textbook, but the general quality of what they publish is very very very high. So many of these books have been key parts of my education including "A short course in bacterial genetics," "Molecular biology of the gene", "A genetic switch", The Archaeal Laboratory Manuals, "Molecular cloning: a laboratory manual" and many others. They publish some good journals too, but since they are not fully Open Access journals, I will not mention them here but hopefully these will become more Open as time goes on.
   
6. Caumsett State Park. Just around the corner from the Banbury Campus it is a delightful location. When I was working on my textbook and living on the Banbury Campus I would try to bike to Caumsett every day for a break.
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7. Biking down (and up) Snake Hill Road. See Google Map here. It is very steep and curvy and very fun and short enough to go up without killing yourself
   View Larger Map
   
8. Alex Gann. He was the original editor for my Evolution textbook. Conjure up an adjective to describe anybody you know. That adjective remarkably describes Alex too. He is anything and everything, good and bad, all rolled into one.
   
9. Barbara McClintock. I am not sure what it is about her that is so fascinating but her persistence about jumping genes is awe inspiring. And of course, she was right about something very important when lots of people told her she was wrong.
   
10. The lab was named after a Billy Joel album. How cool is that?

Microbial genomics and Metagenomics workshop

For those interested in microbial genomics or metagenomics see the announcement here:

The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics, in Walnut Creek, California, January 7-11, 2008. The workshop includes two days of intensive seminars and three days of hands-on tutorials. The goal is to provide training in microbial genomic and metagenomic analysis and to demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research. Participation is limited to 40 attendees (graduate students, postdocs, and faculty or staff scientists). To register for the workshop, submit your application online from the registration page: http://www.jgi.doe.gov/meetings/mgm/

Note the Workshop is FREE. Yes that is right. FREE.

URGENT - IF YOU SUPPORT OPEN ACCESS TO SCIENTIFIC LITERATURE - WRITE YOUR SENATOR NOW

I am posting this which I received in an email.

URGENT CALL TO ACTION: Tell your Senator to OPPOSE amendments that strike or change the NIH public access provision in the FY08 Labor/HHS appropriations bill
--------------------------------

The Senate is currently considering the FY08 Labor-HHS Bill, which includes a provision (already approved by the House of Representatives and the full Senate Appropriations Committee), that directs the NIH to change its Public Access Policy so that participation is required (rather than requested) for researchers, and ensures free, timely public access to articles resulting from NIH-funded research. On Friday, Senator Inhofe (R-OK), filed two amendments (#3416 and #3417), which call for the language to either be stricken from the bill, or modified in a way that would gravely limit the policy's effectiveness.

Amendment #3416 would eliminate the provision altogether. Amendment #3417 is likely to be presented to your Senator as a compromise that "balances" the needs of the public and of publishers. In reality, the current language in the NIH public access provision accomplishes that goal. Passage of either amendment would seriously undermine access to this important public resource, and damage the community's ability to advance scientific research and discovery.

Please contact your Senators TODAY and urge them to vote "NO" on amendments #3416 and #3417. (Contact must be made before close of business on Monday, October 22). A sample email is provided for your use below. Feel free to personalize it, explaining why public access is important to you and your institution. Contact information and a tool to email your Senator are online at http://www.taxpayeraccess.org/nih/2007senatecalltoaction.html. No time to write? Call the U.S. Capitol switchboard at (202) 224-3121 to be patched through to your Senate office.

If you have written in support before, or when you do so today, please inform the Alliance for Taxpayer Access. Contact Jennifer McLennan through jennifer@arl.org or by fax at (202) 872-0884.

Thanks for your continued efforts to support public access at the National Institutes of Health.

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

SAMPLE EMAIL

Dear Senator:

On behalf of [your organization], I strongly urge you to OPPOSE proposed Amendments #3416 and #3417 to the FY 2008 Labor, Health and Human Services and Education Appropriations bill (S.1710). These amendments would seriously impede public access to taxpayer-funded biomedical research, stifling critical advancements in lifesaving research and scientific discovery. The current bill language was carefully crafted to balance the needs of ALL stakeholders, and to ensure that the American public is able to fully realize our collective investment in science.

