Tag: Misc.

Combinging two of my favorite things – chocolate and genomes

Well, the Mars company has really done it now (see Unwrapping the Chocolate Genome -from washingtonpost.com). They are planning to sequence the cacoa genome. Genomes and chocolate. Man are they going to get every bioinformatics person I know to apply to help out with this project …

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.”

So -even though I pondered whether this was science by press release, a friend of mine convinced me it was not and this was just getting out the word on the project. For other details see

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Swimming the Mirror: Poems for My Daughter on KDVS Today at 5 PM

Brad Buchanan will be discussing and reading from his new book of poems, “Swimming the Mirror: Poems for My Daughter” (Roan Press) on KDVS 90.3 FM today (Wednesday) at 5pm. Please consider tuning in. Also available onlne at http://www.kdvs.org/listen/.

Why I am writing about this?  Well Brad and I used to play street hockey together in grad. school at Stanford.  No – neither of us started Google as did other street hockey players from Stanford.  But you should check out Brad’s new book of poems from Roan Press and also can see some of his past stuff at an old blog here.
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, http://www.roanpress.com, which is coming soon”

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Extremophiles getting some props too

With the Mars Lander scratching the surface of the Red Planet looking for indications that life could exist there, the time is ripe for some public education about microbes and extremophiles. And fortunately the press is picking up on this possibility. For example, CNN.COM has picked up an AP story on extremophiles: Life in Earth’s toughest places; how about Mars? – CNN.com

In the article, Alicia Chang from AP writes:

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.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Open Science Highlight — JoVE: Journal of Visual Experiments

I am starting to browse around at JoVE (the Journal of Visualized Experiments).  This is an open journal dedicated to publishing biological research in a visual format.  It is pretty cool.  Some good videos include ones by Jared Ledbetter’s group on studying microbes inside termites (see Layers of Symbiosis – Visualizing the Termite Hindgut Microbial Community
and Extracting DNA from the Gut Microbes of the Termite (Zootermopsis nevadensis)) for example.  Others of interest to this blog include one by Ed Delong’s group on Large-Scale Screens of Metagenomic Libraries. 
Anyway – JoVE is definitely worth checking out … visual presentations are probably the way of the future …
In addition to experiments, JoVE also has some interviews.  For example, I am embedding a nice video from JoVE with a talk by Ed Delong on microbial communities (Microbial communities in nature and laboratory – interview (Video Protocol).   To view the embedded video click the play button below.

http://www.jove.com/index/embed.stp?ID=202

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

How Darwin won the evolution race

There is a cool article in the Observer today on the “race” between Darwin and Wallace on publishing the theory of natural selection (How Darwin won the evolution race | Science | The Observer).

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

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Tree of Life hitting the big screen …

The “Tree of Life” is really hitting the big time. I just found, in a google search, that there is a movie coming out in 2009 called, “Tree of Life (2009).” The plot summary is as follows:

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 powers

And 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

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

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.

You see, my father was a scientist too — an MD who did research at the NIH, focusing mostly on hormone receptors. Given my propensities for putting things on the web and trying to disseminate scientific information, I cam up with a plan last night to create some sort of web page in his honor with some information about his work and his life.

The thing is, I actually know little about his work, because while I was growing up, my parents never really talked about the details of their work (my mom is a scientist too). Sure, we went to the NIH occasionally and most of my parents friends were scientists. And they talked sciency talk. But they did not really discuss details of their work. I think in the end, this is partly why my brother and I did not shun the family business and went into science.

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.

This made me both happy and sad. I was glad to see some of his publications in Pubmed Central (thanks to PNAS and the Biochemistry Journal for putting them there). It was also good to see many available for free, even if this was only at some journals site. So – thanks to journals like J. Biol. Chem. for making the material available online for free. But I was a bit saddened to see how many of his papers, which are now all over 20 years old, being available only for a fee. And I was also a bit saddened to see how many had not yet made it into the digital world.

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

Getting digitized.
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.

  1. 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.Click here to read

  2. 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. Click here to read

  3. 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: 3840164Click here to read

  4. 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.

  5. 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: 6331880Click here to read

  6. 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

  7. 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: 6324804Click here to read

  8. 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: 6704471Click here to read

  9. 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: 6577947Click here to read

  10. 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: 6309801Click here to read

  11. 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

  12. 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. Click here to read

  13. 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: 6186383Click here to read

  14. 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: 6896205Click here to read

  15. 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.

  16. 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: 6895516Click here to read

  17. 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: 7217100Click here to read

  18. 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: 7448753Click here to read

  19. 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: 7016012Click here to read

  20. 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.

  21. Eisen HJ. An antiserum to the rat liver glucocorticoid receptor. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3893-7. PMID: 7001446Click here to read

  22. 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: 6156873Click here to read

  23. 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: 500663Click here to read

  24. 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: 468799Click here to read

  25. 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: 700252Click here to read

  26. 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: 81156Click here to read

  27. 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: 646815Click here to read

  28. 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: 180989Click here to read

  29. Eisen HJ, Ginsberg AL. Letter: Disulfiram hepatotoxicity. Ann Intern Med. 1975 Nov;83(5):673-5. PMID: 1200504. Back issues not currently available.

  30. 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.

  31. 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.

  32. 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: 4357871Click here to read

  33. 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.

  34. 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

  35. 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. 
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Connection between Video Games and Bioinformatics?

The Scientist Magazine has a nice piece on one of my favorite people in all of Science – Sean Eddy. In the article, they discuss how Sean is one of those bioinformatics folks who does not just hack together some code to do something but actually writes really good code for his programs. For those of you who do not know, Sean has made a whole collection of software tools for biologists (see his web site here). Perhaps the most widely used is HMMER, which is designed for making and using hidden markov models. But there are some other good ones he has put out. My favorite is Forester, which was made by Christian Zmasek in his lab and is supposed to be available here, although the site is not working right now (NOTE – Christian has posted a new link for it in the comments). I like this because, well, it is software for “phylogenomic” analysis.

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.

Anyway, glad to see Sean getting positive press. It is well deserved. Now off to play some video games.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Wanted – Summer Intern in Microbial Genomics/Diversity at the Gordon and Betty Moore Foundtion

The Marine-Microbiology Initiative at the Gordon and Betty Moore Foundation is looking a person to work there for the summer. This is

“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


——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Chris Smither on Darwin and Intelligent Design

Entertaining little song by Chris Smither on Evolution/Darwin/Intelligent Design. Scroll to the 2:00 time point if you cannot wait.
Thanks to Iddo Friedberg for the tip.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–