Friday, December 28, 2007
Why "neglected tropical diseases" are going to bite us in the *$
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
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.
Wednesday, December 26, 2007
Happy Hollidays Open Access Movement
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
Wednesday, December 19, 2007
NIH wants proposals on the human microbiome ...
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)
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
* Development of New tools for Computational Analysis of Human Microbiome
Project Data (R21)
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
* Development of New Technologies Needed for Studying the Human Microbiome
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
* Development of New Technologies Needed for Studying the Human Microbiome
* NIH Roadmap Initiatives
* Application Receipt Date(s): February 15, 2008
Phylogenomics makes the big time --- University of Manitoba seeking a "Chair" in Phylogenomics
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
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?
Friday, December 07, 2007
Survival of the fittest M&Ms
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
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.
Tuesday, December 04, 2007
Sharpshooters, dual symbioses and new ways to sequence a genome
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.
Monday, December 03, 2007
An interactive Tree of Life (Web Tool)
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
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:
Saturday, December 01, 2007
Personal Genome Project seeking volunteers
Wednesday, November 21, 2007
New Gardens and Art in the Davis Arboretum
Tuesday, November 20, 2007
Metagenomics leads to discovery of smallest primate
Monday, November 19, 2007
New metagenomics software available
Their summary of the software:
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.
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.
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
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.
Saturday, November 17, 2007
Adaptationomics Award #2 - Washington Post and David Brown
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.
" 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
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
Thursday, November 15, 2007
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. Sereno1*, 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
And of course, the best part, they are free.
Tuesday, November 13, 2007
Out of the ordinary posting - Check out the Predatory Lending Association Website
Judgement Day - Tonight on PBS
For more detail see the NOVA site.
PS - Thanks to Doug Rusch for pointing this out.
Sunday, November 11, 2007
Treat this flu with antibiotics
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.
Saturday, November 10, 2007
Prejudice and DNA
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 UniversityThe 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.
Tuesday, November 06, 2007
Nice pro open access editorial in The Journal Times
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 takingI could not agree more.
Population genomics gets real in Drosophila
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.
Monday, November 05, 2007
New from the Public Library of Science - PLoS Neglected Tropical Diseases
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. ....There is also an interesting population genetic study of Leptospira interrogans.
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.
Good to see this journal out there.
Saturday, November 03, 2007
SF Gate Column on "You big, fat pile of bacteria"
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.
Wednesday, October 31, 2007
Venter on Colbert
Wanted - Good Microbiologist/Molecular Geneticist for UC Davis Section on Microbiology
MICROBIOLOGY AND MOLECULAR GENETICS
The Section of Microbiology, College of Biological Sciences, University of California, Davis, invites applications for two tenure-track positions at the level of Assistant Professor. This is a broadly based search for candidates working on bacterial, archaeal or eukaryotic systems (microbial and non-microbial). Candidates must have an outstanding record of achievement in research and will be expected to develop a strong, externally funded, research program in microbiology and/or molecular genetics. Successful candidates will be expected to participate in normal undergraduate and graduate teaching responsibilities. Department faculty members use microbial and non-microbial systems to study diverse research subjects ranging from environmental microbiology and bacterial gene regulation to single molecule studies of protein-DNA interaction and transcriptional control in mammalian cells. See http://microbiology.ucdavis.edu/ugfaculty.htm for descriptions of faculty research. Due to limits on laboratory space availability, one of the two positions must commence on or after January 1, 2009. Applicants should submit (1) a curriculum vitae, (2) a statement of current and proposed research, (3) copies of no more than two key publications, (4) a statement of teaching interests, and (5) arrange to have at least three letters of recommendation submitted. Applications will only be accepted online at http://microbiology.ucdavis.edu/. Please see the website for details.
While applications will be reviewed until the positions are filled, only applications completed by November 16, 2007 can be assured of full consideration. The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and a respect for differences.
Thursday, October 25, 2007
Ten Things I Love About Cold Spring Harbor Laboratory
- Dolan DNA Learning Center. A pioneer in many aspects of biotechnology and genomics education.
- Banbury Center. Just on the other side of the harbor from the main lab. The Banbury Campus is a truly spectacular place to hang out. I would know. I must have gone there a dozen times while working on my textbook. It has great places to walk to, like down a big hill to a secluded beach. And it is always peaceful and pleasant.
View Larger Map
- The main campus. Also a very pleasant place to hang out. Not quite as nice maybe as Banbury, but still very peaceful and conducive to science.
