Leslie Orgel - Still Speaking Wisely and Openly Even After Death

OK - my mind has been blown. Leslie Orgel, who just passed away recently, has a new Essay in PLoS Biology called "The Implausibility of Metabolic Cycles on the Prebiotic Earth." Anyone interested in the origin of life should check this out.

He had me at the beginning ... and as usual has very clear discussions of the steps needed for life to have originated:

If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear. If, for example, a complex system of nonenzymatic cycles could have made nucleotides available for RNA synthesis, many of the problems of prebiotic chemistry would become irrelevant. Perhaps a simpler polymer preceded RNA as the genetic material—for example, a polymer based on a glycerol-phosphate backbone [5] or a phosphoglyceric acid backbone. Could a nonenzymatic “metabolic cycle” have made such compounds available in sufficient purity to facilitate the appearance of a replicating informational polymer?

The paper then discusses details of various metabolic cycles and why the current evidence is not completely convincing in terms of the exact path that was taken in the origin of life. Note to ID supporters - this does not friggin' mean that he is saying life could not have originated from non living systems. He is simply pointing out that our understanding of it is incomplete. As, by the way, is our understanding of how blood works. But that does not stop us from thinking that blood does in fact, well, work.

Anyway, once you get over the fact that some ID supporters will misuse his work, the end is a great call for what needs to be done:

The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help

Yes, that is right, he got "if pigs could fly" into a paper. He was a great scientist. And it is nice for me to see one more paper of his. And this one, unlike pigs, can fly forever, because it is truly OA.

Syphilis origin solved?

A new paper in PLoS Neglected Tropical Diseases attempts to tackle a rather sensitive topic - the evolutionary origin of treponematoses (i.e., diseases caused by bacteria in the genus Treponema including yaws, pinta, and the one everyone wants to know about - syphilis). The paper, by Kristin Harper and others uses evolutionary reconstructions to try and determine if good old Christopher Columbus played a role in bringing syphilis to the New World.

There was an extensive article about this study in the New York Times on 1/15/08 (by John Noble Wilford). Overall the Times article is good (except Wilford gets the definition of phylogenetic analysis a bit wrong - saying it is the study of the evolutionary relationships between organisms when really it is the study of evolutionary relationships of anything... but hey that is OK).

I confess I am not sure if I am completely convinced by all of Harper et al's arguments concerning the evolution of these bugs. My main concern is that the amount of variation they observe (in ~ 20 genes across these strains) is very very low. And thus the resolution of the phylogenetic trees is quite poor.

Because this is a PLoS paper, it is truly "Open Access" and I can include the Figure here in my blog as long as I cite the original source (see below). If you look at the tree you can see some #s on the branches in the tree. These are based on a statistical test called bootstrapping and the numbers indicate (roughly) how well the tree that is shown represents all of the polymorphisms in the data. The #s are percentages and alas the % support is not very high for many of the branches. So a better resolution of the question of the origin of these diseases will likely require, well, a better resolution on the tree. This in turn will likely require complete genome sequences and perhaps more strains samples. Nevertheless, given the results they have, their arguments seem sound ... and this should stimulate people to gather more genomic data from these bugs.

Also see some other blogs on this

• Neil Woodburn
• John Dennehy (who mentions an article by Carl Zimmer in a non OA publication ... find out which by going to his blog)

Here is Figure 3. It is from Harper KN, Ocampo PS, Steiner BM, George RW, Silverman MS, et al. (2008) On the Origin of the Treponematoses: A Phylogenetic Approach. PLoS Negl Trop Dis 2(1): e148. doi:10.1371/journal.pntd.0000148

Figure 3. This maximum likelihood tree is based on 20 polymorphic regions in the T. pallidum genome. Bootstrap support was estimated with 1,000 replicates in order to assess confidence at branching points and are shown within circles where values are high (>90%). Bootstrap support values for both maximum likelihood and maximum parsimony trees are shown, in that order.

Is that a sex organ on the cover of Nature?

OK --- dipping into the gutter here a bit.  But everyone must check out the cover of Nature this week.  The issue is on the genetics of sex, and I'll be damned if that phycomyces colony on the cover (the one in the back) does not look like some sort of male sexual organ.  

I do not know where to go with this.  It has to be on purpose right?  Is this what they refer to in the cover caption as a "pseudo-sexual" structure?

And I know I am probably not supposed to say this as an obsessed supporter of Open Access publishing but I dream of the day Nature becomes a fully OA journal.   I still think PLoS Biology is a better journal, but Nature definitely has some good stuff there.

International Congress of Genetics --- you should all go ---

OK - I am a bit biased as I am chairing a session at this "International Congress of Genetics" meeting. But it does look pretty good. Plenary talks by Richard Axel, Liz Blackburn, Mario Capecchi, Rudy Kaenisch, Eric Lander, Svante Paabo and Phil Sharp. Sessions on many things, including (hint hint) - metagenomics. Other speakers are listed below. So - you really should consider going ...check out the website here.

