Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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 “
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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 http://www.cs.sjsu.edu/~bamba3.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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