MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'The Tree of Life' source. Wed, 19 Nov 2008 22:55:03 +0100 http://phylogenomics.blogspot.com/2008/11/genomicron-on-science-by-press-release.html Just a quick one here. Ryan Gregory is going on against science by press release - one of my biggest pet peeves. Check it out at:Genomicron: Science by press release.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1968945 Wed, 19 Nov 2008 03:02:00 +0100 1968945 http://phylogenomics.blogspot.com/2008/11/i-see-plos-in-everything-iv-plos-at.html I may see PLoS even when it is not there, but in this picture, which was the group photo for the Metagenomics 2008 meeting at CalIT2, I weaseled my way to the front hoping to get my PLoS bag and PLoS shirt into the picture. And looky there - it worked.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1968946 Wed, 19 Nov 2008 02:44:00 +0100 1968946 http://phylogenomics.blogspot.com/2008/11/eric-e-coli-and-you.html Just a little posting here. I have been playing around with a website called ERIC and thought I would post about it since it seems pretty useful. ERIC - Enteropathogen Resource Integration Center isone of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae. So if you want to learn more about E. coli and its relatives and their genomes, this is a good place to startThis is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Sour... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1960829 Fri, 14 Nov 2008 18:32:00 +0100 1960829 http://phylogenomics.blogspot.com/2008/11/suggestions-for-obamas-cto.html Want to suggest priorities for Obama's CTO? Go to http://www.obamacto.org.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1960830 Fri, 14 Nov 2008 03:23:00 +0100 1960830 http://phylogenomics.blogspot.com/2008/11/plug-of-week-extreme-2008-deep-sea.html Just a little plug here to suggest people might want to check out the web site for a Deep Sea Research Cruise going on right now (Extreme 2008: A Deep-Sea Adventure: University of Delaware). The focus of the cruise is summarized as follows:The scientists will focus on marine viruses and other tiny life called protists and their roles in the food chain. These organisms prey on bacteria, a primary food that sustains the vent ecosystem.Some friends/colleagues of mine are involved in this adventure and it sounds like some cool stuff could come out of it. Also you might want to check out the blog of Lisa Z (ExtremeVirus), who is posting about the cruise.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access adv... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1955297 Thu, 13 Nov 2008 08:41:00 +0100 1955297 http://phylogenomics.blogspot.com/2008/11/this-press-release-deserves-some-sort.html Just got pointed by Ruchira Datta to a new press release from Princeton (Princeton University - Evolution's new wrinkle: Proteins with cruise control provide new perspective) that makes some interesting claims about evolution. Ruchira asked if the press release made sense to me. And alas, it does not. It has all sorts of bizarre evolution claims in it including the followingA team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution...."Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness.""What we have found is that certain kinds of biological structures exist t... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1955298 Thu, 13 Nov 2008 08:27:00 +0100 1955298 http://phylogenomics.blogspot.com/2008/11/underselling-genomics-award-1-david.html I do not normally write too much here about non Open Access publications but this one is so good I had to. Everyone with access to Trends in Microbiology should check out Julian Parkhill's rebuttal to an article written by David Whitworth in the same issue. Whitworth's article is "Genomes and knowledge – a questionable relationship? " and it is in my opinion, filled with some unsuppoerted and over the top statements. In essence, he is arguing that we should stop genome sequencing because there are a bunch of genomes out there already and after all, all that matters is work on model organisms so if you have enough genomes related to your model organism you should move on. Alas I do not have time to detail them here. But fortunately, Parkhill does a great job of responding in his article T... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1955299 Wed, 12 Nov 2008 18:15:00 +0100 1955299 http://phylogenomics.blogspot.com/2008/11/dna-dynasty-company-stealing-and-lying.html Well, just adding my two cents to the pissed off blogosphere regarding a company in Singapore called DNA Dynasty.  