Monday, January 29, 2007

Science World Coming ...

The US Department of Energy and the British Library announced an agreement to develop a new international science portal aimed at sharing scientific information. It sounds like a great thing. Now if only DOE would require Open Access publishing of scientific research that they fund ... that would really show DOE's committment to Open Science. I recommend sending Dr Raymond Orbach, who is leading this initiative, an email message, the address for which you can find at this link at the top of the page.

Saturday, January 27, 2007

Synthetic Biology (faculty job available at U. C. Davis in the Genome Center)

Just heard another talk by Drew Endy about Synthetic Biology and his attempts to make the field work more like Engineering than Biology. Basically, what he is trying to do is to make biological parts (e.g., Biobricks) at the DNA level that would work like circuitry board parts do for making computer chips and related devices. As they get more biological parts, more people will be able to treat synthetic biology in an abstract way - that is they will not need to know per se how the biological parts work, just that they have particular properties.

My favorite part of the field of Synthetic Biology is IGEM, the The international Genetically Engineered Machine competition. Students compete to make cools things from their biological parts. Among the more interesting items that have been made is a bacterallawnthat work as a camera.

In general, I like synthetic biology and the potential it has to produce major benefits for the world, although I wish some of the practitioners were less flippant about the potential risks in the field. And, this minor blog would not be complete without the self interest. THe UC Davis Genome Center has just announced a new faculty position in this area (specifically in cmputational and experimental approaches to network and synthetic biology). So if you are in this field and want to join a great collection of faculty working in diverse areas of genomics, please apply.

Job at Davis

Wednesday, January 24, 2007

Non Open Access publishers getting desperate

Well, this kind of made my day. Nature is reporting that a group of non open access publishers have hired Eric Dezenhall to help them with public relations. Eric Dezenhall is a crisis management consultant (as well as a fiction author) who many may demonize but he certainly seems to be good at what he does. The article at Nature is worth checking out and points to the desperation of these publishers when they see the writing on the wall regarding Open Access. For example, Nature reports a person at AAP the Association of American Publishers says:

"We're like any firm under siege," says Barbara Meredith, a vice-president at the organization. "It's common to hire a PR firm when you're under siege."
Keep up the siege everyone. Their ship is sinking and they are grabbing at the last little pieces of wood they can find.

Tuesday, January 23, 2007

Article in the Christian Science Monitor on PLoS One and related topics

Just saw an interesting article in the Christian Science Monitor on the "end of the scholarly journal" which talks quite a bit about PLoS One. Definitely worth checking out -- many quotes from Chris Surridge of PLoS One and some discussion of Blogs and related sites.

Antibiotic resistant bacteria plaguing US soldiers in Iraq

Very interesting article in Wired magazine about an antibiotic resistant bacteria that is plaguing US soldiers in military hospitals in Iraq. It's got some stuff I would disagree with in there about gene transfer and evolution but overall this is a really good and interesting article about bacterial evolution and antibiotic resistance.

Monday, January 22, 2007

Interesting (but misguided) letter to the editor

There is a funny/interesting letter to the editor in one of the local papers out here. It is basically about how an article on Neanderthals is interesting but how more should be written about current topics in evolution, which sounds great. Then the author proceeds to quote Fisher and Morgan regarding human evolution, not the most modern of research to quote. Anyway, the calculation they made I found to be quite interesting ...

Sunday, January 21, 2007

Blog apologies --- evolution happens

Well, sorry for the limited number of postings here recently. I am working on increasing my own fitness --- we have a baby due next week and my blog has fallen a little behind. I will get back into blogging more in about 3 weeks. If I see anything interesting before then I will post but there may still be a short lull. Now back to getting 1,000,000 things done in one week.

Monday, January 15, 2007

Genomics Gets Nasty

Just saw an entertaining press release about the publication of the genome of the parasite Trichomonas vaginalis. I find this entertaining because it does a remarkable job of capturing the personality of Jane Carlton, the PI on the project, who I used to work with at TIGR.

I particularly like the end

Viewed under the microscope Trichomonas vaginalis moves quickly; it has four undulating flagella and a tail. "It is a gassy organism," says Dr. Carlton. It has special power-generating structures called hydrogenosomes. They produce hydrogen. "So it is releasing hydrogen into the liquid media, making it frothy," she says. "That is why the vaginal discharge is frothy."

The pathogen grows easily in the lab in test tubes containing some liquid media. And it has, as she says, "a real yuck factor to it." A good way to know the microbe is growing well is to smell the contents of the test tube. "It smells foul, it has a fishy odor; really nasty," says Dr. Carlton. "My technician used to get grossed out by that."
While it is true that Jane has no fear about saying things that make some people uncomfortable, it is entertaining to the it in the NYU press release.

The press release is worth reading for another reason - the history of this genome project is different from many other parasites. In this case, the genome was enormously bigger than had been predicted (usually they are smaller than predicted, in part becuase if you over predict the genome size, you will have some extra money in your grant to cover other issues). The press release gives a good impression of how much of a pain it is to run a genome project sometimes.

Anyway - back from a little layoff and just wanted to say - good job Jane.

Thursday, January 04, 2007

Open Access Education?

Thanks to Jacques Ravel for pointing this out. U. C. Berkeley has begun posting many of its science classes as Podcasts which are avilable for download at a special Apple Itunes Site. Also posted are some lectures such as one by George Smoot who just won one of those Nobel Prize thingies. It seems Stanford is doing a similar thing although it does not seem as extensive.

Note sure what other Universities are doing this (I know some classes are podcasting but not clear how many Universities are doing it as extensively as Berkeley).

If anyone else knows of other such efforts please let me know (also see this list of free academic podcasts).

Monday, January 01, 2007

My Open Access New Years Resolutions

Well, 2006 is over and in terms of Open Access to Biomedical type publications, I think it was a pretty good year. The papers being published in Open Access journals continue to get better and better and there are more Open Access journals too. Perhaps to biggest new thing from last year was the start of PLoS One, which is not only an Open Access journal but one that is experimenting with a new type of peer review system.

But of course, more needs to be done. So I am posting here my personal list of Open Access New Years resolutions. These are things I hope to do and hope to convince others to do too (these are in no particular order).

1. Convince more collaborators to publish papers in Open Access journals.

2. Release more of my labs data in a more usable format to Open Data archives (see Bill Hooker's Open Reading Frame blog for more details about doing this).

3. Discuss Open Access to publications and data in all my scientific presentations/talks.

4. Write more blogs about Open Access and its benefits.

5. Convince some existing journals to switch to a more Open Access stance (e.g., I wish this would happen with Journal of Molecular Evolution --- I resigned my position as an Academic Editor when they would not shift but there is still hope).

6. Submit as many of my past papers that were not in Open Access journals to self-archiving repositories (see the comments on my previous blog about this - it seems that this is possible even for Nature papers).

7. Work with Pubmed Central to make self archiving possible there for more papers. Right now it is only possible to submit your own work to Pubmed Central if it was NIH or Wellcome Trust funded.

8. Discuss Open Access with more scientists. Some still have notheard about it and some do not realize what the issues are.

9. Discuss Open Access with more non scientists. To get Congress to pass more rules regarding Open Access, it will help to have more pressure from non scientists. When I have described the current publishing system to non scientists, they are usually astonished by the (1) wasted money and (2) closed nature of much scientific work.

10. Work to get researchers who publish in Open Access journals "extra credit" in promotions, tenure review and grant proposal review. These people are frequently taking risks for the betterment of the scientific community and to advance scientific knowledge. They deserve credit for taking these risks.

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