Has your scientific research been wasted?

I had a good Thanksgiving weekend this year - spending time with family and friends. But as I go back to work this week I have now gotten somewhat depressed over something I did Sunday night. I decided to remove myself from the UC Davis internet proxy to see how many of my past papers that I have published I can obtain without the UC subscriptions. So I went to pubmed, and typed in my name (Eisen JA) and got most of my papers, which are listed at the bottom of this blog (some do not come up due to publication off the pubmed grid or due to co-authors screwing up my initials). (NOTE  - LISTING DELETED 4/09 BECAUSE THE FORMATTING IS ALL MESSED UP)

And then I went to see how many of my papers were freely available and how many were not. What I was most interested in was - what is the deal with papers I wrote before becoming an Open Access convert? For many it is easy to figure out if they are freely available - Pubmed has a link saying "Free in PMC" which refers to Pubmed Central. For others, it was a little trickier.

The results were both good and bad and a summary is below. A few things struck me. First, a lot of my life's work is not readily available without paying other for it. In the day and age of the internet, this means that these papers will simply be read less and less as time goes by. And that makes me very sad. If I had chosen to publish those papers in other journals, anyone in the world could get them at any time. Thankfully I did publish many papers in journals like PNAS, and ASM journals, and NAR - journals that have now decided to release them to Pubmed Central. And also thankfully (but less so) I published some papers in journals that have at least made them freely available on their web sites.

Most surprisingly to me is that a reasonable number of my papers in Nature are freely available on the Nature web site as part of their Genomics Gateway program. Nature deserves serious kudos for doing this and they stand out compared to Elsevier journals (which do not seem to ever do this) and even Science. This is disappointing as Science is published by a scientific society but apparently does not seem to care much about access to publications. Nature, a commercial publisher, is in my opinion doing more for scientific openness than Science. Now, Nature has a long way to go, but I am SO glad I listened to their editors like Chris Gunter and Tanguy Chouard who made a big deal about the Genome papers being free. I did not think it was that big a deal, but in retrospect they were ahead of me in thinking about availability. Plus Nature clearly makes more of an effort to provide free online material than they have to - and certainly make more available than Science.

So in the end - I am sad about my partially wasted past. But I am pleasantly surprised that at least some papers I thought would be more restricted are actually free (although only on the Publishers site for now - Hopefully these journals will submit them to PMC at some point). I guess - you win some and you lose some and some are somewhere in between.

******************
Summary of openness --- other scientists should do this exercise

In Pubmed Central and Open Access

• ASM journals (7) . Thanks ASM. Eisen et al. 1992; Liu et al. 1993; Shafer et al 1997; Fleischmann et al. 2002; Alland et al. 2003; Miller et al 2003; Nelson et al. 2004
  
• Nucleic Acids Research (3). Thanks NAR and Rich Roberts. Eisen et al. 1994; Eisen et al. 1995; Haft et al. 2001.
• PNAS (9); White et al 1998; Nierman et al. 2001; Eisen et al. 2002; Tettelin et al. 2002; Paulsen et al. 2002; Fraser et al. 2002; Seshadri et al. 2003; Seshadri et al. 2004; Schmidt et al. 2005.
• Genome Biology (1) Eisen et al. 2000
• PLoS Journals (6) Wu et al. 2004; Ward et al. 2004; Wu et al. 2005; Wu et al. 2006; Eisen et al. 2006.
• Genetics (1) Tanaka et al.2004.

Available free on publisher's sites (notideal but better than nothing)

• Genome Research (1) Eisen 1998
• MBE (1) Pollock et al 2000.
• Nature (6) Nelson et al 1999; Lin et al. 1999; Eisen 2001; Heidelberg et al. 2000; Eisen 2002; Gardner et al. 2002

Must buy paper

• FEMS Microbiol Lett. Gruber et al 1998
• Human Genetics Wei et al 1998
• Trends in Genetics Eisen 1999
• Mutation Research Eisen and Hanawalt 1999.
• Current Opinion Journals Eisen 2000a; Eisen 2000b Bevan et al. 2001 Nierman et al 2000.
• Methods in Enzymology Nelson et al. 2001.
• Genomics Coleman et al. 2000. Hamilton et al. 2006.
• Research in Microbiology Nierman et al. 2000.
• Theoretical Population Biology Eisen and Wu 2002.
• Env. Microbiol Nelson et al. 2002
• Plant Mol Biol Ermolaeva et al. 2003.
• BBRC Yang et al. 2003
• Genome Biology Review Desjardins et al. 2005.
• IJSEB Badger et al. 2005.
• OMICS Leebens-Mack et al. 2006
• Nature Journals (5) Fraser et al. 2000; Beja et al. 2002; Heidelberg et al. 2002; Read et al. 2003; Heidelberg et al. 2004.
• Science (11) White et al. 1999; Tettelin et al. 2000; Salzberg et al. 2001.; Tettelin et al. 2001; Salzberg and Eisen 2001; Wood et al. 2001; Paulsen et al. 2003; Eisen and Fraser 2003; Methe et al. 2003; Venter et al. 2004; Seshadri et al 2005.
• Photo Res Dassarma et al. 2001

