Archive for April, 2006

Is Mormonism relatively weird or absolutely weird???

By Razib Khan | April 28, 2006 7:00 pm

There’s a hilarious, and often thoughtful, comment thread over at The American Scene. Ross Douthat is a Roman Catholic, and many of his readers are serious intellectual Christians. So, I am always interested when they object to the bizarre and obviously anthropogenic hocus-pocus of Mormonism. Some snips of interest:

dude, mormans are weird. let’s just face it. the whole thing makes me giggle when I talk about it. golden tablets . . . the whole thing is goofy-times.
[later]
Because the theology is “weird,” and the history is even weirder. Captain Moroni? Golden tablets? Steve Young gets his own universe? I mean . . . this just doesn’t sound serious.
I can’t get past “Moroni.” It just sounds like a name that a 19th Century quack would invent.

Response:

Weirder than, say, believing that a man who died two thousand years ago can be eaten in convenient wafer form as a requirement to getting into heaven?

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CATEGORIZED UNDER: Religion

Meow Friday

By Razib Khan | April 28, 2006 12:22 pm

The lion roars…by the way, in case anyone cared, my evil black cat is only up to three birds this spring. I think the worst is over.
Update: More cat below the fold.

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CATEGORIZED UNDER: Blog

The flood of selection rises

By Razib Khan | April 27, 2006 11:20 pm

Over at John Hawks, Has the dam broken on mtDNA selection?. I don’t know if this matters that much scientifically since non-human phylogeography tends to be more cautious than the field of historical human population genetics, but it matters a lot for the public which has been habituated to a steady stream of mitochondrial data being interpreted by popularizers and the press since African Eve.

CATEGORIZED UNDER: Genetics

HIV and human variation

By Razib Khan | April 27, 2006 4:02 am

There is a preprint in the website of The American Journal of Human Genetics titled “Genetic variation in the CCL18 – CCL3 – CCL4 chemokine gene cluster influences HIV-1 transmission and AIDS disease progression.” The title is a mouthful, but the short of it is what we’ve known for a long time, that human genetic variatian responds differently to HIV infection (or the risk of infection). This is surely going to be important, not because the science is a priori killer, but because AIDS is a big public policy issue. Back in the 1990s some people were talking about HIV resulting in the extinction of the human race (OK, I’m mostly talking about my teachers), but real knowledge of evolution would have implied that this is ridiculous. Plagues and pandemics come and go, but the species always bounces back, and we are a numerous large mammal so operational immunity is almost certainly going to be found amongst a small minority (as it has been).
In any case, since the paper is a preprint there isn’t an abstract. Rather, the major points seem to be this: some SNPs are correlated with faster disease progression, and Europeans are also characterized by lower polymorphsim and greater linkage disequilibrium than African Americans on the region of the genome of interest. The linkage disequilibrium manifests in “haplotype blocks” that may be the product of recent powerful selection on loci around which recombination has not had time to break apart the associations generated by the hitch-hiking effect.

CATEGORIZED UNDER: Genetics

Native American HLAs, part II

By Razib Khan | April 26, 2006 9:34 pm

Greg Cochran’s comment below is worth turning into a post:

There’s more to it than that. Tribes often have extremely limited HLA variation, contain only a small subset of the variation that you see in a wider set of Amerindians. Whereas in the old world, even little tiny groups with very low gene flow have lots of different HLA alleles. [Cavalli-Sforza 1994] You’d think that they’d lose those rare alleles by drift, but they don’t – has to be frequency-dependent selection, the same force that has kept alleles around for tens of millions of years. But in the Americas, it appears that those frequency-dependent forces simply did not exist. [Slatkin and Muirhead, 2000]
So, two things going on, which may or may not modify your conclusions. First, a bottleneck, probably: afterwards, a world in which HLA simply does not matter.

We talked about this subsequent to this comment. Basically in small populations subject to a lot of random genetic drift HLA diversity still remains high because stochastic factors run up against powerful negative frequency dependent selection effects. That is, the rarer the allele, the stronger its fitness advantage. So, as drift drives an allele frequency down it begins to run up against countervailing selective pressures. Just as drift is about to run an allele to extinction the break is slammed and it will “bounce back.” This is why HLA variants seem to be almost immortal fragments of the genome.
So what happened with Native Americans? Greg’s point seems to be that Native American groups were not subject to this particular dynamic where HLA is kept diverse within groups, so convential genetic forces of drift were far more powerful on these loci than in other human groups. What’s different? One could posit things like density of population, but the HLA have deep roots well before our own species.