Chairs/Speakers
The following Chairs/Speakers (in alphabetical order) have been confirmed so far: Ruedi Aebersold (ETH Zuerich, Zuerich, Switzerland) Steve Kay (Univ. California, USA) Leif Andersson (Univ. Uppsala, Uppsala, Sweden) Brian Kennedy (Washington Univ., Seattle, USA) Siv Andersson (Univ. Uppsala, Uppsala, Sweden) Daniel Kevles (Yale Univ., New Haven, USA) Hiroyuki Araki (NIG, Mishima, Japan) Amar Klar (NCI, Frederick, USA) Ana Barahona (UNAM, Tialpan, Mexico) Narry Kim (Seoul National Univ., Seoul, South Korea) Cori Bargmann (Columbia University, New York, USA) Arne Klungland (Univ. Oslo, Oslo, Norway) Nick Barton (Univ. Edinburgh, Edinburgh, Britain) Bartha Knoppers (Univ. Montreal, Montreal, Canada) David Baulcombe (Sainsbury Laboratory, Norwich, Britain) Daphne Koller (Stanford Univ., Standford, USA) Stephan Beck (UCL, London, UK) Arash Komeili (Univ. of California, Berkeley, USA) Hugo Bellen (Baylor College of Med., Houston, USA) Charalambos Kyriacou (Univ. Leicester, Leicester, Britain) Jeffrey Bennetzen (Univ. Georgia, Athens, USA) Ruth Lehmann (Skirball Institute, NYU, New York, USA) Shelley Berger (Wistar Inst., Philadelphia, USA) Ottoline Leyser (Univ. York, York, UK) Casey Bergman (Univ. Manchester, Manchester, UK) Thomas Lindahl (CRUK, South Mimms, UK) Anton Berns (nki, Amsterdam, The Netherlands) Klaus Lindpainter (Hoffmann-LaRoche, Basel, Switzerland) Bruce Beutler (Scripps Res. Inst., La Jolla, USA) Edison Liu (Genome Institute, Singapore) Ewan Birney (EMBL, Hinxton, UK) John M. Logsdon (Univ. Iowa, USA) Maria Blasco (CNIO, Madrid, Spain) Trudy Mackay (NCSU, Raleigh, USA) D.I. Boomsma (Netherlands Twin Register, Amsterdam, Netherlands) Partha P. Majumder (Indian Statistical Institute, Kolkata, India) Paola Bonfante (CNR, Torino, Italy) Marjori Matzke (Gregor Mendel Institute, Vienna, Austria) Nancy Bonini (Univ. Penn., Philadelphia, USA) Gunter Meister, MPI, Martinsried, Germany) Peer Bork (EMBL, Heidelberg, Germany) Gilean McVean (Univ. Oxford, Oxford, UK) Dan Bradley (Trinity College Dublin, Dublin, Ireland) David A. Micklos (Cold Spring Harbor, New York, USA) Steve Briggs (Univ. California, San Diego, USA) Andrew Moore (EMBO, Heidelberg, Germany) Maja Bucan (Pennsylvania Univ. Philadelphia, USA) Joe Nadeau (CWR Univ., Cleveland, USA) Margaret Buckingham (Institut Pasteur, Paris, France) Wolfgang Nellen (Univ. Kassel, Kassel, Germany) Edward Buckler (Cornwell Univ., Ithaka, USA) Laura Niedernhofer (Univ. Pittsburg, Pittsburg, USA) Jeremy Burdon (CSIRO-Plant Industry, Canberra, Australia) Jens Nielsen (Biocentrum, Lyngby, Denmark) A. Bernardo Carvalho (Rio de Janeiro Univ., Brazil) Howard Ochman (Uni. Arizona, Tucson, USA) Aravinda Chakravarti (Johns Hopkins Univ., Baltimore, USA) Peter Oefner (Univ. Regensburg, Regensburg, Germany) Deborah Charlesworth (Univ. Edinburgh, Edinburgh, Britain) Steve Oliver (Cambridge Univ., Cambridge, UK) Judy Cho (Yale Univ., New Haven, USA) Allen Orr (Univ. Rochester, Rochester, USA) George Church (Harvard Medical School, Boston, USA) Terry Orr-Weaver (MIT / Whitehead, Cambridge, USA) Andy Clark (Cornwell Univ., Ithaka, USA) Elaine Ostrander (National Human Genome Research Institute, Bethesda, USA) Lynn Cooley (Yale Univ., New Haven, USA) Sven Panke (ETH Zürich, Zürich, Switzerland) Max Cooper (Univ. Alabama, Birmingham, USA) Susan Parkhurst (Fred Hutchinson Cancer Res. Centre, Seattle, USA) Arjan de Visser (Univ. Wageningen, The Netherlands) Martin Parniske (Ludwig-Maximilians-Universität, Munich, Germany) Alain Dessein (Univ. de la Méditérranée, Marseille, France) Renato Paro (ETH Zürich, Basel, Switzerland) Barry Dickson (IMP, Vienna, Austria) Linda Partridge (Univ. College, London, UK) Andrew Dillin (Salk Inst., La Jolla, USA) Dinshaw Patel (Sloan-Kettering Institute, New York, USA) Anna Di Rienzo (Univ. Chicago, Chicago, USA) Hervé Philippe (Univ. Montreal, Montreal, Canada) John Doebley (College of Agricultural & Life Sciences, Madison, USA) Alfred Pühler (Univ. Bielefeld, Bielefeld, Germany) Denis Duboule (Univ. Geneva, Geneva, Switzerland) Nazneen Rahman (Institute of Cancer Research, Sutton, UK) Evan Eichler (Univ. Washington, Seattle, USA) Klaus Rajewsky (Harvard Univ., Boston, USA) Jonathan Eisen (Univ. California, Davis, USA) Erez Raz (MPI, Göttingen, Germany) Hans Ellengren (Evolutionary Biology Centre, Uppsala Univ., Sweden) André Reis (Univ. Erlangen, Erlangen, Germany) Jonathan Flint (Wellcome Trust, Oxford, UK) Hans-Jörg Rheinberger (MPI, Berlin, Germany) Veronica Franklin-Tong (Univ. Birmingham, Birmingham, UK) Francisco Rodriguez-Valera (Univ. Alicante, Spain) Kelly Frazer (Scripps, La Jolla, USA) Outi Savolainen (Univ. of Oulu, Oulu, Finland) Wolf Frommer (Carnegie Institution of Washington, Stanford, USA) John Schimenti (Cornell Univ. New York, USA) Martin Fussenegger (ETH, Zürich, Switzerland) Eran Segal (Weizmann Institute of Science, Rehovot, Israel) Anne-Claude Gavin (EMBL, Heidelberg, Germany) Hee-Sup Shin (KIST, Seoul, South Korea) Michel Georges (Univ. Liège, Liège, Belgium) Akira Shizuo (Osaka Univ., Osaka, Japan) Carla Green (Virginia Univ., Charlottesville, USA) Mikiko Siomi (Univ. Tokushima, Kuramoto, Japan) Jonathan Gressel (Weizmann Inst., Rehovot, Israel) Christina Smolke (Caltech, Pasadena, USA) Anthony Griffiths (Univ. British Columbia, Vancouver, Canada) David Smyth (Monash Univ., Melbourne, Australia) Roderic Guigó (CRG, Barcelona, Spain) Marla Sokolowski (Toronto Univ., Toronto, Canada) Chris Haley (Roslin Inst., Roslin, Britain) Allan Spradling (Carnegie Institution, Baltimore, USA) Mike Hall (Biozentrum, Basel, Switzerland) Didier Stainier (Univ. California, San Francisco, USA) Michael F. Hammer (Univ. Arizona, Tucson, USA) Karen Steel (Sanger Inst., Hinxton, Britain) Min Han (Univ. Colorado, Boulder, USA) Kári Stefánsson (deCODE Genetics, Reykjavik, Iceland) Mitsuyasa Hasebe (National Institute for Basic Biology, Okazaki, Japan) Lars Steinmetz (EMBL, Heidelberg, Germany) Christian Heintzen (Univ. Manchester, UK) Michael Stratton (Sanger Institute, Hinxton, Britain) Steven Henikoff (Fred Hutchinson CRC, Seattle, USA) Azim Surani (Cambridge Univ., Cambridge, Britain) Martin L. Hibberd (Genome Institute of Singapore, Singapore) Joseph Takahashi (Northwestern University, Evanston, USA) Adrian Hill (Oxford Univ., Oxford, UK) Diethard Tautz (MPI, Plön, Germany) Helen Hobbs (Univ. Texas, Dallas, USA) Chau-Ti Ting (National Taiwan Univ., Taipei, Taiwan) Eric Holub (Warwick HRI, Wellesbourne, UK) Franck Uhlman (Cancer Research UK, London, UK) Elisa Izaurralde (MPI, Tuebingen, Germany) John Wakeley (Harvard Univ., Cambridge, USA) Janet Jansson (Swedish Univ. of Agricultural Sciences, Uppsala, Sweden) Detlef Weigel (MPI, Tuebingen, Germany) Urs Jenal (Biozentrum, Basel, Switzerland) Sue Wessler (Univ. Georgia, Athens, USA) Nancy Jenkins (Biopolis, Singapore) Eric Wieschaus (Princeton Univ., Princeton, USA) (Nobel Laureate) Julie Johnson (Univ., Florida, USA) Shinya Yamanaka (Univ. Kyoto, Kyoto, Japan) Regine Kahmann (MPI, Margburg, Germany) Zhu Zhen (Genetics Inst., Beijing, China) Thomas Kaufman (Indiana Univ., Bloomington, USA) Huda Y. Zoghbi (Baylor College of Med., Houston, USA) Stefan Kaufmann (MPI, Berlin, Germany)