To ensure public access to medical research findings, language was included in the in the FY 2008 Labor, Health and Human Services, and Education Appropriations Bill directing the NIH to make a much-needed improvement to its Public Access Policy -- requiring that NIH-funded researchers deposit their manuscripts in the National Library of Medicine's online database to be made publicly available within one year of publication in a peer-reviewed journal. This change is supported by NIH Director Elias Zerhouni, and a broad coalition of educational institutions, scientific researchers, healthcare practitioners, publishers, patient groups, libraries, and student groups -- representing millions of taxpayers seeking to advance medical research.

Amendment #3416 would eliminate this important provision, leaving only a severely weakened, voluntary NIH policy in place. Under the voluntary policy (in place for more than two years) less than 5% of individual researchers have participated -- rendering the policy ineffective. The language in Amendment #3417 would place even further restrictions on the policy, ensuring that taxpayers - including doctors and scientists - are unable to take full advantage of this important public resource.

Supporting the current language in the FY08 LHHS Appropriations Bill is the best way to ensure that taxpayers' investment in NIH-funded research is used as effectively as possible. Taxpayer-funded NIH research belongs to the American public. They have paid for it, and it is for their benefit.

I urge you to join the millions of scientists, researchers, libraries, universities, and patient and consumer advocacy groups in supporting the current language in the FY08 LHHS Appropriations bill and require NIH grantees to deposit in PubMed Central final peer-reviewed manuscripts no later than 12 months following publication in a peer-reviewed journal. Vote NO on Amendments #3416 and #3417.

Whose genome should Roche/454 sequence to make up for selecting Watson's?

In honor of one of my favorite places on the planet, Cold Spring Harbor Laboratory, I am trying to distract some of the negative attention that has come from James Watson's latest choice of words. So I am calling on everyone in the community to come up with recommendations for whose genome Roche should sequence with the 454 technology to make up for the fact that they did Watson's genome. And it would be good if the pick was someone that would make Watson a bit queasy.

Here are my top picks

• Condoleezza Rice. An absurdly powerful, smart, black woman.
• Francis Crick. Someone has to have some of his hair somewhere.
• Rosalind Franklin. Not sure about the hair. But wouldn't it be great if she was one of the reference genomes.
• Francis Collins. Apparently no love lost between Francis and Jim.
  
• Craig Venter. Sure his genome has been nearly completed. But why not do it again with another method.
  

Any other suggestions that would stick in Watson's craw?

Overselling genomics (and men) award #3 - Newsweek Magazine

Newsweek Magazine has a feature on the "10 hottest nerds" that they say are "10 of the most esteemed biologists" in the w0rld. And they ask for their insights into various things. The people are

• Eric Lander
• Leroy Hood
• Craig Venter
• David Botstein
• Svante Paabo
• Philip Sharp
• Rudolph Jaenisch
• Kari Stefansson
• George Church
• Jay Keasling
  

Sure these people have done good things and I truly respect most of them in many ways. But are they kidding me? This is who they pick? First of all, all men? Mostly, all people who have been around the block too. Plus, almost all these people work in something connected to genomics (Lander, Hood, Venter, Botstein, Paabo, and Church are major genomics players; Keasling and Sharp and Stefansson are heavily genomics-based).

They couldn't come up with a single woman? Or anyone doing anything else? Or any new researchers? This whole thing is completely egregious. There are plenty of completely cool things going on in biology that have little if any connection to genomics, that are not men, and/or are not established researchers.

And to get the conversation going here are some people they could have considered to diversify in at least one dimension (i.e., the male versus female thing):

• Kristen Scott
• Hopi Hoekstra
• Pamela Bjorkman
• Philippa Marrack
• Elizabeth Blackburn
• Julie Theriot
• Susan Lindquist
• Andrea Brand
• Joan Steitz
• Lucy Shapiro
• Sharon Long
• Colleen Cavanaugh
• Cindy van Dover
• Mary Claire King
• Rita Colwell
• Claire Fraser
• Nancy Moran
• Katie Pollard
• Linda Partridge
• Sarah Otto
  

I came up with this list in about 20 minutes, based mostly on people I know. And of course, there are TONS of other women in biology who are doing fantabulous research. Even if one did not know anything, a little time on Google pulls up a vast collection of resources -- (e.g., see L'Oreal's for Women in Science page or this Wikipedia page for more suggestions). And of course lets not forget that genomics is not the only thing going on in biology.

So - Newsweek - you are getting my third "Overselling Genomics Award" and on top of that a bonus "Overselling Men" award. All I can say is - what were you thinking?

