Wednesday, May 30, 2007
Now today was the last straw in a long series of annoyances so I am going public with it. My wife had a Dr's appointment with Steve Oliver of the U. C. Davis group here in Davis. Her appointment was at 10 AM. They even called a few nights ago to remind us. So - I stayed at home with our 2 year old and our 4 month old. My wife rushed off, stressed about ditching the 4 month old since he had not eaten at the regular time and she was worried about him getting too hungry while she was gone (we avoid taking kids to Drs offices whenever possible).
So she showed up for her appointment a little early. And then she waited and waited. Finally she went up to the counter and asked what was going on. The receptionist flippantly told her that her appointment was actually at 10:30 but that they tell people it is earlier than it really is because many people are late. In other words, they lie to the patients. I am simply stunned by this. Yes people are late for things. So develop some system to punish the late ones or reward the early ones. But lying to your patients is pathetic. I am once again embarassed to be associated with this system, even if peripherally. So - we are now going to switch to the Sutter group - which I have had great experiences with.
Tuesday, May 29, 2007
This meeting is connected to the new CAMERA Metagenomics Database run out of UCSD (as a Joint Venture with the Venter Institute). I am about to head down to the Scientific Advisory Board meeting for CAMERA. So I am asking anyone out there who is interested in metagenomics to check out CAMERA and let me know what you think. Right now I am I guess kind of an insider/outsider in CAMERA. I am supposed to have a subcontract to Davis to help integrate some phylogenetic tools into the database but alas the Davis office has been a bit lax shall we say about getting my subcontract set up. So until that is set up I guess I am a CAMERA advisor.
Anyway, if anyone has any useful opinions out there about CAMERA I will be happy to share them with those at the SAB meeting.
Dear Sanger Center. You might want to tell google to stop printing your ad that says
"Sanger PhD Programme - www.sanger.ac.uk - Fully funded 4 year studentships in genomics. Deadline 10th Dec 2006"
It seems to be a bit out of date.
Friday, May 25, 2007
Zimmer, for those who are not familiar, is a science writer who also now has a good blog (called The Loom) but is probably best known for his articles in the New York Times and his books. (I have not read all of his books, but his Evolution book is quite good and I have Parasite Rex but alas have not read it yet).
Anyway, Zimmer in his new blog writes about how Open Access science makes his blog easy because he can use a figure from a PLoS paper (on mouse genetic interactions) and rather than sue him, PLoS simply encourages him. I could blather on and on about this (and in fact have - see here for example). But better to just read his words:
And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that "everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish." No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it. In fact, I just did.
I certainly appreciate the importance of copyrights (as the owner of many for my articles and books), but in these situations, keeping information behind a thick wall starts to seem a bit crazy, like the loss of precious bodily fluids. Far from committing some sort of violation to the PLOS paper, I have actually just spread the word about it. A few readers may even go back to read the original. And it was so easy and straightforward for me to do so that I will be very reluctant to bother with anything else.
You go Carl. Welcome to the wonderful world of OA.
Wednesday, May 23, 2007
Anyway - on the drive over, I was listening to KQED's Forum Show and they were doing a story on Avandia, the type II diabetes drug. A recent report on this drug indicates that taking it leads to a significant increase in very negative "side effects" like death. Most interesting and upsetting to me, the lead author of the new study said something to the effect of "our new study was limited significantly because we could not get access to the full results of the clinical trials on Avandia." This is really stunning. Here is a drug making GSK billions of dollars and yet the clinical trial data that underlies the approval of this drug is not readily available for other people to look at. What is wrong with this picture? I though science was about building on prior results. If you can't get the data, how exactly do you confirm what someone else did and how do you build on their results? Apparently, medicine does not follow the same procedures.
So I seethed while in the car. And then, I got stuck in a traffic jam (normally I take the train, but was unable to today). And at the same time, they announced the call in number. So I called -- the first time I have ever even tried to call one of these shows. And on the second try it rang. And a man answered and asked for my first name and my question/comment. And then, I was on the air ... asking about whether there were any attempts to make clinical trial data more readily available (OK, I knew there were attempts, but I was not sure of the details and they needed to be asked on the air anyway).
And if you want to know what I said, and what they said, well listen to the show (I am on at minute ~ 34).
Wed, May 23, 2007 -- 9:00 AMAnd to add to the bonus of being on the air, Jim Bristow, Deputy Director of JGI, was, like me, a bit late to the SAC meeting at JGI. And he came up to me and asked if that was indeed me on the air while I was supposed to be at the meeting. To learn more about clinical trial access, see PLoS Clinical Trials.
Avandia and Diabetes
Listen (RealMedia stream) Download (MP3)
(Windows: right-click and choose "Save Target As." Mac: hold Ctrl, click link, and choose "Save As.")
