Wednesday, July 30, 2008

Best time to appreciate Open Access? When you're really sick and want to learn more about what you have.

Well, I have been out sick for a while. But I am now finally apparently getting better. Thanks to the work of scientists who have developed multiple classes of antibiotics. Anyway, more on that later. While I was out sick I spent a lot of time searching the web for information about nasty, cellulitis causing antibiotic resistant bacterial infections. And I was researching some other health related issues that may have contributed to my getting such an infection. Here are some tidbits I learned during this forced homecation.
  • Complete OA still a long way off. One thing I re-learned during this was that it is incredibly frustrating to see how much of the biomedical literature is still not freely available online. Shame on Elsevier and all the others who are still hoarding this important information.
  • Thanks to those providing OA. Related to the above issue, I came to appreciate was the societies and publishers have decided to go the OA route. I spent a lot of time reading material from ASM, BMC, PLoS, Hindawi, and a few others. And I am grateful to these groups.
  • Google rocks for science searching. Cuil, not so much. If you need to find something about some scientific concept or issue, Google really does a great job. While I was out, Cuil was announced as a possible new competitor for Google in searching. From my experience, Cuil is really really lame for science searches. I like their presentation in a magazine style. But the search results were not so good.
Anyway, enough about me. This is just a quick post to say the Tree of Life will be coming back over the next week or two. I am still out sick. But a clear sign to me that I am getting better is that I finally want to blog again.

Thursday, July 24, 2008

Staying clean

Well, sorry for the lack of posting recently. Out sick thanks to a fun antibiotic resistant bacteria. In honor of that here are some tips to staying clean:

A Germ-Zapper's Guide to Clean (from the Washington Post

hat tip to Doug Rusch for pointing this out and giving me something to do other than worry about bacterial infections)

Wednesday, July 23, 2008

Is your city walkable?

Just got an announcement from a friend of mine who has started a new campaign for trying to "raise America's Walk Score." They have launched a web site with walkability rankings of 2,508 neighborhoods in the largest 40 U.S. cities. If you go to the site and type in your address you can see how you score (Downtown Davis does really well). And if you support walkable communities they have a petition online to encourage Congress to support walking towns ...

Davis Hosting Stage 2 of the Tour of California 2009

Big big news for Davis. Stage 2 of the Tour of California in 2009 will start in Davis (after Stage 1 which starts and ends in Sacramento).

For more information see Velonews here.
Also see the SacBee story here.
  • Stage 1, Saturday, Feb. 14 – Sacramento
  • Stage 2, Sunday, Feb. 15 – Davis to Santa Rosa
  • Stage 3, Monday, Feb. 16 – Sausalito to Santa Cruz
  • Stage 4, Tuesday, Feb. 17 – San Jose to Modesto
  • Stage 5, Wednesday, Feb. 18 – Merced to Clovis
  • Stage 6, Thursday, Feb. 19 – Visalia to Paso Robles
  • Stage 7, Friday, Feb. 20 – Solvang (individual time trial)
  • Stage 8, Saturday, Feb. 21 – Santa Clarita to Pasadena
  • Stage 9, Sunday, Feb. 22 – Rancho Bernardo to Escondido

Thursday, July 17, 2008

Closed Access Award #1: American Psychological Association

Well, I wrote up this award a short time ago and already the story has changed. But I am still giving the award. On Tuesday, Peter Suber reported that

The American Psychological Association may have the worst publisher policy to date for NIH-funded authors. Excerpt:

In compliance with [the NIH OA policy], APA will deposit the final peer-reviewed manuscript of NIH-funded research to PMC upon acceptance for publication. The deposit fee of $2,500 per manuscript for 2008 will be billed to the author's university per NIH policy....

Even after collecting the fee, the APA will not deposit the published version of the article, will not allow OA release for 12 months, will not allow authors to deposit in PMC themselves (and bypass the fee), will not allow authors to deposit in any other OA repository, and will not allow authors to retain copyright.

