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

Open Access Day

Today is Open Access Day.  For more information see here.  It is a big celebration of, well, Open Access to scientific and medical literature.

We are going to have a little shindig at Davis (organized by a grad. student Collin Ellis who is also starting a new organization here on Campus – the UCD-SSOA (Society of Scientists for Open Access).  The shindig will include a live WebCast of OA Day presentations by Richard Roberts (who has one of them Nobel Prize thingies) and Phil Bourne (Editor in Chief of PLoS Computational Biology, and creative mind behind a ton of OA initiatives).  The meeting will be in the Genome Center, GBSF 4202.  FIrst showing of the webcast at 4.  Second showing at 7.  In between I will give a little talk on “Why Open Access is Good for Scientists and the World”.

Hope others will enjoy the day too.  More later …
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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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arXiv reaches 500,000 papers …

Pretty cool that there are 500,000 papers in arXiv (see Slashdot | Free Online Scientific Repository Hits Milestone). Hat tip to Jeremy Peterson for pointing this out. See also Peter Suber on this (Milestone for arXiv)

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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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Open Science Pioneer Award: Douglas Prasher and the Sharing of the GFP Gene

There is a touching and fascinating story in the Cape Cod Times about Douglas Prasher who used to work at Woods Hole Oceanographic Institute. In the 1960s he did some of the pioneering work on GFP (the discovery of which was why Osamu Shimomura, Roger Tsein and Martin Chalfie were given the Nobel Prize in Chemistry this year). Prasher had cloned the gene for GFP but his research funds ran out and he stopped working on GFP (he is currently living in Huntsville Alabama and working as a shuttle driver for a car dealership).

His pioneering work was critical to the later work on GFP and one of the nobel winner Martin Chalfie says

“Prasher’s work was critical and essential for the work we did in our lab,” Chalfie said. “They could’ve easily given the prize to Douglas and the other two and left me out.”

What Prasher did that was so critical was that he gave the cloned gene away to Tsein and Chalfie and others. He was under no obligation per se to give away the gene. But he bears no sour grapes. And he says something fundamentally true about this:

“When you’re using public funds, I personally believe you have an obligation to share,” Prasher said. “I put my heart and soul into it, but if I kept that stuff, it wasn’t gonna go anyplace.”

Sharing of resources is common in science but not universal. And many do it, well, just because it is common practice. But I think we forget sometimes that we have an obligation to share beyond what is common practice. We have an obligation because the advancement of science is why the government (and the public) gives us money to do our work. So, for not harboring sour grapes about missing out on a Nobel Prize, and for emphasizing the “public good” part of sharing scientific resources, I am giving Douglas Prasher an “Open Science Pioneer Award”

See also
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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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Nature using Creative Commons license for genome papers

A new paper that just came out by friends and colleeagues of mine from my days at TIGR (Comparative genomics of the neglected human malaria parasite : Plasmodium vivax) reminded me I wanted to blog about how it is a good thing that Nature is using a Creative Commons License for some (maybe all) genome sequencing papers they publish (at least in the main Nature journal). They do not use the fully open CC license that PLoS/BMC use but hey, it is better than many other journals who claim they are making this “Open.”

The license they use is

“This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence.”

Too bad they do not do this for all the papers they publish. Maybe Chris Gunter can convince them to do that even though she is now at Hudson Alpha. I think when she was at Nature she helped convince them to do this for genome papers.

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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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Biomed Central sold to Springer

Got to run but thought people might be interested in this story. See the scoop at Scientific American. Will post more later. Open access publisher BioMed Central sold to Springer: Scientific American Blog

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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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Rosie Redfield’s Open Access Saga …

Rosie Redfield has an agonizing and interesting series on her blog about her attempts to pay for an article of her’s coming out in the Journal of Molecular Biology to be “Open Access” under the Elsevier OA option (note – this is not fully OA, but it is better than the standard option for this journal). Here are some of her postings worth looking at:

Rosie is one of the true pioneer’s of Open Science, as she has turned her blog into a form of open notebook where she posts discussions about her current research, her papers in progress, grant proposals, and other ideas. Yet the process of trying to pay Elsevier to make her article somewhat more open, and the confusing way “Open Access” is presented by this journal has caused Rosie to (1) give up on the open option for this article and (2) become possibly more enamored with journals that are a bit more committed to Open Access from the beginning.

In her latest post she says

“The Elsevier sponsored-access system is confusing, the policy is not clearly explained, and the necessary information is hard to find.

The Journal of Molecular Biology is an excellent journal, and we’re proud to have our article appear there. The submission and review process went very smoothly, the copy editing was very professionally done, and the 50 free offprints are a nice treat. But I feel strongly that taxpayer-supported research should be published where the taxpayers can see it, so I won’t be submitting to any Elsevier journals in the future.”

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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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Nobel Prize in Medicine Winner is a PLoS One Author …

For You Open Access supporters out there, check out the recent PLoS One paper by Françoise Barré-Sinouss one of the new 2008 winners of the Nobel Prize in Physiology/Medicine.

The paper is Scott-Algara D, Arnold V, Didier C, Kattan T, Pirozzi G, Françoise Barré-Sinoussi, Gianfranco Pancino (2008) The CD85j+ NK Cell Subset Potently Controls HIV-1 Replication in Autologous Dendritic Cells. PLoS ONE 3(4): e1975. doi:10.1371/journal.pone.0001975

You go PLoS One.

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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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Nobel Prize in Medicine for Viral Discoveries

Nobel Prize in Physiology or Medicine goes to Harald zur Hausen, Françoise Barré-Sinoussi and Luc Montagnier for discovery of viruses (HPV and HIV) (see Nobel Announcement – Medicine 2008).

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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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Open genetics: genome rearrangement videos and more

A little late I know, but I was going through my draft postings and I rediscovered this one from July. There is an interesting paper in PLoS Genetics by Aaron Darling et al (full disclosure — Aaron is now working in my lab as a Post Doc … though I started writing this before I realized the paper was his). The paper is about genome rearrangement in bacterial populations (see Dynamics of Genome Rearrangement in Bacterial Populations). Though the science in the paper is quite interesting, the part I want to promote here are the fun genome rearrangment videos in the supplemental material.
//www.youtube.com/get_player

The figure and video are from Darling AE, Miklós I, Ragan MA (2008) Dynamics of Genome Rearrangement in Bacterial Populations. PLoS Genet 4(7): e1000128. doi:10.1371/journal.pgen.1000128.

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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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Open Access Pioneer Award #4: Carl Malamud and Public.Resource.Org

This is not about science but I think this guy deserves an award.  I just read an interesting and funny story in the S.F. Chronicle (Sebastopol man puts code manuals online) by Matthew Stannard about Carl Malamud who has been putting building codes, plumbing codes and other codes online at Public.Resource.Org.
Basically, he is doing this because many of the codes are only available for a fee.  He says

“Not everybody is going to read the building code, but everybody who wants to should be able to without putting 100 bucks in the slot,” Malamud said. “Primary legal materials are America’s operating system.”

And though his work has been questioned by some (who would like to make money off of the codes) he appears to be on solid legal ground. 

“It’s very clear in American law that you can’t get intellectual property protection for law,” said Pamela Samuelson, co-director of the UC Berkeley Center for Law and Technology. “Law belongs to everybody.”

So for this work, I am giving Malamud by Open Access Pioneer Award (#4).  Keep up the good work.

For more see (among many):
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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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