Monday, June 30, 2008
Top five metaphors Darwin considered and rejected for "The Tree of Life"
Well, as I am desperately trying to prevent Hollywood from corrupting the term "Tree of Life" and I got to thinking. Why did Darwin and others have to use the metaphor of a tree to represent the branching history of organisms through evolutionary time? Why did other metaphors not get used? Well, thanks to a little research I did by communicating with Darwin directly (as I did when he announced his endorsement of Obama), I have found out that Darwin went through many other metaphors before settling on the "Tree of Life." (note the tree-like figure here which is based on the one figure in the Origin of Species).
And here are the top 5 other such metaphors for what is now known as "The Tree of Life"
- The coral of life. Darwin particularly liked this one as he did some work on marine organisms. But ultimately he rejected it because he was worried about anti-evolutionists killing coral to get back at Darwin.
- The watershed of life. Rivers exhibit branching patterns much like trees. The big problem Darwin saw was that sometimes separate river branches reconnect to each other, which did not follow his model for descent. If only Darwin knew about lateral gene transfer.
- The blood vessels of life. Darwin was desperate to find visceral connections for people to evolution. This one would have been great. The big problem here was the "going" and "coming" nature of arteries and veins.
- The shrub of life. Thus turns out to have been one of Darwin's favorites because it captures the richness of diversity more than a sparsely branching tree. However, shrub, even then, was used as a derogatory term to refer to height challenged individuals. And Darwin did not want to upset this key constituency so he avoided this term.
- The lungs of life. While this has some positive features (e.g., it is unidirectional like a tree), thankfully Darwin did not stick to this or we would have competition from "LOL" for all the domain names.
Other possibilities included "the Plumbing System of Life" and "the Highway Map of Life". If you know of others Darwin may have considered, let me know.
Friday, June 27, 2008
Calling all evolutionary biologists - protect the "Tree of Life" from extinction by Hollywood
- Jonathan Eisen's "Tree of Life" blog (no selifsh interest here)
- Tree of Life Web Project
- Tree of life (science) - Wikipedia, the free encyclopedia
- Green Tree of Life at Berkeley
- Fungal Tree of Life Project
- Beetle Tree of Life project
- Fly Tree of Life project
- Mammal Tree of Life project
- Cypriniformes Tree of Life project
- Liverwort Tree of Life Project
- Early Bird Tree of Life project
- Early Bird Tree of Life project
- Angiosperm Tree of Life project
- Cnidaria Tree of Life Project
- Decapoda Tree of Life Project
- The Evilutionary Biologist John Dennehy talks about the tree of life in his post titled "Tree of life".
- Nodalpoint is helping out.
- Jeremy at Another Blasted Weblog is saving the tree.
Thursday, June 26, 2008
Jelly Bellies in the New York Times
Combinging two of my favorite things - chocolate and genomes
Some little notes on the project:
- They plan to release the data for public use: "Mars plans to make the research results free and accessible through the Public Intellectual Property Resource for Agriculture, a group that supports agricultural innovation, as they become available. The intent is to prevent opportunists from patenting the plant's key genes."
- They are doing this in a collaboration with IBM
- Good quote by Howard Shapiro: "We have the ability as a private company to take charge of the future," Howard-Yana Shapiro, global director of plant science for Mars, said."
Wednesday, June 25, 2008
Swimming the Mirror: Poems for My Daughter on KDVS Today at 5 PM
Roan Press is a new Sacramento area publisher. In the email I got they say
"Please mark your calendars for Roan Press's first Book Launch Party at the Book Collector (1008 24th Street) on July 23 at 7:30 pm. Roan Press is a new Sacramento publisher with an interest in poetry, fiction, books of essays and other genres. We particularly welcome submissions from Northern California writers, but are open to work from anyone, anywhere. Please also watch for our website, www.roanpress.com, which is coming soon"
Tuesday, June 24, 2008
Overselling genomics award #4: University of Western Ontario and Graham Thompson on honeybee altruism
The press release however, goes way way overboard in interpreting their results and claiming "New Discovery Proves 'Selfish Gene' Exists." They imply throughout the press release that prior work simply suggested that selfish genes were theoretically possible in this case and that now with their results they have been proven. For example they quote the lead author Graham Thompson:
This means that the 'selfish' gene does exist, not just in theory but in reality.This is way beyond an overstatement. Their results are nice and interesting but they are part of a continuum of work on bees (and other selfish systems) and do not in any obvious way suddenly prove the existence of this selfish gene compared to prior work that they imply was just guesswork. I am personally baffled by the extent of this claim -- basically ignoring work by many others as well as work in a variety of systems outside of bees. They end the press release with the following:
"This basically provides a validation for a huge body of socio-biology," says Thompson, who adds the completion of Honey Bee Genome Project in 2006 was crucial to this discovery.For that last statement, I am thus giving them my "Overselling genomics award" #4. But they easily could have gotten a few others.
Hat tip to T. Ryan Gregory for pointing this out. And you should check out his new Genomics by press release "award" at his blog Genomicron. I will probably be writing about the same story soon.
