Archive for January, 2007

What science fiction writer am I?

By Razib Khan | January 27, 2007 5:36 pm

Pretty cool. Via Afarensis.

I am:
Arthur C. Clarke

Well known for nonfiction science writing and for early promotion of the effort toward space travel, his fiction was often grand and visionary.

Which science fiction writer are you?

CATEGORIZED UNDER: Blog

Anisogamy

By Razib Khan | January 26, 2007 6:08 pm

Matt has a “Basic Concepts” post on Anisogamy.

CATEGORIZED UNDER: Evolution

Kat

By Razib Khan | January 26, 2007 11:06 am

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CATEGORIZED UNDER: Blog

Basic concepts – linkage disequilibrium

By Razib Khan | January 24, 2007 11:35 am

Thinking about it today, I realized there is a “Basic Concept” that I think I should touch upon, and that is linkage disequilibrium (LD). Notice the wiki link? I do that whenever I mention LD because it is such an essential concept for some of the evolutionary ideas which I am interested in, but often not necessarily a transparent or clear one to the lay person.
chrom1.jpgIts lack of obviousness isn’t due to complexity, LD is pretty simple, rather there are particular background ideas which one needs to firmly have in mind before one can easily grasp it. For this reason I’ve placed an image of a chromosome to the left. LD is not a purely intrachromosomal concept, but, I believe a biophysical model is important in understanding it, so I will use this image for illustrative purposes in the following post. So, you know that the human genome is divided physically into chromosomes, and each chromosome consists of two sister strands of DNA, chromatids. As you see to the left diploid organisms have two copies of a gene, alleles, at each “locus.” A locus is obviously an abstract concept, it is basically a synonym for a gene. Assuming we have “gene” under our belts we can now conceive of a strand of DNA which is saturated with various genomic regions, introns, exons, intra and intergenic regions, etc. The details aren’t particularly relevant to LD, just remember that locus 1 and locus 2 on the same chromosomal strand are a particular physical distance apart.

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CATEGORIZED UNDER: Genetics

Species

By Razib Khan | January 24, 2007 1:16 am

John Wilkins has a long post on species concepts.

CATEGORIZED UNDER: Blog

Basic concepts – 8th grade math

By Razib Khan | January 23, 2007 11:03 am

Many fellow ScienceBloggers are doing a “Basic Concepts” series. Here are some of them:

Mean, Median, and Mode
Normal Distribution
Force
Gene
Central Dogma of Molecular Biology
Evolution
Clade

Instead of thinking up something new I’ve decided to repost a an older post where I cover the “basic” equations and models which I pretty much assume in many of my posts. The post below….

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CATEGORIZED UNDER: Uncategorized

W.D. Hamilton & group selection & ideology

By Razib Khan | January 22, 2007 11:57 pm

My post below, Group selection & the naturalistic fallacy, elicited some interesting comments. First, I mentinoed W.D. Hamilton’s allusion to a relationship between fascism & group selection. Here is what he said:

‘Liberal’ thinkers should realize from the outset that fervent ‘belief’ in evolution at the group level, and especially any idea that group selection obviates supposedly unnecesssary or non-existent harsh aspects of natural selection, actually starts them at once on a course that heads straight towards Fascist ideology….

(page 385, Defenders of the Truth)

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CATEGORIZED UNDER: Evolution

10 Questions for György Buzsáki

By Razib Khan | January 22, 2007 12:11 pm

amnestic does 10 Questions for György Buzsáki.

CATEGORIZED UNDER: Biology

Genetic stochasticity & environments

By Razib Khan | January 22, 2007 10:34 am

So I near the end of my survey of chapter 5 of Evolutionary Genetics: Concepts & Case Studies.1 Today, we address environmental variation, but I think sometimes the end is the beginning, so I quote:

Random environment models have many technical aspects…that make them difficult to analyze. As a result, they have ben largely ignored in population genetics. This is unfortunate as it is clear that environments do change and that adaptive evolution is driven by these changes.

The last sentence made me think, “No shit sherlock.” This is a pretty deep indictment of population genetics, since for many environmental fluctuation and it impact on allele frequencies is the heart of evolution. I don’t know much about ecological genetics myself, so the formalism was somewhat unfamiliar to me, but I will offer what seems to be the most perplexing equation derived from a single locus diallelic model assuming two selection coefficients (i.e., each allele is randomly affected by the environment):
E{Δp} = σ2epq(1/2 – p)
[update – this was a major transcription error, I think the confusion in the comments will be cleared up now]
This models the mean change in allele frequency for p, with σ2 representing the expected variance of the change, and q naturally being simply 1 – p. I’ll let the text express the peculiarity of the equation:

…when p 0 and when p > 1/2 E{Δ} < 0. This indicates that selection pushes p toward 1/2, on average…E{Δ} suggests that random changes in the fitnesses of a model that does not maintain polymorphism will turn it into a model of balancing selection that does maintain polymorphism