- Meetings and Courses. They have quite a collection of well known meetings and courses. Personally, I have a place near and dear to my heart for the main Genomes meeting, which I used to go to often. It was the place where I first talked about "Phylogenomics" as a means to predict gene function and this was how I got my first taste of the lab.
- Books from CSHL Press Of course I am a bit biased since they just published my evolution textbook, but the general quality of what they publish is very very very high. So many of these books have been key parts of my education including "A short course in bacterial genetics," "Molecular biology of the gene", "A genetic switch", The Archaeal Laboratory Manuals, "Molecular cloning: a laboratory manual" and many others. They publish some good journals too, but since they are not fully Open Access journals, I will not mention them here but hopefully these will become more Open as time goes on.
- Caumsett State Park. Just around the corner from the Banbury Campus it is a delightful location. When I was working on my textbook and living on the Banbury Campus I would try to bike to Caumsett every day for a break.
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- Biking down (and up) Snake Hill Road. See Google Map here. It is very steep and curvy and very fun and short enough to go up without killing yourself
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- Alex Gann. He was the original editor for my Evolution textbook. Conjure up an adjective to describe anybody you know. That adjective remarkably describes Alex too. He is anything and everything, good and bad, all rolled into one.
- Barbara McClintock. I am not sure what it is about her that is so fascinating but her persistence about jumping genes is awe inspiring. And of course, she was right about something very important when lots of people told her she was wrong.
- The lab was named after a Billy Joel album. How cool is that?
Wednesday, October 24, 2007
Microbial genomics and Metagenomics workshop
The U.S. Department of Energy Joint Genome Institute (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics, in Walnut Creek, California, January 7-11, 2008. The workshop includes two days of intensive seminars and three days of hands-on tutorials. The goal is to provide training in microbial genomic and metagenomic analysis and to demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research. Participation is limited to 40 attendees (graduate students, postdocs, and faculty or staff scientists). To register for the workshop, submit your application online from the registration page: http://www.jgi.doe.gov/meetings/mgm/
Note the Workshop is FREE. Yes that is right. FREE.
Saturday, October 20, 2007
URGENT - IF YOU SUPPORT OPEN ACCESS TO SCIENTIFIC LITERATURE - WRITE YOUR SENATOR NOW
URGENT CALL TO ACTION: Tell your Senator to OPPOSE amendments that strike or change the NIH public access provision in the FY08 Labor/HHS appropriations bill
The Senate is currently considering the FY08 Labor-HHS Bill, which includes a provision (already approved by the House of Representatives and the full Senate Appropriations Committee), that directs the NIH to change its Public Access Policy so that participation is required (rather than requested) for researchers, and ensures free, timely public access to articles resulting from NIH-funded research. On Friday, Senator Inhofe (R-OK), filed two amendments (#3416 and #3417), which call for the language to either be stricken from the bill, or modified in a way that would gravely limit the policy's effectiveness.
Amendment #3416 would eliminate the provision altogether. Amendment #3417 is likely to be presented to your Senator as a compromise that "balances" the needs of the public and of publishers. In reality, the current language in the NIH public access provision accomplishes that goal. Passage of either amendment would seriously undermine access to this important public resource, and damage the community's ability to advance scientific research and discovery.
Please contact your Senators TODAY and urge them to vote "NO" on amendments #3416 and #3417. (Contact must be made before close of business on Monday, October 22). A sample email is provided for your use below. Feel free to personalize it, explaining why public access is important to you and your institution. Contact information and a tool to email your Senator are online at http://www.taxpayeraccess.org/nih/2007senatecalltoaction.html. No time to write? Call the U.S. Capitol switchboard at (202) 224-3121 to be patched through to your Senate office.
If you have written in support before, or when you do so today, please inform the Alliance for Taxpayer Access. Contact Jennifer McLennan through email@example.com or by fax at (202) 872-0884.
Thanks for your continued efforts to support public access at the National Institutes of Health.
On behalf of [your organization], I strongly urge you to OPPOSE proposed Amendments #3416 and #3417 to the FY 2008 Labor, Health and Human Services and Education Appropriations bill (S.1710). These amendments would seriously impede public access to taxpayer-funded biomedical research, stifling critical advancements in lifesaving research and scientific discovery. The current bill language was carefully crafted to balance the needs of ALL stakeholders, and to ensure that the American public is able to fully realize our collective investment in science.