Can openness stop wars?

Thanks to Doug Rusch for pointing me to this video of a talk by Michael Shermer. It is a bit over the top, but I like the bit at the end suggesting that open access to information can basically stop wars.

Not sure I buy into the whole argument, but I do think that keeping scientific information behind closed walls is generally a bad idea ....

PCR Humor

Not much to say - other than thanks to Jenna Morgan for sending this ...

Oakley Keeping his Eye on Evolution

I saw an interesting talk today and thought I would post on it. I was not expecting to be able to go to the talk as I was supposed to be at a workshop in San Francisco but had to bail on it because my kids have been sick. But I did go in to Davis for a brief spell to go to a seminar by Todd Oakley who gave a talk here today.

It was a generally insightful phylogenomic tour of the evolution of opsins and eyes in animals. He also mentioned a paper he had recently in PLoS One on Animal Opsin evolution. This is from the work of his graduate student David Plachetzki and it does a nice job of doing "phylogenomic" analysis in the way I think of phylogenomics -- that is -- a integration of evolutionary and genomic analyses. (NOTE - I think it is kind of lame that people use the term phylogenomics, which I coined by the way, to refer to "using genomes to infer evolutionary trees). It is a paper worth checking out if you are interested in the origin of novelty.

I am putting links here to some of their figures and embedding them in this blog because, well, I can since PLoS One uses a broad Creative Commons license. For example - see Figure 6 from their paper below (the citation is Plachetzki DC, Degnan BM, Oakley TH (2007) The Origins of Novel Protein Interactions during Animal Opsin Evolution. PLoS ONE 2(10): e1054. doi:10.1371/journal.pone.000105).

Figure 6. Ancestral state reconstruction of G protein-binding interactions for each metazoan opsin-mediated phototransduction cascade obtained by simulated mutational mapping [64] (see methods).For each class of opsin, the P value of the reconstructed ancestral G α interactions is represented in pie graphs. Ancestral G protein interactions in phototransduction cascades mediated by ciliary, rhabdomeric and G_o opsins can be significantly resolved (P>0.95) but the ancestral states of the rhabdomeric+G_o, and cnidops clades are equivocal. ML state reconstructions shown for each node as colored branches. Red, G_i/t; Blue, G_q; Green, G_o; Black, no G protein interaction (as is the case for RGR/Retinochrome opsins); Grey, equivocal reconstruction from ML. Reconstructed ancestral amino acid motifs of the 4th cytoplasmic loop region of opsin are shown along branches in logos. Maximum vertical height scales to P = 1.0. We obtained clear reconstructed states for most of the residues in a conserved tripeptide motif (residues 310, 311 and 312, horizontal bar) for the ciliary, rhabdomeric and G_o /RGR nodes. For the most part, the remainder of the residues in can be unequivocally reconstructed to the level of Dayhoff classes. B = HRK, X = LIVM, J = GATSP, Z = DENQ..

























See also Figure 2

"Figure 2. Unrooted metazoan-wide phylogeny of opsins, new cnidarian genes in bold, branches proportional to substitutions per site. Circles at nodes indicate Bayesian posterior probabilities (White = 1.0, Red>0.90, Blue>0.80, Green>0.70, Yellow>0.60, Black>0.50). cil = ciliary, rh = rhabdomeric."

Science and the presidential election

Nothing really new from me here but saw some good blogs on the topic of science and the presidential election.

Steve Salzberg has summary information and some comments here.
Popular Mechanics has some info here
The ever active Bora has some comments here
Wired has a bit here

My little bit .... I think science is clearly not strongly supported by the current administration. However, scientists need to be careful about how they word things, since in the end, we are asking for money from taxpayers to, well, pay our salaries and pay for our work. This is one of the reasons I am very strongly in support of "open science." The more open we scientists are, I think, the easier it is to justify to the "public" that we deserve some of their/our money. That is not to say that lots of taxpayer money is not completely wasted on other things. And even not completely open science is frequently good for the world. But openness should help make scientists not seem so ivory toweresque and would show that we want to give back in exchange for what we are given.

More fun at Long's

OK. Just had to post something because this is getting comical. I went in to Long's in E. Davis the other day to pick up some prescription refills. I had requested the refills online through the Long's web site and received an email saying they were reads. When I got in to the store, they told me that the refills were not ready. This is funny because this was about the 15th or so time in a row that my prescriptions were not ready when I was told they would be. One time it was problems with the online system. Another time it was that they needed a new prescription from my Doctor. Sure prescriptions expire and that is not really Long's fault. But apparently, when my prescriptions expire they decide to send faxes to a doctor I used to have in Maryland, even though I moved over two years ago. I came in like four times once over two weeks and every time they person at the counter would say "We faxed a request to Dr. So and So' and I would say "That person has not been my doctor for years. My new doctor is Dr. So and So in Davis." and they would sit there and click away at the keyboard supposedly fixing things and then they would say "OK, we will send it to the new doctor" And then I would come back and the person would say "We faxed your doctor in Maryland but he has not responded". This happened over and over and over. I began to view it as a game. How many times could I come to the pharmacy and could they get something wrong? The good things was, the people at the Long's pharmacy were very very nice. The bad thing was, something always seemed to go wrong. For a while I tried to use their automated prescription refill system, but that always went wrong too. So instead now, since I live near Long's and go to the Nugget all the time, I view my trips to the Long's Pharmacy as kind of an experiment in how many different ways my prescriptions can get screwed up.

Shameless Self Promotion ---- Another Good Review on my New Evolution Textbook

Well, again, here is another shameless self promotion. We got another good review of the new Evolution Textbook on which I am a co-author. This one is by Dan Hartl and was in Nature OK, it is not an Open Access review, but as I have said before, I am obsessed about open access to research articles, not book reviews, etc.

