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

Explorit Videos on Youtube

A variety of videos are available from the Explorit Science Center on YouTube. They are worth browsing.

——–
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.

——–

Icky Stuff at Long’s




All I can say is I am glad I check my medicines before I take them.  I went to Long’s in East Davis the other day to pick up some insulin and was given a box of my insulin pens.  When I got home I found that there was only one insulin pen in the box and that pen was used.  Not exactly confidence boosting in my pharmacy.  Only later did I figure out what happened which was even scarier.  This was insulin I had returned months before because of a defect that Long’s was supposed to send back to the manufacturer (I had called the company who had handled this very well, and they told me a free box would be at Long’s and that Long’s would return the unused portion to them).  So I guess Long’s put it in the fridge and did not return it and then saw my name on it and gave it back to me.  Yuck.  Even worse, they did it again, I think the next time I went in.  Double yuck.  

Note that I wrote this when it happened but decided not to post it (but saved it in my blogger account), since it seemed a bit too personal. But now (2009) I am having problems with Long’s again and I figured I would make live some of my old postings about Long’s.

——–
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.

——–

Kudos to New Scientist’s "24 myths and misconceptions" about evolution

New Scientist has a pretty good article on myths and misconceptions about evolution (see Evolution: 24 myths and misconceptions).

They really hit on many of my pet peeves on evolution. Among my favorites:

Many of these fit in well with my Adaptationomics Award which I will start giving out again soon ….

——–
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.

——–

Help save Davis’ Schools …

Normally I do not put too many things about Davis here as I post them on my Davis Blog here. But I am cross posting today since I know many people from Davis read this blog.

There is a financial crisis of sorts going on in Davis. Please consider donating to the Davis Schools Foundation by May 15 in order to prevent cancellation of programs and/or termination of teachers.

See the video below which was made to showcase Davis’ children and what we stand to lose if we don’t all act fast!

See also Jamie Madison’s blog.

——–
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.

——–

Save Davis’ Schools

There is a financial crisis of sorts going on in Davis. Please consider donating to the Davis Schools Foundation by May 15 in order to prevent cancellation of programs and/or termination of teachers.

See the video below which was made to showcase Davis’ children and what we stand to lose if we don’t all act fast!

——–
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.

——–

SPARC and Science Commons release guide to creating institutional open acces policies

A nice new release from SPARC and Science Commons is out. They put together a guide to creating institutional open access policies (see Press Release)

In the guide they have an overview of the new Harvard Open Access policy, suggestions for what one can do on one’s own campus and a plan of action for bringing about policy change. I know I am going try some of their suggestions here at Davis as I am hoping Davis and the UC in general adopts a policy like Harvard’s (they mention the UC consideration of such a policy in their site)

——–
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.

——–

Science Commons » Blog Archive » Rockefeller U. Press Uses CC Licenses to Reduce Permission Barriers

Good Open Access news from Rockefeller Press. They have decided to change their publishing policies and are making them much more open. Emma Hill, who used to work at PLoS Biology and is now the Editor of J. Cell Biol. from Rockefeller has an editorial (with Mike Rossner) about the change including details of the new policy and some of the reasons for the change.

Among the changes they make and some of the reasons why

  • Giving copyright to the authors.
    • This is a good thing and about time for them to do it. They say: “Preying on authors’ desire to publish, and thus their willingness to sign virtually any form placed in front of them, scientific publishers have traditionally required authors to sign over the copyright to their work before publication. “
  • Adopting a Creative Commons license.
    • They say “What does this Creative Commons License mean? It means that our published content will be open for reuse, distribution, data mining, etc., by anyone, as long as attribution is made to the original work. Share-alike means that any subsequent distribution must follow the rules set out in this license. Non-commercial means that published work can be reused without permission, as long as it is for noncommercial purposes.”
    • This to me is the most important part of their policy. CC licenses change everything – they make it easy for everyone to use the material.
  • They retain an exclusive license for 6 months. After the 6 months, the material has the full CC license and can be distributed anywhere as long as it is attributed and not for commercial use.

Overall, I think this change is a good thing. It is still not the full Open Access I prefer, but it is a great step in the right direction. Also see a blog by Science Commons discussing the new policy – see Science Commons. They are overwhelmingly positive. See also Peter Suber here.

On extra nice thing about the policy is they are making it retroactive for all their publications in the past. So lots of Rockefeller press stuff from the past has now become much more open.

——–
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.

——–

Metagenomics just keeps getting bigger …

Yet another tip of the hat form the scientific community to the growing field of metagenomics. Today Ed Delong, one of the pioneers of using metagenomic methods to study microbes, was elected to the National Academy of Sciences. Congrats to Ed for this well deserved recognition (now I note, he has done many things in ocean microbiology that are not metagenomics … but we will pretend here that this was all about his metagenomics work).

