genetics
grrlscientist | October 4, 2007tags: researchblogging.org, Brown paper wasp, Polistes fuscatus, hymenoptera, evolution, eusociality, social behavior
Brown paper wasp , Polistes fuscatus.
Fairport, New York, USA. 2003.
Many thanks to Alex Wild for sharing his amazing images here.
Thanks to Elizabeth Tibbetts for the species identification.
[larger view]
Eusociality, or "true social behavior", is the most extreme form of cooperative sociality known. Due to its seemingly altruistic nature, eusociality has provided many interesting challenges for evolutionary theory. Eusociality, as exemplified by ants, bees and wasps, is…
grrlscientist | October 3, 2007tags: researchblogging.org, treatment-emergent suicidal ideation, suicide, citalopram, celexa, SSRI, black box warning
Despite what the news might have you believe, it is quite rare for a depressed person to exhibit increased suicidal thinking after they have begun treatment with an SSRI, such as citalopram (celexa). According to the statistics, so-called "treatment-emergent suicidal ideation" occurs only in approximately 4% of all people taking citalopram, whereas this same phenomenon also occurs in 2% of all placebo-treated cases. However, in those unusual cases where suicidal ideation…
razib | October 3, 2007Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome:
Structural variation of the genome involves kilobase- to megabase-sized deletions, duplications, insertions, inversions, and complex combinations of rearrangements. We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify structural variants (SVs) ~3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an…
razib | October 2, 2007My ideas about skin color & diet aren't original. I am pretty sure that I originally read them in Great Human Diasporas by L.L. Cavalli-Sforza. Here's the extract:
In Europe the development of agriculture has lead to the spread of cereals as the primary foodstuff over the last ten thousand years. Unlike meat, particular fish liver, cereals contain no vitamin D. They do, however, contain a precursor taht becomes vitamin D if exposed to the ultraviolet light from the sun's rays absorbed through the skin. Cereal eaters can produce enough vitamin D to survive and grow normally if they are…
pharyngula | October 1, 2007
All of us mammals have pretty much the same set of genes, yet obviously there have to be some significant differences to differentiate a man from a mouse. What we currently think is a major source of morphological diversity is in the cis regulatory regions; that is, stretches of DNA outside the actual coding region of the gene that are responsible for switching the gene on and off. We might all have hair, but where we differ is when and where mice and men grow it on their bodies, and that is under the control of these regulatory elements.
A new paper by Fondon and Garner suggests that there…
razib | October 1, 2007Vitamin D deficiency and skin color are two biological topics I've focused on a lot. The latter may have a relationship to the former insofar as light skin is better at synthesizing Vitamin D at low radiation levels (i.e., at high latitudes). Additionally, some of the genes that are under recent natural selection (within the last 10,000 years), such as OCA2 & SLC24A5, are related to pigmentation (specifically, the lightening of skin or eye color). At my other blog I've reproduced some ethnographic data which shows deviation from expectation of skin color in various populations assuming…
pharyngula | October 1, 2007Casey Luskin has to be a bit of an embarrassment to the IDists…at least, he would be, if the IDists had anyone competent with whom to compare him. I tore down a previous example of Luskin's incompetence at genetics, and now he's gone and done it again. He complains about an article by Richard Dawkins that explains how gene duplication and divergence are processes that lead to the evolution of new information in the genome. Luskin, who I suspect has never taken a single biology class in his life, thinks he can rebut the story. He fails miserably in everything except revealing his own ignorance…
pharyngula | September 30, 2007Cosma has to go and show off with a magisterial demonstration of why he is the smartest man on the internet: he's written an exceptionally thorough description of heritability and IQ. It's not a light read (statistics and genetics!), but it's probably the most informative thing I've read in a month or more.
