genetics
pharyngula | February 24, 2008The author of All-Too-Common Dissent has found a bizarre creationist on the web; this fellow, Randy Stimpson, isn't at all unusual, but he does represent well some common characteristics of creationists in general: arrogance, ignorance, and projection. He writes software, so he thinks we have to interpret the genome as a big program; he knows nothing about biology; and he thinks his expertise in an unrelated field means he knows better than biologists. And he freely admits it!
I am not a geneticist or a molecular biologist. In fact, I only know slightly more about DNA than the average college…
razib | February 23, 2008I'm 5 feet 8 inches tall. 1.73 meters. In the United States that's somewhat on the short side, most of the charts suggest I'm around the 30th percentile for white men. Of course, I'm not white. In any case, though I'm on the short side for the typical American male, I'm a giant in my family. My father is 5 feet 4 inches. My mother is around 5 feet now. They're possibly shorter than they were due to age, but they would have been short in the United States no matter what. As I was growing up, and surpassed my parents in my mid-teens, I assumed that their relative lack of height was a…
razib | February 23, 2008...yes, true. On a typical single locus (on some loci, such as SLC24A5, most of the variation is between groups). But that doesn't mean that you can't use genetics to differentiate population clusters. Here are 938 individuals (the points) from 51 world populations (the color of the points) displayed on a figure with the two largest principle components of the variation.
From Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. Also see Lewontin's Fallacy.
razib | February 23, 2008A new paper came out in Science this week, Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation, that's getting some media play. The second-to-last author is L. L. Cavalli-Sforza, and the general combination of means and ends on display in The History and Geography of Human Genes, is all over it. From the introduction:
We first studied genetic ancestry of each individual without using his/her population identity. This analysis considers each person's genome as having originated from K ancestral but unobserved populations whose contributions are described by K…
awild | February 22, 2008
The smallest insect I've ever photographed made the cover of the scientific journal Genetics this week. Encarsia pergandiella, an aphelinid wasp not even a millimeter long, was the subject of a study by Perlmann, Kelly, and Hunter documenting the reproductive consequences of infection by bacterial parasite.
The wasp lab is downstairs from ours, so it wasn't much trouble to schlep my equipment over for an afternoon session. The goal was to create a set of images to submit to the journal as potential covers, and I was more than happy to have the opportunity to shoot these charismatic little…
razib | February 20, 2008I haven't had time to read them, but John Hawks already commented:
A flush of papers this week (two today in Nature, one tomorrow in Science) describe new analyses of SNPs across the genome. Two of the papers sample SNPs in global samples numbering more than 500 individuals.
...and Yann Klimentidis.
clock | February 20, 2008Brendan Bohannan, Richard W. Castenholz, Jessica Green and their students and postdcos at the Center for Ecology and Evolutionary Biology at University of Oregon are currently doing a Journal Club on the PLoS ONE article The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples, which is part of the PLoS Global Ocean Sampling Collection. Please join in the discussion.
clock | February 19, 2008I tried to understand what DNA barcoding is, as everyone is talking about it. And I tried reading a couple of papers about it - I am a biologist, so I should have understood them, but nope, I was still in the dark.
So, what does one do? Waits for a science blogger to explain it. And so it happens, Karen explained it yesterday. I read it. Slowly and carefully. Only once. And I grokked it all!
gregladen | February 19, 2008Comparing living chimpanzees to living humans, in reference to the species that gave rise to these two closely related species, is one way to frame questions about the evolution of each species.
Generally, it is useful to address evolutionary questions by comparing two living species with the reconstructed "last common ancestor" (LCA) of those species. All of the similarities and differences between the LCA and the living form, in each lineage, represent evolutionary "stories" (that could even be worked out as hypotheses). Similarities indicate important, long-maintained adaptations, and…
mikethemadbiologist | February 15, 2008The editors of the journal Nature write:
(Nature 451, 745-746 (14 February 2008) | doi:10.1038/451745b; Published online 13 February 2008)
Genetics benefits at risk
A rogue senator needs to be bypassed.
