In a mystical world of folklore, several individuals embrace in a race to find the Tree of Life, said to give immortality, fertility, and other supernatural powersAnd if that does not excite you, well, maybe this will. The cast includes Brad Pitt, Sean Penn and a few other big shots. Stay tuned here for more updates, or check out the wikipedia page for the movie here. Also see: Brad Pitt and The Tree of Life, Brad Pitt Scales Tree of Life, Malick's Tree of Life caught on camera, Brad Pitt looks young in Tree of Life movie
Tuesday, June 17, 2008
Tree of Life hitting the big screen ...
Monday, June 16, 2008
Obama on Teaching Evolution
He was asked about the teaching of intelligent design and evolution in public schools. His response:
I'm a Christian, and I believe in parents being able to provide children with religious instruction without interference from the state. But I also believe our schools are there to teach worldly knowledge and science. I believe in evolution, and I believe there's a difference between science and faith. That doesn't make faith any less important than science. It just means they're two different things. And I think it's a mistake to try to cloud the teaching of science with theories that frankly don't hold up to scientific inquiry.
McCain seems to have gone silent on this issue although I have pointed out that in the past that he was clear about science being taught in science classes. Seems like he is trying to steer clear of this issue. What ever happened to the straight talking McCain?
Freeing My Father's Scientific Publications
Today is Father's Day. It was a great day for me, hanging out with my kids and wife and doing things around town here in Davis (we kind of made it Father's Weekend and did some activities on Saturday too). Despite the wonderful weekend, this day is also filled with melancholy for me when I think about my father, Howard Eisen, who died when I was a freshman in college. I miss him greatly. But whenever I think about him I think about how he almost certainly would be really proud that his two sons (me and my brother Michael at Berkeley) are now scientists.
So, of course, being the obsessed Open Access advocate, the first thing I decided to look at was what publications of my fathers I could get my hands on. This was both to read them and to make them available on this tribute page.
So - my first step in this journey was to search Pubmed for Eisen HJ. And then I had to remove the publications by another Eisen HJ. And so I was left with 35 publications in PubMed (I know he had some other articles as well as chapters in books and such but this is a good start). So then I asked - which of these were available online in one way or another. According to Pubmed 24/35 were available online. Of those available online:
- Pubmed Central: 3
- Free access: 13
- Fee access: 8
- Unavailable: 11.
So - what to do next? Well, my goal is to get access to all his papers and then to free them up to the world. So my first step was to see if any of the ones that Pubmed did not have links for might be available online anyway. And indeed a few were. For example, Pediatric Research back issues are available online. And these are free. In addition, his papers in Biochemistry, J. Steroid Biochemistry and Advances in Genetics is available for a fee but it is not linked from Pubmed. So with this information the new tally was
- Pubmed Central: 3
- Free access: 14
- Fee access: 11
- Unavailable: 7
So for those 7 that are currently unavailable (at least anywhere I could find) digitally, my next step is to try and lobby the journals to make them available. For some journals, this has some hope (well, not per se my lobbying, but they may make them available). For example, Endocrinology has some back issues available but just not all the way back to some of my father's publications in that journal. So, I wrote to the journal Endocrinology using the link from the journal site and asked what their plans were for older issues. And I will post here if I get a response. (( UPDATE - THESE ARE TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.)) I am doing the same for all the other unavailable publications, although some of the journals seem to not exist anymore.
Convincing "free" access journals to deposit old papers in PMC.
My next goal is to see if the "free" access journals have any plans to submit stuff to Pubmed Central. Yes, I know PMC is not perfect, but I believe it is better to have things in PMC than just on a journals website. So I am writing to all these journals to find out if they have any plans to deposit this material.
Freeing up the "fee for access" papers.
My final initial goal, and probably the most challenging, is to figure out ways to make the papers that are current "fee for access" available for free. If these were my papers, I suppose I could put many of the PDFs on my own web site. Perhaps I can do this for my father's publications (does the right to do this get passed down?). Of course, first I have to get the PDFs and it just seems weird to me to have to pay to get access to papers my father wrote. Another possibility is that the journals would let me pay an OA fee to free up these old papers. I am going to look into that although I cannot really afford it. A final possibility would be to get the papers into PMC without the journals explicit agreement. Perhaps because my father was a government employee, the copyright would allow depositing in PMC? I do not know.
So right now, the process is incomplete. I am actually learning a good deal about OA from looking into older papers rather than just all the new papers I tend to focus on. And hopefully in the process I can free up all of my father's papers so that his scientific legacy does not fade away as rapidly due to lack of access. And then next maybe I can focus on my grandfather's publications.
Anyway -- here is a list of my father's publications with links and/or comments on their availability.
- Simons SS Jr, Pumphrey JG, Rudikoff S, Eisen HJ. Identification of cysteine 656 as the amino acid of hepatoma tissue culture cell glucocorticoid receptors that is covalently labeled by dexamethasone 21-mesylate. J Biol Chem. 1987 Jul 15;262(20):9676-80. PMID: 3597435.
- Cresteil T, Jaiswal AK, Eisen HJ. Transcriptional control of human cytochrome P1-450 gene expression by 2,3,7,8-tetrachlorodibenzo-p-dioxin in human tissue culture cell lines. Arch Biochem Biophys. 1987 Feb 15;253(1):233-40. PMID: 3813564.