CATEGORIZED UNDER: Genetics

Induction, deduction and abduction….

By Razib Khan | April 26, 2006 4:28 am

Evolgen says:

Let’s focus on two things: the hypothetical deductive method and essential information that you must know to be able to read the science section of a newspaper.

Hm. Amen. Sort of. Scientists in many fields needed to be straight-jacketed into the “hypothetico-deductive” model for a reason. I remember a phylogeneticist telling a group of us why the hypothetico-deductive method was crucial in his own work, before his time taxonomists would get into arguments where they would justify their opinion about systematic relationships with an operational “Cuz I said so!” Testing hypotheses is essential for science. That being said, scientists do more than test truths derived from their models.

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CATEGORIZED UNDER: Science

The First Human

By Razib Khan | April 25, 2006 8:35 pm

The San Jose Mercury News has a review up of Ann Gibbons’ The First Human: The Race to Discover Our Earliest Ancestors. It concludes:

But too many pieces are still missing from the puzzle — including fossils of the ancestors of our closest relatives, chimpanzees and gorillas — to allow for a clear picture of the evolutionary lineage.
So in the end, “The First Human” is a bit like a detective story without a conclusion, or like a detective story that puts Sherlock Holmes, Hercule Poirot, Sam Spade, V.I. Warshawski, Easy Rawlins and Gil Grissom all in the same room, gives them a handful of clues, and lets them argue endlessly about the solution. The characters in Gibbons’ book are almost as colorful and cantankerous as those fictional sleuths. Science writing is rarely this entertaining.

Bones will not tell the whole story. Expect a different sort of excavation, that is, inferences from the genes of humans alive today, to bring to light a lot of the tale in the next few years.

CATEGORIZED UNDER: Evolution

One founding for Native Americans

By Razib Khan | April 25, 2006 2:01 am

Earlier this week I hinted that I had a priori genetic reasons for being skeptical of a “two wave” theory for the peopling of the New World. Well, I was going to do some literature searches and slap something together that was meaty, but I don’t have time, so I’ll just offer up an attenuated but sufficient outline of what my issue is.
First, look at this map and note the “Amerindians” and other populations. Now, look at this table and note the level of heterozygosity of Amerindians vs. other populations. In short, Amerindians are notoriously genetically homogenous on the MHC loci compared to other human populations.

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CATEGORIZED UNDER: Genetics

Unity in diversity, last response to John Wilkins

By Razib Khan | April 24, 2006 6:49 pm

John put up his last thoughts on race, and Evolgen chimed in with his ruminations.
First, nice exchange. Quick points….

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CATEGORIZED UNDER: Genetics

Chimpanzees attack a taxi & kill a driver!

By Razib Khan | April 24, 2006 3:32 pm

Check out John Hawks’ commentary on this story about chimpanzees attacking a taxi and killing the driver. Never forget that we are a relatively gracile species.

CATEGORIZED UNDER: Anthroplogy

I say "race" and you say "population substructure"

By Razib Khan | April 23, 2006 5:50 pm

John responds to the “race” response from Matt & I. I’m not interested in making a point-by-point response to the response because I don’t think the “objective” difference in opinion is that great, rather, it seems to be that we are clashing in the turbulent waters of nominalism.
First, I will respond to what I believe is the perception by John that I am conceiving of race as an essential and fundamental taxonomical unit. I don’t hold to that. I’ve rejected the Platonic conception of race before. The problem that “race based public policy” often has is that the legal system is deterministic, and probablistic entities like subpopulations don’t fit into neat categories. I don’t deny that human populations exhibit spatial and temporal gradients. I stated before that my attitude toward population substructure is instrumentalist. I am happy to treat human beings as fundamentally the same, having equal rights before God & Nature. This the basal starting point, but, we often just stop there.

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CATEGORIZED UNDER: Genetics

Race

By Razib Khan | April 22, 2006 8:27 pm

John Wilkins has a post on race where he expresses skepticism about its biological reality. He comment was in response to a post on my other blog (by another individual), but I’ll stand by it.
I’ve talked abut race in the past, and I’m not into the topic at this point since it is going over old ground, but a few quick responses….

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CATEGORIZED UNDER: Genetics

Living Neandertals & another idea about the Hobbits

By Razib Khan | April 21, 2006 11:14 pm

Just a note for those of you who don’t read my other weblog, Greg Cochran has two new ideas that we’re trying to guess at. First, he’s got a new theory about the origin/evolution about the Hobbits of Flores. Second, he thinks it might be a possibility that there are living Neandertals. Anyway, I’m throwing this out there because I won’t be too surprised if Greg can convince Nick Wade to write a story in the Grey Lady about this stuff at some point in the near future….

