Tag: Misc.

I write with sadness that Jeremy Knowles has passed away. Knowles was a Professor at Harvard, had been Dean of the Faculty of Arts and Sciences at Harvard, and an HHMI Trustee, among many things. I did not know him well, but I did have a recent scientific exchange with him regarding analysis we were doing of the Tetrahymena genome. Knowles has asked a question to Peter Bruns, who is a Tetrahymena guru (and also was at HHMI). The question related to intron splice junctions and whether that might support a paper he had written in 1992. The science here is not important.

I wrote back, basically saying we were sequencing the genome but alas our data might not be useful for his question since most of what we were doing at the time was predicting gene splice sites not actually determining them for real. And I said, in fact, much of the data in Genbank was also predictions not real cDNAs.

I expected him to be a bit disappointed. But instead, he wrote back to Peter:

Peter:
Thank you! Jonathan’s response confirms that I was right to ask an expert. For if I had gone fishing in the gene bank pool, I should probably have drowned. I shall wait, calmly.
best,
Jeremy

What I was struck with was his sense of humor and warmth, which emanated from this and a few other simple email messages. Based on these communications, I was looking forward to interacting with him again as we are now writing up a paper including all of our new cDNA data (real sequences, not predictions). I am sorry to see him go.

As someone who studies the “Tree of Life” in terms of evolution (the tree of life is an evolutionary tree relating all life forms) and who even named his blog after this, I am fascinated by different portrayals of the Tree of Life. We can see lots of things like the Tree of Life in the real word. Much of this is due to the use of the Tree of Life imagery by various religious groups. Some of it is more connected to evolution in some way. But whatever the inspiration, there are some pretty nice representations out there. And I am posting one of them today. At UC Davis the UC Davis Arboretum is a really spectacular place. I go walking there all the time and take my kids to play there and watch the ducks and other animals. One day, I was walking near some gardens that they have been renovating for a while, when I saw they had unveiled some new artwork.

Below are some pictures of this artwork.  I am going to start posting more “Tree of Life” art here in the future and would love to get examples from people out there too.

http://picasaweb.google.com/s/c/bin/slideshow.swf

A quick post — here are some relatively new interesting papers in metagenomics that are fully Open Access

• A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. Schloss & Handelsman BMC Bioinformatics 2008, 9:34
  
• Picoeukaryotic sequences in the Sargasso Sea metagenome. Piganeau et al. Genome Biology 2008, 9:R5
• Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PLoS ONE. 2008; 3(2): e1584
• The airborne metagenome in an indoor urban environment. PLoS ONE. 2008 3(4):e1862.

Well, I signed up for emails from the Bill and Melinda Gates Foundation, hoping to apply for some of their trillions of dollars to do a little bit of research.

And I got an email today I would like to share, since, well, they said I should share it. And here it is ..

The Bill & Melinda Gates Foundation is now accepting grant proposals for Grand Challenges Explorations, a US$100 million initiative to help scientists pursue innovative ideas for solving major global health problems.

Grant proposals are being accepted online at www.gcgh.org/explorations until May 30, 2008, on the following topics:

— Creating new ways to protect against infectious diseases
— Creating drugs or delivery systems that limit the emergence of resistance
— Creating new ways to prevent or cure HIV infection
— Exploring the basis for latency in TB

Initial grants will be $100,000 each, and projects showing success will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the topics and application instructions are available at www.gcgh.org/explorations.

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. If you don’t submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world’s greatest health challenges.

###
Bill & Melinda Gates Foundation

Guided by the belief that every life has equal value, the Bill & Melinda Gates Foundation works to reduce inequities and improve lives around the world. In developing countries, it focuses on improving health, reducing extreme poverty, and increasing access to technology in public libraries. In the United States, the foundation seeks to ensure that all people have access to a great education and to technology in public libraries. In its local region, it focuses on improving the lives of low-income families. Based in Seattle, the foundation is led by CEO Patty Stonesifer and Co-chairs William H. Gates Sr., Bill Gates, and Melinda French Gates.

Just got an email announcing a new issue of Davis Life Magazine which I meant to post about here previously. It is a nice little web magazine about, well, life in Davis.

Well, the News is abuzz with discussion of a controversy involving lung cancer studies that were funded by tobacco associated money (e.g., see MSNBC and TIME and the NY Times). The issue is that apparently the source of the money was hidden through some sort of laundering of the money through a foundation.

As many readers know, I am a bit obsessed with open access to scientific research publications. This here is a case where the need for openness goes well beyond publications. Here there is a need for openness about funding and conflicts of interest and the roles of all participants. In this case, I am not sure what could have been done by the journals involved to vet the funding of the project more carefully. But nevertheless, science in general can be severely hurt whenever there are cases of even the appearance of conflict of interest. I do believe that open access journals help in this in that anyone, anywhere, can look at the publication as well as the descriptions of the funding sources and the authors contributions. The more eyes we have on research products, the more likely problems will be discovered and (possibly) the less likely it will be to happen again.

Way to go Amanda Plunkett – featured on the UC Davis front page and in the UC Davis Magazine.

Well, the new NIH policy is not perfect, but it is a good first step. And I must say, I got a tingle of excitement when I got this email from the UC Davis Administration:

March 20, 2008

I am writing to alert you to a new requirement for investigators who receive funding from the NIH. Under the Consolidated Appropriation Act of 2008, the NIH will require that all NIH-funded investigators submit or arrange for the submission of an electronic version of their final, peer-reviewed manuscripts accepted for publication to the National Library of Medicine’s PubMed Central. PubMed Central (PMC) is the NIH’s publicly-accessible, digital archive of full-text, peer-reviewed journal articles. This new law requires manuscripts to be made publicly available via PMC no later than 12 months after the official date of publication. Please note:

1. This requirement applies to all peer-reviewed articles that arise, in whole or in part, from direct costs funded by NIH, or from work of NIH staff, that are accepted for publication on or after April 7, 2008.

2. UC Davis investigators are responsible for ensuring that any publishing or copyright agreements concerning submitted articles fully comply with this requirement. To satisfy this obligation, UC Davis investigators should enclose a copy of the one-page letter prepared by the UC Office of the President with any articles submitted to publishers for possible publication either at the time the article is submitted or with the publication agreement. The subject letter is available at: http://www.ucop.edu/raohome/cgmemos/08-05a.pdf).

3. The final, peer-reviewed manuscript submitted to PMC must include all graphics and supplemental material that are associated with the article.

4. Beginning May 25, 2008, anyone submitting an application, proposal or progress report to the NIH is also required to include the PMC reference number when citing applicable articles arising from NIH-funded research. This requirement applies to proposals submitted to the NIH for the May 25, 2008 due date, as well as subsequent due dates.

5. Certain publishers have agreed to automatically submit articles to PMC on behalf of the authors. The list of these publishers can be accessed at http://publicaccess.nih.gov/submit_process_journals.htm

Even if a publisher is on this list, UC Davis investigators should verify that their published articles will be submitted to PMC in compliance with the law. If the publisher is not on the list, UC Davis investigators are responsible for submitting their articles to PMC and verifying receipt of the article.

6. Failure to comply with this policy may jeopardize future NIH funding.

Additional information about this law is available at http://publicaccess.nih.gov. Also, the UC Davis Library can provide further assistance to investigators. Please see http://www.lib.ucdavis.edu/dept/hsl/resources/other/nihmandate/ or contact the Library’s sciences department heads: