Eisen Lab Blog

Prejudice and DNA

There is an article in this Sundays’ New York Times by Amy Harmon about prejudice’s possibly being revived and stoked by the oncoming personal genomics revolution. I think there is no doubt this is coming. The problem is really two fold in my opinion.

First, as reflected in the story, it is pretty clear that despite the claims of some researchers who seem like they simply want to avoid the subject, we will start to see more findings of genetic differences among populations. . For example, Marc Feldman from Stanford (who by the way was on my thesis committee) is quoted as saying

“There are clear differences between people of different continental ancestries,” said Marcus W. Feldman, a professor of biological sciences at Stanford University

The second part of the problem, in my opinion, is an extension of something I complain about routinely here – the overselling of genomics. In this case we have a double effect. First, is the effect of “DNA.” Somehow, when analysis of DNA is part of a study or story, people seem to overestimate its importance. Then comes the genomics-effect. Since genomics is about “all” the DNA, it carries even more weight than normal DNA studies. On the one hand, this is reasonable, as genomics does give a more thorough picture than past genetic studies. But on the other hand, genomics gets oversold as somehow telling the whole story. In this regard I buy the argument in the Harmon story reflected in the quote by David Altschuler that

it is so clear that the economic and social and educational differences have so much more influence than genes. People just somehow fixate on genetics, even if the influence is very small.”

I certainly think personal genomics is going to reveal lots of interesting connections between genes and various phenotypes. But there is no doubt data from personal genomics will lead to the amplification of prejudices and biases already present.

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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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Nice pro open access editorial in The Journal Times

The Journal Times has a new editorial in support of Open Access publishing.

Key phrase:

While open access to information won’t eliminate the development work, by continuing to limit public access to the information for which the public has paid, we risk losing that vital moment of inspiration which leads to something that makes our lives easier, or healthier, or to a whole new industry. It’s not a risk we can afford to keep taking

I could not agree more.

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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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Population genomics gets real in Drosophila

There has been lots and lots of talk about “population genomics” in the last few years. For microbes, people have been doing this type of genome wide survey within populations for some time. But for multicellular organisms there have been only a few studies and most of these were limited in scope. Now comes a in depth study of Drosophila simulans published in PLoS Biology. This project, led by colleagues of mine at UC Davis (David Begun is first author, Chuck Langley is senior author) did “light” whole genome sequencing (at the Washington University Genome Sequencing Center) of seven lines of D. simulans and one line of D. yakuba.

There is lots of interesting population genomics, population genetics and evolutionary analysis in this paper. If anyone out there is interested in personal genomics or human population genomics in any way, it is worth checking out this paper as a model for what can be done in multicellular eukaryotes.

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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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New from the Public Library of Science – PLoS Neglected Tropical Diseases

Well, obviously most people will not want to get one of these “Neglected” tropical diseases, but if you do, one would bet you will be surfing the web trinyg to find out more about it.

And alas, most of the research on such diseases is hidden behind journal restrictions. That was, until now.

Check out the PLoS NTDS Web Site to or Bora’s blog to learn more.

Also check out the editorial by Margaret Chan, the Director General of the World Health Organization. She says

The launch of PLoS Neglected Tropical Diseases marks yet another turning point in the long and notorious history of some of humanity’s oldest diseases. ….

The free availability of leading research articles will benefit decision-makers and diseases control managers worldwide. It will also motivate scientists, both in developing and developed countries.

There is also an interesting population genetic study of Leptospira interrogans.

Good to see this journal out there.

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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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SF Gate Column on "You big, fat pile of bacteria"

There is an interesting column on SFGate.com about microbes living in and on people. By Mark Morford, SF Gate Columnist

He talks about eating earthworms as a kid.

Of course, it turns out, biologically speaking, that big, dirty earth-muncher probably did my immune system, my intestinal tract and all the happy bacteria therein a world of good. It’s true.

Furthermore he says

we as an overpampered culture are probably not getting enough nasty buggy immune-system-boosting microbes in our diet, in our meats, in our mouths. And therefore we should probably, you know, eat a bit more crap.

I am not sure I would go as far as suggesting eating crap, but I second the notion that we as a society have to stop being obsessed with getting rid of all bacteria. Bacteria are overall good.

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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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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.

http://www.comedycentral.com/sitewide/video_player/view/default/swf.jhtml

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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 – 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.

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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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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.
    [googlemaps https://maps.google.com/maps?f=q&hl=en&geocode=&time=&date=&ttype=&q=cold+spring+harbor,+ny&ie=UTF8&t=h&om=1&s=AARTsJp3e5KgjeAd4nPGwvhPk7OmTHUonA&ll=40.892656,-73.469782&spn=0.009732,0.012875&z=15&output=embed” frameborder=”0″ height=”300″ scrolling=”no” width=”300″>
    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. http://maps.google.com/maps?f=q&hl=en&geocode=&time=&date=&ttype=&q=cold+spring+harbor,+ny&ie=UTF8&t=h&om=1&s=AARTsJp3e5KgjeAd4nPGwvhPk7OmTHUonA&ll=40.927132,-73.470726&spn=0.038909,0.051498&z=13&output=embed
    View Larger Map
  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
  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?
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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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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.

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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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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
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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.

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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.

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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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