- Eisen LP, Reichman ME, Thompson EB, Gametchu B, Harrison RW, Eisen HJ. Monoclonal antibody to the rat glucocorticoid receptor. Relationship between the immunoreactive and DNA-binding domain. J Biol Chem. 1985 Sep 25;260(21):11805-10. PMID: 3840164
- Antakly T, Eisen HJ. Immunocytochemical localization of glucocorticoid receptor in target cells. Endocrinology. 1984 Nov;115(5):1984-9. PMID: 6208016. UPDATE - TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.
- Harmon JM, Eisen HJ, Brower ST, Simons SS Jr, Langley CL, Thompson EB. Identification of human leukemic glucocorticoid receptors using affinity labeling and anti-human glucocorticoid receptor antibodies. Cancer Res. 1984 Oct;44(10):4540-7. PMID: 6331880
- Reichman ME, Foster CM, Eisen LP, Eisen HJ, Torain BF, Simons SS Jr. Limited proteolysis of covalently labeled glucocorticoid receptors as a probe of receptor structure. Biochemistry. 1984 Oct 23;23(22):5376-84. PMID: 6391542
- Nebert DW, Eisen HJ, Hankinson O. The Ah receptor: binding specificity only for foreign chemicals? Biochem Pharmacol. 1984 Mar 15;33(6):917-24. Review. PMID: 6324804
- Nebert DW, Brown DD, Towne DW, Eisen HJ. Association of fertility, fitness and longevity with the murine Ah locus among (C57BL/6N) (C3H/HeN) recombinant inbred lines. Biol Reprod. 1984 Mar;30(2):363-73. PMID: 6704471
- Foster CM, Eisen HJ, Bloomfield CD. Covalent labeling of rat thymocyte and human lymphoid glucocorticoid receptor. Cancer Res. 1983 Nov;43(11):5273-7. PMID: 6577947
- Karenlampi SO, Eisen HJ, Hankinson O, Nebert DW. Effects of cytochrome P1-450 inducers on the cell-surface receptors for epidermal growth factor, phorbol 12,13-dibutyrate, or insulin of cultured mouse hepatoma cells. J Biol Chem. 1983 Sep 10;258(17):10378-83. PMID: 6309801
- Mariani G, Kortright KH, Eisen HJ, Adamson RH, Waldmann TA. A methodological approach for the study of protein synthesis by cell cultures in vitro. J Nucl Med Allied Sci. 1983 Jul-Sep;27(3):237-47. PMID: 6198498
- Simons SS Jr, Schleenbaker RE, Eisen HJ. Activation of covalent affinity labeled glucocorticoid receptor-steroid complexes. J Biol Chem. 1983 Feb 25;258(4):2229-38. PMID: 6687388.
- Tukey RH, Hannah RR, Negishi M, Nebert DW, Eisen HJ. The Ah locus: correlation of intranuclear appearance of inducer-receptor complex with induction of cytochrome P1-450 mRNA. Cell. 1982 Nov;31(1):275-84. PMID: 6186383
- Legraverend C, Hannah RR, Eisen HJ, Owens IS, Nebert DW, Hankinson O. Regulatory gene product of the Ah locus. Characterization of receptor mutants among mouse hepatoma clones. J Biol Chem. 1982 Jun 10;257(11):6402-7. PMID: 6896205
- Nebert DW, Negishi M, Lang MA, Hjelmeland LM, Eisen HJ. The Ah locus, a multigene family necessary for survival in a chemically adverse environment: comparison with the immune system. Adv Genet. 1982;21:1-52. Review. PMID: 7036691. Available online for fee but not linked from Pubmed.
- Eisen HJ, Schleenbaker RE, Simons SS Jr. Affinity labeling of the rat liver glucocorticoid receptor with dexamethasone 21-mesylate. Identification of covalently labeled receptor by immunochemical methods. J Biol Chem. 1981 Dec 25;256(24):12920-5. PMID: 6895516
- Hannah RR, Nebert DW, Eisen HJ. Regulatory gene product of the Ah complex. Comparison of 2,3,7,8-tetrachlorodibenzo-p-dioxin and 3-methylcholanthrene binding to several moieties in mouse liver cytosol. J Biol Chem. 1981 May 10;256(9):4584-90. PMID: 7217100
- Stevens J, Eisen HJ, Stevens YW, Haubenstock H, Rosenthal RL, Artishevsky A. Immunochemical differences between glucocorticoid receptors from corticoid-sensitive and -resistant malignant lymphocytes. Cancer Res. 1981 Jan;41(1):134-7. PMID: 7448753
- Nebert DW, Eisen HJ, Negishi M, Lang MA, Hjelmeland LM, Okey AB. Genetic mechanisms controlling the induction of polysubstrate monooxygenase (P-450) activities. Annu Rev Pharmacol Toxicol. 1981;21:431-62. Review. PMID: 7016012
- Marković RD, Eisen HJ, Parchman LG, Barnett CA, Litwack G. Evidence for a physiological role of corticosteroid binder IB. Biochemistry. 1980 Sep 30;19(20):4556-64. PMID: 7426614. Available online to purchase though no listed in Pubmed.