The issue is that selection coefficients associated with the alleles represented by p and q are random, as opposed to an overdominant scenario where the heterozygote, e.g., A1A2, is more fit than A1A1 & A2A2. In this case the maintenance of polymorphism fits our intuition insofar as one would expect that both alleles would persist to maintain an optimal frequency of the heterozygote. But the assumptions that this model started out with was not a case where the heterozygote exhibited an advantange, rather, it was one compatible with positive directional selection, which exhausts genetic variation over time. The author, John Gillespie, finds the results curious and perplexing.
One could make several inferences. Perhaps the model that, with its one locus and two alleles, is so simple that its assumptions deviate too far from the reality which it is trying to capture. The mathematics need further exploration and this may simply be a “quirk” which will be resolved later. Another possibility is that the model is telling us something real about nature, that we are missing a great deal in the population genetic models which are predicated on “bean bag genetics,” that nature’s contingent complexity can not be so easily parsed into a few elegant parameters. Fundamentally, I think the “salvation” lay in the empirical world, particular in computational genomics, which can expand beyond the over simplifications of one locus diallelic analytic models. We may lose the ability to define the world by a single equation, but the reality is that the biological world is riddled with so many exceptions that we may have to settle for a finite but reasonable numbef of sui generis models.
1- Previous posts: I II, III, IV & V.

CATEGORIZED UNDER: Genetics

Group selection & the naturalistic fallacy

By Razib Khan | January 21, 2007 6:38 pm

Over at Bora’s place he talks about a paper on group selection. In regards to the scientific idea and its broad relevance to evolutionary biology, I am mildly skeptical. That being said, this comment drew my attention:

While endorsing DS Wilson’s Unto Others, Richard Lewontin mentioned an unsavory aspect of group selection (NYROB, 10/22/98): namely, war is a mechanism of the differential survival and reproduction of whole groups. Out-group aggression goes hand in hand with in-group cooperation. It is very advisable to be mindful of the Naturalistic Fallacy when considering group selection.

The Naturalistic Fallacy derives from G.E. Moore’s examination of the assumption that what is “good” can be derivable from natural properties (e.g., physical pleasure sensation), and is often conflated with David Hume’s is-ought problem, the idea that what is is what ought, to be. Regardless of which meaning the commenter had in mind, I think the point was that outgroup vs. ingroup dynamics, and their somewhat nasty implications, should be kept in mind when examining the validity of group selection.

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CATEGORIZED UNDER: Evolution

Robert Trivers wins the Crafoord Prize

By Razib Khan | January 20, 2007 11:54 am

A reader just informed me that Bob Trivers just won the Crafoord Prize in bioscience! For those who would like to become more familiar with Trivers’ work, I highly recommend Natural Selection and Social Theory. Genes in Conflict is also a good read if you want some molecular level evolutionary exposition. Finally, Trivers looms large in both Mother Nature and Defenders of the Truth. If you don’t know anyting about Trivers, I suggest this Edge Special Event.
Robert Trivers introduced concepts such as reciprocal altruism in the 1970s which revolutionized social theory, and serve as the atomic units upon which higher order explanations of animal (and human) behavior often build. In Defenders of the Truth Ullica Segerstrale chronicles how Trivers was in many ways the “mad genius” (literally, he has bipolar disorder) behind E.O. Wilson leading up the publication of Sociobiology. In many ways Trivers’ approach in evolutionary biology is that of a neoclassical economist, reductionistic, logical and couched in simplifying formalisms. Of course this has its draw backs, but, I believe it is an essential base on which other models and paradigms may be scaffolded.

CATEGORIZED UNDER: Genetics

Katz

By Razib Khan | January 19, 2007 10:44 am

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CATEGORIZED UNDER: Blog

Sign up for A Week of Science

By Razib Khan | January 19, 2007 12:12 am

There is now a sign up page for A Week of Science. Basically I’ll take the feeds and load them up on Justscience.net with Feedpress the day before the 5th. You can see the current list here. You can insert the sign up page with this code into you’re own site (remove the styling if you wish of course):

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CATEGORIZED UNDER: Uncategorized

Steve Weinberg's brilliant ignorance

By Razib Khan | January 18, 2007 12:36 pm

PZ and John have commented on a Steve Weinberg review of The God Delusion. This prompts me to offer up a cheap reflection which I’ve been meaning to air since watching Beyond Belief 2006, Steve Weinberg was, to my eye, the most ignorant and complacent of all the speakers and panelists, while at the same time being likely the most incandescently brilliant of them all. Weinberg is a great physicist, but having him review The God Delusion is like giving Leon Kass The Party of Death. On a related note, over at The Secular Outpost, Taner Edis wonders if Sam Harris shouldn’t know something about the religions which he criticizes. Now, mind you, I do not tend to value theology very highly. Unlike other Nevilles I tend to fault Dawkins et. al. more for their lack of psychological sophistication than philosophical depth. But the point stands.
Addendum: Let me add that I can’t but feel some joy that a brilliant man such Steven Weinberg is an atheist, one of “my kind.” But I have to admit that that joy is diminished watching him engage someone like Scott Atran, who though lacking in the mental acuity and raw firepower of a Weinberg, knows the lay of the land (religion that is) well enough to make the mighty seem like fallen fools.