Technology development guru George Church -- aka the information exhibitionist -- is playing a salutary social role with his Personal Genome Project. Church is in the process of gathering phenotypic data and sequencing portions of the genomes of ten volunteers, including himself.... He intends to study how the genes of these people -- all but one of whom have revealed their identities --…
razib | February 15, 2008Very cool paper, Adaptations to Climate in Candidate Genes for Common Metabolic Disorders (Open Access):
The human species inhabits a wide geographical range encompassing a diversity of climates, and adaptation to these climates likely played an important role in shaping genetic and phenotypic variation among populations. We hypothesized that spatially varying selective pressures related to climate shaped the frequencies of genetic variants in the energy metabolic pathway. To test this hypothesis, we examined patterns of genetic variation in 82 candidate genes for common metabolic disorders…
gregladen | February 12, 2008"Disease" is a big word. I'd like to address this question by focusing on the difference, or lack of difference, between a poison, a disease, and a yummy thing to eat. It turns out that they may all be the same. Yet different.
Phenylketonuria (fee-null-keet-o-noo-ria), mercifully also known as "PKU" (pee - kay - you) is a disorder in which the amino acid phenylalanine is not broken down by an enzyme (phenylalanine hydroxylase) and thus accumulates in the body as phenylpyruvic acid.
This is bad because phenylpyruvic acid interferes with normal development of neural tissues.
In western…
gregladen | February 10, 2008A very important and truly wonderful paper in Nature described a tour-de-force analysis of the Mammalian Evolutionary Record, and draws the following two important conclusions:
The diversification of the major groups of mammals occurred millions of years prior to the KT boundary event; and
The further diversification of these groups into the modern pattern of mammalian diversity occurred millions of years later than the KT boundary event.
[This is a repost from gregladen.com]
The KT boundary event is the moment in time when a ca. 10 km. diameter object going very fast hit the earth in the…
gregladen | February 9, 2008Bad News: It's a Big Lizard!!
According to a report noted in Evolving in Kansas, Komodo Dragons have been hatched in Sedgwick County without fertilization by a male.
There are two of them, both males. (Isn't that interesting?) ...
I think they should name them Jesus and Brian.
razib | February 7, 2008Innate social aptitudes of man is a controversial paper. As noted in the biographical introduction to it William D. Hamilton states that his friend Robert Trivers referred to it as the "fascist paper" (see Natural Selection and Social Theory for Trivers' perspective on his relationship with Hamilton). Not because Trivers himself thought it was fascist, rather, that was simply the perception of most who read and criticized the paper. The most vociferous critic was the biological anthropologist Sherwood L. Washburn (see Defenders of the Truth for a detailed exposition of Washburn's many…
gregladen | February 5, 2008Natural Selection is the key creative force in evolution. Natural selection, together with specific histories of populations (species) and adaptations, is responsible for the design of organisms. Most people have some idea of what Natural Selection is. However, it is easy to make conceptual errors when thinking about this important force of nature. One way to improve how we think about a concept like this is to carefully exam its formal definition.
[repost from gregladen.com]
In this post, we will do the following:
Discuss historical and contextual aspects of the term "Natural Selection…
razib | February 5, 2008I hope you have yesterday's post "out of your system." I will admit here that I don't know if I was particularly intelligible, but the prose and formalism of Hamilton's paper isn't exactly the picture of transparency. I find his later works much more intelligible; I suspect part of it has to do with the fact that Hamilton was responding and extending a tradition of evolutionary genetic modeling which reached back to R. A. Fisher and continued into the 40s and 50s. Reading a paper in 2008 which presupposes familiarity with a corpus of work from nearly three generations in the past can be a…
razib | February 4, 2008Inclusive fitness is something you've heard of before no doubt. J. B. S. Haldane, one of the greatest evolutionary geneticists of the 20th century, once quipped that he would "...lay down [his] life for two brothers or eight cousins," a succinct expression of the subset of this framework which is bracketed under kin selection. The logic is pretty self-evident, but in the 1960s a lonely graduate student in England, William D. Hamilton, toiled away attempting to formally explain the mystery of altruism. The fruit of his labors were two papers, The genetical evolution of social behaviour - I and…
gregladen | February 3, 2008There many ways of dividing up and categorizing Natural Selection. For example, there are the Natural Selection, Sexual Selection and Artificial Selection, and then there is the Modes of Selection (Stabilizing, Directional, and Disruptive) trichotomy.
We sense that these are good because they are "threes" and "three" is a magic number. Here, I'm focusing on the Mode Trichotomy, and asking that we consider that there are not three, but four modes of Natural Selection. This will cause tremors throughout the Evolutionary Theory community because Four is not a magic number, but so be it.
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