- Eisen HJ. An antiserum to the rat liver glucocorticoid receptor. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3893-7. PMID: 7001446
- Hannah R, Simkins R, Eisen HJ. Synthesis of alpha-fetoprotein and albumin by fetal mouse liver cultured in chemically defined medium. Dev Biol. 1980 Jun 15;77(2):244-52. PMID: 6156873
- Okey AB, Bondy GP, Mason ME, Kahl GF, Eisen HJ, Guenthner TM, Nebert DW. Regulatory gene product of the Ah locus. Characterization of the cytosolic inducer-receptor complex and evidence for its nuclear translocation. J Biol Chem. 1979 Nov 25;254(22):11636-48. PMID: 500663
- Rechler MM, Eisen HJ, Higa OZ, Nissley P, Moses AC, Schilling EE, Fennoy I, Bruni CB, Phillips LS, Baird KL. Characterization of a somatomedin (insulin-like growth factor) synthesized by fetal rat liver organ cultures. J Biol Chem. 1979 Aug 25;254(16):7942-50. PMID: 468799
- Simkins RA, Eisen HJ, Sparks JW, Glinsmann WH. Development of glucogenesis from galactose by fetal rat liver explants in organ culture. Dev Biol. 1978 Oct;66(2):353-60. PMID: 700252
- Simkins RA, Eisen HJ, Glinsmann WH. Functional integrity of fetal rat liver explants cultured in a chemically defined medium. Dev Biol. 1978 Oct;66(2):344-52. PMID: 81156
- Eisen HJ, Glinsmann WH. Maximizing the purification of the activated glucocorticoid receptor by DNA-cellulose chromatography. Biochem J. 1978 Apr 1;171(1):177-83. PMID: 646815
- Eisen HJ, Glinsmann W. Partial purification of the glucocorticoid receptor from rat liver: a rapid, two-step procedure using DNA-cellulose. Biochem Biophys Res Commun. 1976 May 17;70(2):367-72. PMID: 180989
- Eisen HJ, Ginsberg AL. Letter: Disulfiram hepatotoxicity. Ann Intern Med. 1975 Nov;83(5):673-5. PMID: 1200504. Back issues not currently available.
- Eisen HJ, Glinsmann W. Partial purification of glucocorticoid receptor from rat liver using DNA-cellulose. J Steroid Biochem. 1975 Jul;6(7):1171-3. PMID: 170470. AVAILABLE FOR FEE BUT NOT LINKED FROM PUBMED.
- Glinsmann WH, Eisen HJ, Lynch A, Chez RA. Glucose regulation by isolated near term fetal monkey liver. Pediatr Res. 1975 Jul;9(7):600-4. PMID: 125868. AVAILABLE FREE EVEN THOUGH MEDLINE DOES NOT HAVE LINK.
- Eisen HJ, Goldfine ID, Glinsmann WH. Regulation of hepatic glycogen synthesis during fetal development: roles of hydrocortisone, insulin, and insulin receptors. Proc Natl Acad Sci U S A. 1973 Dec;70(12):3454-7. PMID: 4357871
- Eisen HJ, Glinsmann WH, Sherline P. Effect of insulin on glycogen synthesis in fetal rat liver in organ culture. Endocrinology. 1973 Feb;92(2):584-8. PMID: 4682869. Wrote to ask if they will become available. UPDATE - TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.
- Hellman DE, Eisen HJ, Goodman HM. The effects of hypophysectomy on phosphorylase activity in adipose tissue and muscle. Horm Metab Res. 1971 Sep;3(5):331-5. PMID: 4332655
- Eisen HJ, Goodman HM. Growth hormone and phosphorylase activity in adipose tissue. Endocrinology. 1969 Feb;84(2):414-6. PMID: 4303531. Wrote to ask if they will become available. UPDATE - TO BE MADE AVAILABLE SOON ACCORDING TO HIGHWIRE PRESS.
Sunday, June 15, 2008
Connection between Video Games and Bioinformatics?
Anyway - it is a nice article about Sean, especially the parts talking about how his background in video games contributed to his success in bioinformatics. Back to something I said above, Sean is without a doubt one of my favorite people in science. There are many reasons for this but here are a few.
- He is very open with ideas.
Once, at a conference, I gave a talk on this bizarre new pattern we had found when we were comparing the genomes of E. coli and V. cholerae. We had found that when we did genome-level alignments of these species there was an X-like pattern (see our paper on this here). Anyway, in the talk I said something to the effect of "we have no friggin idea how these X-like alignments could be generated" And Sean, I think in the quesiton session, pointed out that in another paper of ours we had seen what appeared to be symmetric inversions occurring around the origin of replication and that could create the X-alignment. And lo and behold he was right. We got the paper, but in a large part it was his push that got us looking at the inversions sooner than we would have. - He is very open with science.
Most of Sean's work is on the open side of science. Open Source software. Open Access publications. Open everything. And I should point out that it was a talk by Sean that catalyzed my conversion into an Open Science supporter. I was attending a meeting in Ft. Lauderdale to discuss data release policies for genome projects. This meeting led to the "Ft Lauderdale Agreement" on data release, by the way. A the meeting there were many genomics players like Eric Lander and Francis Collins who were trying to push for not completely open data release policies where genome centers could release data but there would be constraints placed on the use of the data so that the genome centers would be the first to be able to publish genome scale analysis of an organisms genome sequence.
