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.
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.
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
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.
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.
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.
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
Any other suggestions that would stick in Watson’s craw?
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
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):
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?
Just a quick note to suggest people check out Mendel’s Garden at “Discovering Biology in a Digital World“
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 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.
Jonathan Eisen's Lab 