Not only are they purveying complete crap in terms of genetics/genomics (e.g., they say they have a genetic test to determine the innate abilities of your children) but they have apparently stolen the logo of the DNA Network of which I am a member.  Lovely.  I figure, if we make enough blogging noise, then when people search for them with google they will at least also see some of our postings.  So here is mine.  See alsoNilsPauloBill This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1943407 Sat, 08 Nov 2008 08:07:00 +0100 1943407 http://phylogenomics.blogspot.com/2008/11/metagenomics-2008-meeting-notes.html I am going to post notes here for the Metagenomics 2008 meeting.#1 - most everyone here seems really happy about the election#2 - mooched a ride this morning to the conference site from some of the folks who run "The Seed" and related annotation and analysis servers.  I have written about them before but people really should check them out if you are interested in microbial genome analysis. #3 - Alex Worden is talking now about picoeukaryotes.  Alex does some of the coolest environmental microbiology out there and just happens to focus on groups of organisms that are frequently ignored.  She just said a key quote "Physiology is not a bulk or an average property" basically saying what I say which is that an environment is not simply a bag of genes.  That is we need to remember that the... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1939204 Wed, 05 Nov 2008 16:31:00 +0100 1939204 http://phylogenomics.blogspot.com/2008/11/metagenomics-meeting-competing-with.html Well, I apologize but I am not going to post anything today about the metagenomics meeting in San Diego since I came late today as I wanted to be at home for the beginning of the election.  But I made my way down to San Diego and made it to dinner.  The dinner "entertainment" was a talk by one of the grand gurus of ocean microbiology - Steven Giovannoni.  Alas, even he realized that he was competing with people wanting to know about the election and I confess I spent most of his talk hitting reload on my phone and surfing between sites.  So I have no notes to post about his talk.  But I can say that I am happy about the election.  And tomorrow I will try to post some notes about talks.  But I may be still too happy to take notes ...This is from the "Tree of Life" blog ( http://phylo... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1933323 Wed, 05 Nov 2008 06:29:00 +0100 1933323 http://phylogenomics.blogspot.com/2008/11/more-about-how-i-feel-from-my-iphone.html This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1933324 Wed, 05 Nov 2008 04:22:00 +0100 1933324 http://phylogenomics.blogspot.com/2008/11/how-i-feel-drawn-on-my-iphone.html This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1933325 Wed, 05 Nov 2008 04:18:00 +0100 1933325 http://phylogenomics.blogspot.com/2008/11/charles-darwin-reiterates-endorsement.html Charles Darwin has again spoken from the grave. In February I reported how Darwin endorsed Obama in the primary against Hilary Clinton (The Tree of Life: Charles Darwin Endorses Obama as the "Natural Selection") (note - his candidacy took off immediately after the 2/5 endorsement). And Darwin is getting in his own November surprise for the election tomorrow. Darwin spoke through a variety of media (I am using this term in reference to the plural of medium - people who speak to the dead .. but I am not sure whether media or mediums is the plural) and said"This one is such a complete no brainer. Obama is so far and away the fitter candidate. Plus if Palin and McCain do not believe in my greatest work, well they can ..." (we cannot print the rest)So there it is. Of course, most living well kn... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1930296 Mon, 03 Nov 2008 16:57:00 +0100 1930296 http://phylogenomics.blogspot.com/2008/10/conflict-between-religion-and-evolution.html Not to beat a dead horse here, but some people out there still think there is a absolute conflict between religious beliefs and believing that evolution occurs.  And if you still think that, you might want to check out the schedule for the Vatican Conference on Evolution (and related topics) that is going on right now (see here for the PDF and here for an outline).  Held at the Vatican from Oct 31 - Nov 4 and sponsored by the Pontifical Academy of Sciences is a conference on "Scientific Insights into the Evolution of the Universe and of Life."  