To ensure public access to medical research findings, language was included in the in the FY 2008 Labor, Health and Human Services, and Education Appropriations Bill directing the NIH to make a much-needed improvement to its Public Access Policy -- requiring that NIH-funded researchers deposit their manuscripts in the National Library of Medicine's online database to be made publicly available within one year of publication in a peer-reviewed journal. This change is supported by NIH Director Elias Zerhouni, and a broad coalition of educational institutions, scientific researchers, healthcare practitioners, publishers, patient groups, libraries, and student groups -- representing millions of taxpayers seeking to advance medical research.
Amendment #3416 would eliminate this important provision, leaving only a severely weakened, voluntary NIH policy in place. Under the voluntary policy (in place for more than two years) less than 5% of individual researchers have participated -- rendering the policy ineffective. The language in Amendment #3417 would place even further restrictions on the policy, ensuring that taxpayers - including doctors and scientists - are unable to take full advantage of this important public resource.
Supporting the current language in the FY08 LHHS Appropriations Bill is the best way to ensure that taxpayers' investment in NIH-funded research is used as effectively as possible. Taxpayer-funded NIH research belongs to the American public. They have paid for it, and it is for their benefit.
I urge you to join the millions of scientists, researchers, libraries, universities, and patient and consumer advocacy groups in supporting the current language in the FY08 LHHS Appropriations bill and require NIH grantees to deposit in PubMed Central final peer-reviewed manuscripts no later than 12 months following publication in a peer-reviewed journal. Vote NO on Amendments #3416 and #3417.
Thursday, October 18, 2007
Whose genome should Roche/454 sequence to make up for selecting Watson's?
Here are my top picks
- Condoleezza Rice. An absurdly powerful, smart, black woman.
- Francis Crick. Someone has to have some of his hair somewhere.
- Rosalind Franklin. Not sure about the hair. But wouldn't it be great if she was one of the reference genomes.
- Francis Collins. Apparently no love lost between Francis and Jim.
- Craig Venter. Sure his genome has been nearly completed. But why not do it again with another method.
Monday, October 15, 2007
Overselling genomics (and men) award #3 - Newsweek Magazine
- Eric Lander
- Leroy Hood
- Craig Venter
- David Botstein
- Svante Paabo
- Philip Sharp
- Rudolph Jaenisch
- Kari Stefansson
- George Church
- Jay Keasling
They couldn't come up with a single woman? Or anyone doing anything else? Or any new researchers? This whole thing is completely egregious. There are plenty of completely cool things going on in biology that have little if any connection to genomics, that are not men, and/or are not established researchers.
And to get the conversation going here are some people they could have considered to diversify in at least one dimension (i.e., the male versus female thing):
- Kristen Scott
- Hopi Hoekstra
- Pamela Bjorkman
- Philippa Marrack
- Elizabeth Blackburn
- Julie Theriot
- Susan Lindquist
- Andrea Brand
- Joan Steitz
- Lucy Shapiro
- Sharon Long
- Colleen Cavanaugh
- Cindy van Dover
- Mary Claire King
- Rita Colwell
- Claire Fraser
- Nancy Moran
- Katie Pollard
- Linda Partridge
- Sarah Otto
So - Newsweek - you are getting my third "Overselling Genomics Award" and on top of that a bonus "Overselling Men" award. All I can say is - what were you thinking?
Sunday, October 14, 2007
Check out Mendels Garden at DBIADW
Friday, October 12, 2007
Appendix story in need of an asterix and appendix and a retraction
That was the topic of a series of news stories and a press release last week that somehow I did not blog on even though Thomas Goetz sent me the story. I was busy at a conference mind you but this is such easy pickings. This has got to be one of the poorer science reporting jobs done in a while and also one of the most misleading press releases I have seen. In the press release there are a series of phrases that make it seem like the scientists have discovered a major function for the appendix:
Appendix Isn't Useless At All: It's A Safe House For Good BacteriAND
William Parker, Ph.D. is one of a team of scientists to discover that the appendix has a function -- protecting beneficial bacteria.
And the reporting seems to have bought this hook line and sinker. See
- The appendix does have a use – re-booting the gut
- Appendix: It’s not useless after all
- Scientists discover true function of appendix organ
- Purpose of Appendix Believed Found
- Study: Yes...your appendix has a purpose
We propose that the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogenThe key word here is "propose." In the paper, they do not actually really show direct evidence for any function. And the title of the journal should hint at this - the Journal of Theoretical Biology. It is a place for scientists to put out new hypotheses, including those that have little evidence behind them. Nothing is wrong with such a journal. Hypotheses are a good thing.