So if you are looking for a new OA journal to submit some systems biology related papers, you should try here. And maybe with a little effort, we can convince Nature it is worth doing for more of their journals.
Thursday, May 17, 2007
To all you microbiologists out there. Are you bored with what you are doing? Looking for something important and challenging to do? Sick of working on yet another human pathogen? Switch to working on a topic relating to limiting global warming and climate change (note if you want to learn more about global climate change check out the recent New Scientists article here which I found out about from the Davis Egghead Blog). Among the topics you could work on:
Tuesday, May 15, 2007
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.
Thursday, May 10, 2007
I wrote about the meeting previously in my blog.
The speakers were Eric Allen (UCSD-SIO), Doug Bartlett (UCSD-SIO), Weizhong Li (UCSD), Victor Markowitz (JGI), Jonathan Eisen (UCD), Victoria Orphan (Caltech), Adam Martiny (UCI), Jessica Green (UCM), Kimmen Sjolander (UCB), and Steven Brenner (UCB). All Powerpoint presentations are available in PDF format.
Monday, May 07, 2007
Basically there appear to be two camps emerging. The anti-science group (not what they called them in the Times article but that is what they are) who cannot reconcile Darwinism (or many other scientific tenets) with their religious beliefs. And on the other side are conservatives who not only accept evolution by natural selection as a fact, but embrace it as supporting many of their conservative ideals. This second pro-evolution conservative clade includes fundamentalist types who, like Francis Collins, believe that evolution by natural selection is indirectly the hand of God. The pro-evolution clade also includes political and social conservatives, who are not particularly religiously conservative.
I found the article fascinating in many ways because finally philosophical conservatives are taking a stand against the religious right. For example:
“I do indeed believe conservatives need Charles Darwin,” said Larry Arnhart, a professor of political science at Northern Illinois University in DeKalb, who has spearheaded the cause. “The intellectual vitality of conservatism in the 21st century will depend on the success of conservatives in appealing to advances in the biology of human nature as confirming conservative thought.”
Also --- from the article
What both sides do agree on is that conservatives who have shied away from these debates should speak up. Mr. Arnhart said that having been so badly burned by social Darwinism, many conservatives today did not want “to get involved in these moral and political debates, and I think that’s evasive.”
Yet getting involved is more important than ever, after “the disaster” of “President Bush’s compassionate conservatism,” he said, because the only hope for Republicans is a “fusion of libertarianism and traditionalism, and Darwinian nature supports that conservative fusion.”
So I say to all you social or political conservatives who think that anti-evolution talk is not necessary and potentially damaging, come out come out wherever you are. The time is now for evolutionary biologists to embrace these conservatives. Not because they agree or disagree with their politics. But because evolutionary biology does not itself make ANY moral judgements nor force one to make any political decisions. It is science. Just as quantum physics does not support the right or the left, evolutionary science is apolitical. That is not to say that evolutionary science cannot be used to inform political and social and moral decisions. It is just that evolutionary science is not about those things. It is about studying the way the world works.
See the SF-GATE article here.
Obama is quoted as saying
"Rather than restricting the product of those debates, we should instead make sure that our democracy and citizens have the chance to benefit from them in all the ways that technology makes possible."I could not agree more. Now if only that were the case for all scientific research.
Thanks to Melinda Simmons for pointing this out
I have tried to convince people there are connections between the two in the past. But the best article I have seen on this is, for better or worse, about my brother. What a scam he has pulled at Berkeley. He is teaching a course (with James Fraser) ostensibly about bioinformatics in some way. What is is really about? Baseball statistics. They are not even trying to pretend it is about bioinformatics. But they apparently hope that some of the stats rubs off enough that some students get into bioinformatics.
As an ex-baseball player I have some smpathy for their approach. Also, it was at a baseball game that my brother first convinced me that Open Access science was the way to go. But I think focusing on stats is the wrong way to use an interest in baseball to get an interest in biology. I think it would be better to get Drew Endy and his cohort into using one of their synthetic biology competitions to make some good new steroids. And then the stats course could be used to analyze the differences with and without the new drugs.
Saturday, May 05, 2007
I think this is a stunner,” Dr. Collins said. “This is like the seat of the soul of the genome."
Now, I have commented before about how Dr. Collins is doing a pretty good job about keeping his religious beliefs separate from his work. And since he is a strong supporter of evolutionary biology I like to give him the benefit of the doubt (I personally agree with him that there is no need for a conflict between evolutionary biology and non fundamentalist religious beliefs). But I think "the seat of the soul of the genome" is a bit much.
I frequently criticize researchers who observe something in the genome and immediately come up with an adaptive explanation for the observation. Such adaptationist, just so story responses, are common in molecular biology and many areas of biology and were written about extensively by Gould and Lewontin and others. But now I guess we have a new category of adaptationist-like explanations. Striking findings in a genome can now be called "just soul stories."