Among the speakers: Takashi Gojobori, Werner Arber, H.Em. Cardinal Christoph Schönborn, Martin Rees, Stephen Hawking, David Baltimore, Luca Cavalli-Sforza, Christian de Duve, Francis Collins (who is the only one of the speakers with God in the t... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1927849 Sat, 01 Nov 2008 04:33:00 +0100 1927849 http://phylogenomics.blogspot.com/2008/10/genome-technology-runs-table-on-open.html Wow.  Again, wow.  Genome Technology Magazine has dedicated in essence an entire issue to Open Access and they have a whole series on interesting things to say about it.  In addition they are making the issue available under a Creative Commons License so everyone can check it out.  Among the articles are:Ready or Not, Here Comes Open AccessOpen Access: What Does It All Mean?Many Flavors of Open AccessAn Acquisition, an Association, and a CelebrationPubMed Central: The 'Mildly Destabilizing' CompromiseReluctant Publishers and the Birth of PLoSSo everyone - go check it out.  And give them some props.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (So... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1924539 Fri, 31 Oct 2008 18:14:00 +0100 1924539 http://phylogenomics.blogspot.com/2008/10/nature-endorses-obama-for-president.html Nature has an editorial (America's choice : Article : Nature) on the US Presidential Election that is worth looking at. For those interested in the Cliff Notes Version they end the piece with"This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama."For more detail, I think the key point is here:On a range of topics, science included, Obama has surrounded himself with a wider and more able cadre of advisers than McCain. This is not a panacea. Some of the policies Obama supports — continued subsidies for corn ethanol, for example — seem misguided. The advice of experts is all the more valuable when it is diverse: 'groupthink' is a problem in any job. Obama seems to understand... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1918053 Wed, 29 Oct 2008 18:26:00 +0100 1918053 http://phylogenomics.blogspot.com/2008/10/plos-biology-at-5-future-is-open-access.html Just a quick one here. All those interested in Open Access should look at this editorial on PLoS Biology from the PLoS Biology staff PLoS Biology - PLoS Biology at 5: The Future Is Open AccessThis is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1914710 Wed, 29 Oct 2008 03:27:00 +0100 1914710 http://phylogenomics.blogspot.com/2008/10/tomorrows-table-on-todays-table-x-2.html So - I was having breakfast with my daughter this morning and she was in a funky mood.  She wanted some stories so to make life easy and not get up, I opened up the only thing near the table to read - a copy of Nature Biotechnology that I received for free in the mail (not sure why) - and was going to show her some pictures of things.  And there was a review of my friend and colleague Pam Ronald's book "Tomorrow' Table."  And so I told my daughter that this was a story about a book by my friend Pam and reminded her about how we had gone over to Pam's house and how she worked in the office next to mine.  And then I asked my daughter if she wanted to see Pam's book, which I had in the office and she said yes.  And so I got the book and then we told stories about Pam.  So - here in livi... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1914711 Tue, 28 Oct 2008 16:09:00 +0100 1914711 http://phylogenomics.blogspot.com/2008/10/palin-announces-opposition-to-research.html Sarah Palin today has followed up her attack on fruit fly research by condemning much of the NIH Budget and a variety of other scientific earmarks.  At a town hall meeting yesterday while campaigning in Guam, Palin said"We asked federal agencies to give us a summary of key words relating to research projects and we found an enormous number of them focused on homosapiens. I kid you not."When asked by a teenage audience member to explain what was wrong with this research Palin said"You probably are a homosapiens no? Or have many friends that are?  What we need to do is spend money on helping people change and not on studying these homosapiens"The teen tried to respond but was escorted forcefully out of the hall by security while Palin continued on in her meeting.  At the end of the meeti... