Another education use of Open Access publications

I was reminded of another important use of Open Access publications last week when I gave a talk at Chico State University. Chico St. is one of the California State Universities (I guess it’s formal name is California State University, Chico). The people in the Biology Department there invited me to give a talk (I think this was because of the press coverage of my PLoS Biology paper on the symbionts of the glassy winged sharpshooter – a pest of great concern throughout California since it transmits Pierce’s Disease in grapes).

I had a great visit and a nice drive to and from Chico. I met with lots of faculty doing interesting stuff. And after my talk we went to a local pub with some faculty and students. I had opened up my talk discussing the benefits of Open Access publication and how it was just as important as databases like Genbank (In fact, I think it is a good idea to discuss the importance of OA in scientific presentations in general – spreading the word). And much of our conversation at the pub centered on Open Access.

The most interesting thing I found out was that for one of the journal club/discussion courses that they have there, they only use papers from OA journals like PLoS journals. There were two major reasons for this. (1) As a woefully underfunded university (note – read this Arnold), they do not have funds for their libraries to subscribe to a diversity of journals and (2) using OA publications means they can post all the publications or links to them on a web site for students and do not have to make them closed access / password protected to prevent illicit sharing of non Open publications.

So – another benefit of Open Access publishing. Easing access even o major universities in the US, and making it easier to use research papers as part of course readers and course web sites.

Science and Education Win Another Round …

Well, the good news keeps pouring in for science education and the teaching of evolution. The Cobb County School Board, which had tried to insert religious points of view into the teaching of evolution, have backed down. They had placed stickers on biology textbooks that read

This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered

Yet, of course they did not label any other area of science in this way. AP reports that

The Cobb County school board signed an agreement filed in U.S. District Court on Tuesday agreeing never to use a similar sticker or to undermine the teaching of evolution in science classes.

It is nice to see that they have had a change of heart, or at least have realized that they would lose this fight. Either way, science and education win this round. Unfortunately, the proponents of Intelligent Design, will try again and again. And they should be fought every step of the way to keep them from attacking the teaching of evolution in science classes.

Evolution Pumpkins

Evolution fans have to check out the pumpkins at this site. I found the site by browsing around the “ClutterMuseum” blog (I was checking it out because the author poster to my blog about Davis, CA). Now, I know the FSM (Flying Spaghetti Monster) can be considered an in your face response to the intelligent design movement. But personally, the ID movement needs to be made fun of even more and the FSM is one of the best ways to do that. For more information you can read the “About” part of this blog.

Evolution and Politics

Scientists are acting up again. The New York Times reports that

75 science professors at Case Western Reserve University in Cleveland have signed a letter endorsing a candidate for the Ohio Board of Education.

This is great news if you ask me. Scientists seemed to be emboldened to play more of a role in politics. I think this is due to some of the recent pushes from anti-science coalitions, like the supporters of “intelligent design” as a scientific theory (which it is clearly not).

We desperately need more of this type of thing – with scientists speaking up. I do not want scientists to choose sides in truly political debates. And I hope scientists will avoid being too arrogant – such as when some suggest science can solve all the worlds woes. But when sound science is being ignored or belittled by politicians, scientists should speak up. The evolution debate is but one example. There are many more issues where sound science is being misused or ignored (e.g., global warming).

So – I recommend all scientists consider doing something to get involved. Lend your support to the folks in Ohio (e.g., Lawrence Krauss organized the group to write the letter). Or join an organization like SEFORA a new science based political action group. But just don’t sit on the side and say “scientists should not get involved.” If all scientists keep doing that, we are in deep trouble.

Genomics Education Bus

I just got back from the new version of the old GSAC meeting. It is now called GME or Genomes, Medicine and the Environment (or, as we like to call it – stuff Craig Venter is interested in these days). The meeting is organized by the Venter Institute and this year was one of the better versions of this meeting. There were some really interesting talks in a few topic areas (I will try and post some details about these later). But to me, the most interesting part was seeing the Venter genomics education bus (part of their Genomics Discovery program) on tour. They use this bus to go around to high schools and other places to do some genomics education.