Not available anywhere

• Older paper published in the Journal of Molecular Evolution Eisen 1995.
• Older paper in Methods in Molecular Biology Eisen 1997
• Older paper in Nature Medicine Eisen et al. 1997

Vic Fazio Yolo Wildlife Area - A Stunning Place 5 Minutes from Davis

I am astonished so few people I have met talk about the Vic Fazio Yolo Wildlife Area that is located between Davis and Sacramento. It is a stunning place in terms of bird life and also in terms of just being able to go for a little hike near to town.

I first tried to go there last winter, but there were sings up saying the whole place was closed due to flooding. I guess I forgot about it until last month, when I was searching for things to do with my 21 month old daughter. She really loves water and birds, so I figured I would give it a try.

So I headed out with my Burley Bike Trailer in the back of the car (if I knew how close it really was I probably would have biked there). And we went over at about 10 AM on a really foggy day. All it takes is a little drive towards Sacramento. And bam - you are there. I had no idea where to go in the preserve and ended up at a little trailer that was taking hunting registrations. But the "official" there told me where there were some nice places to walk around. And we parked and then went for an hour walk. And we saw 1000s upon 1000s of ducks and shorebirds and many hawks as well as a lot of other types. My daughter did not want to leave.

I have now gone back two other times and each time has been very nice. One of the trips there we were able to see a giant flock of what looked like snow geese off in the distance towards Sacramento, and we also saw a Sora Rail as well as many other relatively hard to find species. Given that this place is SO close to Davis, I am surprised I have not seen more people there.

For more information check out

• Yolo Basin Foundation
• Davis Wiki Site Information About Vic Fazio Wildlife Area
• Interesting historical note
  

What is that NEXTgencode Advertising on My Site

So I saw this add on my site for NextGenCode. It was very cryptic so I went to their site.

They make their site seem like they are a Biotech company promoting genetic engineering as a tool in life enhancement. But looking at their articles and other material it became clear this was a spoof of some sort. The best part of their web site are the ads, like the one for Anhedonia and the one for Losing Blondes (about blondes going extinct in 200 years). I was guessing that this was some spoof put out by people to make fun of the synthetic biology field, but then I gave in a decided to google the company.

This is when I found the Wall Street Journal article that says they are a marketing ploy for a Michael Crighton novel. (I had not clicked on the link about a book stealing trade secrets form the company, but if you do, you get a story about Crighton's novel stealing their ideas). While some may find the slight of hand they are using here to be deceptive or malicious, I think it is pretty funny. It did not take long for me to figure out it was a spoof of some sort and it was kind of fun trying to figure it out.

Good to see that my site is being used for important advertising. Some day I will discuss the ads on my site for Intelligent Design proponents.

Here are some additional stories about Nextgencode

• Nextgencode.co.UK site - Different than the .com site
• Chris Abraham pooh-poohing the creativity of the Nextgencode site
• Nextegencode YouTube vids
• Time Magazine article
• Hollywood Reporter article

Of course, any blog about Crighton would be incomplete without mentioning his scientific "credibility" or the debate about it. He has clearly written some interesting science-related books over the years and in many of them the science is not completely absurd. But his anti-global warming book, State of Fear, made Crighton seem like an anti-science advocate. Personally, I never read the book so I cannot comment about the issue directly. But here are some stories about the book for people to look at.

• NRDC article
• Earth Institute article
• Mother Jones article

A call for Open Access supporters to favor grant proposals from researchers promising Open Access publishing

In the world of scientific research, perhaps the most critical step is the acquisition of funding to do research. A key component of grant reviews these days are "Release Policies" for data, tools and research materials. In general, the more "Open" one is with these release policies, the more likely one is to get a grant. This of course makes great sense. If one is going to keep ones data or tools or material private for as long as possible, then one is not advancing science as rapidly as someone else who did the same work but also released everything rapidly.

I believe now is the time for the same thing to be done regarding Open Acces publishing. One can use the same litmus test here. Imagine two grant proposals, to do identical work. And furthermore, asssume the researchers will succeed in their work. And one researcher promised to publish in an Open Access manner while the other promises to publish in a non Open manner. Again, assuming everything else is equal, I think the proposal promising Open Access publishing HAS to be scored higher than the one promising non Open publishing.

Certainly in NSF proposals this could be considered as a component of the Broader Impact criteria and people should write it into their grants. If anyone has any ideas about how this could be specifically incorporated into NIH or DOE or other grants please let me know.