Other people elected of particular relevance to this blog — David Hillis, a great evolutionary biologist, and Rosemary Grant, of Darwin’s finches fame.

——–
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.

——–

Francisco J. Ayala – Evolution – Scientists Who Believe in God – – New York Times

Good to see someone other than Francis Collins getting some press about bridging the gap between evolution and religion. Today it is Francisco Ayala, an evolutionary biologist at UC Irvine. There is an interesting story about him in the New York Times today (Francisco J. Ayala – Evolution – Scientists Who Believe in God ).

Now, I thought I knew a good deal about Ayala but I did learn a bit in the article about his life and background (e.g., he was a Dominican priest, which I did not know). I personally think the “religion” vs. “evolution” debate is pretty silly much of the time and succumbs to the modern obsession with controversy. Ayala’s new book “Darwin’s Gift to Science and Religion” apparently addresses this issue and I hope it does a better job than Collins’ book, which I found to be wanting in many areas. Of course, I guess I am a bit biased since I have had a soft spot for Ayala for many years and since he just wrote a very positive review of my new Evolution textbook. Now, if Collins wrote a positive review, I do not think I would like his book any more, but who knows …

——–
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.

——–

Reminder About the NIH Public Access Policy

To all interested in Open Access publishing


Here is an email I just got from NIH

April 28, 2008

Dear Members of the NIH Research Community:

I am writing to remind you that the mandatory NIH Public Access Policy (http://grants.nih.gov/grants/guide/notice-files/NOT-OD-08-033.html) applies to final peer-reviewed manuscripts accepted for publication on or after April 7, 2008. Making published research funded by NIH accessible to everyone, including health care providers, patients, educators and scientists, helps advance science and improve human health. We all have a role to play in achieving this goal, and I appreciate your efforts to make the NIH Public Access Policy successful.

The NIH Public Access Policy implements Division G, Title II, Section 218 of PL 110-161 (see http://publicaccess.nih.gov/policy.htm), which was signed into law late last year. Compliance with this Policy is a legal requirement and a term and condition for all active grants and contracts awarded as of April 7, 2008. Failure to comply may trigger one or more enforcement actions, depending on the severity and duration of the non-compliance.

Please see the Public Access Web site for the tools you need to comply with the Policy. The Web site houses Frequently Asked Questions (FAQs), training information, and other resources.

To ensure compliance with the Policy, please remember to:

Address Copyright – Make sure that any copyright transfer or other publication agreements allow your paper to be submitted to NIH in accordance with the Policy.

Submit Papers upon Acceptance for Publication

1. Some journals will submit the final published article on your behalf, without your involvement. See http://publicaccess.nih.gov/submit_process_journals.htm for a list of these journals.

2. For any journal other than those on this list, please:

a. When submitting a paper for publication, inform the journal that the final peer-reviewed manuscript is subject to the NIH Public Access Policy.

b. Make sure that any copyright transfer or other publication agreement allows the final peer-reviewed manuscript to be submitted to NIH in accordance with the Policy. For more information, see the FAQ Whose approval do I need to submit my article to PubMed Central? and consult with your Institution.

c. Submit the final peer-reviewed manuscript to NIH upon acceptance for publication at http://www.nihms.nih.gov/. See the Submission Process for more information.

Cite Papers

§ When citing your NIH-funded papers in NIH applications, proposals or progress reports, please include the PubMed Central reference number (PMCID) for each paper.

§ NIH will monitor compliance through citations. Effective May 25, 2008, when your NIH Program Officer reviews your progress report or application, he or she will be expecting a PMCID in the citation of every applicable paper that arose out of your NIH funding, or a manuscript submission system reference number (NIHMSID) if the PMCID has not been issued. See Section C of our FAQ for examples.

§ If you publish through a journal listed under http://publicaccess.nih.gov/submit_process_journals.htm, there might be a slight delay in assignment of a PMCID. That is okay. We have signed agreements with these journals that allow NIH to resolve submission with them without your involvement. To facilitate your Program Officer’s job, we ask that you indicate ‘PMC Journal- In Process’ until the PMCID is available.

The NIH Public Access Policy is a legal requirement and represents an important opportunity for science and medicine. We are very interested in your feedback on the Policy and are soliciting input through a request for information from March 31, 2008 to May 31, 2008. Please send any comments or suggestions to http://publicaccess.nih.gov/comments.htm.

Sincerely,

Norka Ruiz Bravo, PhD

NIH Deputy Director for Extramural Research

——–
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.

——–