Friday, October 31, 2008

Conflict between religion and evolution? Not according to the Papal Conference on Evolution ...

Not to beat a dead horse here, but some people out there still think there is a absolute conflict between religious beliefs and believing that evolution occurs. And if you still think that, you might want to check out the schedule for the Vatican Conference on Evolution (and related topics) that is going on right now (see here for the PDF and here for an outline).

Held at the Vatican from Oct 31 - Nov 4 and sponsored by the Pontifical Academy of Sciences is a conference on "Scientific Insights into the Evolution of the Universe and of Life." Among the speakers: Takashi Gojobori, Werner Arber, H.Em. Cardinal Christoph Schönborn, Martin Rees, Stephen Hawking, David Baltimore, Luca Cavalli-Sforza, Christian de Duve, Francis Collins (who is the only one of the speakers with God in the title of his talk) and Maxine Singer. Sounds like a pretty good conference and I really wish I had been invited. But suffice it to say that (1) the Pope has strong religious beliefs and (2) that the Pope and the Vatican are enthusiastic about evolution as a science.

Too bad one of our VP candidates seems still stuck on the notion that we need to teach "the controversy" about evolution. Just what controversy is that?

Genome Technology Runs the Table on Open Access ...

Wow. Again, wow. Genome Technology Magazine has dedicated in essence an entire issue to Open Access and they have a whole series on interesting things to say about it. In addition they are making the issue available under a Creative Commons License so everyone can check it out. Among the articles are:

So everyone - go check it out. And give them some props.

Wednesday, October 29, 2008

Nature Endorses Obama for President

Nature has an editorial (America's choice : Article : Nature) on the US Presidential Election that is worth looking at. For those interested in the Cliff Notes Version they end the piece with

"This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama."

For more detail, I think the key point is here:

On a range of topics, science included, Obama has surrounded himself with a wider and more able cadre of advisers than McCain. This is not a panacea. Some of the policies Obama supports — continued subsidies for corn ethanol, for example — seem misguided. The advice of experts is all the more valuable when it is diverse: 'groupthink' is a problem in any job. Obama seems to understands this. He tends to seek a range of opinions and analyses to ensure that his own opinion, when reached, has been well considered and exposed to alternatives. He also exhibits pragmatism — for example in his proposals for health-care reform — that suggests a keen sense for the tests reality can bring to bear on policy.

They basically reiterate my concern for the McCain-Palin platform regarding science but they do not really go far enough. McCain and Palin have expressed decidedly anti-science positions recently (well, Palin has expressed them previously too). And thus it is not simply what advisors they surround themselves with but whether they would listen to any of them. Sadly the hints are that McCain and Palin will not listen to scientific advisors on many issues. Obama has made it clear that he will. Not that he puts science above all else (nor should he) But at least he will listen and make rational decisions that include science as a component. McCain and Palin seem dead set against "evidence" of any kind much of the time (note - McCain still exhibits occasional glimpses of the reasonable person he used to be on some issues like Global Warming - but these are few and far between).

Hat tip to Oliver M. for sending this around ...

Tuesday, October 28, 2008

PLoS Biology at 5: The Future Is Open Access

Just a quick one here. All those interested in Open Access should look at this editorial on PLoS Biology from the PLoS Biology staff PLoS Biology - PLoS Biology at 5: The Future Is Open Access

Tomorrow's Table on Today's Table x 2

So - I was having breakfast with my daughter this morning and she was in a funky mood. She wanted some stories so to make life easy and not get up, I opened up the only thing near the table to read - a copy of Nature Biotechnology that I received for free in the mail (not sure why) - and was going to show her some pictures of things. And there was a review of my friend and colleague Pam Ronald's book "Tomorrow' Table." And so I told my daughter that this was a story about a book by my friend Pam and reminded her about how we had gone over to Pam's house and how she worked in the office next to mine. And then I asked my daughter if she wanted to see Pam's book, which I had in the office and she said yes. And so I got the book and then we told stories about Pam. So - here in living color is a picture of my daughter and Tomorrow's Table the book and the review of Tomorrow's Table on my table, today.

Monday, October 27, 2008

Links on Outdoor Art in Davis from DavisLife Magazine

Just got some links to a collection on outdoor art in Davis from people at DavisLife magazine.