Sometimes things in this journal have lots of evidence and in other cases they do not. In this case I do not think they present any direct evidence and the evidence they present is at best circumstantial and unconvincing. Basically, they lay out a hypothesis that the appendix may have some role in the immune system. Then they highlight a further series of circumstantial connections and inferences to come to the idea that the appendix may have some role in harboring "beneficial" microbes in the gut.
It is an interesting theory. It could be true. But the evidence they present is very very circumstantial and weak at best. They seem to claim that stronger evidence would be impossible to obtain since doing experiments on humans is not easy. But given the large number of people who have had their appendices removed, one could actually do a retrospective study of how well such people recover from pathogen attacks or the use of antibiotics. Until such a study is done, it would be wrong to say these authors discovered anything. What they did is propose a hypothesis for a function of the appendix. The hypothesis might stimulate discussions and some research but lets not oversell it.
In many ways you could consider their hypothesis much like the hypothesis that microbial life existed on Mars. This Mars idea is plausible. But there is currently no evidence for it. Imagine if the reporters said "Life found on Mars" in relation to a paper proposing that life might have existed on Mars. The reporting here is no different - though the stories got it wrong. In part this is because the press release is so misleading. But reporters have got to go beyond the press release or the initial story. Just see Carl Zimmer's blog for a great example of bad reporting.
Genomics by Press Release Award #1
Yesterday, researchers in South Africa announced that they had sequenced the genome of a XDR strain of the bacterium (Mycobacterium tuberculosis) that causes TB. I sniffed around this story because someone who used to work for me, James Sakwa, was mentioned in some of the stories.
The stories proclaim how quickly the researchers were able to sequence this genome with quotes like
(It) took us just over a week, using other technology it would have taken up to a year," he told AFP.This sounded a lot like other claims of rapid genome sequencing ... and I was skeptical since just doing some shotgun sequencing, with whatever method, does not lead to a complete genome. Alas, it looks like my skepticism is valid. The AP reports
The complete genome sequencing data has not yet been shared with other scientists. Previous tuberculosis strains have already been mapped, and some experts are uncertain how quickly the research will result in new diagnostics or treatments.So - there is apparently no paper associated with their work. And the data is not being shared. So in that spirit, I am announcing here that I have sequenced the genome of
How Al Gore changed my life and Congratulations on a well deserved Novel Prize
Senator Al Gore '69 spoke to Science A-30 class (as well as many others) in the end of November. His main focus was change in the global environment (i.e greenhouse effect, pollution, ozone depletion, deforestation, etc.) and what can and should be done about such issues. Senator Gore's interest in the environment, now almost a crusade, was sparked in a class he took at Harvard from Prof. Ravel. Gore suggested that the first step that we as a nation, and as a species, must take is to recognize that there is a problem. He referred to the classical biology example of the frog in a pot of water. If the temperature of the water is increased rapidly then the frog will be leaping at the opportunity to get out. However, if the temperature of the pot is increased gradually the frog may not sense anything, and will cook in its own innocence. According to Gore, today's society is prone to such a way of thinking. Society is least likely to recognize those changes in the environment that occur over long periods of time. It is like the Far Side cartoon in which a caveman asks his friend if the ice wall looks a bit closer today.I went up and talked to Gore afterwards and found him truly inspiring. It was this discussion that helped guide me to start a new Environmental Issues journal at Harvard and to do various other things for Earth Day 1990. Anyway, all I can say is congratulations to Al Gore, a Nobel Prize well deserved for someone who has been working to help our planet for at least 20 years.
So, the first step is to recognize that changes are going on, and that they are more that just gradual, that they are completely new in quality and quantity. The main problem today as compared to two thousand years ago is that the changes are happening too fast. The population is increasing at a rate never seen before. Rapidly increasing levels of greenhouse gases may lead to changes in climate and temperature that will be too fast for many organisms to respond. Extinction rates, already higher than any time since the "great" dinosaur extinction, may increase even more as organisms get wiped out by the environmental changes. Ozone depletion over the antarctic may just be a warning of a decrease over the temperate and tropical areas. The subsequent increase in UV light levels at the surface of the earth could have catastrophic effects. Industrialists and many government officials suggest that "science" will be able to cure these problems in the future
This same type of graph can be shown for ozone depletion, deforestation, pollution, soil erosion, and species depletion. However, as long as their is a lack of consensus as to the amount of change, and to the degree that any of these changes will affect human's (especially those alive today), there will be little change in government policy. In essence, Gore says, we are doing what the frog did.