At the time I was working at TIGR and I supported this notion of basically letting people search for a few genes of interest but preventing them from doing genome analyses. And then Sean got up and gave a talk and, well, blew my mind. I am sure I have notes somewhere from the meeting but basically what he said was - the genome projects whole point is to generate genome data for people to do genome-level analysis. So how on earth can we justify preventing exactly the type of analysis that the projects were designed to generate. He was not saying that we should not somehow protect the genome centers. What he was saying was that for the benefit of science, we need to find a way to allow people to do genome-level analyses immediately on the data. And he also said that the risks of releasing ones data with no restrictions are much less than everyone claims. I think he convinced many people that genome centers needed to open up their data release policies a bit more. And he convinced me.
And so I went home from that meeting and decided to release the data from as many of my genome projects as I could, with NO restrictions (e.g., this is what we did with Tetrahymena). And also, this new found belief in openness helped pave the way for my conversion to being an Open Access publishing supporter.
Future of Microbiology Funding at NSF?
A million minds getting together can be confusing but might end up being really cool
WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org webcite.I got really lost reading this I confess. But I moved on since the overall concept seemed quite intriguing, even if I did not get it completely. But it did not get much clearer further on. For example consider their description of a "knowlet"
OK ... I got lost every time I tried to read this in detail. I do think they could benefit greatly by translating their paper from the language used by people who work on text mining to a broader presentation.The future outlook to integrate data mining (for instance gene co-expression data) with literature mining, as formulated in the review by Jensen et al. [2], is at the core of what we aim for at the text mining/data mining interface. To support the capturing of qualitative as well as quantitative data of different natures into a light, flexible, and dynamic ontology format, we have developed a software component called Knowlets™. The Knowlets combine multiple attributes and values for relationships between concepts.
Scientific publications contain many re-iterations of factual statements. The Knowlet records relationships between two concepts only once. The attributes and values of the relationships change based on multiple instances of factual statements (the F parameter), increasing co-occurrence (the C parameter) or associations (The A parameter). This approach results in a minimal growth of the 'concept space' as compared to the text space (Figure 1).
But reading between the lines here, this is a new, apparently open access system to try and get community annotation for "Concepts" and for relationships among concepts in biological sciences. Those concepts could include a wide range of things, including genes, genomes, proteins, as well as more standard concepts like functions. Whatever this system is, it seems worth checking out.
I leave you with their ending:
Once widely used and augmented, this resource could become an open, yet quality assured and comprehensive, environment for collaborative reference and knowledge discovery.Now that I can say I understand and it sounds good to me. If anyone out there has any more insight into this, please give your input.
Saturday, June 14, 2008
Deep microbes get all the love
In the blogs of hers that I have read (note to New York Times --- your system of allowing access to the blog archive really sucks) I recall there being many references to microbes, even when the focus was not on microbes per se. And this week the whole darn blog is about them small little organisms. In this weeks blog, she writes about microbes living in the deep biosphere (some of my favorites) (see Meet the Intraterrestrials).
So - check out her blog. And encourage her to keep writing about microbes. We know they are cool but she can help convince all those others who are not yet microbe fans of this fact too.
Friday, June 13, 2008
Open Metagenomics: Selenium in the Oceans
In this study, we report a comprehensive analysis of Sec utilization in marine microbial samples of the GOS expedition by characterizing the GOS selenoproteome. This is the first time that the microbial selenoprotein population is described in a global biogeographical context. Our analysis yielded the largest selenoprotein dataset to date, provided a variety of new insights into Sec utilization and revealed environmental factors that influence Sec utilization in the marine microbial world.
Wednesday, June 11, 2008
An Open Access pioneer - Trent Reznor
And now he is going even further and in essence putting his music into the public domain as much as possible (see his web site NIN.com for more detail). For example
"Mr. Reznor even posts online all the raw digital tracks from Nine Inch Nails albums for anyone to remix. “I’m done with them,” he said. “Why not?”And he is doing this even though the $$$ for producing his music does not come from the government. He does it in part because he wants his ideas and music to spread and he wants to contribute to musical development. There are obvious parallels between what he (and others) are doing in music and those who develop Open Source software and those who release their data and publications to be as free as possible. I know I am not the first to discuss this, but just thought I would put it out there.
Wanted - Summer Intern in Microbial Genomics/Diversity at the Gordon and Betty Moore Foundtion
"a short-term opportunity for an advanced undergraduate or graduate student who would enjoy delving into the genes and genomes of the microbes sequenced as part of the Microbial Genome Sequencing Project (a.k.a the "Moore 155")."For further details and links see the GBMF job ad. Note applications are due June 16, 2008. Here is more detail on what they are looking for:
Since 2004, the Microbial Genome Sequencing Project (MGSP) funded by the Marine Microbiology Initiative has produced the complete genome sequences of a diverse array of Bacteria and Archaea. To date, the genomes of over 130 microbes have been sequenced, annotated using automated computer algorithms, and deposited in public databases. The primary objective for the internship will be to research and synthesize information about the genome content, isolation habitats, and ecology for these microorganisms.
Specific goals include:
- -Synthesize important new discoveries from scientific publications resulting from the MGSP
- -Compare genomes to seek novel patterns of gene content as a function of organism’s habitat and physiology
- -Build 16S rRNA phylogenetic trees for major Bacterial and Archaeal clades for inclusion on the moore.org website
- -Research the primary scientific literature relating to viruses (phage) that infect MGSP microorganisms to investigate the influence of phage on microbial evolution and ecology
Preferred Qualifications/Skill Set:
- -Advanced biological sciences or computer sciences undergraduate or graduate student preferred
- -Strong research, writing, and oral communication skills
- -Strong interest and knowledge of microbial evolution and ecology
- -Experience working with microbial genomes or gene sequences preferred
Chris Smither on Darwin and Intelligent Design
Thanks to Iddo Friedberg for the tip.