Tuesday, May 01, 2007
FOR IMMEDIATE RELEASE
72 New Members Chosen By Academy
The election was held this morning during the business session of the 144th annual meeting of the Academy. Those elected today bring the total number of active members to 2,025. Foreign associates are nonvoting members of the Academy, with citizenship outside the
The National Academy of Sciences is a private organization of scientists and engineers dedicated to the furtherance of science and its use for the general welfare. It was established in 1863 by a congressional act of incorporation signed by Abraham Lincoln that calls on the Academy to act as an official adviser to the federal government, upon request, in any matter of science or technology.
Additional information about the Academy and its members is available online at http://www.nasonline.org.
Newly elected members and their affiliations at the time of election are:
ACUÑA, Mario H.; senior astrophysicist and project scientist, International Solar Terrestrial Physics Program, NASA Goddard Space Flight Center, Greenbelt, Md.
AGARD, David A.; investigator, Howard Hughes Medical Institute, and professor, department of biochemistry and biophysics,
AMBROS, Victor R.; professor of genetics,
ANDERSON, David J.; investigator, Howard Hughes Medical Institute, and Roger W. Sperry Professor of Biology, California Institute of Technology, Pasadena
ATWATER, Brian F.; geologist, western earthquake hazards team, U.S. Geological Survey, and affiliate professor, department of earth and space sciences, University of Washington, Seattle
AWSCHALOM, David D.; professor of physics and of electrical and computer engineering, department of physics,
BAKER, Tania A.; investigator, Howard Hughes Medical Institute, and E.C. Whitehead Professor Biology, Massachusetts Institute of Technology,
BAWENDI, Moungi G.; professor of chemistry and Keck Professor of Energy, Massachusetts Institute of Technology,
BELLUGI, Ursula; professor and director, Laboratory of Cognitive Neuroscience, Salk Institute for Biological Studies, La Jolla,
BLOCK, Steven M.; professor of applied physical and biological sciences,
BRENNER, Michael B.; Theodore Bevier Bayles Professor of Medicine,
BRYANT, Robert L.; J.M. Kreps Professor, department of mathematics,
CANFIELD, Donald E.; professor of ecology,
CARROLL, Sean B.; investigator, Howard Hughes Medical Institute, and professor of molecular biology and genetics,
CLARK, Noel; professor, department of physics,
COOK, Karen S.; Ray Lyman Wilbur Professor of Sociology, department of sociology,
DANGL, Jeffrey L.; associate director, Carolina Center for Genome Sciences, and John N. Couch Distinguished Professor, University of North Carolina, Chapel Hill
DOONER, Hugo K.; professor, Waksman Institute, Rutgers, The State University of New Jersey,
DRAINE, Bruce T.; professor, department of astrophysical sciences,
DRUKER, Brian J.; investigator, Howard Hughes Medical Institute, and JELD-WEN Chair of Leukemia Research, Oregon Health & Science University, Portland
DURRETT, Richard; professor,
EDGAR, Robert S.; professor emeritus,
EMANUEL, Kerry A.; Breene M. Kerr Professor, program in atmospheres, oceans, and climate, department of earth, atmospheric, and planetary sciences, Massachusetts Institute of Technology, Cambridge
EMR, Scott D.; investigator, Howard Hughes Medical Institute, and director, Institute of Cell and Molecular Biology, Cornell University, Ithaca, N.Y.
ESTELLE, Mark; Carlos O. Miller Professor of Developmental Biology, department of biology,
ESTES, Mary K.; professor and Cullen Foundation Endowed Chair, department of molecular virology and microbiology, Baylor College of Medicine,
FALKOWSKI, Paul G.; professor, Institute of Marine and Coastal Sciences and department of geological sciences, Rutgers, The State University of New Jersey, New Brunswick
FAYER, Michael D.; David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry, department of chemistry,
FLEMING, Graham; Melvin Calvin Distinguished Professor of Chemistry,
FRAKER, Pamela J.; professor of food science and human nutrition and distinguished professor of biochemistry,
GABRIELSE, Gerald; Leverett Professor of Physics,
GINSBURG, David; investigator, Howard Hughes Medical Institute, and James V. Neel Distinguished University Professor, University of Michigan Medical School,
GOLDMAN, Allen M.; Institute of Technology Professor of Physics, and head,
GOTTLIEB, David; Ford Foundation Professor,
GRONENBORN, Angela M.; professor of pharmacology, and director, Structural Biology Program,
HILDEBRAND, John G.; Regents Professor and professor of neurobiology, biochemistry and molecular biophysics, entomology, and molecular and cellular biology, and director, Arizona Research Laboratories Division of Neurobiology, University of Arizona, Tucson
HOBBS, Helen H.; investigator, Howard Hughes Medical Institute, and director, McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas
HOUSE, James S.; Angus Campbell Collegiate Professor of Sociology and Survey Research, Institute for Social Research,
JOHNSON, William L.; Ruben and Donna Mettler Professor of Materials Science, Engineering, and Applied Science, California Institute of Technology, Pasadena
JOHNSON-LAIRD, Philip N.; Stuart Professor of Psychology, department of psychology,
KIESSLING, Laura L.; professor of chemistry and biochemistry,
KOWALCZYKOWSKI, Stephen C.; distinguished professor of microbiology and of molecular and cellular biology, and director, Center for Genetics and Development,
LAITIN, David; James T. Watkins IV and Elise V. Watkins Professor of Political Science, department of political science, Stanford University, Stanford, Calif.
