Archive for July, 2006

Introgression in wolves & dogs

By Razib Khan | July 31, 2006 10:25 pm

Apropos of our discussion of evolution and dogs, and introgression, here is a new paper I stumbled upon in Molecular Ecology, Detecting introgressive hybridization between free-ranging domestic dogs and wild wolves (Canis lupus) by admixture linkage disequilibrium analysis. Linkage disequilibrium is basically the non-random association of alleles across loci. For example, imagine that you have alleles A1 and A2 at locus A, and B1 and B2 at locus B. Imagine that these two locii are on separate chromosomes (just to make it clearer, though they don’t have to be). In a randomly mating population A1 and B1 or B2 should not be correlated together in the same organism’s genome anymore than you would expected based on their frequencies. But sometimes gene-gene interactions result in the coadapted fitness of two alleles, so that A1 + B1 is more fit than A1 + B2 (imagine, if you will, higher spontaneous abortion of fetuses with A1 + B2). Nevertheless, today linkage disequilibrium is more often used to study the impact of selective and demographic forces operant upon the genome across the span of history than coadapted complexes. A strong powerful selective event on one locus, say Z, might drag adjacent regions of the genome along via a “hitch-hiking” event during the selection sweep (this is why researchers tend to look around the region coding for lactase to confirm that their technique works). As time passes recombination should break apart linkage disequilibrium, so the extent of the current associations can be highly informative. And so it is with this paper.

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CATEGORIZED UNDER: Genetics

All the Science Blogs fit to blog (about)

By Razib Khan | July 31, 2006 10:12 pm

Don’t have time to read all the Science Blogs? Don’t worry, Bora’s put together a literal tapas of selections, part I, part II, part III and part IV.

CATEGORIZED UNDER: Blog

Baruch Spinoza, the first of "us"

By Razib Khan | July 31, 2006 10:04 am

Alex points me to this Rebecca Goldstein op-ed in The New York Times marking the excommunication of Baruch Spinoza. I am actually reading Goldstein’s biography of Spinoza, Betraying Spinoza: The Renegade Jew Who Gave Us Modernity, and just finished Matthew Stewart’s The Courtier and the Heretic: Leibniz, Spinoza, and the Fate of God in the Modern World. Most of you probably know the name Spinoza from Einstein’s assertion that he “believe in Spinoza’s God,” the pantheistic entity which suffused existence itself.
Update: James H. has more at The Island of Doubt.

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CATEGORIZED UNDER: Religion

Bonus Kat

By Razib Khan | July 28, 2006 10:57 am

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CATEGORIZED UNDER: Genetics

Introgression related papers

By Razib Khan | July 27, 2006 11:11 pm

I suspect the basic general process of introgression is clear to most of you, though I will get back to it soon. But here are some papers with candidate genes (click “related” for more references):
RRM2P4, <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=14513410&query_hl=5&itool=pubmed_docsum"dystrophin, xp21.1 and 17q21.31. Also, I should add in the amusing evidence that archaics and moderns had sexual intercourse (amusing, but scientific nonetheless). Finally, a more theoretical paper that just came out.
There are other possibilities, like MC1R, but that could also be frequency dependent selection. More to come soon, I promise….

CATEGORIZED UNDER: Genetics

SEED on grandmothers

By Razib Khan | July 27, 2006 10:42 pm

Seed has a piece on the discoveries relating to menopause and its importance to the “Grandmother Hypothesis.” Unlike male decline in fertility menopause is a specific and deliberate sequence of proactive processes by the female body to shut down reproductive capacity. Something like this is almost certainly functionally significant, and anthropological work which seems to show cross-cultural evidence of lower infant mortality in the presence of a maternal grandmother in the household is another important avenue in the overall program.

CATEGORIZED UNDER: Genetics

Doing your homework

By Razib Khan | July 27, 2006 8:09 pm

Below the fold, readers, this is what I mean by doing your technical homework.

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CATEGORIZED UNDER: Blog

Introgression, what's in a word?

By Razib Khan | July 26, 2006 10:56 pm

Here is the definition from Wiki:

Introgression is a term used in genetics, particularly plant genetics, to describe the movement of a gene from one species into the gene pool of another by backcrossing an interspecific hybrid with one of its parents. Introgression of a transgene from a transgenic plant to a wild relative as the result of a successful hybridization is an example.

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CATEGORIZED UNDER: Genetics

2 X 2 Design (Adoption + IQ)

By Razib Khan | July 26, 2006 10:22 pm

Since Jonah posted on the French IQ study profiled in The New York Times Magazine, I thought I’d point to an analysis of the data by a co-thug over at GNXP Classic. Warning, if 2 X 2 ANOVA bores you, prepare to be bored. Otherwise, enjoy.
Update: Alex has more analysis.

CATEGORIZED UNDER: Genetics

Limelight on a stupid commenter

By Razib Khan | July 26, 2006 9:31 pm

Update: It maybe that “idiot commenter” speaks English as a second language , and so was not expressing his skepticism with sufficient nuance for my taste. That being said, this post stands as a warning to those who would waste my time.
-God Bless, Razib
This commenter starts out by admitting that he didn’t follow all my reasoning in my post on Neandertal admixture, but proceeds to take a patronizing tone. What bullshit. I know that some of my posts make recourse to terms which are a bit technical, in fact, terms which I myself didn’t grasp well until a few years ago, and whose conceptual implications and structure were somewhat fuzzy until only recently. But, it really isn’t rocket science, and the basic analytic framework isn’t much beyond 8th grade algebra, at least in its most general and broadest scope.