I agree with Peter that this is a stunningly inane move on their part (for more discussion see Suber's follow up here). They are basically saying that to carry out a simply electronic submission they will charge $2500.

Apparently someone convinced them this was not the brightest thing in the world to do as they are now reconsidering this move (I learned about this reconsideration from the Scientist magazine blog here ... you need to register to read the blog). This blog reports
A statement sent to The Scientist today from APA Publisher Gary VandenBos said: "A new document deposit currently being re-examined and will not be implemented at this time...APA will soon be releasing more detailed information about the complex issues involved in the implementation of the new NIH Public Access Policy."

VandenBos was not available for further comment.
Even though they are reconsidering their policy, since they have not out and out rescinded it, I am still giving the American Psychological Association my first "Closed Access Award" for this incredibly silly move

Tuesday, July 15, 2008

Conflict of interest and openness

The New York Times had a long and extensive article on conflicts of interest in medicine. See Times article here. 

I was pleasantly surprised to see them discuss the concept that open access to data can help correct for bias if it occurs by allowing others to redo analyses.  For example: 

“Having everyone stand up like a Boy Scout and make a pledge isn’t going to quell suspicion,” said Dr. Donald Klein, an emeritus professor at Columbia, who has consulted with drug makers himself. “The only hope to rule out bias is to have open access to all data that’s produced in studies and know that there are people checking it” who are not on that company’s payroll.
Unfortunately the Times does not raise the issue of access to the publications themselves.  Clearly having the data is good.  But if nobody can read the papers and they can just read the press releases that come from the papers, we are all doomed.

I see PLoS in everything

Seen recently at the California Railroad Museum. I guess the people from Nature were right - PLoS One is leaving its mark everywhere.

Sunday, July 13, 2008

Stanford - Promoting open access while selling access to "closed" journals

Some people may have seen the press Stanford got a few weeks ago regarding the Open Access initiative of their School of Education. For some more information on this see
  • Stanford's Education School Requires Open Access

  • Stanford University School of Education's Open Access Mandate—Harvard Medical School Next?

  • Science Commons » Blog Archive » A new open access mandate at Stanford

  • Certainly sounds like a good move on their part. And then I got an interesting thing in the mail from the Stanford Alumni Association (I earned my PhD from Stanford) trying to get me to join the association (see letter below). What was the selling point? If I joined I would get access to newspapers, periodicals and even scientific journals, through their library. So Stanford is all for OA in some places. But while they have access to closed journals, they will use that as a recruitment tool to join the Alumni Association. Seems to me like a better way to push for Open Access would be for all of Stanford to take the School of Education's position and for the university to immediately cancel all subscriptions to completely closed access journals.

    Saving Money and Gas and the Planet by Not Travelling

    A UC Davis professor has been getting some local press for NOT going to a meeting . Well, OK that is not exactly the point. He (Timothy Morton) gave his talk remotely by video taping it and then having the people in Scotland watch the DVD and then talk to him.  The reason for the news coverage is that by doing this this saves both money and carbon output.  Given that I have been canceling trips left and right recently for some medical reasons, I like this idea.  

    I even gave a talk over iChat to a metagenomics gathering in Berlin that was organized by Dan Falush.   I was supposed to go to to this workshop last week as a run up for the International Congress of Genetics (which I have also bailed on but they did not offer to let me speak remotely).  

    I might add that doing a talk by iChat worked out OK ... we probably needed speakers for the computer on the other end and microphones so I could hear the discussion.  And not sure my talk was any good.  But technically, iChat worked out fine.

    So what I am now going to say is that I am canceling the trips for environmental reasons ...

    Saturday, July 12, 2008

    Day 2 on the pump

    Well, Day 2 has begun. And I confess I still find the whole thing to be freaky. I had a rough night trying to sleep with the pump by my side and the tube connected to me. At one point it fell out of my pocket and onto the floor. In addition, my 3.5 year old daughter woke up screaming few times wanting daddy to come to her room. So I rushed into her room, once forgetting to pick up the pump from the bed and nearly dragging it on the floor.