Tuesday, June 10, 2008
Good luck Chris Gunter ...
As for what Chris will do at HudsonAlpha, the press release says she "will work closely with Dr. Richard M. Myers, HudsonAlpha director, to raise awareness about HudsonAlpha and its research programs on a national level." RIck was the person who helped push me to formalize my ideas behind "phylogenomics" many years ago when we were both at Stanford and so now two of my favorite genomics folks will be in Alabama. I guess HudsonAlpha is a place to keep an eye on ...
Getting John Henry and his hammer into a scientific paper
His point here is to talk about man versus machine and to then discuss the recent article in PLoS Biology on a "Darwinian Machine" which I wrote about previously. (I think he is also making a bit of a play on words with the hammerhead ribozyme, but I am not sure). Anyway, Ellignton's article is worth checking out. I especially like the endingThe steam drill was on the right hand side,
John Henry was on the left,
Says before I let this steam drill beat me down,
I'll hammer myself to death”—The Ballad of John Henry (American, traditional)
Machine-based continuous evolution should be the best of all worlds, combining man's mental ability to chart the future with automated control of selection stringency with the still unpredictable mode and tempo of evolution's relentless drive.
Figure from Ellington's PLoS Biology paper. I can put it here because it is a fully Open Access paper using a broad Creative Commons license. All I have to do is cite the source. And so I am. Andy Ellington. PLoS Biol 6(5): e132 doi:10.1371/journal.pbio.0060132
Figure reportedly by Angel Syrett (see comments).
Monday, June 09, 2008
Plant kin recognition? (Caution - Anthropocentrism ahead)
They report
The sea rocket, researchers report, can distinguish between plants that are related to it and those that are not. And not only does this plant recognize its kin, but it also gives them preferential treatment.And
Dodder is unable to grow its own roots or make its own sugars using photosynthesis, the process used by nearly all other plants. As a result, scientists knew that after sprouting from seed, the plant would fairly quickly need to begin growing on and into another plant to extract the nutrients needed to survive.
But even the scientists studying the plant were surprised at the speed and precision with which a dodder seedling could sense and hunt its victim. In time-lapse movies, scientists saw dodder sprouts moving in a circular fashion, in what they discovered was a sampling of the airborne chemicals released by nearby plants, a bit like a dog sniffing the air around a dinner buffet.
The notion that plants sense and respond to their surroundings is apparently controversial. Or, maybe a better way to put it is, the attempts to compare plant to animal neural functions is controversial. So much so that many plant scientists got together to say enough is enough
Thirty-six authors from universities that included Yale and Oxford were exasperated enough to publish an article last year, “Plant Neurobiology: No Brain, No Gain?” in the journal Trends in Plant Science. The scientists chide the new society for discussing possibilities like plant neurons and synapses, urging that the researchers abandon such “superficial analogies and questionable extrapolations.”
I personally think there is an enormous amount of anthropocentrism here. Sure, plants may not have true brains. But even though many people like to think of animals in general and humans in particular as the be all end all of evolution, last time I checked, plants have been evolving for a long time. And there is no reason to think that they do not have all sorts of cool and wacky ways to sense and respond to the world around them.
The same anthropocentric point of view has led scientists to grossly underestimate the complexity of phenomena in microbes too. Microbes in fact can sense and respond to kin, they can count, they can tell time, they have immune systems. In other words, whether small or large, furry or not, simple or complex (in appearance) lots of cool things have evolved in lineages that do not lead up to humans.
Well, everyone. As we continue to delve into the biology of non animals more deeply, we are going to find all sorts of cool things out there. And yes, some of it will be even more complex and interesting and wacky than what we see in animals.
For other stuff on this story see
Sunday, June 08, 2008
Conflicts of interest, full disclosure, and ethical blogging
- Science blogging ethics from Omphaloskepsis
- Help build the science blogging ethics wiki from Adventures in Ethics and Blogging
- The ethics of science blogging: help set the agenda.
- NC Science Blogging 2008: Ethics
- Hope for Pandora: Blogging Codes of Ethics
- The Scientist : NewsBlog : Science blogging conf.: Ethics, please ...
- Wired Science . Correlations | PBS
- Weblog Ethics Survey Results
Saturday, June 07, 2008
More Airport Dinosaurs - Denver This Time
Friday, June 06, 2008
A science blogger on Science writing about a science blog ...
But I was tired and it did not come out so well when I said "A science blogger wrote about science blogging and how Science wrote about my blog". And the person just stared at me.
Anyway, all I know now is that it is a lot easier to talk about when Nature writes about "science" blogging
You know the conference you are at is too big when ....
Now - I confess I was really impressed with how ASM handled this enormous meeting I was just at. If you are going to have a big meeting, ASM does a smashing job. And I can see how such big meetings can have their appeal - the diversity of work and activities relating to Microbiology are amazing. However, big meetings are still not my cup of tea.
So here is my top 10 list of "You know the conference you are is too big when ...". All are based on experiences from this meeting.