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CATEGORIZED UNDER: Genetics

Logical consistency is irreligious

By Razib Khan | July 25, 2006 9:42 pm

Jason says in a post which addresses the religion & science issue:

Either the Bible is the holy and inerrant word of God, or it is an ancient document written by people with no more claim to authority than any other document that has survived from that time. It’s hard to find a logically consistent middle ground.

I regularly made this argument until a few years ago. It generally remains my own personal view, though my estimation of the likelihood of the first possibility is so low that I don’t know if it is judgement that is worth making when social considerations are removed. I stopped making the argument Jason is pointing to when I read this:

disconforming evidence only seems to make believers try harder to understand the deeper truth and to strengthen religious beliefs. For example, after reading a bogus article on a new finding from the Dead Sea Scrolls that seemed to contradict Christian doctrine, religious believers who also believed the story reported their religious beliefs reinforced.

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CATEGORIZED UNDER: Religion

I think Stephen Jay Gould would be appalled

By Razib Khan | July 24, 2006 10:35 pm

I am a little unsure whether this article in The Washington Post titled And the Evolutionary Beat Goes On . . ., beginning with the sentence “Stephen Jay Gould would have been pleased,” is a subtle joke or not. The journalist has a science background, and has even covered the evolution “controversy,” but that doesn’t really prepare you to dive into the brand new world of evolutionary genomics.
Here is the short of it. First, biases on the table, to say that I am not a Gouldian is charitable. I would argue that evidence of recent human evolution and diversification seems to be positively un-Gouldian. Here is the Wiki summary of Gould’s ideas in Gould’s words:

A new species can arise when a small segment of the ancestral population is isolated at the periphery of the ancestral range. Large, stable central populations exert a strong homogenizing influence. New and favorable mutations are diluted by the sheer bulk of the population through which they must spread. They may build slowly in frequency, but changing environments usually cancel their selective value long before they reach fixation. Thus, phyletic transformation in large populations should be very rare-as the fossil record proclaims. But small, peripherally isolated groups are cut off from their parental stock. They live as tiny populations in geographic corners of the ancestral range. Selective pressures are usually intense because peripheries mark the edge of ecological tolerance for ancestral forms. Favorable variations spread quickly. Small peripheral isolates are a laboratory of evolutionary change.

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CATEGORIZED UNDER: Genetics

10 Questions with Charles Murray

By Razib Khan | July 24, 2006 9:00 am

Over at GNXP Classic our resident virgin Matt McIntosh poses 10 questions for Charles Murray, author of The Bell Curve.

CATEGORIZED UNDER: Blog

Fisher, Wright and evolution of dominance

By Razib Khan | July 23, 2006 4:26 pm

Robert Skipper has an enormous post on R.A. Fisher & Sewall Wright’s theories of dominance. I think Wright was more in the right on this issue, remember, it is easier to break (lose function) than make (gain function).

CATEGORIZED UNDER: Genetics

Politics & foreign policy

By Razib Khan | July 23, 2006 2:44 pm

More unsolicited opinion on current events from me over at Nation Building.

CATEGORIZED UNDER: Politics

The Genetical Theory of Natural Selection, preface & chapter 1

By Razib Khan | July 22, 2006 6:13 pm

I have mentioned a few times that I am re-reading The Genetical Theory of Natural Selection by R.A. Fisher. I read it a few years back when I didn’t know anything about evolutionary theory, so I believe this run through will be more frutiful. For those of you who don’t know, R.A. Fisher was possibly the most important evolutionary biologist, and probably most important statistician, of the 20th century. Along with Sewall Wright and J.B.S. Haldane he created the field of theoretical population genetics which the Neo-Darwinian Synthesis takes as an a priori starting point. I know that in the current craze over evolutionary developmental biology, “evo-devo,” and the importance given over to the modulation of gene expression, some are indicating that the old paradigms are being overthrown. I don’t believe this is true, and in fact, like James F. Crow I believe that new empirical techniques from genomics will revive the importance of theoretical insights which for many decades remained untestable.

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CATEGORIZED UNDER: Genetics

Bumping uglies with the Neandertal (aka but they did interbreed!)

By Razib Khan | July 21, 2006 10:08 pm

Update: Update at the bottom….
In reference to the sequencing of the Neandertal genome, Kambiz at Anthropology.net states:

I have one little gripe with the New York Times article. Wade quotes a geneticist, Dr. Bruce Lahn saying there is, “evidence from the human genome suggests some interbreeding with an archaic species.” Has he not read Paabo’s paper 2004 PLoS paper, “No Evidence of Neandertal mtDNA Contribution to Early Modern Humans?” There is significant mtDNA evidence to stongly conclude that humans and Neandertals did not interbread directly.

I left a comment on that website, but I will elaborate a bit here. In reference to Bruce Lahn, he almost certainly has read that paper, but,
1) mtDNA can take you only so far.
2) Lahn is implicitly pushing a new paradigm in how we view human origins, a “genocentric” perspective, to borrow a phrase.
To understand in detail about why mtDNA must be viewed with caution, read RPM’s take down of its use in molecular ecology, or John Hawks’ post which addresses the issue from a paleoanthropological angle. If you want it short and sweet: one locus isn’t going to tell you the whole story, and that is more and more true as you push back into time. Reading the mtDNA lineage is reading the mtDNA lineage, not the sum totality of our evolutionary genomic history.

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CATEGORIZED UNDER: Evolution

Mendel's Garden is up!

By Razib Khan | July 21, 2006 2:18 pm

Mendel’s Garden is up!

CATEGORIZED UNDER: Genetics

Definitive Neandertal sequencing post

By Razib Khan | July 21, 2006 12:48 pm

Not here, over at John Hawks’.

CATEGORIZED UNDER: Evolution

Katz in 100 degree heat

By Razib Khan | July 21, 2006 11:36 am

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CATEGORIZED UNDER: Blog
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