Palin announces opposition to research on Homo sapiens

Sarah Palin today has followed up her attack on fruit fly research by condemning much of the NIH Budget and a variety of other scientific earmarks. At a town hall meeting yesterday while campaigning in Guam, Palin said

"We asked federal agencies to give us a summary of key words relating to research projects and we found an enormous number of them focused on homosapiens. I kid you not."

When asked by a teenage audience member to explain what was wrong with this research Palin said

"You probably are a homosapiens no? Or have many friends that are? What we need to do is spend money on helping people change and not on studying these homosapiens"

The teen tried to respond but was escorted forcefully out of the hall by security while Palin continued on in her meeting. At the end of the meeting Palin returned to the topic of science research and said "If elected, the McCain-Palin ticket will reallocate federal funds to eliminate waste on topics like homosapiens and fruit flies. Enough is enough."

Sunday, October 26, 2008

Proposition 8 - My Vote

I generally shy away from non sciency topics here but occasionally a few slip in. And as I was filling out my absentee ballot I just felt I had to post something about California's horrendous Anti-Gay-Marriage Proposition 8. Originally, I was going to post a picture of my no vote on my absentee ballot but then I read this New York Times article about how many states have laws that say something like

"No person shall photograph, videotape, or otherwise record the image of a voted official ballot for any purpose not otherwise permitted under law."

So instead of a picture I am going to simply put words here. And since a picture is worth 1000 words, here are mine.

No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8.

Evidence Based Healthcare and Baseball

Love the Op Ed piece in the Friday New York Times entitled "How to take American Healthcare from Worst to First." First, one reason I love this article is it is discussing how we need to move to more "Evidence Based" medicine. You may be amazed to know that much of medicine is not evidence based but that is the sad truth. When I first heard about how not all medicine was evidence based medicine (in a talk by David Cox when I was a grad. student) I was blown away. Anyway, the article is worth a read from this point of view.

More amazingly is the author list -- Billy Beane (general manager of the Oakland A's), Newt Gingrich, and John Kerry. What a combination. They make the argument that medicine needs a wholesale change in the way it is done just like baseball is shifting to more evidence based decisions. It is a nice analogy. Too bad the current administration believes that simply thinking about something is the equivalent to evidence. And also too bad that McCain-Palin seem to be following in the trend of Bush to not hold "evidence" in high regard. I wonder what Newt (who is a big science and technology advocate) thinks of the recent anti-science push of the Republicans in power.

Saturday, October 25, 2008

McCain Palin going after fruit flies

As if scientists did not have enough reasons to vote against McCain-Palin who seem to have decided that Bush was overly supportive of science. Now Palin is attacking of all things "fruit-fly research." Lovely. Proof that they are both clueless (not knowing what a fruit fly is probably) and anti-science at the same time. For more on this see:

Tuesday, October 21, 2008

Brain Doping April 1 Joke still getting some press

Well, my April 1 collaborative joke on brain doping is still getting some press. See El Pais which reports

Como muestra, algo que empezó como una broma. "Los centros del NIH (los Institutos de Salud de Estados Unidos) pedirán a todos los científicos que quieran optar a sus ayudas y subvenciones a que pasen pruebas antidopaje para comprobar que no han tomado estimulantes cognitivos para aumentar su rendimiento intelectual". Una supuesta World Anti-Brain Doping Authority (WABDA) se encargaría de los análisis. Es el mensaje de una nota de prensa falsa. Una fake lanzada en Internet el pasado 1 de abril, el día de los inocentes en Estados Unidos, por Jonathan Eisen, biólogo evolucionista de la Universidad de California. Comenzó como una travesura, pero el rumor acabó por extenderse por la red.

La broma apunta, sin embargo, a un debate abierto entre la comunidad científica. Si se controla el dopaje en deportes como el ciclismo, ¿por qué no controlarlo en la comunidad científica, donde también compite el intelecto por conseguir becas, ayudas e incluso premios en reconocimiento de su inteligencia? Esa era la reflexión original que, según explica Eisen, le llevó a colgar su broma de Internet. Sin embargo, también afirma que nunca aceptaría que se realizasen ese tipo de controles.