CATEGORIZED UNDER: Science

A week of Just Science, what it's about

By Razib Khan | January 18, 2007 12:06 am

RPM and Chris have hit most of the points in regards to the Just Science project. To be short, what it’s not about is anti-science. Just one week, that’s all. It certainly isn’t about traffic or comment response. It isn’t about ease of posting, expressing a clever opinion, but rather a tight exposition of a difficult concept. And it isn’t about any one blogger, and it isn’t about you, it’s about science. Myself, I don’t have the marginal time to spend writing one deep scientific post a day, so I’m putting things in the queue right now. I’m going to set up Just Science as an aggregator weblog. In other words, for a week in early February the website will bring together scientific content from all the blogs who take up the challenge, and you can then use that feed to keep track of the posts.

CATEGORIZED UNDER: Blog

Four Stone Hearth

By Razib Khan | January 17, 2007 7:24 pm

Martin has Four Stone Hearth up, go check it out!

CATEGORIZED UNDER: Anthroplogy

Imagine, what if there was no anti-science?

By Razib Khan | January 17, 2007 12:49 pm

A Week of Science. More later (I’m on board obviously)….

CATEGORIZED UNDER: Blog

"Hard-wired" for God

By Razib Khan | January 17, 2007 10:14 am

Both Jason Rosenhouse and Rand Simberg have offered in the past few days that they have never exhibited an inclination to accept theism. Jason wonders:

I have very clear memories of attending Sunday school as a kid, and spending most of that time thinking my teachers were putting me on. Do I lack something that other people have? Are there genes that predispose people to belief or non-belief?

There certainly are such genes involved in predisposition to religiousness. There is non-trivial heritability toward religious zeal. By heritability I mean the proportion of popuation level variation in a trait than can be explained by variation in the genes. This is a subtle point: just because a constellation of genes may affect the propensity toward religiosity, that does not imply that there were selection for religious belief. Rather, it maybe that religion is a phenomenon which is a byproduct of normal human psychological processes. And just as humans exhibit variation on a whole host of psychological characteristics, so any trait which emerges as a side effect of said traits shall also exhibit variation.

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CATEGORIZED UNDER: Religion

Neandertal-Modern hybrid skull?

By Razib Khan | January 16, 2007 10:59 am

There is news about a skull which is about 40,500 years old found in Europe that exhibits a hybrid Neandertal-Modern morphology:

However, there were some important differences: apparently independent features that are, at best, unusual for a modern human. These included frontal flattening and exceptionally large upper molars with unusual size progression which are found principally among the Neanderthals.

Prof Chris Stringer of the Natural History Museum, London, commented on the PNAS paper’s suggestion of interbreeding: “How often it happened and its importance to the bigger picture of modern human origins are unclear, but my view from the available evidence is that it was probably a rare event. I thus take a different view from colleagues such as Joao Zilhao and Erik Trinkaus who see signs of a significant Neanderthal input in early Cro-Magnons.

Stringer is an Out of Africanist who believes that modern humanity emerged recently from the ancestral continent and replaced other archaic populations. But, as noted by the introgression story, rare breeding events can have salient genetic and evolutionary consequences. The key is to establish interfertility beyond a doubt, and then the genetic logic that positively favored alleles are likely to spread and fix across the subspecies boundary becomes compelling. This is only one skull, and though other “hybrid” finds have been recovered, I suspect that the total number will always remain small. Genetic methods will be essential in filling in the gaps in our knowledge, but these morphological finds are necessary elements in constructing the theoretical superstructure because genetic methods are by their nature conjectural and must be interpreted through particular assumptions.
The paper will be out soon in PNAS.

CATEGORIZED UNDER: Evolution

Race & modern genomics

By Razib Khan | January 15, 2007 9:13 am

p-ter has an interesting post where he explores some current findings about human population substructure. He begins:

First, an important preliminary– there are millions of places in the human genome where any two given people could possible differ, either by a single base change, the addition of an entire chunk of DNA, the inversion of a chunk of DNA, or whatever. Keep that in mind: millions and millions of places (for a database of many of the single base changes, see the HapMap). Now, the intuitive argument: after humans arose in Africa, they dispered themselves throughout the world. By both chance and in response to selection due to their new environments, populations in different parts of the world ended up with different frequencies of those millions of DNA variants. Simple enough. Now, below the fold, I will present the evidence that 1. the patterns of genetic variation form clusters on a world-wide scale, 2. genetic clusters coincide with what is commonly called “race”, and 3. genetic variation between clusters is relevant phenotypically.

Jason Rosenhouse has posted on race recently as well. You can find some of my own opinions on the topic here. Ultimately, I think asking questions about race/population substructure is very interesting because I find human evolutionary genetics very interesting. 2 years ago Armand Leroi could plausibly say we didn’t know how skin color was genetically controlled. Today he wouldn’t be able to say that.

CATEGORIZED UNDER: Biology
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