    I spent much of the AM trying to figure out how I was supposed to take a shower with this thing. I disconnected the tubing but was not sure how wet I could let the port on my belly get. So I washed the rest of me and was careful with the port.

    I decided to skip work today. Just could not deal with it. And I spent the AM doing some yard work and the PM making jam and freezing some of our summer fruit growing in our yard. And I still was a bit freaked out by the whole thing.

    So we decided to go out for dinner and though it was nice to be able to punch in how much I was going to eat and get a bolus from my pump, I still found the whole thing stressful. I did not know what to do with the tubing nor exactly how to carry the pump around. Then we went out for ice cream and eventually came home. So - Day 2 survived but still not exactly relaxing.

    UC Davis Med School's conflict of interest policies among best

    A little late on tis post but still wanted to point out this story in the Davis student newspaper (California Aggie - UC Davis Med School's conflict of interest policies among best). They report that:
    The American Medical Student Association recently conducted a ranking of medical schools based on their policies regarding free gifts from pharmaceutical companies. UC Davis was one of only seven schools nationwide who received a grade of "A" - meaning the school has a comprehensive policy that restricts pharmaceutical company representatives' access to both campuses and academic medical centers.
    Good to see this. I find the layers of real and potential conflicts of interest in medical research in general to be very poorly handled by the community. Not that basic science is immune to this problem either but it seems worse in medical research. For some scathing commentary on conflict of interest in medical research, keep an eye on Steven Salzberg's blog. Every once in a while he has some juicy stuff to discuss.

    Good sources for Air Quality Information for Davis

    Just in case anyone needs it here are a couple of good sources for air quality information for Davis and the area

    Friday, July 11, 2008

    Do you get permission to engineer your microbe?

    Well, lots of researchers manipulate microbes in various ways in the lab. They delete genes. They make mutants They insert genes. Sometimes, they insert antibiotic resistance genes to help with the genetic manipulations they are doing.

    Do researchers always think about the potential risks of what they are doing? Well, probably not. Most of the time that is OK as the risks are negligible. But some of the time, there are real risks to consider. One example of a real risk is the introduction into some pathogen of genes encoding a form of antibiotic resistance not seen normally in that pathogen. If that strain escapes from the lab, it could, in theory, spread into the real world and make treating infections by that pathogen more difficult.

    All Things Considered had a very interesting story on "Making Drug-Resistant Germs In The Lab" about exactly this issue a few days ago where they discussed how one researcher submitted to an NIH oversight panel a request to carry out this type of experiment. It seems as though very few researchers actually submit requests to carry out these experiments, even though many are doing it. NPR also discussed how the CDC reviews requests to manipulate certain really nasty pathogens and that most of the requests have been granted. Unfortunately, I cannot find a transcript for this story to quote, but it is really worth listening to.

    Wanted -Microbial Genomics Lead at JGI

    The Joint Genome Institute, where I work part of the time, is seeking a lead scientist for their Microbial Genomics work.
    Sr. Research and Management Opportunity

    The DOE Joint Genome Institute (JGI) in Walnut Creek, CA has an exciting Staff Scientist opportunity available. Will be responsible for leading the JGI's Microbial Genome Program including the development of an independent research program in microbial genomics. Will manage all aspects of the program from application review through sequencing and genome analysis. Will be expected to collaborate with external scientific communities, present scientific data and publish results independently and with collaborators. Will also participate as a member of the JGI senior management team. This position reports to the Deputy Director of Scientific Programs.
    For more information see here. If you want to play a leadership role in microbial genomics, this job is for you.

    How will I survive? iPhone Upgrade crashed ...

    Well, not my normal posting here. But I have been trying to use my iPhone more and more for blogging and was excited about some of the new software upgrades that were made available today. And so I started the upgrade. And the iTunes server has apparently crashed and now my phone is stuck in "Emergency calls only" mode. So much for mobile blogging for today at least.