Monday, October 20, 2008

Roan Press Web Site Live

Well, I wrote about Roan Press ("Sacramento's Small Literary Publisher") a while ago (see here) since a friend of mine from grad. school Brad Buchanan had published a new poetry book through them and was on the air on KDVS. And now the Roan Press web site is live. You can order Brad's book Swimming the Mirror there (and see a review here). Brad will be doing a reading at the Avid Reader in Sacramento (1600 Broadway) at 1 PM on October 26.

Friday, October 17, 2008

Blocked Access Bummer #1

I have decided to start posting when I want to read an article at home but cannot due to lack of access (even though I might have it at work). Today's bummer is I wanted to read an article by Joel Sachs on "Resolving the first steps to multicellularity" but I could not get it because I do not have access to Trends in Ecology and Evolution at home. Bummer. Looks like it could be good.

Thursday, October 16, 2008

Larry Moran on Phylogenomics, my new paper, and species

Just a quick note to encourage people to check out Larry Moran at The Sandwalk blogging about my new phylogenomics paper (with Martin Wu) and talking about whether one can use species as a term for bacteria.

At Davis Today - Chris Somerville on Cellulosic Biofuels

Quick Post Today --- For THose Interested in Biofuels --- you might be interested in this

Distinguished Lecturer
Dr. Chris Somerville
Director, Energy Biosciences Institute (EBI)
Presents On:
“Cellulosic Biofuels”
UC Davis ARC Ballroom October 16, 2008, 3:00-4:00 PM

Tuesday, October 14, 2008

Happy Open Access Day: Back to Genome Biology for Me

Well, good timing on this one. A new paper from Martin Wu in my lab has recently been accepted to Genome Biology and the provisional PDF was posted online 10/13. The paper ( A simple, fast, and accurate method of phylogenomic inference ) describes a new program Martin wrote called AMPHORA and shows how it can be used to build phylogenetic trees based on concatenated alignments of housekeeping proteins and also for metagenomic phylotyping using a diversity of protein markers. As today is Open Access Day I thought I would just put in a plug for this OA paper and thank Martin for his great work and commitment to Open Access.

I should note - I really really like Genome Biology as a journal - even though they have been rejecting many of my papers lately (or maybe in part because of this). I am really glad this one got in there. I published my first fully OA paper in Genome Biology in 2000 (on symmetric genome inversions in bacteria and archaea -- a paper co-authored with Steven Salzberg, Owen White and John Heidelberg - see Evidence for symmetric chromosomal inversions around the replication origin in bacteria). It is one of my favorite papers from my entire career, as in it we report on a pattern that turns out to appear to be one of the few rules of bacterial and archaeal genome evolution. Anyway - glad to be back in Genome Biology.

Open Access Day: Video of a Talk I Gave About OA

Well, I was going to write all this blather about OA. But I realized it would be easier to share a video of a talk I gave at U. Washington on Open Access as part of their Biomedical Research Integrity Series (U. Washington Program). I cannot figure out how to download/embed the video so instead I am just posting the links. If someone has software for downloading it and wants to help me embed it and/or upload to YouTube and SciVee that would be great ((NOTE - VIDEO IS NOW EMBEDDED BELOW THANKS TO FRANCOIS MICHONNEAU) . Here are the links:

Lecture #2, Responsible Authorship:

Thursday, August 7, 2008; Speaker: Jonathan Eisen, Ph.D., "Responsible Authorship and the Ownership of Scientific Knowledge: Thoughts on Open Access Publishing"
To view the lecture, click here: Flash Player version, Windows Media Player version, or QuickTime Player version (for QuickTime players you may have to open the player and paste the url: rtsp://media.depts.washington.edu/uwbri/BRI_Eisen_2008.mov)

Open Access Day: Thanks to OA Journals Staff

Well, today is a big day for Open Access, as it is, well, Open Access Day. And one thing I really wanted to put out there is that I think we all should say a big thanks to all of those who have worked tirelessly at various OA journals to help move OA into the mainstream and to produce a vast collection of fully open biomedical and scientific literature.

As I am involved in PLoS journals in many ways, I want to thank all of the staff who work behind (and sometimes in front) of the scenes there. There is a relatively full list of these people here. And I am publishing that list here too, with, along with a heartfelt thank you. Thank you. You all rock. And we should also thank all the staff at other OA Publishers (e.g., BMC). You rock too.