Check out Mendels Garden at DBIADW

Just a quick note to suggest people check out Mendel's Garden at "Discovering Biology in a Digital World"

Appendix story in need of an asterix and appendix and a retraction

The appendix. What is it good for?

That was the topic of a series of news stories and a press release last week that somehow I did not blog on even though Thomas Goetz sent me the story. I was busy at a conference mind you but this is such easy pickings. This has got to be one of the poorer science reporting jobs done in a while and also one of the most misleading press releases I have seen. In the press release there are a series of phrases that make it seem like the scientists have discovered a major function for the appendix:

Appendix Isn't Useless At All: It's A Safe House For Good Bacteri

AND

William Parker, Ph.D. is one of a team of scientists to discover that the appendix has a function -- protecting beneficial bacteria.

And the reporting seems to have bought this hook line and sinker. See

• The appendix does have a use – re-booting the gut
• Appendix: It’s not useless after all
• Scientists discover true function of appendix organ
• Purpose of Appendix Believed Found
• Study: Yes...your appendix has a purpose

The problem? Wanna know what they actually did in their paper? Well if you have a subscription to the Elsevier published Journal of Theoretical Biology you can go read the paper here. If you do not have a subscription I quote some of the abstract for you

We propose that the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen

The key word here is "propose." In the paper, they do not actually really show direct evidence for any function. And the title of the journal should hint at this - the Journal of Theoretical Biology. It is a place for scientists to put out new hypotheses, including those that have little evidence behind them. Nothing is wrong with such a journal. Hypotheses are a good thing.

Sometimes things in this journal have lots of evidence and in other cases they do not. In this case I do not think they present any direct evidence and the evidence they present is at best circumstantial and unconvincing. Basically, they lay out a hypothesis that the appendix may have some role in the immune system. Then they highlight a further series of circumstantial connections and inferences to come to the idea that the appendix may have some role in harboring "beneficial" microbes in the gut.

It is an interesting theory. It could be true. But the evidence they present is very very circumstantial and weak at best. They seem to claim that stronger evidence would be impossible to obtain since doing experiments on humans is not easy. But given the large number of people who have had their appendices removed, one could actually do a retrospective study of how well such people recover from pathogen attacks or the use of antibiotics. Until such a study is done, it would be wrong to say these authors discovered anything. What they did is propose a hypothesis for a function of the appendix. The hypothesis might stimulate discussions and some research but lets not oversell it.

In many ways you could consider their hypothesis much like the hypothesis that microbial life existed on Mars. This Mars idea is plausible. But there is currently no evidence for it. Imagine if the reporters said "Life found on Mars" in relation to a paper proposing that life might have existed on Mars. The reporting here is no different - though the stories got it wrong. In part this is because the press release is so misleading. But reporters have got to go beyond the press release or the initial story. Just see Carl Zimmer's blog for a great example of bad reporting.

Genomics by Press Release Award #1

Well, I have tried to hold off giving out awards here since I kind of botched my last attempt at this. But here goes.

Yesterday, researchers in South Africa announced that they had sequenced the genome of a XDR strain of the bacterium (Mycobacterium tuberculosis) that causes TB. I sniffed around this story because someone who used to work for me, James Sakwa, was mentioned in some of the stories.

The stories proclaim how quickly the researchers were able to sequence this genome with quotes like

(It) took us just over a week, using other technology it would have taken up to a year," he told AFP.

This sounded a lot like other claims of rapid genome sequencing ... and I was skeptical since just doing some shotgun sequencing, with whatever method, does not lead to a complete genome. Alas, it looks like my skepticism is valid. The AP reports

The complete genome sequencing data has not yet been shared with other scientists. Previous tuberculosis strains have already been mapped, and some experts are uncertain how quickly the research will result in new diagnostics or treatments.

So - there is apparently no paper associated with their work. And the data is not being shared. So in that spirit, I am announcing here that I have sequenced the genome of Albert Einstein Marie Curie and Al Gore Barbara McClintock this morning on my new EXCERCYCLER machine we invented here in Davis. It is a new green sequencing technology that is powered by a bicycle and the sequence data is generated by feeding pieces of DNA into the front derailer and sequence comes out of the back derailer. See hazy image below.

How Al Gore changed my life and Congratulations on a well deserved Novel Prize

My life changed a great deal in 1989 when Al Gore came to speak at Harvard for the Environmental Action Committee in which I was involved. In honor of his Nobel Peace Prize here are my notes from his talk which I had intended to write up for a Biology Department newsletter but never did. I never finished the notes but here is the start.

