- 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.
Wednesday, July 30, 2008
Best time to appreciate Open Access? When you're really sick and want to learn more about what you have.
Thursday, July 24, 2008
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?
Davis Hosting Stage 2 of the Tour of California 2009
- 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
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.
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.
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 policy...is 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."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
VandenBos was not available for further comment.
Tuesday, July 15, 2008
Conflict of interest and openness
“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
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
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
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
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
Friday, July 11, 2008
Do you get permission to engineer your microbe?
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
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.
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
Thursday, July 10, 2008
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?
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
"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
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 implicationsBut the subtitle is even better
Pond scum can undo pollution, fight global warming and alleviate world hungerThere 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
- 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.
- Analysis of some financial information suggests that PLoS Biology and Medicine currently are not breaking even
- PLoS One is apparently wildly successful and thus is brining in some money to PLoS.
- 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)
- Therefore, the entire PLoS Publication model is a failure.
- Does Nature really think that there ever was a single "model" for how PLoS should be evaluated?
- If so, where is the documentation of what this model actually was?
- 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.
- Does not Nature supplement some of their bigger journals with their higher volume other journals?
- 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?
- 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?
- Drug Monkey: Nature offers a completely objective and unbiased review of PLoS.
- Greg Laden
- Peter Suber
- Alex Holcombe/Ceptional Nature targets financial weakness of PLoS journals
- Plausible Accuracy
- Bora at Blog Around the Clock
- Bill Hooker
- Health Science and Libraries Blog
- Questionable Authority
- Neurotic Physiology When Journals Pounce
- Class of the business models from A Man with a PhD
- Bjorn Brembs
- Hank at Scientific Blogging
- Timo Hannay at Nature
- Nature Re-Attacks Open Access and PLoS
- Nature vs. PLoS by John Dupuis
- Commentary: Open access equals bulk publishing? by Lars Jensen
- The ‘threatening’ success of PLoS; now heard aloud!
- Science Literature and Changing Times
- The future of scientific publishing
- PLoS, Nature and the community backlash
- PLoS In Nature : The Big Picture
- New salvos in the publishing wars
- Science Commons’ John Wilbanks on the Declan Butler article
- PLoS and the future of publishing - as framed by Nature
- OA and the broader social good
- The economics of open access, part two
- What’s the deal with PLoS One?
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
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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