In the review Hartl tells a story about an encounter with Max Delbrück at Cold Spring Harbor where Delbruck implied that molecular aspects of evolution were uninteresting. Hartl goes on to say many nice things about our book (he does get on our case about having problems on the web and not in the book - but hey nobody is perfect). My favorite from the review is the following

Textbooks in evolutionary biology have gen-
erally kept pace with these changes and several
excellent books are available. This new one by
Barton and colleagues is among the best. The
production quality is superb in layout, compo-
sition, typesetting, colour palette, illustrations
and gorgeous half-tones; and the writing is
excellent, as one might expect from such a stel-
lar cast of experts in population genetics, palae-
ontology, human genetics, bacterial genomics
and developmental biology (respectively).

Thanks Dr. Hartl. And a much belated thanks for a personal encounter that I had with you many years ago where you were MUCH more encouraging to me about working on bacterial genomes than Delbruck was to you about molecular evolution.

Microbial communities highlighted by MIT Technology Review: The Year in Biotech

The MIT Technology review has an interesting piece on the "Year in Biotech". See Technology Review: The Year in Biotech

The selected key items that they discuss:

• Personal genomics
• Microbial communities
• Stem cells without embryos
• Brain repair
• Human genetic variation

Good to see microbial communities getting selected for this type of thing --- they are after all the next big thing.

In memory of Sam Karlin

I just got an email telling me that Sam Karlin had passed away. Sam, for those who do not know, was one of the luminaries in bioinformatics and mathematical biology. You can learn a bit more about him by going to this site which relates to a workshop that was help in honor of his 80th birthday.

His passing saddens me greatly. Sam was a curmudgeony guy at times, but also a great scientist and teacher. He was one of my mentors when I was in graduate school at Stanford. I was kind of a fish out of water --- trying to learn boinformatics in a lab that studies the cell biology of DNA repair processes. So I took a course from Sam Karlin and Volker Brendel and then spent three years meeting on and off with Sam in his office discussing various aspects of genome and gene sequence analysis. We did not always agree. But I think I learned more about bioinformatics from those meetings with Sam than from anything else I have done in my career.

Sam reminded me a lot of my grandfather (who was a physicist). We would meet to ostensibly talk about RecA (my favorite protein) or DNA composition (Sam's favorite thing at the time) or evolution or something or other. But Sam turned every meeting into some type of lesson about bioinformatics. We rarely got to our end goal, but that did not really matter.

So - in his honor I am going to start a new section of this blog --- the Something about Math in Biology or the SAM in Biology section ... stay tuned.

NOTE Lee Altenberg has a memorial page to him, consisting of his doctoral advisor genealogy:

Why "neglected tropical diseases" are going to bite us in the *$&#

Malaria. Chagas. Filariasis. Dengue fever. Onchocerchiasis. Trachoma. Cholera. Leishmaniasis. Yaws. Leprosy.

Neglected tropical diseases. You certainly don't want to get them (I have had at least one). And they are not as neglected as they used to be with some money being dedicated to them (e.g. from the Gates Foundation) and their own PLoS journal dedicated to them and even famous people blogging about them. The World Health Organization pushes for them to get more attention.

But given that these diseases kill and injure BILLIONS of people and cause untold amounts of economic damage, they clearly still do not get what they deserve, in terms of research dollars and drug development efforts, etc.

Well, listen up people in the non-tropical (a.k.a. developed) world. Even if the "let's help others" line does not light your fire, you better start worrying about these diseases. That is because many of these diseases are on the march in part due to global warming and will likely soon be a bigger part of our life in the developed world.

There has been lots in the press and web about this but it still seems to get ignored which is why I am blogging about it here. For example see

• NPR story from 2002
• Union of Concerned Scientists article
• BBC article from 1999

The thing that reminded me of this issue was a 12/23/07 New York Times article discussing the spread of the tropical virus that causes chikungunya into Europe for the first time.

So, next time you are lingering in Berlin or New York or Moscow and you feel a weird itch. Or have a fever that just won't go away. Or have strange swellings where you never had them before. Don't just look for diseases that were once common wherever you are. Start to think about things like Dengue (my favorite, since I have had it). And maybe just maybe, you should start to worry about these things BEFORE you get them. And support efforts to make these diseases not so neglected.

Happy Hollidays Open Access Movement

Well there is damn good news on the Open Access to scientific literature front. President Bush signed the big spending bill today that includes a provision requiring all papers coming from NIH funded work to be made freely available after 1 year. From the Washington Post:

Under the bill's terms, scientists getting grant money from the National Institutes of Health would now have to submit to the NIH a final copy of their research papers when those papers are accepted for publication in a journal. An NIH database would then post those papers, free to the public, within 12 months after publication.

I am giddy with excitement about this. Congratulations to all who lobbied so hard for this, such as Heather Joseph from SPARC. Her quote from the Post article is helpful here:

"The basic reason we went to bat so hard for this was because we thought it was the right thing to do with taxpayers' science," Joseph said. "Now there will be $29 billion in taxpayer investments freely available to the public," she said, referring to the NIH medical research budget

NIH wants proposals on the human microbiome ...

NIH has an press release regarding the new Roadmap Initiative on the Microbiome. I quote from it below:

Bethesda, Md., Wed., Dec. 19, 2007 – The human body contains trillions of microorganisms, living together with human cells, usually in harmony. Because of their small size, however, microorganisms make up only about one to two percent of the body's mass. Many microbes maintain our health, while others cause illness. Yet, surprisingly little is known about the role this astounding assortment of bacteria, fungi and other microbes play in human health and disease. To better understand these interactions, the National Institutes of Health (NIH) today announced the official launch of the Human Microbiome Project. The human microbiome is the collective genomes of all microorganisms present in or on the human body.

"The human microbiome is largely unexplored," said NIH Director Elias A. Zerhouni, M.D. "It is essential that we understand how microorganisms interact with the human body to affect health and disease. This project has the potential to transform the ways we understand human health and prevent, diagnose and treat a wide range of conditions."

Part of the NIH's Roadmap for Medical Research, the Human Microbiome Project will award a total of $115 million to researchers over the next five years. Initially, researchers will sequence 600 microbial genomes, completing a collection that will total some 1,000 microbial genomes and providing a resource for investigators interested in exploring the human microbiome. Other microbial genomes are being contributed to the collection by individual NIH institutes and internationally funded projects. A meeting between international partners was recently convened to discuss forming an international consortium.

Researchers will then use new, comprehensive laboratory technologies to characterize the microbial communities present in samples taken from healthy human volunteers, even for microbes that cannot be grown in the laboratory. The samples will be collected from five body regions known to be inhabited by microbial communities: the digestive tract, the mouth, the skin, the nose, and the female urogenital tract. Demonstration projects will subsequently be funded to sample the microbiomes from volunteers with specific diseases. This will allow researchers to correlate the relationship between changes in a microbiome present at a particular body site to a specific illness.