    Phylojeanomics and The Jeans of Life

    Well after the PLoS Nature dust up, I thought we needed a little humor in our lives.  So here is an old Levis add with a distinct evolution theme.  Maybe Jindal should propose a Levis boycott?

    Thursday, July 10, 2008

    Starting pumping

    Well after 24 years of Type I diabetes I am now switching from multiple daily injections to using a pump. Not sure if this will be a permanent shift but it is worth a try.

    I note, I have been in excellent control with the injections and do not really find them that annoying. But lately I have had some issues with control (both on the high and low end) and I thought it would be worth trying the pump.

    So I went to my doctor, who happens to also have Type I diabetes. And he recommended I go on the Medtronic Paradigm 722 pump. And so, without much fanfare I did it.

    It took a month or so for the paperwork from my insurance to work through the system and I was approved for the pump. And then they sent me a big box with all sorts of stuff in it. And I scheduled an appointment with a Medtronic tutor who would show me how to use it.

    And that is what I did today. I went in to my doctor's office and me the tutor. And we went through the basics (I had spent about two hours playing around with the pump the day before). And then we got some insulin from the doctor and she showed me how to connect the tubing. And then I connected myself (using one of the Medtronic Quick-Set systems).

    It was not too painful, but I got some sort of stress response - pale and sweaty - much like the last time I gave blood. But I got through that and felt a bit better. And then I was sent home. Just like that I was a cyborg on the pump.

    I confess - despite being a biologist (Professor) and having lots of knowledge about how these things work, I spent the rest of the day kind of freaking out with a tube connected to my belly fat. Nothing rational in the freak out session - just felt weird being connected to this pump when normally I would just give a shot and then be "free." Oh well, we will see how it goes. I even went from the doctor's office to a meeting I had on my campus about teaching a new course and managed to not completely flip out and run out of the meeting.

    And then I went home and kind of sulked around the house while I tried to figure this thing out. So - not too bad but not sure I like this thing. When using injections between shots I could at least pretend to be somewhat normal. Now with a tube sticking into my side that is not going to happen.

    Forget Lincoln-Douglas - How about a Lincoln-Darwin debate?

    In case you did not see it - it is worth seeing the discussion of Lincoln vs. Darwin in Newsweek (How Darwin and Lincoln Shaped Us).  They set up the discussion by pointing out that they had the same birthday.  They say Lincoln was more important.  Not going to argue but not sure they are right.  My favorite section on this article:
    This questioning spirit is one of the most appealing facets of Darwin's character, particularly where it finds its way into his published work. Reading "The Origin of Species," you feel as though he is addressing you as an equal. He is never autocratic, never bullying. Instead, he is always willing to admit what he does not know or understand, and when he poses a question, he is never rhetorical. He seems genuinely to want to know the answer. He's also a good salesman. He knows that what he has to say will not only be troubling for a general reader to take but difficult to understand—so he works very hard not to lose his customer. The book opens not with theory but in the humblest place imaginable: the barnyard, as Darwin introduces us to the idea of species variation in a way we, or certainly his 19th-century audience, will easily grasp—the breeding of domestic animals. The quality of Darwin's mind is in evidence everywhere in this book, but so is his character—generous, open-minded and always respectful of those who he knew would disagree with him, as you might expect of a man who was, after all, married to a creationist.