I'm sure I'm going to have to read it a few more times before I've absorbed it all.
razib | September 28, 2007This post is more of a personal note...here are three papers that are really cool must reads:
Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, et al. (2007) Localizing Recent Adaptive Evolution in the Human Genome. PLoS Genet 3(6): e90 doi:10.1371/journal.pgen.0030090
Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biol 4(3): e72 doi:10.1371/journal.pbio.0040072
Tang K, Thornton KR, Stoneking M (2007) A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome. PLoS Biol 5(7):…
razib | September 28, 2007Yesterday I put up a post where I attempted to use a visual analogy for what I believe might be evolutionary forces operative over short periods of time that result in phenotypic diversification across populations with recent common ancestry. But what about the flip side? In the case yesterday the basic genetic substratum, the preponderance of the genome, was not subject to powerful diversifying forces because only drift was presumably operating over short periods of time. It was on selectively salient slices of the genome where differences came into sharp focus quickly. But there is an…
razib | September 27, 2007In my post The new races of man I tried to offer a verbal exposition of my current thinking as to how and why human physical variation shows the patterns we see around us. In short, I believe that powerful selective forces have reshaped a subset of the human genome in similar and different ways across a range of populations over the past 10,000 years. Empirically, I would predict that the physical appearance we denote as stereotypically "Chinese" or "Swedish" or "West African" might be rather recent ecotypes, adapted to new circumstances, both environmental and cultural. The types we see…
razib | September 24, 2007The Boston Globe has a long piece titled DNA unraveled. With the subtitle like "A 'scientific revolution' is taking place, as researchers explore the genomic jungle" you know what to except, lots of adjectives and a healthy dollop of hyperbole. I guess I lean toward the side of the conservatives in the article, but ultimately it doesn't matter, nature always has the last laugh.
Update: Eye on DNA has a more thorough comment on this article and many others in the latest round up. Always worth checking out!
razib | September 22, 2007Well, you may not have blue eyes, but many people do. The post below suggests that there is still a lot of confusion on how eye color is inherited, but now in 2007 we are coming close to clearing up many issues. A paper which came out early this year, A Three-Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation (Open Access), suggests that about 3/4 of the eye color variation in Europeans (from pale blue to dark brown) can be explained by polymorphism around the OCA2 gene. In other words, eye color comes close to being a monogenic Mendelian…
razib | September 21, 2007Do any readers know of work which tracks the correlation between characteristics such as blonde hair and blue eyes (within population where these are extant at high frequencies, but not fixed)? I am also interested in geographic distributions. In part I'm interested in exotic combinations, for example, look below the fold....
clock | September 20, 2007Earlier studies have indicated that a gene called FOXP2, possibly involved in brain development, is extremely conserved in vertebrates, except for two notable mutations in humans. This finding suggested that this gene may in some way be involved in the evolution of language, and was thus dubbed by the popular press "the language gene". See, for instance, this and this for some recent research on the geographic variation of this gene (and related genes) and its relation to types of languages humans use (e.g., tonal vs. non-tonal). Furthermore, a mutation in this gene in humans results in…
razib | September 20, 2007I've talked about MHC a fair amount, mostly because of its evolutionary significance, so if you are interested in the topic Mystery Rays for Outer Space is starting a series ion the topic. Check out the first post. Also, PLOS Genetics has a new paper on MHC.
sporte | September 19, 2007But I'm certain that you will find some interesting things.
Mendel's Garden will be ready for harvest, here on Sunday, October 7th, and I need your help.
You won't need to stay on the path, but I would like you to submit your best genetics & molecular biology articles by midnight, Friday October 5th.
Either send your articles to me: digitalbio at gmail dot com
or use the handy-dandy submission form.
With your help, Mendel's Garden is certain to bloom with earthly delights.
razib | September 19, 2007From PLOS One, Gain-of-Function R225W Mutation in Human AMPKγ3 Causing Increased Glycogen and Decreased Triglyceride in Skeletal Muscle:
We have identified for the first time a mutation in the skeletal muscle-specific regulatory γ3 subunit of AMPK in humans. The γ3R225W mutation has significant functional effects as demonstrated by increases in basal and AMP-activated AMPK activities, increased muscle glycogen and decreased IMTG. Overall, these findings are consistent with an important regulatory role for AMPK γ3 in human muscle energy metabolism.
Costford SR, Kavaslar N, Ahituv N,…
razib | September 18, 2007Michael Lynch in Nature Reviews Genetics, The evolution of genetic networks by non-adaptive processes:
Although numerous investigators assume that the global features of genetic networks are moulded by natural selection, there has been no formal demonstration of the adaptive origin of any genetic network. This Analysis shows that many of the qualitative features of known transcriptional networks can arise readily through the non-adaptive processes of genetic drift, mutation and recombination, raising questions about whether natural selection is necessary or even sufficient for the origin of…