There are quite a few criticisms to Gore's approach. Technology, that wonderful thing that has brought us strip mining, and artificial hearts, may be able to, in the future, reverse some of those things we are doing now. So why limit growth, when we can clean up later. It's like when I was a kid, "But mom, I'll clean up after Tom and Jerry" knowing full well that I wouldn't and running the risk of getting attacked by one of the dust balls under my dresser. However, if I made a real mess, such as one that would stain something, I had to clean it up then and there. The problem is that everyone seems to think all of these processes that are taking place in the atmosphere are reversible when in fact they may not be. Species depletion clearly is not. And if the other processes are allowed to run amok, we will likely have one big mess on our hands.
UPDATE: Found my notes from his talk. I scanned them in and am posting here
Thursday, October 11, 2007
Biofools on Eye in the Sky
Monday, October 08, 2007
Ten things to NOT do at a conference
- Go way over your allotted time to speak. Even if the chair of a session lets you do this, don't. It is rude to the audience and to other speakers.
- Lack empathy for your audience. Take a few minutes to imagine what the audience might want to get from your talk. Some of the speakers here are much more concerned with what they will get from the presentation.
- Use a lot of slides with way way way too small text or images.
- Answer cell phone calls in the middle of the audience. Yes, that's right, scientists can be jackasses. Imagine that.
- Corner people who are on the way to the restroom. Let people go.
- Make an opening statement when asking questions like "That was a great talk" or "That was an interesting talk" or anything like that. Don't be a suckup. Just ask your question.
- Be rude to the meeting helpers when you forget something. Come on. If you are not registered for the meeting it is most likely that you screwed something up, not the meeting.
- Ask many follow up questions after your question. If you want to have a discussion, buy a beer for someone. If you have a straightforward question that is answerable - ask it. If you want to make a simple statement, fine. If you want to go on and on ... get a room.
- Write in your blog in the back of the room (hey, I did not say I was perfect).
- Have too little time for breaks. The best part of conferences is the coffee and other breaks. No need to have too many talks. Have lots of breaks.
I am sure there are other things to not do ... but these are those that come to mind right now.
GME 2007 - Getting feedback on PLoS ONe
Sunday, October 07, 2007
GME 2007 - Genomes, Medicine and the Environment
NOTE - I AM POSTING SOME NOTES IN THE COMMENTS ON THIS ENTRY.
|Opening Remarks, J. Craig Venter, Ph.D., JCVI|
|Colleen Cavanaugh, Ph.D., Harvard University - "Genomic Insights into Chemosynthetic Symbioses"|
|Nancy Moran, Ph.D., The University of Arizona - "Genomics of Symbiotic Bacterial Communities within Insects"|
|Hamilton Smith, M.D., J. Craig Venter Institute - "Toward a Minimal Cell"|
|Steve Briggs, Ph.D., University of California, San Diego - " Development and Application of Protein Profiling Methods"|
|Yuri Gorby, Ph.D., J. Craig Venter Institute - "Electromicrobiology: The Role of Bacterial Nanowires in Extracellular Electron Transfer"|
|Edward Bayer, Ph.D., Weizmann Institute of Science - "Bioengineering of Cellulosomes: Prospects for Conversion of Biomass to Bioenergy" |
|12:00-2:00||Lunch, Sunset Ballroom |
|John Heidelberg, Ph.D., University of Southern California - "Genomic, Metagenomic and Functional Analyses of Cyanobacteria from Hot-Spring Microbial Mats"|
|Gene Tyson, Ph.D., Massachusetts Institute of Technology - "Metatranscriptomic Analysis of Microbial Communities in the North Pacific Subtropical Gyre"|
|Syed Hashsham, Ph.D., Michigan State University - "Understanding Microbial Community Succession in Response to Substrate Shock using Roche 454 GS FLX Sequencing System"|
|David Schwartz, M.D., National Heart, Lung & Blood Institute Toxicology Program - "Environmental Genomics and Human Health"|
|Ren Bing, Ph.D., University of California, San Diego School of Medicine - " Annotating the Human Genome - a ChIP-chip Approach"|
|Russell M. Gordley, B.A., Scripps Research Institute - " Evolution of Programmable Zinc Finger-recombinases with Activity in Human Cells "|
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