Senator Al Gore '69 spoke to Science A-30 class (as well as many others) in the end of November. His main focus was change in the global environment (i.e greenhouse effect, pollution, ozone depletion, deforestation, etc.) and what can and should be done about such issues. Senator Gore's interest in the environment, now almost a crusade, was sparked in a class he took at Harvard from Prof. Ravel. Gore suggested that the first step that we as a nation, and as a species, must take is to recognize that there is a problem. He referred to the classical biology example of the frog in a pot of water. If the temperature of the water is increased rapidly then the frog will be leaping at the opportunity to get out. However, if the temperature of the pot is increased gradually the frog may not sense anything, and will cook in its own innocence. According to Gore, today's society is prone to such a way of thinking. Society is least likely to recognize those changes in the environment that occur over long periods of time. It is like the Far Side cartoon in which a caveman asks his friend if the ice wall looks a bit closer today.

So, the first step is to recognize that changes are going on, and that they are more that just gradual, that they are completely new in quality and quantity. The main problem today as compared to two thousand years ago is that the changes are happening too fast. The population is increasing at a rate never seen before. Rapidly increasing levels of greenhouse gases may lead to changes in climate and temperature that will be too fast for many organisms to respond. Extinction rates, already higher than any time since the "great" dinosaur extinction, may increase even more as organisms get wiped out by the environmental changes. Ozone depletion over the antarctic may just be a warning of a decrease over the temperate and tropical areas. The subsequent increase in UV light levels at the surface of the earth could have catastrophic effects. Industrialists and many government officials suggest that "science" will be able to cure these problems in the future

This same type of graph can be shown for ozone depletion, deforestation, pollution, soil erosion, and species depletion. However, as long as their is a lack of consensus as to the amount of change, and to the degree that any of these changes will affect human's (especially those alive today), there will be little change in government policy. In essence, Gore says, we are doing what the frog did.

There are quite a few criticisms to Gore's approach. Technology, that wonderful thing that has brought us strip mining, and artificial hearts, may be able to, in the future, reverse some of those things we are doing now. So why limit growth, when we can clean up later. It's like when I was a kid, "But mom, I'll clean up after Tom and Jerry" knowing full well that I wouldn't and running the risk of getting attacked by one of the dust balls under my dresser. However, if I made a real mess, such as one that would stain something, I had to clean it up then and there. The problem is that everyone seems to think all of these processes that are taking place in the atmosphere are reversible when in fact they may not be. Species depletion clearly is not. And if the other processes are allowed to run amok, we will likely have one big mess on our hands.

I went up and talked to Gore afterwards and found him truly inspiring. It was this discussion that helped guide me to start a new Environmental Issues journal at Harvard and to do various other things for Earth Day 1990. Anyway, all I can say is congratulations to Al Gore, a Nobel Prize well deserved for someone who has been working to help our planet for at least 20 years.

----------
UPDATE: Found my notes from his talk.  I scanned them in and am posting here

Biofools on Eye in the Sky

Eye on the Sky's (Michael Ferrari) has a little post on Biofoolery and Water usage. In it he links to the new NAS report on this topic.

Ten things to NOT do at a conference

Well, overall I am liking the GME meeting I am at. But not all of it. And some things here are instructional for what NOT to do at a conference, either as an attendee or as a presenter or as an organizer. Here are some of them

DO NOT:

1. Go way over your allotted time to speak. Even if the chair of a session lets you do this, don't. It is rude to the audience and to other speakers.
2. Lack empathy for your audience. Take a few minutes to imagine what the audience might want to get from your talk. Some of the speakers here are much more concerned with what they will get from the presentation.
3. Use a lot of slides with way way way too small text or images.
4. Answer cell phone calls in the middle of the audience. Yes, that's right, scientists can be jackasses. Imagine that.
5. Corner people who are on the way to the restroom. Let people go.
6. Make an opening statement when asking questions like "That was a great talk" or "That was an interesting talk" or anything like that. Don't be a suckup. Just ask your question.
7. Be rude to the meeting helpers when you forget something. Come on. If you are not registered for the meeting it is most likely that you screwed something up, not the meeting.
8. Ask many follow up questions after your question. If you want to have a discussion, buy a beer for someone. If you have a straightforward question that is answerable - ask it. If you want to make a simple statement, fine. If you want to go on and on ... get a room.
9. Write in your blog in the back of the room (hey, I did not say I was perfect).
10. Have too little time for breaks. The best part of conferences is the coffee and other breaks. No need to have too many talks. Have lots of breaks.

