drinking the koolaid
Last year Kathryn O’Donnell and Jef Boeke published a review in Cell on Piwis and their role in maintaining transposon silencing in the germline genome. Together with an additional short review by Seto et. al. on Piwi proteins, a compelling picture of Piwis is just beginning to emerge … Read the rest of this entry »
I’ve been mentioned on Bio::Blogs #17 (the one Santa brought us)! This has provided the necessary motivation to mention some good posts I’ve read recently on Blogs:
Pedro Beltrao over at Public Rambling has a good post on the recent Cell paper by Lécuyer on Global Analysis of mRNA Localization. This paper has been on my radar because I’ve been working with the BioGRID lately and therefore thinking a bit about how to infer missing network connections.
The recent article at PLoS ONE by Keller and Harel entitled “Beyond the Gene” attracted some attention in the blogs I read. Jason Stajich over at Fungal Genomes and Comparative Genomics highlights some problems with the jargon introduced by Keller (post here) and RPM at evogen rips the article to shreds on a number of grounds, including the dreaded “adaptionist claptrap” (post here). I can honestly say that I got more from reading these two posts than from the article itself. (I reviewed a good article related to the “adaptionist claptrap” in my very first post.)
Finally, while not a literature review, I enjoyed the recent post Good Programming versus Biological Intuition over on Bioinformatics Zen.
Over the holidays I read a Review article entitled “From genotype to phenotype: buffering mechanisms and the storage of genetic information” by S.L. Rutherford.
Most models of evolution focus on DNA variation, either between individuals or between populations. However, reality is a bit more complicated, as most natural selection acts on variation among phenotypes rather than genotypes. The mapping from phenotype to genotype is complicated by the fact that genetic buffering allows for the buildup and storage of genetic variation in phenotypically normal populations.
“A more realistic picture of genetic networks will emerge from combining the perspectives of molecular and developmental genetics with those of population and evolutionary genetics. Understanding how specific genes are modulated relative to genetic and environmental variation is essential to understanding the course of evolution.”
Last week a review by Michael Lynch came out in Nature Reviews Genetics entitled, “The evolution of genetic networks by non-adaptive processes”.
In this review, Lynch takes a population genetics perspective on network evolution. Using relatively simple but powerful mathematical models of basic evolutionary processes, Lynch shows that many of the characteristic properties of networks (metabolic, developmental, and regulatory) that have been highly advertised lately (such as complexity, organization, robustness, evolvability, etc.) are just a basic consequence of the underlying nucleotide evolutionary process.