CATEGORIZED UNDER: Evolution

Religious intolerance in the USA

By Razib Khan | April 21, 2006 6:10 pm

How deep do the seams of tolerance run in this country? Sometimes you wonder…ultimately, I’m pessimistic about the human love of liberty. I tend to agree with Matt McIntosh that to some extent American defense of individual freedoms is based on custom & tradition rather than reasoned acceptance of core principles. In any case I had a book on my shelf which I just had some spare time to open today, America and the Challenges of Religious Diversity, and I saw this table:

  Spiritual Shoppers (%) Christian Inclusivists(%) Christian Exclusivists(%) All Respondents (%)
Percentage who said they favored:
Making it illegal for Muslim groups to meet in the United States 15 27 27 23
Making it illegal for Hindu groups to meet in the United States 12 25 24 20
Making it illegal for Buddhist groups to meet in the United States 12 24 23 20
N (897) (677) (1,006) (2,910)

Of course, the standard caveat applies that many respondents are probably too dumb to understand the questions.

CATEGORIZED UNDER: Religion

Friday cat picture

By Razib Khan | April 21, 2006 1:06 pm

Check out the tail, Agnostic….

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CATEGORIZED UNDER: Blog

Bayesian Estimation of the Timing and Severity of a Population Bottleneck from Ancient DNA

By Razib Khan | April 20, 2006 10:25 pm

Check out this cool paper in PLOS Genetics:

In this first application of the approximate Bayesian computation approach using the serial coalescent, we demonstrated the estimation of historical demographic parameters from ancient DNA. We estimated the timing and severity of a population bottleneck in an endemic subterranean rodent, Ctenomys sociabilis, over the last 10,000 y from two cave sites in northern Patagonia, Argentina….We found a decrease from a female effective population size of 95,231 to less than 300 females at 2,890 y before present: a 99.7% decline. Our study demonstrates the persistence of a species depauperate in genetic diversity for at least 2,000 y and has implications for modes of speciation in the incredibly diverse rodent genus Ctenomys. Our approach shows promise for determining demographic parameters for other species with ancient and historic samples and demonstrates the power of such an approach using ancient DNA.

I hope John Hawks and the gang can get their buddies to lend them some ancient DNA! The character of human evolutionary bottlenecks is a major issue in how we view the origin of our own species. There is other cool stuff about founder effect speciation (founder flush?) and the evolution of sociality via kin selection.
Here’s the Eureka Alert summation.

CATEGORIZED UNDER: Genetics

Comments, you can hold 'em if you are a retard<sup*

By Razib Khan | April 20, 2006 8:50 pm

Since I will use vulgar language, this post will be mostly below the fold.

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CATEGORIZED UNDER: Blog

Pagan & Christian

By Razib Khan | April 20, 2006 3:29 am

The late 4th century witnessed the death of the pagan world and the rise of the early medieval era. Today, our culture focuses on the here & now and we neglect the past. But the past is important because we can learn from the rivers explored by our ancestors. In our modern age of religious pluralism, poised between the past and the future, I am often struck by how apropos the dispute between the pagan Prefect of Rome, Symmachus, and the great Christian cleric Ambrose, seems.
Here is Symmachus:

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CATEGORIZED UNDER: History

The chimeric robot

By Razib Khan | April 19, 2006 9:44 pm

Richard Dawkins pioneered the popularization of the “selfish gene” concept in the book of the same name in the 1970s, and yet it is clear that most people haven’t really internalized this idea. Otherwise, how to explain the success of books like The Journey of Man and The Seven Daughters of Eve which explicitly conflate population history and gene history to the point where one would assume a 1:1 covariance.

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CATEGORIZED UNDER: Genetics

Genetic thugs in the house!

By Razib Khan | April 19, 2006 12:07 pm

I’ve been a bit anal about genetic drift over the past few days. The reason is simple, replace “random genetic drift” with “sampling error”, and note how ridiculous some of the things scientists will say to journalists when they come a callin’ sound all of a sudden. “Hm…no, I haven’t done research in this area, but it seems like sampling error could generate that sort of pattern.” “Well, it could be sampling error, they can’t prove it isn’t.” I’m not saying that random genetic drift isn’t a good null hypothesis, I’m just saying that it is a deux ex machina that sounds good when you can’t think of anything else, operationally a skyhook.

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CATEGORIZED UNDER: Genetics
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