I am sure there are other things to not do ... but these are those that come to mind right now.

GME 2007 - Getting feedback on PLoS ONe

While at the GME meeting - I have now been approached by 3 people saying they really liked the discussion I initiated on PLoS One for a paper on metagenomics a few weeks ago. They were not saying they liked my comments but that there was an active discussion about some important topics. I think the function on PLoS One has great potential to engage the broad scientific community in discussions that might have previously been limited to journal clubs. So it is nice to see (1) that people are reading stuff on PLoS One and (2) that they seem to like the commenting function.

GME 2007 - Genomes, Medicine and the Environment

I am now at the "Genomes, Medicine and the Environment" conference in San Deigo. It looks to be quite good and diverse. Here is the schedule for Monday. I will try and post notes either as they happen or later tonight. First note --- my undergrad. advisor, Colleen Cavanaugh is showing some cool pictures of deep sea organisms and their symbionts that chemosynthesize for them. She says "genomics is literally like opening a window into our science, because we cannot culture any of these symbionts." And now she is talking about our paper on the symbionts of the giant clam, Calyptogena magnifica. It is really cool for me to see this -- Colleen was the person who got me interested in microbes and symbioses and even though I only worked in her lab for 1.5 years, it changed my life and scientific career.

NOTE - I AM POSTING SOME NOTES IN THE COMMENTS ON THIS ENTRY.

Opening Remarks, J. Craig Venter, Ph.D., JCVI
	Synthetic Biology
	Colleen Cavanaugh, Ph.D., Harvard University - "Genomic Insights into Chemosynthetic Symbioses"
	Nancy Moran, Ph.D., The University of Arizona - "Genomics of Symbiotic Bacterial Communities within Insects"
	Hamilton Smith, M.D., J. Craig Venter Institute - "Toward a Minimal Cell"
	BioEnergy
	Steve Briggs, Ph.D., University of California, San Diego - " Development and Application of Protein Profiling Methods"
	Yuri Gorby, Ph.D., J. Craig Venter Institute - "Electromicrobiology: The Role of Bacterial Nanowires in Extracellular Electron Transfer"
	Edward Bayer, Ph.D., Weizmann Institute of Science - "Bioengineering of Cellulosomes: Prospects for Conversion of Biomass to Bioenergy"
12:00-2:00	Lunch, Sunset Ballroom
	Environmental Genomics
	John Heidelberg, Ph.D., University of Southern California - "Genomic, Metagenomic and Functional Analyses of Cyanobacteria from Hot-Spring Microbial Mats"
	Gene Tyson, Ph.D., Massachusetts Institute of Technology - "Metatranscriptomic Analysis of Microbial Communities in the North Pacific Subtropical Gyre"
	Syed Hashsham, Ph.D., Michigan State University - "Understanding Microbial Community Succession in Response to Substrate Shock using Roche 454 GS FLX Sequencing System"
	David Schwartz, M.D., National Heart, Lung & Blood Institute Toxicology Program - "Environmental Genomics and Human Health"
	Human Metagenomics
	Ren Bing, Ph.D., University of California, San Diego School of Medicine - " Annotating the Human Genome - a ChIP-chip Approach"
	Russell M. Gordley, B.A., Scripps Research Institute - " Evolution of Programmable Zinc Finger-recombinases with Activity in Human Cells "

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.

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

• Gnats Gnot Gnice
• Indians work out the bugs
• Pest control
• No idea the place was bugged
• Tribe swats Yanks again, eyes sweep CLEVELAND 2, NY 1 (11)
• GNAT THIS TIME
• Joba, Yankees can't avoid the plague
• Indians Feel the Buzz
• Bug off Yanks: Tribe takes 2-0 series lead
• Indians continue to bug Yanks
• Bitten and beat, Yanks seek cure
• Indians bug Yankees with itch to win
• YANKS VICTIM OF INSECTICIDE
• NOW THEY'RE IN A SWARM OF TROUBLE
• JOBA BUGGIN'
• No bugs about it: Indians roll
• Yankees bug out
• Indians work out the bugs
• Tribe win? Gnaturally
• Perfect swarm

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.

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.

PLoS One Commentary Expansion and Metagenomics of Warm Waters

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.