LIBCHABER, Albert J.; professor of physics, The Rockefeller University, New York City
LOVEJOY, Claude Owen; university professor,
MARDER, Eve E.; professor of neuroscience, department of biology,
McMULLEN, Curtis T.; professor,
MICALI, Silvio; professor, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology,
MILLER, Christopher; investigator, Howard Hughes Medical Institute, and professor,
MOERNER, William E.; Harry S. Mosher Professor,
MORGAN, M. Granger; university professor and head, department of engineering and public policy,
OLSON, Peter L.; professor of geophysical fluid dynamics,
PACALA, Stephen W.; Frederick D. Petrie Professor, department of ecology and evolutionary biology,
PLOG, Stephen; Commonwealth Professor, department of anthropology,
PLOTT, Charles R.; Edward S. Harkness Professor of Economics and Political Science, division of humanities and social sciences, California Institute of Technology,
RICHMOND, Timothy J.; professor, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zurich, Switzerland
SCHILLER, Peter H.; professor, Massachusetts Institute of Technology,
SCHRAMM, Vern L.; professor and chair, department of biochemistry, Albert Einstein College of Medicine of
SEIDMAN, Jonathan G.; Henrietta B. and Frederick H. Bugher Professor of Cardiovascular Genetics,
SHULMAN, Gerald I.; investigator, Howard Hughes Medical Institute, and professor of medicine and cellular and molecular physiology, Yale University School of Medicine,
SPENCER, Charles S.; curator of anthropology, and chair, division of anthropology, American
SPERGEL, David N.; professor, department of astrophysical sciences,
SREENIVASAN, Katepalli R.; Martin Professor of Engineering and distinguished university professor,
STARK, Harold M.; professor of mathematics,
TABIN, Clifford J.; professor, department of genetics,
WELLEMS, Thomas E.; chief, laboratory of malaria and vector research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
WILL, Clifford M.; James S. McDonnell Professor of Physics,
WISE, Mark B.; John A. McCone Professor of High Energy Physics, California Institute of Technology,
YOKOYAMA, Wayne M.; investigator, Howard Hughes Medical Institute, and Sam and Audrey Lowe Levin Professor of Medicine and of Pathology, Washington University School of Medicine,
YOUNG, Michael W.; vice president of academic affairs and Richard and Jeanne Fisher Professor, The Rockefeller University, New York City
Newly elected foreign associates, their affiliations at the time of election, and their country of citizenship are:
ASKONAS, Brigitte A.; visiting professor, Imperial College of Science, Technology, and Medicine,
CIECHANOVER, Aaron J.; distinguished professor, faculty of medicine, Technion,
DELIGNE, Pierre; professor, Institute for Advanced Study,
GRANT, Peter R.; professor,
IIJIMA, Sumio; professor, department of materials science and engineering,
ITO, Masao; director, RIKEN Brain Science Institute, Saitama (
IZQUIERDO, Ivan A.; professor of medicine and head, Memory Center, Institute of Biomedical Research, Pontifical Catholic University of Rio Grande, Porto Alegre (Brazil)
KINGMAN, John; director, Isaac Newton Institute for Mathematical Sciences,
LI, Aizhen; Shanghai Institute of Microsystem and Information Technology, Chinese
LORDKIPANIZDE, David O.; director,
MARASAS, Walter F.O.; director, Programme on Mycotoxins and Experimental Carcinogenesis Unit, Medical Research Council, Tygerberg (
PINGALI, Prabhu L.; director, division of agricultural and development economics, United Nations Food and Agricultural Organization,
SALAS, Margarita; research professor,
SEEBACH, Dieter; professor of chemistry emeritus, laboratory of organic chemistry, Swiss Federal Institute of Technology,
TAKEICHI, Masatoshi; director, Center for Developmental Biology, RIKEN,
WHITE, Simon D.M.; director, Max Planck Institute for Astrophysics, Garching,
WOODMAN, Ronald F.; executive president, Geophysical Institute of Peru, Mayorazgo (
ZHANG, Qifa; professor and director, National Key Laboratory of Crop Genetic Improvement,