"We now understand that there are more microbial cells than human cells in the human body. The Human Microbiome Project offers an opportunity to transform our understanding of the relationships between microbes and humans in health and disease," said Dr. Alan Krensky, the director of the Office of Portfolio Analysis and Strategic Initiatives (OPASI), which oversees the NIH Roadmap for Medical Research.

While the term "microbiome" may be relatively new in biomedical research, most people are familiar with some of the effects - both good and bad - that microbes can have on our health. Consider the example of the biggest reservoir of microbes in humans: the digestive tract. The human gut harbors many beneficial microorganisms, including certain bacteria called probiotics. There is evidence these probiotics, found in dietary supplements, yogurt and other dairy products as well as various soy products, can stimulate the immune system and improve digestive functions. In contrast, previous research suggests that variations in the composition of microbial communities may contribute to chronic health conditions, including diabetes, asthma, obesity and digestive disorders.

"Microbes play a significant role in the health of the digestive tract and many digestive diseases result when the microbial environment is out of balance," said Griffin P. Rodgers, M.D., M.A.C.P., director of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), and co-chair of the Human Microbiome Project's Implementation Group. "The Human Microbiome Project will help us better understand the microbial environment in the gut, as well as provide us with the tools and technology to expand our exploration into this field of research."

Traditionally, microbiology has focused on the study of individual species as isolated units, making it difficult to develop and inventory all of the microbes in and on the human body. Because their growth is dependent upon a specific natural environment, it's difficult to recreate microbe-host interactions in the laboratory. Advances in next generation DNA sequencing technologies relying on a process called metagenomic sequencing will be used. Instead of isolating each microbe, all of the DNA within the collected samples will be sequenced.

"Our goal is to discover what microbial communities exist in different parts of the human body and to explore how these communities change in the presence of health or disease," said National Human Genome Research Institute Director, Francis S. Collins, M.D., Ph.D., co-chair of the Human Microbiome Project Implementation Group. "In addition, we will likely identify novel genes and functional elements in microbial genomes that will reshape the way we think about and approach human biology."

NIH recently awarded $8.2 million to four sequencing centers, to start building a framework and data resources for the Human Microbiome Project. One-year awards were given to the sequencing centers at the Baylor College of Medicine, Houston, and Washington University School of Medicine, St. Louis, which are part of the NHGRI Large-Scale Sequencing Research Network; and the Broad Institute of MIT/ Harvard, Cambridge, Mass., and the J. Craig Venter Institute, Rockville, Md., which are funded through the National Institute of Allergy and Infectious Diseases (NIAID) Microbial Genome Sequencing Centers Program.

The objectives of this initial work are to sequence the genomes of 200 microbes that have been isolated from the human body as part of the 1,000 microbial genomes collection. Researchers will also begin recruiting healthy volunteers who will donate samples from the five body regions. NHGRI, NIAID, and the National Institute of Dental and Craniofacial Research (NIDCR) have led the initial phases of the project.

"The recent emergence of faster and cost-effective sequencing technologies promises to provide an unprecedented amount of information about these microbial communities, which in turn will bolster the development and refinement of analytical tools and strategies," said NIAID Director Anthony S. Fauci, M.D., co-chair of the Human Microbiome Project's Implementation Group.

Following the precedents set by other large-scale genomics efforts, such as the Human Genome Project and the International HapMap Project, data from the Human Microbiome Project will be swiftly deposited in public databases, including those supported by the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/mapview), part of the National Library of Medicine. The project also will fund the establishment of a Data Analysis and Coordinating Center, which will coordinate data access and develop data retrieval tools for the research community.

Also following on the lead of those efforts, the Human Microbiome Project will monitor and support research on the ethical, legal and social implications of the research. Areas of focus include the clinical and health implications of using probiotics, potential forensic uses of microbiome profiles, bioterrorism and biodefense applications, the application of new technologies from the project, and patenting and privacy issues.

"Examining and addressing the emerging ethical, legal and social implications of metagenomics research is central to our goal of one day moving any resulting diagnostic, prevention, or treatment tools into the clinic in a safe and effective manner," said NIDCR Director Lawrence Tabak, D.D.S., Ph.D., co-chair for the NIH Human Microbiome Project Implementation Group.

Additional information about the Human Microbiome Project is available at www.nihroadmap.nih.gov/hmp. For more information about funding opportunities, go to: www.nihroadmap.nih.gov/hmp/grants.asp. A high resolution image of the bacteria, Entercoccus faecalis, a microbe that lives in the human gut, is available in color at www.genome.gov/pressDisplay.cfm?photoID=20023, or in black and white at www.genome.gov/pressDisplay.cfm?photoID=20024.

The Human Microbiome Project is part of the NIH Roadmap for Medical Research. The Roadmap is a series of initiatives designed to pursue major opportunities and gaps in biomedical research that no single NIH institute could tackle alone, but which the agency as a whole can address to make the biggest impact possible on the progress of medical research. Additional information about the NIH Roadmap can be found at www.nihroadmap.nih.gov.

The National Institutes of Health (NIH) -"The Nation's Medical Research Agency" - includes 27 Institutes and Centers and is a component of the U. S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments and cures for both common and rare diseases. For more information about NIH and its programs, visit www.nih.gov.

Though I risk introduce more competition for myself here I thought I would add some key links to the calls for proposals:


* Development of New tools for Computational Analysis of Human Microbiome
Project Data (R01)
* (RFA-RM-08-008)
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
* http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-08-008.html
*
*
* Development of New tools for Computational Analysis of Human Microbiome
Project Data (R21)
* (RFA-RM-08-009)
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
* http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-08-009.html
*
*
* Development of New Technologies Needed for Studying the Human Microbiome
(R01)
* (RFA-RM-08-010)
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
* http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-08-010.html
*
*
* Development of New Technologies Needed for Studying the Human Microbiome
(R21)
* (RFA-RM-08-011)
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
* http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-08-011.html

Phylogenomics makes the big time --- University of Manitoba seeking a "Chair" in Phylogenomics

Now I know Phylogenomics has hit the big time.

University of Manitoba is looking for a chair in the emerging area of phylogenomics. See below. PS - Good job phylogenomics. You have made it.


From their ad:

UNIVERSITY OF MANITOBA – CANADA RESARCH CHAIR – TIER II
Phylogenomics Chair, Department of Biological Sciences, Faculty of Science
Position # 06661 and 06662

The University of Manitoba is seeking applications or nominations for a Canada Research Chair established by the Government of Canada to enable Canadian Universities to foster world-class research excellence (http://www.chairs.gc.ca). Our Strategic Research Plan (http://www.umanitoba.ca/admin/vp_research/research_chairs.html) identifies a Tier II Chair in the Faculty of Science in the area of Phylogenomics as a priority.