So I call on researchers who support Open Access publishing in any way to start to bring this up on grant panels and in grant reviews. And to score proposals accordingly. That is, if someone has a record of publishing in Open Access journals, they should be moved up a notch compared to others. Just how much is a "notch". That should be up to individuals. But it is the principle here that is important - publishing in Open Access journals should be a component of grant reviews.

Kofi Annan urges restrictions onf biotechnology

Reuters is reporting on a speech by Kofi Annan, Secretary General of the United Nations, in which he

warned of “catastrophic” results if recent advances in biotechnology, including gene manipulation and work with viruses, fell into the wrong hands.

He also said

“We lack an international system of safeguards to manage those risks,” he said. “Scientists may do their best to follow rules for responsible conduct of research. But efforts to harmonize these rules on a global level are outpaced by the galloping advance of science itself.”

He even suggests that the time is ripe for international governing bodies much like was done for nuclear energy in the 1950s. Is this a ploy to use the current animosity towards biotechnology in Europe to give the UN something new to do? Clearly, the US would not sign on to such things with the current administration (or probably any administration). But I certainly find it interesting that he is pushing this. I wonder if he is specifically worried about synthetic biology too or if this is just more concern for genetic engineering in general.

Neanderthals and Humans

So - we now have data and papers relating to some genome sequencing of DNA apparently from a Neanderthal fossil. I must say, even though I am a skeptic of much of the work on ancient DNA, I find the idea of sequencing the genome of a Neanderthal to be pretty cool. Perhaps more importantly than the scientific uses of this information, the sequencing is a brilliant public relations coup for genome sequencing. It is also a potentially useful tool in science and evolution education.

I will spare everyone my worries the scientific value of this work for now and am just using this post to collect links that I have found to be useful regarding Neandethal ancient DNA.

• Open Access Review on Ancient DNA (from PLoS Biology)
• NY Times article by Nick Wade from July
• Smithsonian Site on Neanderthals
• Neanderthal Museum
• Wikipedia entry on Neanderthals
• Smithsonian Magazine article on Svante Paabo

I will add more links in the next few days - or people can add them with comments

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.

Long's Drug's Plant Graveyard

I went to Long's today on Covell to drop off and then pick up a prescription. In the time I was waiting I decided to check out their "Garden Center." I was just curious and did not have high expectations when I went in. Well, I can say without a doubt that I was underwhelmed. It was more like a plant graveyard than a Garden Center. There were multple dead trees in pots there, some of which were not even upright anymore. And many of the perennials seemed dead too. It looked like nobody had even been in there in weeks. You would think at some point they would reduce their prices to try and sell stuff before it died but apparently not - the prices were nothing special even on the nearly dead stuff.

I have been checking out the various nurseries and garden cente's in the area looking for a few things to jazz up the yard. Ace Hardware is OK but I almost never end up getting anything there despite browsing for a while. Redwood Barn on the other hand, is a dream come true. We just bought a lovely tree there - not too expensive - but that is beside the point. Most importantly, the workers there know their stuff and spent the time with me to discuss what type of tree we wanted and they came up with 4-5 suggestions. Perhpas Long's shold ditch their Garden Center or maybe just let it grow wild.

UC Davis Research Blog

Well, U. C. Davis (where I work) shows that it is both hip and dedicated to Science research with a new "Research Blog" put out by its University Communications office. It is called Egghead and its goal is:

Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

I am not sure how many other Universities have an officially sanctioned blog from the press office, but I could not find any.

My favorite post at Egghead so far is the one about a website called Adopt a Microbe. There is
absolutely no Davis connection to this site yet the wrote a tiny blurb about it anyway. I hope they continue to do things like this - it can get tedious if the blog is all about promoting Davis research only. It will certainly get read more if there is a diversity of stuff there.

It is good to see that Biology is the top subject there ... not that there is anything wrong with other fields but one of the reasons I wanted to move to U. C. Davis was because of the amazing diversity of biology-related research going on on campus.

Now if they could only get a weekly podcast going ...

If anyone out there knows of other Universities with interesting Blogs from the press office, let me know.

Hidden Gem in Davis - Farmer's Kitchen Cafe

The Farmer's Kitchen Cafe, which is part of the Natural FoodWorks Store, is possibly the biggest hidden gem of a restaurant in Davis. They specialize in :

delicious, homemade bioregional foods, free of gluten and casein. Your food is made with locally grown and organic fruits and vegetables, free range meats and wild fish. No aluminum pans, no hydrogenated fats, no microwaved foods, no unnatural additives.