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1911385 Mon, 27 Oct 2008 14:30:00 +0100 1911385 http://phylogenomics.blogspot.com/2008/10/evidence-based-healthcare-and-baseball.html Love the Op Ed piece in the Friday New York Times entitled "How to take American Healthcare from Worst to First."  First, one reason I love this article is it is discussing how we need to move to more "Evidence Based" medicine.  You may be amazed to know that much of medicine is not evidence based but that is the sad truth.  When I first heard about how not all medicine was evidence based medicine (in a talk by David Cox when I was a grad. student) I was blown away.  Anyway, the article is worth a read from this point of view.  More amazingly is the author list -- Billy Beane (general manager of the Oakland A's), Newt Gingrich, and John Kerry.  What a combination.  They make the argument that medicine needs a wholesale change in the way it is done just like baseball is shifting to m... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1908836 Sun, 26 Oct 2008 22:15:00 +0100 1908836 http://phylogenomics.blogspot.com/2008/10/mccain-palin-going-after-fruit-flies.html As if scientists did not have enough reasons to vote against McCain-Palin who seem to have decided that Bush was overly supportive of science. Now Palin is attacking of all things "fruit-fly research." Lovely. Proof that they are both clueless (not knowing what a fruit fly is probably) and anti-science at the same time. For more on this see:Sarah Palin: Ignorant and anti-science [Pharyngula]Palin Balks at Scientific ResearchSarah Palin: Ignorant and anti-scienceGenetically IgnorantThink Progress » Memo To Palin: Fruit Fly Research Has Led To ...Palin.. fruit flies…and ignoranceThis is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1907703 Sat, 25 Oct 2008 17:26:00 +0100 1907703 http://phylogenomics.blogspot.com/2008/10/brain-doping-april-1-joke-still-getting.html Well, my April 1 collaborative joke on brain doping is still getting some press. See El Pais which reportsComo muestra, algo que empezó como una broma. "Los centros del NIH (los Institutos de Salud de Estados Unidos) pedirán a todos los científicos que quieran optar a sus ayudas y subvenciones a que pasen pruebas antidopaje para comprobar que no han tomado estimulantes cognitivos para aumentar su rendimiento intelectual". Una supuesta World Anti-Brain Doping Authority (WABDA) se encargaría de los análisis. Es el mensaje de una nota de prensa falsa. Una fake lanzada en Internet el pasado 1 de abril, el día de los inocentes en Estados Unidos, por Jonathan Eisen, biólogo evolucionista de la Universidad de California. Comenzó como una travesura, pero el rumor acabó por extenderse por ... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1892041 Tue, 21 Oct 2008 08:48:00 +0100 1892041 http://phylogenomics.blogspot.com/2008/10/blocked-access-bummer-1.html I have decided to start posting when I want to read an article at home but cannot due to lack of access (even though I might have it at work).  Today's bummer is I wanted to read an article by Joel Sachs on "Resolving the first steps to multicellularity" but I could not get it because I do not have access to Trends in Ecology and Evolution at home.  Bummer.  Looks like it could be good. This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1886442 Fri, 17 Oct 2008 14:37:00 +0100 1886442 http://phylogenomics.blogspot.com/2008/10/larry-moran-on-phylogenomics-my-new.html Just a quick note to encourage people to check out Larry Moran at The Sandwalk blogging about my new phylogenomics paper (with Martin Wu) and talking about whether one can use species as a term for bacteria.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1883384 Fri, 17 Oct 2008 02:50:00 +0100 1883384 http://phylogenomics.blogspot.com/2008/10/at-davis-today-chris-somerville-on.html Quick Post Today --- For THose Interested in Biofuels --- you might be interested in thisDistinguished LecturerDr. Chris SomervilleDirector, Energy Biosciences Institute (EBI)Presents On:“Cellulosic Biofuels”UC Davis ARC Ballroom October 16, 2008, 3:00-4:00 PMThis is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1883385 Thu, 16 Oct 2008 17:36:00 +0100 1883385 http://phylogenomics.blogspot.com/2008/10/happy-open-access-day-back-to-genome.html Well, good timing on this one. A new paper from Martin Wu in my lab has recently been accepted to Genome Biology and the provisional PDF was posted online 10/13. The paper ( A simple, fast, and accurate method of phylogenomic inference ) describes a new program Martin wrote called AMPHORA and shows how it can be used to build phylogenetic trees based on concatenated alignments of housekeeping proteins and also for metagenomic phylotyping using a diversity of protein markers. As today is Open Access Day I thought I would just put in a plug for this OA paper and thank Martin for his great work and commitment to Open Access.I should note - I really really like Genome Biology as a journal - even though they have been rejecting many of my papers lately (or maybe in part because of this). I am r... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1873102 Tue, 14 Oct 2008 08:03:00 +0100 1873102 http://phylogenomics.blogspot.com/2008/10/open-access-day-video-of-talk-i-gave.html Well, I was going to write all this blather about OA. But I realized it would be easier to share a video of a talk I gave at U. Washington on Open Access as part of their Biomedical Research Integrity Series (U. Washington Program). I cannot figure out how to download/embed the video so instead I am just posting the links. If someone has software for downloading it and wants to help me embed it and/or upload to YouTube and SciVee that would be great. Here are the links:Lecture #2, Responsible Authorship: Thursday, August 7, 2008; Speaker: Jonathan Eisen, Ph.D., "Responsible Authorship and the Ownership of Scientific Knowledge: Thoughts on Open Access Publishing" To view the lecture, click here: Flash Player version, Windows Media Player version, or QuickTime Player version... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1873103 Tue, 14 Oct 2008 07:30:00 +0100 1873103 http://phylogenomics.blogspot.com/2008/10/open-access-day-thanks-to-oa-journals.html Well, today is a big day for Open Access, as it is, well, Open Access Day. And one thing I really wanted to put out there is that I think we all should say a big thanks to all of those who have worked tirelessly at various OA journals to help move OA into the mainstream and to produce a vast collection of fully open biomedical and scientific literature. As I am involved in PLoS journals in many ways, I want to thank all of the staff who work behind (and sometimes in front) of the scenes there. There is a relatively full list of these people here. And I am publishing that list here too, with, along with a heartfelt thank you. Thank you. You all rock. And we should also thank all the staff at other OA Publishers (e.g., BMC). You rock too.PLoS Staff Peter Jerram, Chief Executive Officer Finan... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1873104 Tue, 14 Oct 2008 07:10:00 +0100 1873104 http://phylogenomics.blogspot.com/2008/10/open-access-day.html Today is Open Access Day.  For more information see here.  It is a big celebration of, well, Open Access to scientific and medical literature.We are going to have a little shindig at Davis (organized by a grad. student Collin Ellis who is also starting a new organization here on Campus - the UCD-SSOA (Society of Scientists for Open Access).  The shindig will include a live WebCast of OA Day presentations by Richard Roberts (who has one of them Nobel Prize thingies) and Phil Bourne (Editor in Chief of PLoS Computational Biology, and creative mind behind a ton of OA initiatives).  The meeting will be in the Genome Center, GBSF 4202.  FIrst showing of the webcast at 4.  Second showing at 7.  In between I will give a little talk on "Why Open Access is Good for Scientists and the World".... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1873105 Tue, 14 Oct 2008 07:01:00 +0100 1873105 http://phylogenomics.blogspot.com/2008/10/arxiv-reaches-500000-papers.html Pretty cool that there are 500,000 papers in arXiv (see Slashdot | Free Online Scientific Repository Hits Milestone). Hat tip to Jeremy Peterson for pointing this out. See also Peter Suber on this (Milestone for arXiv)This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1870887 Sat, 11 Oct 2008 23:31:00 +0100 1870887 http://phylogenomics.blogspot.com/2008/10/open-science-pioneer-award-douglas.html There is a touching and fascinating story in the Cape Cod Times about Douglas Prasher who used to work at Woods Hole Oceanographic Institute. In the 1960s he did some of the pioneering work on GFP (the discovery of which was why Osamu Shimomura, Roger Tsein and Martin Chalfie were given the Nobel Prize in Chemistry this year). Prasher had cloned the gene for GFP but his research funds ran out and he stopped working on GFP (he is currently living in Huntsville Alabama and working as a shuttle driver for a car dealership).His pioneering work was critical to the later work on GFP and one of the nobel winner Martin Chalfie says"Prasher's work was critical and essential for the work we did in our lab," Chalfie said. "They could've easily given the prize to Douglas and the other two and left me ... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1870888 Sat, 11 Oct 2008 14:49:00 +0100 1870888 http://phylogenomics.blogspot.com/2008/10/nature-using-creative-commons-license.html This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence."Too bad they do not do this for all the papers they publish. Maybe Chris Gunter can convince them to do that even though she is now at Hudson Alpha. I think when she was at Nature she helped convince them to do this for genome papers.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the Univ... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1862825 Thu, 09 Oct 2008 07:48:00 +0100 1862825 http://phylogenomics.blogspot.com/2008/10/bimed-central-sold-to-springer.html Got to run but thought people might be interested in this story. See the scoop at Scientific American. Will post more later. Open access publisher BioMed Central sold to Springer: Scientific American BlogThis is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1859597 Tue, 07 Oct 2008 16:01:00 +0100 1859597 http://phylogenomics.blogspot.com/2008/10/rosie-redfields-open-access-saga.html Rosie Redfield has an agonizing and interesting series on her blog about her attempts to pay for an article of her's coming out in the Journal of Molecular Biology to be "Open Access" under the Elsevier OA option (note - this is not fully OA, but it is better than the standard option for this journal). Here are some of her postings worth looking at:Open Access and other sliminess at ElsevierMore Elsevier hassles about open accessThe saga continues...Open access frustration more powerful than princip...More from Elsevier (names removed...)Rosie is one of the true pioneer's of Open Science, as she has turned her blog into a form of open notebook where she posts discussions about her current research, her papers in progress, grant proposals, and other ideas. Yet the process of trying to pay E... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1859598 Tue, 07 Oct 2008 15:15:00 +0100 1859598 http://phylogenomics.blogspot.com/2008/10/nobel-medicine-winner-is-plos-one.html For You Open Access supporters out there, check out the recent PLoS One paper by Françoise Barré-Sinouss one of the new 2008 winners of the Nobel Prize in Physiology/Medicine.The paper is Scott-Algara D, Arnold V, Didier C, Kattan T, Pirozzi G, Françoise Barré-Sinoussi, Gianfranco Pancino (2008) The CD85j+ NK Cell Subset Potently Controls HIV-1 Replication in Autologous Dendritic Cells. PLoS ONE 3(4): e1975. doi:10.1371/journal.pone.0001975You go PLoS One. This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1853654 Mon, 06 Oct 2008 09:48:00 +0100 1853654 http://phylogenomics.blogspot.com/2008/10/novel-in-medicine-for-viral-discoveries.html Nobel Prize in Physiology or Medicine goes to Harald zur Hausen, Françoise Barré-Sinoussi and Luc Montagnier for discovery of viruses (HPV and HIV) (see Nobel Announcement - Medicine 2008).This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1853655 Mon, 06 Oct 2008 09:40:00 +0100 1853655 http://www.blogger.com/video-play.mp4?contentId=ce9d1b5ba4e02c62&type=video%2Fmp4http://phylogenomics.blogspot.com/2008/10/open-genetics-genome-rearrangement.html A little late I know, but I was going through my draft postings and I rediscovered this one from July. There is an interesting paper in PLoS Genetics by Aaron Darling et al (full disclosure -- Aaron is now working in my lab as a Post Doc ... though I started writing this before I realized the paper was his). The paper is about genome rearrangement in bacterial populations (see Dynamics of Genome Rearrangement in Bacterial Populations). Though the science in the paper is quite interesting, the part I want to promote here are the fun genome rearrangment videos in the supplemental material. The figure and video are from Darling AE, Miklós I, Ragan MA (2008) Dynamics of Genome Rearrangement in Bacterial Populations. PLoS Genet 4(7): e1000128. doi:10.1371/journal.pgen.1000128.This is from th... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1852665 Sat, 04 Oct 2008 14:57:00 +0100 1852665 http://phylogenomics.blogspot.com/2008/10/open-access-pioneer-award-4-carl.html This is not about science but I think this guy deserves an award.  