    Wednesday, July 09, 2008

    Evolution education, Jindal and the election

    There is an interesting piece on the "Science Education Act" in Louisiana in the New Scientist (see New legal threat to school science in the US ). by Amanda Gefter. This act seems to be designed to "lip ID in "through the back door" and is promoting itself as a bill for "Academic Freedom" Personally, I am all for academic freedom, including the ability to study and discuss all sorts of controversial things. However, it is clear this is not what the bill is really about. It is about teaching religion as science. The New Scientist reports
    "Supporters of the new law clearly hope that teachers and administrators who wish to raise alternatives to evolution in science classes will feel protected if they do so. The law expressly permits the use of "supplemental" classroom materials in addition to state-approved textbooks. The LFF is now promoting the use of online "add-ons" that put a creationist spin on the contents of various science texts in use across the state, and the Discovery Institute has recently produced Explore Evolution, a glossy text that offers the standard ID critiques of evolution (see "The evolution of creationist literature"). Unlike its predecessor Of Pandas and People, which fared badly during the Dover trial, it does not use the term "intelligent design"."
    All I can say is that if McCain picks Bobby Jindal (the governor of LA and supporter of this bill) as his running mate it will be the ultimate proof that McCain is no longer the independent thinker he used to be and is instead a complete tool of others.

    It is worth reading this article if you care about science education.

    Tuesday, July 08, 2008

    Overselling genomics Award #5: Duckweed will save the world

    OK. I really wanted to leave this one alone because it involves the Joint Genome Institute (JGI) where I work part of the time. And I really like JGI and what it is doing in many aspects of genomics. But this one is just so over the top that I could not leave it alone. There is a press release from Rutgers that came out regarding a new project to sequence the duckweed genome (see News: Duckweed genome sequencing has global implications) and the Eureka release here

    And this one is just so over the top in terms of overselling I do not know where to begin. First, they had me at the title
    Duckweed genome sequencing has global implications
    But the subtitle is even better
    Pond scum can undo pollution, fight global warming and alleviate world hunger
    There is really little else to say. I commend the JGI and DOE for supporting this work as it sounds reasonable and work on this organism may have many uses. But, umm, this was the most obvious "Overselling genomics award" I have ever given.

    Wednesday, July 02, 2008

    Only Nature could turn the success of PLoS One into a model of failure

    Now, mind, you I like Nature as a publishing unit. They publish some very fine journals. Now, most of them are not Open Access, so I choose not to publish there if I can avoid it. But I still like them. And many of the editors and reporters there are excellent - smart, creative, insightful and such. But Nature the publisher can also be completely inane when it comes to writing about Open Access and PLoS. In a new article by Declan Butler, Nature takes another crack at the PLoS "publishing model"

    The problem with PLoS now is ... wait for this ... the success of PLoS One. PLoS One it turns out is publishing a lot of papers (including one by me, today). And bringing in a decent amount of money to PLoS apparently (note for full disclosure - I am involved in PLoS Biology as "Academic Editor in Chief" and PLoS Computational Biology as an Academic Editor ... although I should note I am not involved in financial discussions at PLoS in any way).

    So why is the success of PLoS One a problem? Well, because it allows Nature to do the old good cop bad cop routine and to write, again, about the "failings" of the PLoS publication model. Now, mind you, the article does not quote a single source for what the PLoS publication model is. But they do say it has failed. From what I can tell here is the logic of the failure argument:
    1. Nature believes PLoS' model for success revolved solely around PLoS Biology and PLoS Medicine and some of the other other PLoS journals being self sustaining after a few years.
    2. Analysis of some financial information suggests that PLoS Biology and Medicine currently are not breaking even
    3. PLoS One is apparently wildly successful and thus is brining in some money to PLoS.
    4. PLoS One publishes a lot of papers (they discuss this a bit and imply that this is a bad thing because some of the papers must be bad. Note - they do not back this up with any evidence. Silly for me to ask a science journal to use evidence)
    5. Therefore, the entire PLoS Publication model is a failure.
    The problems with this logic are, well, large. Here are some:
    1. Does Nature really think that there ever was a single "model" for how PLoS should be evaluated?
    2. If so, where is the documentation of what this model actually was?
    3. Even if there was a PLoS model and even if it turns out to be not exactly what PLoS is doing now, what is the big deal? If you were a stockholder of any company and they told you "we are never going to change our business model no matter what happens in the world around us" I would recommend you not buy their stock. It is simply farcical to expect any entity to stick to a single simple model forever.
    4. Does not Nature supplement some of their bigger journals with their higher volume other journals?
    5. Most companies these days use high profile entities such as PLoS Biology and PLoS Medicine to attract attention to other portions of their company in order to help bring in money. Is this somehow not allowed by PLoS? Doesn't Nature do the same thing?
    6. If you look at the figure Nature shows of PLoS $$$, it shows income rising in 2007 and expenses going down. How did that get turned into a bad thing?
    So - I still do like Nature publishing because much of the time it has high quality stuff. It even has high quality stuff commenting/criticizing the Open Access movement and pointing out some of the challenges with it. But this article by Butler is not an impressive piece of work. I really wanted to give him an award but could not think of what to give.