The emerging field of Phylogenomics uses an exciting comparative approach to research that integrates the study of the evolution of species using genomic data and the study of genome function using phylogenetic data, and can powerfully inform a broad spectrum of biological research

Performance enhancing drugs - I confess

Yup, that is right. I took steroids today. I hope this does nto rule out my chances of getting into the hall of fame. But hey, I am going to be up front about it so I wanted to post here in case there is a future investigation into performance enhancing drugs among scientists.

What I took was cortisone, by injection for tendinitis in my fingers. The shot, given by a doctor, hurt like nothing else. But I needed it to recover from an injury. This injection hopefully will let me return in a few weeks to "normal" in terms of my typing. And I am sure all of you out there will be happy about that.

So - the question is - am I cheating? Or is using steroids to recover from an injury OK (see Andy Pettite). What if I got the steroids to make my typing faster. Would that be cheating?

Survival of the fittest M&Ms

Fantastic evolution post on the best of Craigslist.

The post starts off with

Whenever I get a package of plain M&Ms, I make it my duty to continue the strength and robustness of the candy as a species. To this end, I hold M&M duels.

And then, after a crushing test of fitness

Occasionally I will get a mutation, a candy that is misshapen, or pointier, or flatter than the rest. Almost invariably this proves to be a weakness, but on very rare occasions it gives the candy extra strength. In this way, the species continues to adapt to its environment.

Then the winning M&M is sent to Mars with a note

Please use this M&M for breeding purposes.

Best part - Mars sent him a coupon for free M&Ms which he considers "grant money." Who said evolution can't be fun.

Thanks to Michael Eisen for pointing this out.

Fired for (not believing in evolution) promising to do sucky science

The Boston Globe reports on a story about a post doc (Nathanial Abraham) from Woods Hole Oceanographic Institution who was fired recently, apparently because he does not believe in evolution. Apparently, even though Abraham was supposed to focus on comparative and evolutionary studies in the lab of Mark E. Hahn, at some point Abraham told Hahn he did not believe in evolution.

This raises the question - that the Globe asks

"Can people work in a scientific field if they don't believe in its basic tenets?"

I think the answer in this is a bit slippery. If someone does not believe in evolution, but in their work still uses evolutionary analyses and perspective I am not sure what one should do. But Abraham apparently went further and said he would not even discuss evolution in papers on the project. This is reflected in a letter from Hahn quoted in the Globe:

". . . You have indicated that you do not recognize the concept of biological evolution and you would not agree to include a full discussion of the evolutionary implications and interpretations of our research in any co-authored publications resulting from this work," Hahn wrote in the letter, which the commission provided to the Globe. "This position is incompatible with the work as proposed to NIH and with my own vision of how it should be carried out and interpreted."

This then becomes more than "not believing" in evolution outside of work. This is clearly a stance that could jeopardize the quality and integrity of the papers coming out of the project (imagine if I said I was going to write all genome papers from now one based on my belief that DNA is not the material of inheritance but instead that membranes are).

So this looks like a case where the issue is much clearer than in some other cases reported recently. Abraham basically was telling his boss "I vow to do sucky science." And for this, I think it is perfectly reasonable that he got canned.

PS - Thanks for Iddo Friedberg for pointing this story.

Also - see PZ Myers' post about this for much more detail.

Sharpshooters, dual symbioses and new ways to sequence a genome

Those interested in symbioses and in new sequencing methods should look at a paper that just came out in PNAS by John McCutcheon and Nancy Moran (OK - I am a bit biased - this work is related to something I did previously with Nancy). Their paper reports a further dissection of a dual symbioses in sharpshooters (a group of insects that feed on xylem sap). The dual symbioses involves two types of bacteria that live inside specialized cells in the gut of these insects.



Previously, my group had worked with Nancy to sequence the genome of one of the symbionts (Baumannia) as well as part of the genome of the second one (Sulcia). Nancy was interested in this symbioses for many reasons including that as obligate xylem feeders the sharpshooters almost certainly were not getting gall the nutrients they needed in their diet. Based on what was known about bacterial symbionts in other sap feeding insects (e.g., aphids) it seemed likely that the symbionts of the sharpshooters were making the missing nutrients for their host. However, all previous genomic based studies had been done on phloem feeding insects like aphids. Phloem and xylem are the two main circulatory systems in plants. Phloem tends to be nutrient rich, although still not rich enough for the aphids to live on it alone. Thus the aphids rely on bacterial symbionts to make amino acids missing in the phloem.

Xylem is generally much poorer in nutrients and this Nancy wanted to compare the genomes of the symbionts of xylem feeders with those of phloem feeders. Nancy and others had done preliminary work on the sharpshooters showing that they had multiple symbionts living inside cells in their gut and that one of the symbionts (which she named Baumannia after Paul Baumann who she had worked with previously) was closely related to the Buchnera symbionts found in aphids.

So Nancy approached me when I was at TIGR and asked if I would be interested in helping her sequence the Baumannia genome. I said yes (secretly, truth be told, I would have tried to sequence the genome of a rock if Nancy asked. She is perhaps the smartest person I know in all of science and is always doing the coolest types of research. Plus, I figured, I might also be able to interact with her husband, Howard Ochman, who also does cool stuff).

Of all the possible sharpshooters (the symbionts are found in all sharpshooters), Nancy chose to focus on the glassy winged sharpshooter because it is an important pest organism (it is a vector for Pierce's disease in grapes).


So - we (well, the core facility at TIGR under my supervision) sequenced the Baumannia genome using DNA that Nancy had isolated from dissections of the gut of glassy winged sharpshooters. In analysis of the genome we (well, again, the royal we --- in this case Dongying Wu in my lab did most of the analysis) found, among many things, that Baumannia appeared to be making vitamins and cofactors for the host. But alas, we also found something missing --- Baumannia did not appear to be able to make amino acids for the host. Since xylem was likely to be missing amino acids that all animals require in their diet, we had figured that Baumannia must be making them for the host. So we were vexed.



That was, until Nancy pointed out (or reminded us - since she probably had mentioned it before) that there was another symbiont living in the gut of these insects --- a symbiont called Sulcia. She suggested that we look at the DNA sequence pieces that did not assemble with the Baumannia genome and look for any that might encode genes similar to genes from the group of bacteria in which Sulcia is found. And, 1.5 years later, after much informatics and lab work, we obtained about 130 kb of the genome of this second symbiont and found that it encoded at least some of the essential amino acid synthesis pathways that could make the needed amino acids for the host. And we stopped there, published a paper in PLoS Biology proposing the existence of a dual symbiosis with one symbiont making vitamins and cofactors and the other making amino acids, and moved on to other things.

Now in this new paper, Nancy's lab has returned to this symbioses and has finished the genome of Sulcia (the genome is available here in Genbank). And the story just gets cooler and cooler. With this complete genome they get a more detailed picture of the symbiosis than we were able to obtain, and are able to really reconstruct the whole system (and correct some mistakes we had made in our paper). My favorite thing in their paper is Figure 3 which you can find here (I am not sure about the PNAS policy of putting the image in my blog since this does not seem to be an Open article). This figure shows their reconstruction of what could be called to community metabolism. Interestingly it appears the symbionts depend on each other and are not just passing things on to the host separately.