I just read an interesting and funny story in the S.F. Chronicle (Sebastopol man puts code manuals online) by Matthew Stannard about Carl Malamud who has been putting building codes, plumbing codes and other codes online at Public.Resource.Org.Basically, he is doing this because many of the codes are only available for a fee.  He says"Not everybody is going to read the building code, but everybody who wants to should be able to without putting 100 bucks in the slot," Malamud said. "Primary legal materials are America's operating system."And though his work has been questioned by some (who would like to make money off of the codes) he appears to be on solid legal ground. "It's very clear in American law that you can't ge... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1851052 Fri, 03 Oct 2008 17:17:00 +0100 1851052 http://phylogenomics.blogspot.com/2008/10/who-do-nobel-laureates-endorse-guess.html Not much more to say - just thought I would post a link to this posting from "A Vote for Science" by Michael Stebbins (A Vote For Science : 61 Nobel Laureates in Science Endorse Obama)This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1851051 Fri, 03 Oct 2008 17:17:00 +0100 1851051 http://phylogenomics.blogspot.com/2008/10/twisted-tree-of-life-award-2-science.html Well, I love Science Friday. I listen to podcasts of it now almost every day when I bike to work. It is a brilliant show, covering a wide range of science and science related topics in depth. Plus it is freely downloadable in a variety of formats. And they have a great website too. But every once in a while they get something a bit wrong. Yesterday, on my way home from a new introductory biology class we are teaching at Davis on "The Tree of Life" (which I will write more about later), I was listening to a Science Friday about Fungi (Science Friday Archives: The Fabulous Fungi). And unfortunately, in the introduction, Joe Palca started off with a pretty outdated discussion of the tree of life.When you ask people to name the kingdoms, most people get the big ones, animals, plants, bacteria.... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1847982 Thu, 02 Oct 2008 14:56:00 +0100 1847982 http://phylogenomics.blogspot.com/2008/10/sarah-palins-still-dangerous-views-on.html Well, Palin has clearly revised her public position on teaching evolution.  In part of her interview with Katie Couric it was addressed (I got the transcript here. )Couric: Do you believe evolution should be taught as an accepted scientific principle or one of several theories?Palin: Oh, I think it should be taught as an accepted principle. And, you know, I say that also as the daughter of a school teacher, a science teacher, who has really instilled in me a respect for science. It should be taught in our schools. And I won't ever deny that I see the hand of God in this beautiful creation that is Earth, especially coming from one of the most beautiful states in the Union and traveling around this country also in this last month. My goodness, just seeing, you know, the beautiful landscape... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1844795 Wed, 01 Oct 2008 15:56:00 +0100 1844795 http://phylogenomics.blogspot.com/2008/09/congrats-to-gary-andersen-developer-of.html The Phylochip, developed by Gary Andersen, of Lawrence Berkeley National Lab, and colleagues, has won a Wall Street Journal, Technology Innovation Award. For more see the Wall Street Journal here. Their phylochip is a microarray which can be used to rapidly survey rRNAs from different organisms and get a measure of the types and abundances of organisms present in a sample. It is similar in concept although different in design from a rRNA chip that was used by David Relman, Pat Brown, Chana Palmer and others. Not sure why the chip from Brown et al did not also win the award (it probably was not nominated, or something like that), but still, always good to see cool things in microbiology win awards like this.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonat... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1841085 Wed, 01 Oct 2008 00:32:00 +0100 1841085 http://phylogenomics.blogspot.com/2008/09/joe-derisi-and-open-science-featured-on.html Well, I already gave him one of my awards, so what else could he do?  Anyway, always good to see Open Science getting promoted and nice to see Voice of America running a story on Joe Derisi after his Heinz Award and featuring this openness (listen to an MP3 of the radio story here).  