    See also (thanks to Bora for pointing out a bunch of these links)

    My first PLoS One paper .... yay: automated phylogenetic tree based rRNA analysis
    Well, I have truly entered the modern world. My first PLoS One paper has just come out. It is entitled "An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)" and well, it describes automated software for analyzing rRNA sequences that are generated as part of microbial diversity studies. The main goal behind this was to keep up with the massive amounts of rRNA sequences we and others could generate in the lab and to develop a tool that would remove the need for "manual" work in analyzing rRNAs.

    The work was done primarily by Dongying Wu, a Project Scientist in my lab with assistance from a Amber Hartman, who is a PhD student in my lab. Naomi Ward, who was on the faculty at TIGR and is now at Wyoming, and I helped guide the development and testing of the software.

    We first developed this pipeline/software in conjunction with analyzing the rRNA sequences that were part of the Sargasso Sea metagenome and results from the word was in the Venter et al. Sargasso paper. We then used the pipeline and continued to refine it as part of a variety of studies including a paper by Kevin Penn et al on coral associated microbes. Kevin was working as a technician for me and Naomi and is now a PhD student at Scripps Institute of Oceanography. We also had some input from various scientists we were working with on rRNA analyses, especially Jen Hughes Martiny

    We made a series of further refinements and worked with people like Saul Kravitz from the Venter Institute and the CAMERA metagenomics database to make sure that the software could be run outside of my lab. And then we finally got around to writing up a paper .... and now it is out.

    You can download the software here. The basics of the software are summarized below: (see flow chart too).
    • Stage 1: Domain Analysis

      • Take a rRNA sequence
      • blast it against a database of representative rRNAs from all lines of life
      • use the blast results to help choose sequences to use to make a multiple sequence alignment
      • infer a phylogenetic tree from the alignment
      • assign the sequence to a domain of life (bacteria, archaea, eukaryotes)

    • Stage 2: First pass alignment and tree within domain
      • take the same rRNA sequence
      • blast against a database of rRNAs from within the domain of interest
      • use the blast results to help choose sequences for a multiple alignment
      • infer a phylogenetic tree from the alignment
      • assign the sequence to a taxonomic group

    • Stage 3: Second pass alignment and tree within domain
      • extract sequences from members of the putative taxonomic group (as well as some others to balance the diversity)
      • make a multiple sequence alignment
      • infer a phylogenetic tree
    From the above path, we end up with an alignment, which is useful for things such as counting number of species in a sample as well as a tree which is useful for determining what types of organisms are in the sample.

    I note - the key is that it is completely automated and can be run on a single machine or a cluster and produces comparable results to manual methods. In the long run we plan to connect this to other software and other labs develop to build a metagenomics and microbial diversity workflow that will help in the processing of massive amounts of sequence data for microbial diversity studies.

    I should note this work was supported primarily by a National Science Foundation grant to me and Naomi Ward as part of their “Assembling the Tree of Life” Program (Grant No. 0228651). Some final work on the project was funded by the Gordon and Betty Moore Foundation through grant #1660 to Jonathan Eisen and the CAMERA grant to UCSD.

    Wu, D., Hartman, A., Ward, N., & Eisen, J. (2008). An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) PLoS ONE, 3 (7) DOI: 10.1371/journal.pone.0002566

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