Another important aspect of their paper is that it is the first (as far as I know) example of a genome being finished using a combination of the two hot new sequencing methods - 454/Roche and Illumina/Solexa. Basically they used the Roche/454 method to provide deep coverage of the Sulcia genome and then used Illumina/Solexa sequencing to get accurate sequence data for the types of sequence for which the Roche method does not work well.

So - check out the paper in PNAS. You won't regret it.

An interactive Tree of Life (Web Tool)

Thanks to Michael Ferrari who has pointed out a cool new phylogenetics visualization tool called the "Interactive Tree of Life"

Put out (I believe) by Peer Bork's group, this tool allows users to upload their own trees and then view and manipulate them from anywhere. Seems like Peer is trying to become the Google of phylogenetics.

Wanna sequence a microbial genome? Try applying to this NSF-USDA

Contrary to rumors that I had heard (and I confess was spreading too) the NSF and USDA have announced the continuation of their Microbial Genome Sequencing program. This is by far and away my favorite grant program pretty much ever. I have gotten funding for most of my favorite projects through this program. So - I hate to bring in competition, but I thought I should post an announcement here:

Microbial Genome Sequencing Program FY2008
As a collaborative, interagency effort, the National Science Foundation (NSF), and the Cooperative State Research, Education, and Extension Service (CSREES) of the U.S. Department of Agriculture invite research proposals (i) to support high-throughput sequencing of the genomes of microorganisms, and (ii) to develop and implement strategies, tools and technologies to make currently available genome sequences more valuable to the user community.

Full Proposal Deadline: February 19, 2008

The link for the solicitation should be up later today at:
http://www.nsf.gov/publications/pub_summ.jsp?ods_key=nsf08511

Personal Genome Project seeking volunteers

The Personal Genome Project is seeking volunteers. The project would sequence (at least part of) your genome. In exchange you would agree to have the data released openly and also have some data about you released as well. I think it this could become a phenomenal medical resource and I am happy some people are volunteering for this. I probably would not do it myself - mostly out of concern for the privacy of my children and relatives. But hey - if you want to do it - all the power to you. Go to their website to sign up.

New Gardens and Art in the Davis Arboretum

Just a quick posting here. Went for a walk yesterday in the Davis arboretum and saw some nice new artwork and a new garden over near the end of the path. Here are some pictures.

Metagenomics leads to discovery of smallest primate

Check out the post at Suicyte Notes on the discovery of a very very small novel primate from analyzing metagenomic data. Man, metagenomics rocks.

New metagenomics software available

A new publication in BMC Bioinformatics by Eppley et al. is available describing Strainer. Strainer is a metagenomics analysis software package focused on population genetics, from the Banfield lab. The software is available here.

Their summary of the software:

Background
Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes.

Results
We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events.

Conclusions
The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.

How to keep track of genome projects - GOLD - Genomes Online Database

A new paper on GOLD - the Genomes On Line Database has been published in Nucleic Acids Research. GOLD is an amazing resource for those interested in microbial genomes ... there are so many genome projects out there that it is VERY hard to keep track of them. GOLD does this for you.

Plus it has data organized in nice ways (like by phylogenetic trees) and you can also download all the information. If you want a nice survey of genome projects, check out the statistics page.

Adaptationomics Award #2 - Washington Post and David Brown

This is a bit late, but I am now giving out my second "Adaptationomics Award" to David Brown, for his article in the Washington Post on "How science is rewriting the book of genes." This award is for somehow misusing genomics to push forward ideas that are excessively adaptationist (i.e., somehow claiming that something must be adaptive simply because it is observed to exist). I have given out one before (see here).

The article by Brown itself reports on some moderately recent changes in human genetics. Among the items discussed are "junk DNA", alternative splicing, and "inefficiencies" in genetic machinery. Some of the discussion in the article in interesting. But it is the last topic, the "inefficiencies" that really gets to me.

It starts off

"It used to be a rule -- actually, more of an assumption -- that the genetic machinery of living organisms was never intentionally wasteful or inaccurate. It turns out this isn't always true, either."

First of all, there is no "intention" in genetic machinery (or by implication, in evolution). I note that this is one of the hallmarks of adaptationism (and adaptationomics) - the anthropomorphizing of DNA.

Then Brown describes some recent papers suggesting that for some protein coding genes, there are (get ready for this) phenotypic differences in alleles that have only synonymous differences. That is, these alleles code for the same protein but use different codons for certain amino acids. Now, never mind that it has been known for 20+ years that codon usage is under selection in some cases (e.g., see papers by Hiroshi Akashi such as this one).

What gets me here is that the discussion that centers on the notion that some synonymous differences are either "inefficient" or "wasteful" and that there MUST be an explanation as to why a cell would do this.

He asks

" Why would evolution favor this built-in inefficiency?"

No - nowhere in the discussion has there been any evidence presented that evolution "favors" this kind of thing (by favor, I assume he means something akin to positive selection, but emotions make evolution so much closer no?). So it would be better to ask "Is this under positive selection" or, in emotional terms "Does evolution favor this?"

And the next discussion is even more adaptationistic. Here he discusses "nonsense mediated decay" whereby translation is terminated in the middle of making a protein. Brown then asserts that this wastefulness must have some adaptive explanation. And he does this by a painful analogy:

Think of a cell as containing a factory that makes both tractors and tanks. In peacetime, few tanks are made, but the knowledge and capacity is never lost. Most tanks are built halfway and then broken down, with the parts sent back up the assembly line for reuse.

But then comes great stress; say the cell is experiencing too much heat or not enough oxygen or food. That's where nonsense-mediated decay (NMD) comes into play. It's suddenly wartime, but instead of refitting the factory to make tanks, all the cell has to do is give the order to take the half-made tanks to completion.

Umm -- I do not even know where to begin with this. Is he implying that the ribosome needs to keep its wheels greased in order to know how to make the protein when it is needed? I am not clean. But regardless, the implication is clear --- there MUST be an adaptive explanation for all examples of NMD. Just in case oyu did not see the push for adaptationism --- the end sentence reminds us:

Just the right amount of wrong instructions and wasteful habits -- that's what evolution has built into all of us.

Ick. And thus my Adaptationomics award #2.

Now THAT is personal genomics

Those interested in the coming personal genomics world should check out Amy Harmon's article in the New York Times. Harmon discusses her own foray into getting sampled herself - a personal story on personal genomics. Oh - so ripe for word play. For a good discussion of the paper and some of the related issues see Matthew Herper's blog here.

I personally think the whole field has rushed a wee bit ahead of the science (which reminds me to point out - if you are looking for a new career, I think genetic/genomic counselor is going to be one of the hottest jobs of the future). But nevertheless, I plan to get tested, so I must not think the science is that off.