- People communicate within the conference venue by email and cell phones
- They give you a foldout map showing the locations of all the different venues/activities/
- Colleagues contact you electronically after your talk rather than in person
- The lines for food are longer than the lines for security at the airport
- There are more:
- counters at the registration booth than at the airport ticket area
- meeting staff than scientists at the last conference you attended
- promotional booths than active players in Major League Baseball (OK, we are not quite there with this meeting but we are close)
- The abstract book weighs more than your laptop computer
- People use GPS to find their way in the conference center (I wish I had pictures but I saw this happening)
- The bus/shuttle scheduling system is more complex than the travelling salesman problem
- You need to plan your own schedule by searching a database
- You do more walking inside the conference center than outside
Wednesday, June 04, 2008
ASM Phylogenomics Notes
Tuesday, June 03, 2008
Yet another reason to avoid big meetings
Monday, June 02, 2008
Chancellor of UC Davis stepping down
Begin forwarded message:
From: Chancellor Vanderhoef <lnvanderhoef@ucdavis.edu>
Date: June 2, 2008 3:28:58 PM CDT
To: UC Davis Family:;
Subject: Leadership Transition
Dear Members of Our UC Davis Family,
I can't imagine greater good fortune than to have spent the past 24 years at UC Davis, first as provost, then, since 1994, as chancellor. Along the way, there have been challenges to be sure, but, together, we have helped this remarkable university to reach higher, to be bolder and to achieve great distinction. For those years and those opportunities, I will always be grateful.
So it is with conflicting emotions that I announce today that next year, our centennial year, will be my last as chancellor. I will step down on June 30, 2009. Following a sabbatical leave, I will return to the life of a faculty member, and will do whatever I can to support UC Davis as its chancellor emeritus.
To make our centennial year my last has been my plan for some time now -- a decision made finally realizing that there'd never be a stopping point if I waited for every initiative to be completed. Our 100th birthday seemed to me a particularly fitting time for a transition in leadership, as we look back with pride at our first century, and as we look forward to a second century that's sure to be as transformational as our first.
As well, announcing now provides our new UC president, Mark Yudof, with ample time to recruit a chancellor who will continue to elevate UC Davis among the nation's most distinguished universities. Ours will be his first opportunity to recommend a new UC chancellor to the regents.
So as we wrap up one academic year and anticipate the start of my last as chancellor, know that I approach this coming year as I did my first -- inspired by the opportunity, and keen to turn plans into action.
And, as was true then and even more so now, I am grateful for all that my wife, Rosalie, has done to support me and UC Davis -- particularly her tireless work to raise funds for the Mondavi Center for the Performing Arts and to introduce schoolchildren to the arts. To those many, many people with whom we've worked closely over the years, there's not enough room in this letter to express our appreciation. We'll try to catch you, one by one.
Sincerely,
Larry N. Vanderhoef
Chancellor, UC Davis
June 2, 2008
UC Davis Chancellor Larry N. Vanderhoef to Step Down in June 2009
Chancellor Larry N. Vanderhoef, who led UC Davis' climb up the ranks of the nation's finest universities while he helped open the campus's doors to the disadvantaged and advocated academic diplomacy to help resolve global conflict, announced today that he will step down in June 2009, at the end of the campus's centennial year.
Vanderhoef, appointed in 1994 as UC Davis' fifth chancellor, is one of the nation's longest-serving university leaders and is widely credited for nurturing future university presidents and provosts. He came to the campus in 1984, first serving as executive vice chancellor and then provost/executive vice chancellor. After what will be a full quarter century of service to UC Davis, he will take a yearlong sabbatical, and then return to the faculty as a professor of plant biology. He will also continue to support the campus as chancellor emeritus.
"I can't imagine greater good fortune than to have spent the past 24 years at UC Davis," Vanderhoef said in a letter today to the campus community. "Along the way, there have been challenges to be sure, but together we have helped this remarkable university to reach higher, to be bolder and to achieve great distinction. For those years and those opportunities, I will always be grateful."
The University of California System's top leaders -- UC's current president, Robert Dynes, and incoming President Mark Yudof -- led the chorus of many who praised Vanderhoef for his distinguished tenure.
Dynes pointed out that Vanderhoef "has been the senior chancellor of the UC system for several years, and all the other chancellors and I look to him for wisdom and experience." Yudof, outgoing president of the University of Texas, said that, from afar, he has "watched the campus go from relative obscurity to the front ranks among the nation's research universities."
Expanded access and opportunity
The first in his family to complete high school, and one of the very few in his Wisconsin foundry town to find his way to college, Vanderhoef has dedicated his time as chancellor to removing barriers to higher education. He elevated the campus's Division of Education to a new School of Education when other universities were downsizing theirs, expanded partnerships with community colleges, encouraged disadvantaged elementary school students to stay on track through the innovative "Reservation for College" program, and partnered with leaders of regional communities of color to raise awareness of UC Davis.
Enormous strides
On his watch, UC Davis has grown and prospered. The campus was invited in 1996 to join the prestigious Association of American Universities, representing the top 62 research universities in North America. Research funds, won competitively by UC Davis' faculty, increased from $169 million to more than $500 million annually. The campus has risen in national rankings, too. UC Davis is now ranked 8th among all U.S. universities in contributions to society (Washington Monthly) and 11th among U.S. public universities (U.S. News & World Report). Private gifts have jumped from $40 million to nearly $200 million a year, with more than $1 billion cumulatively raised in support of programs -- including $100 million from the Gordon and Betty Moore Foundation to launch a new School of Nursing, $35 million from Robert and Margrit Mondavi to name the Mondavi Center for the Performing Arts and the Robert Mondavi Institute for Wine and Food Science, and a $10 million gift from alumnus Maurice Gallagher to help fund a new building -- Maurice J. Gallagher Jr. Hall -- and endowment for the Graduate School of Management.