Monday, June 23, 2008
Extremophiles getting some props too
But if there were past or present life on the red planet -- a big if -- scientists speculate it would likely be similar to some extreme life on Earth -- microscopic and hardy, capable of withstanding colder-than-Antarctica temperatures and low pressures.AND
Most living things on Earth thrive not only in the presence of water, but also need sunlight, oxygen and organic carbon. But the range of conditions in which life can survive has been expanded with recent discoveries of micro-organisms trapped in glaciers and rocks or living in volcanic vents and battery acid-like lakes.The AP article is quite reasonable, as far as science reporting goes. However, there is some stink going on in the bloggosphere about AP bullying bloggers regarding fair use so you might want to check out AP: Stupid, it hurts! and AP Files 7 DMCA Takedowns Against Drudge Retort and AP/Drudge Retort “Resolution” Leaves Fair Use Questions Unanswered.
UC Davis Bodega Marine Lab getting some props
The article lead in is all you really need to know:
Mention Bodega Bay, and the first thing that comes to mind - even now, 45 years later - is Tippi Hedren getting her head pecked by a gaggle of sociopathic seagulls. The town's visitor center hands out 8,000 maps a year pinpointing where Alfred Hitchcock filmed the most memorable scenes of the 1963 classic "The Birds."
But each year, 10,000 to 12,000 people travel to a spectacular spot west of town to visit a less-famous site, the Bodega Marine Laboratory, a UC Davis outpost where about 100 graduate students and scientists study underwater life along the Northern California coast.
Each Friday afternoon, from 2 to 4, docents lead free, hourlong tours that wind through parts of the sprawling complex. It soon becomes clear that visiting a marine lab isn't anything like visiting for-profit aquariums, with their polished tanks and fancy signs. Here, the only live exhibits are a tide pool and three small aquariums.
Mind you, Bodega Bay itself is not the most happening town in the world. But it has a few stores, restaurants and cafes (which they review some of in the Chronicle article). The lab is also the site for the "Workshop in Applied Phylogenetics." One cool thing about this workshop is that the organizers have begun building a Wiki to gather information on phylogenetic methods and tools and this wiki is open to everyone to use and contribute to. So if you are interested in phylogenetics you might want to check out the wiki and start adding to it. And you might want to keep an eye out for announcements for next years course.
Open Science Highlight -- JoVE: Journal of Visual Experiments
Saturday, June 21, 2008
How Darwin won the evolution race
When I read this I cannot help wonder what would have happened if this race had happened today. With publishing and the spread of ideas occurring at a much slower pace in the past, Darwin could afford a bit of time to polish up all the lines of thought and evidence presented in the Origin of Species. It is really his work on building up such evidence that helped convince people of the importance of natural selection. So - if this had happened today - Darwin and Wallace would certainly have been on Science Friday. Lots of bloggers would have written about it. But would Darwin have taken the time to polish up his loose ends or would he have just rushed out his short paper on natural selection and then gotten caught up in the hype and debate?
Anyway, the article has some good bits both about the history and about the acceptance (or lack thereof) of evolution and natural selection today. My favorite lines is:
Natural selection is simply too important for society to live without it, he (Steven Jones) argues. It is the grammar of the living world and provides biologists with the means to make sense of our planet's myriad plants and animals
Friday, June 20, 2008
Tree of Life Runners Web Notes 6-20-2008
- Interesting Open Access papers to look at:
- PLoS Genetics: Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project
- PLoS Computational Biology: A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation
- Evolution in the news:
- Other science news:
- Open Access blogging:
- What Happens If This Government-Sponsored Research Finds Raw Milk Really Is Good for Us? (a bit of a conspiracy theory but also entertaining
Street View for Davis on Google Maps
View Larger Map
Oh - and here I am .... loading my car up for a trip.
View Larger Map
Wednesday, June 18, 2008
Prochlorococcus on Science Friday
Are You Intellectually Clean?
For the honour of humanity and the integrity of the academy, I declare I have not, nor ever will, use any drug for an intellectual advantage. See, www.academicoath.com
Freeing My Father's Scientific Publications Update
I wrote to the powers that be at the journal "Endocrinology" asking about when back issues might be made available. And I got a VERY quick reply from someone from Highwire Press which is the place that puts out Endocrinology on the web
Dear Jonathan Eisen,The person who wrote back was almost apologetic about how long this might take but I am personally very pleased. Given that Endocrinology says the make all articles more than a year old available for free, this likely means that my father's three papers in Endocrinology will soon be available for free online. This then changes my tally to:
The Endocrine Society is currently in the process of loading back issues for all of their journals. It will most likely be six months before back content is online.
Pubmed Central: 3
Free access: 17
Fee access: 11
Getting better. Of course, I want them all to be as widely available as possible so I am still going to work to move everything up the list towards Pubmed Central. Also, my brother suggests (in the comments to my previous post) that since my father was a government employee we should be able to just post his papers online. I think this is a good option but I still will be working on the "official" channels to see what happens.
Since I made the original posting there have been some useful comments about what I might do on some other sites. See for example, this FriendFeed discussion (I have just discovered FriendFeed and it seems quite cool but I am not sure if everyone can see this discussion or not so please let me know if this link does not work).
I will keep posting on my progress as well as what I learn about Copyright, Free Access, etc.
Tuesday, June 17, 2008
ASM Bloggers Breakfast and Lost Notes
Tree of Life hitting the big screen ...
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
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
- Markoviƒá 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. , 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 the first installment, I am pointing people to a new paper on PLoS Genetics "Trends in Selenium Utilization in Marine Microbial World Revealed through the Analysis of the Global Ocean Sampling (GOS) Project" by Yan Zhang, Vadim N. Gladyshev (hat tip to Katie Pollard for pointing out this paper).
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 ending
The 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)
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
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