Wednesday, November 21, 2007
Tuesday, November 20, 2007
Monday, November 19, 2007
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.
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
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.
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
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.
And of course, the best part, they are free.
Tuesday, November 13, 2007
Sunday, November 11, 2007
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
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
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.
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
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
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.