Under Vanderhoef's leadership and direction, UC Davis has also made great strides in recruiting a diverse and accomplished faculty and student body. Student enrollment has grown from 22,000 to 30,000, and the faculty has increased by 44 percent. More than 4 million square feet of classroom, lab, clinical, performance and office space have been added. And an ailing county hospital in Sacramento has been transformed into an academically distinguished and financially sound regional medical center.
Among Vanderhoef's most ambitious undertakings is a new south entry to the campus, anchored by the state-of-the-art Mondavi Center, the soon-to-open Robert Mondavi Institute and the under-construction Graduate School of Management, conference center and hotel buildings. On another campus flank will soon rise West Village, an innovative and environmentally sensitive neighborhood that will provide affordable housing for students, faculty and staff, as well as a Village Square and community college center -- a first within UC.
International academic diplomacy
But Vanderhoef's interests and influence have stretched far beyond northern California. In 2004, for example, in the face of considerable concern and disapproval, the chancellor led what he was told was the first high-level university delegation to visit Iran since that country's 1979 revolution. Vanderhoef wrote in a journal at the time, "We're not going to Iran to make a political statement, nor are we seeking publicity. We're simply one university wanting to talk to another university about ways in which we can work together. And, perhaps in the process, one small step can be taken toward a return to normalcy in the Middle East."
Vanderhoef has been asked to return to Iran this November, this time as a member of a small delegation of university presidents sponsored by the Association of American Universities.
Principled decisions in the face of criticism
Certainly, Vanderhoef's 2004 trip to Iran was not the first of the tough decisions he has made as a UC Davis leader. Indeed, it was a fiscal crisis in the early 1990s, when Vanderhoef was then provost and executive vice chancellor, that proved his mettle and ultimately positioned him to be chancellor. He oversaw painfully deep cuts and staff layoffs, yet in a collaborative way that restored a sense of stability and fairness to a campus in tumult. It was then that he initiated his series of brownbag chats that continue today, offering faculty, staff and students a regular opportunity to meet and talk with him.
When the UC regents in 1995 ended the use of race, ethnicity and gender in admissions, Vanderhoef vocally opposed the action, believing that without an immediate alternative to provide access for the disadvantaged a generation of students would be lost. Soon after, when it was UC Davis' turn to be featured at a regents meeting, he brought the diverse Gospel Choir to perform, and brought the regents to their feet.
In 2003, Vanderhoef made another controversial decision -- announcing that UC Davis would move from Division II to Division I athletics, knowing that the faculty as a whole would not be supportive. The chancellor said then that the campus really had no alternative. "We are seeking, in an evolving landscape, firm ground upon which to continue and to enhance a program that is centered around the student-athlete and the teacher-coach," he said at the time. The Big West Conference would offer Davis a better academic, philosophical and competitive "fit," he said, and align it with sister campuses UC Irvine, UC Riverside and UC Santa Barbara. In this, the first official Division I season at UC Davis, the Aggies sent 11 teams to NCAA postseason play.
In 1993, Vanderhoef disappointed students at the School of Law with his decision that broadcast media could not be barred from covering the commencement speech of U.S. Supreme Court Justice Harry Blackmun, a condition of the justice's speaking. Blackmun withdrew, and the unhappy graduates signaled their discontent by passing around a jar of sourballs at commencement. New York Newsday, however, wrote that "Maybe [Vanderhoef] is the one who ought to be on the Supreme Court."
Nurturing university leaders
To be sure, Vanderhoef has never been one to seek out controversy to raise his own profile. On the contrary, this unassuming and down-to-earth Midwesterner has always been more interested in bringing recognition to UC Davis than to himself, and in growing new academic leaders along the way.
In the past 15 years, more than a dozen UC Davis administrators have gone on to president and provost positions at major universities around the country. They credit Vanderhoef's collegial and collaborative approach to problem solving, and his belief in delegating both authority and responsibility, with providing junior administrators the experience to move on and up.
"That type of experience, particularly with an excellent, diverse team, provides strong leadership development," said Virginia Hinshaw, former UC Davis provost and executive vice chancellor and current president of the University of Hawaii-Manoa.
"Larry Vanderhoef sets a positive tone at the top for good behavior among administrators, and I believe this brings out the best in people," said Mark McNamee, former dean of biological sciences at UC Davis and now provost of Virginia Tech.
Still, Vanderhoef has garnered many personal accolades. Recognized for his "passion to make things happen," he was honored by the Sacramento (California) Business Journal as one of the 20 people who have contributed most substantially to California's capital region over the past 20 years. The Sacramento Metropolitan Chamber of Commerce named him Sacramentan of the Year in 2004, and the Arts and Business Council of Sacramento presented him with its Prelude to the Season Outstanding Contribution Award in 2003. And in 2006, the Northern California World Trade Center and the California Business, Transportation and Housing Agency presented him with the International Leadership Award, in recognition of his efforts to increase the campus's international engagement.