Although the service there can be a little slow, that is part of the point. This is not a fast food restaurant. It is fresh, in season, homemade, and usually organic or at least local. Last time I went I had the chicken noodle soup, which was, I have to say, even better than mom used to make. It has a nice simple clear broth, a smattering of flavorful veggies and chicken, and a good helping of clearly top of the line noodles. I also had an organic eggplant sandwich with pesto and feta cheese that was nearly perfect. The eggplant was creamy and intermixed with the pesto into a spread with no hint of the bad eggplant flavors one can get sometime. Plus, there is a great basket of miscellaneous crayons and toys that our daughter spent much of the time playing with.

This is one of my favorite places in Davis and definitely worth a visit, especially if you are into sustainable, organic or local foods. Check it out at 624 4th Street or at their website.

Sea Urchin Genome and the Ridiculous Evolutionary Claims of Genome Researchers

All I can say is "AAAAARGH"

A sea urchin genome has been sequenced and there are some really interesting findings that have been reported based on analysis of the genome. For example, there appears to have been a large expansion of genes involved in the innate immune system in the species sequenced, Strongylocentrotus purpuratus.

All the good science aside, what most struck me were some of the ridiculous quotes attributed to some of the researchers in this project in stories and press releases. For example, in an article on MSNBC, George Weinstock says

“The sea urchin is surprisingly similar to humans,"
"Sea urchins don't look any more like humans than fruit flies, but about 70 percent of sea urchin genes have a human counterpart whereas only about 40 percent of fruit fly genes do."

Apparently, George was glossing over the reason this organism was chosen for sequencing in the first place. If you go to the NHGRIs web site you can get the white paper written that led to the selection of this species for sequencing. Perhaps the most important reason is that evolutionarily the sea urchin is closer to humans than fruit flies are. Therefore, it should only be a surprise to someone who does not know the evolutionary position of this species.

Perhaps even more appalling is the discussion of the apparent large number of genes for light sensory systems in this species. Again, Weinstock is quoted:

“There is not a lot of light at the bottom of the ocean, so it is not clear what they might be ‘seeing,'" Weinstock said. "This is certainly an area that will be studied intensively as a result of the genome project.”

I can only view this as some sort of joke. First of all, blind cavefish still have the genes for light perception even though they do not see. This is because it takes time for such genes to disappear. Second, apparently George has never really thought about where this species of sea urchin is found. It is found in the intertidal zone -- hardly the dark depths of the ocean. I could go on and on but I will just get more annoyed. In this case, Weinstock has proven that many Genome Scientists are almost completely clueless about the organisms they are working on. Which is a shame. Becuase sea urchins are fascinating creatures and the fact that they are more closely related to humans than are most other invertebrates is one of the main reasons they have been a focus on so much research up until now. Oh well ...

Paramecium whining

I just got an announcement from Linda Sperling, announcing the publication of a paper on the Paramecium genome

Dear ciliate researcher,

We are pleased to announce that the Paramecium genome article is now available as an advanced online publication at the following address:

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05230.html

We thank all of you for your interest and support.

Jean Cohen and Linda Sperling



Linda Sperling
Centre de Génétique Moléculaire
CNRS
Avenue de la Terrasse
91198 Gif-sur-Yvette CEDEX
FRANCE

sperling@cgm.cnrs-gif.fr
+33 (0)1 69 82 32 09 (telephone)
+33 (0)1 69 82 31 50 (fax)
http://paramecium.cgm.cnrs-gif.fr/

She sent this to an email list for ciliate researchers. I am writing about this in my blog because a blog is where you are supposed to write things these days when you are pissed off. Why am I pissed off about this? Well, the Paramecium paper makes no mention whatsoever of our paper on the genome of a close relative of Paramecium (Tetrahymena thermohila for those interested) which was published in August. And they do not even explicitly mention the Tetrahymena genome project (even though they say they took our data and used it). I guess I am not too surprised since their paper is published in Nature, which recently seems to be taking many liberties with referencing things in Open Access journals (ours was in PLoS Biology).

What is most annoying about this whole thing is that Linda Sperling is on the Scientific Advisory Board of our project, and has been privy to all of our work from the inside and was I am sure fully aware of our paper being accepted long before theirs was. Common courtesy in science would have been for them to have made a reference to our paper in press or at least our project. But for whatever reason, they carefulyl crafter their words to make no mention of our work. Interestingly, here is the email I sent to the same ciliate list on August 29, 2006

For those interested, our paper on the Tetrahymena MAC genome has been published online at PLoS Biology

http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040286

Jonathan Eisen

Strikingly, their paper was then accepted August 31, 2006. I hate to believe in conspiracies, but it seems just a little too coincidental that their was accepted just after ours was published. And yet still no mention of our work in their paper. Hmmm ...

Fortunately, since our paper was in PLoS Biology, they cannot say "sorry - we did not have access to it." Whatever they say, I can say clearly that Linda Sperling will not be invited to our next SAB meeting.