For other interesting discussions see

• The Quantified Self
• Deepak Singh
• Greg Laden

Open Access dinosaurs and way to go Paul Sereno

Well, I met Paul Sereno, the dinosaur hunter, for the first time at SciFoo camp (for more about that see here). I confess I was skeptical when he said he was committed to Open Access. But now he has really proven his OA chops. He has a new paper in PLoS One on some friggin cool dinosaur fossils.

The paper is "Structural Extremes in a Cretaceous Dinosaur" by Paul C. Sereno^1*, Jeffrey A. Wilson², Lawrence M. Witmer³, John A. Whitlock², Abdoulaye Maga⁴, Oumarou Ide⁴, Timothy A. Rowe⁵

Check it out at PLoS One.

Excellent Free Science Education Videos from HHMI

I just got in the mail some of the free science education DVDs I ordered from the Howard Hughes Medical Institute. The first one I have looked at is quite good (it is on evolution, of course). I recommend people browse the HHMI catalog here. These could be useful for students as well as for actual courses.

And of course, the best part, they are free.

Out of the ordinary posting - Check out the Predatory Lending Association Website

In the spirit of Craig Venter sequencing his own microbiome and the the PISD spoof of PRISM, which I have written about before, people should check out the new Predatory Lending Association website.

Judgement Day - Tonight on PBS

Tonight ()Tuesday, 11/13, from 8-10 pm) NOVA is running a documentary on the Kitzmiller vs. Dover evolution trial.

For more detail see the NOVA site.

PS - Thanks to Doug Rusch for pointing this out.

Treat this flu with antibiotics

A big problem these days is the overuse of antibiotics. One of the reasons antibiotics are overused is that people use them for viral illnesses not bacterial ones. But the NY Times Book Review has an example of a "flu virus" that if you have it, you should use antibiotics on. In a review of Craig Venter's new book in this Sunday's Times, Peter Dizikes refers to one of Venter's achievements in sequencing the first genome:

But he never found a comfortable place in the fledgling government project to chart the human genome and in 1992 joined a new private group, the Institute for Genomic Research. There, Venter and colleagues became the first researchers to chart the whole genome of any organism (the flu virus), among other landmarks, and refined a technique allowing scientists to piece together genomes from small bits of DNA, minimizing the ponderous genetic surveying then in use.

Fine and dandy, except it was not the flu virus, but a bacterium sometimes referred to as H. flu, also known as H. influenzae. It does cause an illness that can resemble the flu, but it is definitely a bacterium. If the Times gets it wrong, one cannot really expect the public to get it right can we? I am not sure what the solution here is, but maybe we should stop saying things are "flu-like" when we mean "flu-like symptoms." Or maybe we need better diagnostics for the home, so that people can figure out what they have more easily.

Prejudice and DNA

There is an article in this Sundays' New York Times by Amy Harmon about prejudice's possibly being revived and stoked by the oncoming personal genomics revolution. I think there is no doubt this is coming. The problem is really two fold in my opinion.

First, as reflected in the story, it is pretty clear that despite the claims of some researchers who seem like they simply want to avoid the subject, we will start to see more findings of genetic differences among populations. . For example, Marc Feldman from Stanford (who by the way was on my thesis committee) is quoted as saying

“There are clear differences between people of different continental ancestries,” said Marcus W. Feldman, a professor of biological sciences at Stanford University

The second part of the problem, in my opinion, is an extension of something I complain about routinely here - the overselling of genomics. In this case we have a double effect. First, is the effect of "DNA." Somehow, when analysis of DNA is part of a study or story, people seem to overestimate its importance. Then comes the genomics-effect. Since genomics is about "all" the DNA, it carries even more weight than normal DNA studies. On the one hand, this is reasonable, as genomics does give a more thorough picture than past genetic studies. But on the other hand, genomics gets oversold as somehow telling the whole story. In this regard I buy the argument in the Harmon story reflected in the quote by David Altschuler that

it is so clear that the economic and social and educational differences have so much more influence than genes. People just somehow fixate on genetics, even if the influence is very small.”

I certainly think personal genomics is going to reveal lots of interesting connections between genes and various phenotypes. But there is no doubt data from personal genomics will lead to the amplification of prejudices and biases already present.

Nice pro open access editorial in The Journal Times

The Journal Times has a new editorial in support of Open Access publishing.

Key phrase:

While open access to information won’t eliminate the development work, by continuing to limit public access to the information for which the public has paid, we risk losing that vital moment of inspiration which leads to something that makes our lives easier, or healthier, or to a whole new industry. It’s not a risk we can afford to keep taking

I could not agree more.

Population genomics gets real in Drosophila

There has been lots and lots of talk about "population genomics" in the last few years. For microbes, people have been doing this type of genome wide survey within populations for some time. But for multicellular organisms there have been only a few studies and most of these were limited in scope. Now comes a in depth study of Drosophila simulans published in PLoS Biology. This project, led by colleagues of mine at UC Davis (David Begun is first author, Chuck Langley is senior author) did "light" whole genome sequencing (at the Washington University Genome Sequencing Center) of seven lines of D. simulans and one line of D. yakuba.

There is lots of interesting population genomics, population genetics and evolutionary analysis in this paper. If anyone out there is interested in personal genomics or human population genomics in any way, it is worth checking out this paper as a model for what can be done in multicellular eukaryotes.

New from the Public Library of Science - PLoS Neglected Tropical Diseases

Well, obviously most people will not want to get one of these "Neglected" tropical diseases, but if you do, one would bet you will be surfing the web trinyg to find out more about it.

And alas, most of the research on such diseases is hidden behind journal restrictions. That was, until now.

Check out the PLoS NTDS Web Site to or Bora's blog to learn more.

Also check out the editorial by Margaret Chan, the Director General of the World Health Organization. She says

The launch of PLoS Neglected Tropical Diseases marks yet another turning point in the long and notorious history of some of humanity's oldest diseases. ....

The free availability of leading research articles will benefit decision-makers and diseases control managers worldwide. It will also motivate scientists, both in developing and developed countries.

There is also an interesting population genetic study of Leptospira interrogans.

Good to see this journal out there.

SF Gate Column on "You big, fat pile of bacteria"

There is an interesting column on SFGate.com about microbes living in and on people. By Mark Morford, SF Gate Columnist

He talks about eating earthworms as a kid.

Of course, it turns out, biologically speaking, that big, dirty earth-muncher probably did my immune system, my intestinal tract and all the happy bacteria therein a world of good. It's true.

Furthermore he says

we as an overpampered culture are probably not getting enough nasty buggy immune-system-boosting microbes in our diet, in our meats, in our mouths. And therefore we should probably, you know, eat a bit more crap.

I am not sure I would go as far as suggesting eating crap, but I second the notion that we as a society have to stop being obsessed with getting rid of all bacteria. Bacteria are overall good.