Early in his career, he was named an Eisenhower Fellow, a recognition given to emerging leaders from around the world to promote positive relationships and interactions between countries. He was awarded honorary doctoral degrees by Purdue University and Inje University in Korea, and an honorary professorship by China Agricultural University. He holds B.S. and M.S. degrees in biology from the University of Wisconsin, Milwaukee, and a Ph.D. in plant biochemistry from Purdue University.
Nationwide search
A nationwide search for a new Davis chancellor will be initiated, and a committee with regent, faculty, staff, student, alumni and foundation board representatives will be named to advise Yudof, the incoming UC president, in the selection of Vanderhoef's successor.
UC Davis, a land-grant institution, is a leader in interdisciplinary study, offering more than 100 academic majors and 86 graduate programs. It is the only campus in the UC system with schools of Education, Law, Management, Medicine, and Veterinary Medicine. The campus's breadth of academic and outside-the-classroom programs, commitment to providing an attentive and research-enriched education, determination to address society's needs and consideration of campus community members as family are truly distinctive.
What others are saying about Chancellor Larry Vanderhoef's distinguished tenure at UC Davis:
UC President Robert Dynes: "I heartily congratulate Larry for all he has accomplished. Larry has been the senior chancellor of the UC system for several years, and all the other chancellors and I look to him for wisdom and experience. During his tenure as chancellor, UC Davis has grown in size, stature and excellence, and everyone within UC is proud of it. Congratulations to a friend for a stellar accomplishment."
UC President-designate Mark Yudof: "Larry has done a remarkable job during his tenure at UC Davis. I have, from afar, watched the campus go from relative obscurity to the front ranks among the nation's research universities. I offer him my heartiest congratulations, and I am looking forward to working with him during his final year."
UC Provost Rory Hume: "Chancellor Vanderhoef has served both UC Davis and the UC system as a whole with great distinction. During his long period of leadership Davis has grown enormously in academic distinction, and in size. It has substantially broadened the scope of its academic programs, while retaining its highly valuable, distinctive nature. Much credit for those advances rests directly with Larry Vanderhoef. He has also been a superb citizen of the UC system, wise, measured, supportive and decisive. We could ask for no better colleague and friend."
Robert Berdahl, president of the Association of American Universities and former UC Berkeley chancellor: "Larry Vanderhoef has been an extraordinarily successful chancellor of UC Davis. Under his leadership, Davis emerged as one of the outstanding public universities in America. He has provided leadership within the University of California, where his voice and judgment are widely respected by the other chancellors, and he has been an effective leader on the national stage as well, including at AAU. His leadership has always been marked by intelligence, thoughtfulness, and generosity of spirit. I am proud to consider him a colleague and friend."
Vice Provost for Undergraduate Studies Patricia Turner: "It has been my privilege to serve on Larry Vanderhoef's leadership team. When he appointed me to my first senior position, I was relatively untested. He recognized managerial and leadership abilities I did not even see in myself. I believe his ability to identify and support strong leaders stands as one of his most significant gifts to the campus. As well, he has an uncanny ability to connect with undergraduate students and takes seriously their comments and suggestions. For the past 14 years, UC Davis students have been very fortunate to have a chancellor who prioritized their academic and extra-curricular well-being."
Robert and Margrit Mondavi, in nominating Chancellor Vanderhoef for a 2006 CEO Leadership Award: "Chancellor Vanderhoef's leadership has elevated the accomplishments and the reputation of UC Davis, and has inspired the support of people like us, who share his vision and see opportunities for creating a lasting legacy through investment in a remarkable university. We share with Larry Vanderhoef a commitment to innovation and excellence, and to the risk-taking that's inevitably required to be successful."
Then-Assemblyman Darrell Steinberg, in supporting Chancellor Vanderhoef's 2004 selection as "one of the 20 people who have contributed most substantially to California's capital region over the past 20 years": "When Larry arrived at UC Davis...he brought with him a commitment to not only guide UC Davis to the top tier of national universities but to ensure that the university was engaged with its broader community....UC Davis has clearly flourished under Larry's leadership and consequently has contributed substantially to the state's and the region's prosperity."
Fear and Loathing in Boston for the ASM Meeting
OK
Saturday, May 31, 2008
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Davis Really Is Friendly
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Friday, May 30, 2008
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Thursday, May 29, 2008
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Wednesday, May 28, 2008
Top 10 Things Francis Collins Might Do After NHGRI
- 1. The 1000 genome songs project. He is already further along in this than the 1000 genomes project ...
- 2. Get a job at Craig Venter's Synthetic Genomics. Hey, Collins says he wants to try something new. And Craig has a history of hiring people who used to work at funding agencies.
- 3. Sequence Jesus' genome. More on this later.
- 4. Run the World Anti Brain Doping Agency (WABDA). We need a crusader to run the organization.
- 5. Start a blog. Hey, there are worse things one could do with free time. Not many. But there are some.
- 6. Start a genomic information anti-discrimination lobbying firm. Like others in government, he really should try to make money off of legislation he helped pass.
- 7. Dancing with the stars. He could even sing along too.
- 8. Start giving talks about genetic inferiority of various races and genders. Or did someone who once ran NHGRI already do that?
- 9. Try and apply for some of NHGRI's money. Oh wait, he does not run a huge sequencing center, so he may not qualify.
- 10. Make jewelry out of disk shaped beads. Also known as sequinsing.
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