Just before coming to the meeting, the bus apparently rolled into New Orleans (see Wired news story here). Lots of people like to complain about Venter and his style, but whatever you may think of him, I think this bus is a great idea. We desperately need more people who do science making an effort to interact with and educate people about scientific research. And since this bus is outfitten with lab equipment and various genome-related toys, it can go into a neighborhood without the best science labs and help introduce students to the fun and excitement of modern science.

Note – the photo was taken by me at the GME meeting in Hilton Head, SC. In the photo are Lisa McDonald, Jennifer Colvin, and (I think) Darryl Bronson.

Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics

Just got back from the 14th Annual International Meeting on Microbial Genomics, where I gave talk on microbial symbiont genomics. This was one of the best meetings I have been to in a while. It had the right combination of everything including:

  1. Many excellent talks and posters (OK, in the interest of not upsetting people for not saying their talk or poster was great, I will not make a big list of all the ones I thought were good, but I will give a few highlights below).
  2. Excellent location (UCLAs Lake Arrowhead Conference Center, which is in the mountains east of Los Angeles). This is a place that is very conducive to getting to know colleagues and it almost forces interaction among people. There is one central building where there is a dining hall, a nice deck if you want to eat outside, the conference room, rooms for posters, and a large living room for hanging out. The rooms for sleeping are mostly great (e.g., mine was a split level condo like structure with a living room and a bedroom/bath on floor one and a bedroom/bath on floor 2). And being in the mountains is very pleasant. Plus there is a pool, jacuzzi, and sports facilities that are very nice. The only annoying thing is that the Lake itself, which is 100 yards away, but it really almost private, with most of the shoreline occupied by houses and private docks.
  3. Good food. The food is not spectacular or anything but better than the food at 90% of the conferences I have been at.

In terms of talks, there were quite of few that were both interesting topics and very well presented. For example, Jessica Green from U. C. Merced gave a great talk about spatial distributions of microorganisms, Julian Parkhill from the Sanger Center put together a really nice story about mechanisms by which microbial pathogens generate phenotypic diversity, and Julie Huber from MBL impressed many with her talk about the “Deep Rare Biosphere.”

But to me, the best two talks were ones on science education reform by two people from UCLA. Erin Sanders-Lorenz presented a summary of her course she has been teaching at UCLA that has students doing “phylogenomic” analysis which takes them from isolating and culturing organisms from environmental samples to building evolutionary trees of genes isolated from these cultured species.. This seemed like a very creative, hand on, novel way to teach students the excitement of science and some things about evolution. It sounded so well thought out that I asked for (and got) a copy of her lab manual.

Much as I liked this class, the one described by Cheryl Kerfeld knocked my socks off. She described a program they have developed at UCLA called the Undergraduate Genomics Research Initiative. This is an interdepartmental multi-course collaboration with the central theme involving the sequencing and analysis of the genome of a bacterium called Ammonifex degensii. The various courses are organized around a central course on genome sequencing. The linked courses include ones in many different departments at UCLA as well as various courses at other universities. They have clearly given enormous thought to how to do a truly project based course which likely will catch students attention and interest much more than standard lectures or standard labs.

There have been other successful hands on genome sequencing courses before – perhaps the first being one by Brad Goodner at Hiram College who had students participate in the sequencing and analysis of the genome of Agrobacterium tumefaciens (e.g., see a press release here). The Kerfeld UCLA UGRI program sounds like it has gone to the next level by integrating many courses across departments and by having creative ways to encourage participation of students in multiple aspects of the project. It really is worth giving a look at the UCLA UGRI program’s web site.

Other tidbits about the meeting:

  • Jeffrey H. Miller from UCLA organized it
  • This is the same Jeffrey Miller who identified most of the mutator genes in E. coli with a really creative genetic screen
  • There was another Jeffrey Miller from UCLA at the meeting (will leave this up to google for people to figure out who this other Miller is).