And they even interviewed me because of my blog about him.  Blogs and the "real" news merge closer and closer every day.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1841086 Tue, 30 Sep 2008 20:00:00 +0100 1841086 http://phylogenomics.blogspot.com/2008/09/humorous-sciency-signs-2-squirrel.html Here is another funny science related sign. I think this was from the Grand Canyon or somewhere near there, taken by my mother, many years ago.Like I needed any more justification to not trust organisms bigger than a large protist.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1837280 Tue, 30 Sep 2008 04:09:00 +0100 1837280 http://phylogenomics.blogspot.com/2008/09/wanted-evolutionary-genomicist.html Todd Oakley, of UCSB and more importantly, the Evolutionary Novelty Blog, forwarded this to me.  UCSB is looking for an Asst. Prof. in Evolutionary Genomics.  If only they had said "Phylogneomics" then I would have written a longer posting ...See here for more detail. Also see the ad on Oakley's blog.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1837281 Mon, 29 Sep 2008 22:38:00 +0100 1837281 http://phylogenomics.blogspot.com/2008/09/science-faux-pas-4-nature-wishes-their.html I know others have written about this already but I had to add this to my collection of Science Faux Pas because it is pretty good.  Nature had a recent issue that was covering the US election.  And look at the front and back cover ... they claim it was an accident but hard to imagine given the posing/color matching.  I note I first heard about this from Bora on FriendFeed. And now the Times Online has a whole story on it.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1837282 Mon, 29 Sep 2008 14:45:00 +0100 1837282 http://phylogenomics.blogspot.com/2008/09/700-billion-will-buy-lot-of-taq-lb.html I know, my research tends to me expensive as I work on deep sea organisms and do genomics and such.  But for $700 billion, a lot could get done in my work areas.  Here are some things one could get for that amount of money that directly relate to my work (this was inspired by a conversation with Drew Endy Friday)1,400,000 Roche 454 Sequencing Machines (for $500,000 each).  If you had money for reagents, that would get you a lot of sequencing.70 million bacterial genomes (at $10,000 each for the shotgun sequencing)280,000 liters (yes that is right, liters) of Taq polymerase (at 100$/40 ul)29.16 billion liters of sterilized LB broth (from Sigma at 12$/500 ml).  That is one deep lake of LB.7 billion copies of my Evolution textbook7 million people years of computational biologists to analy... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1834743 Sun, 28 Sep 2008 04:58:00 +0100 1834743 http://phylogenomics.blogspot.com/2008/09/humorous-sciency-signs-1-please-do-not.html I am starting yet another thread here --- my favorite humorous science related signs.  This one is from Alaska.  Not sure what Sarah Palin would think of this one, but that is another topic.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1834744 Sat, 27 Sep 2008 20:05:00 +0100 1834744 http://phylogenomics.blogspot.com/2008/09/drew-endy-talking-at-davis-tomorrow.html For those from UC Davis or the area who read the blog and have an interest in genetic engineering or synthetic biology or open science, you should come to this talk.Genome Center ColloquiumStorer Life Sciences Endowment PresentsDrew Endy, PhDStanford University"Post-Synthesis Genetics & Engineering Biological Simplicity"Friday, September 26, 200810:00 a.m., 1005 GBSF AuditoriumFor more on Drew Endy, well, use google of course or go here:Edge: ENGINEERING BIOLOGY: A Talk with Drew EndyWired 13.01: Life, ReinventedIT Conversations | O'Reilly Media Open Source Conference | Drew EndyYouTube - iGEM - Drew Endy Defining Synthetic Biology (video)Synthetic Biology Debate with Drew Endy and Jim Thomas at Fort ...MIT World » : The Implications of Synthetic BiologySeedmagazine.com | MIND08 | Dre... The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1829206 Fri, 26 Sep 2008 02:51:00 +0100 1829206 http://phylogenomics.blogspot.com/2008/09/science-faux-pas-3-editirs-in-chief.html The pictire seys it all.  Note - we think this was the restaurant's fault.This is from the "Tree of Life" blog ( http://phylogenomics.blogspot.com ) of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis.. (Source: The Tree of Life) The Tree of Life blogs http://www.medworm.com/rss/comments.php?id=1829207 Fri, 26 Sep 2008 02:43:00 +0100 1829207