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.

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.

Read More

Click below the fold….

I predicted this is November 1998, yes I did Tony, you remember! Check out chunky Britney dancing.

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.

I think I’m probably breaking some rule of blogger etiquitte by performing the dreaded fact-check manoeuver on Colby Cosh just after he linked to my other blog. But it always makes me wince when people I respect stake out strong positions where they’re demonstrably wrong on the facts, so I’m afraid I cannot let this pass:

Africans aren’t helpless animals–they know what works against malaria. Unfortunately, what works against malaria is DDT. But any country that proposes a program of household DDT application faces starvation at the hands of European bureaucrats and consumers. The nets are an unnecessarily expensive and epidemiologically phony sauve-qui-peut measure, a work-around for what could be described as the greatest ongoing mass murder ever perpetrated.

This is one of those strange memes that gets into the air and becomes part of the conventional wisdom, despite the fact that if you dig deep enough the whole thing turns out to be baseless. (Other examples include what Everybody Knows about the industrial revolution or the great depression.)

Cosh seems like he usually has pretty good bullshit detectors, and I would have thought that alarm bells would have started ringing when (if?) he noticed that one of the articles he cites was by Dr Rutledge Taylor, the man who directed the film 3 Billion and Counting. Hello there, lying with statistics! The film’s site claims that “Africa loses nearly 3000 women and children on a daily basis … to malaria alone”. That’s 100 million per year, which is pretty impressive considering that according to the CIA world factbook total world death rate is closer to 60 million per year (9/1000*6.5 billion). [See edits below.]

But let that pass, and let’s look at the allegation made against the EU. Let’s see what the EU ambassador to the US has to say on the matter (emphasis mine):

The European Union has no objection to the safe spraying of houses with DDT for malaria control, but it does have concerns about illegal agricultural uses. The E.U., like the United States and 149 other countries that signed the Stockholm Convention on Persistent Organic Pollutants in 2001, believes that the use of DDT in agriculture should be phased out.

Nations have the right to use DDT for public health protection, and the convention includes an exemption to allow such uses. It even sets out conditions for the safe use of DDT in malaria control — a use unlikely to leave residues in crops.

It is up to Uganda how to fight malaria, and DDT is one tool in that fight. The European Union continues to assist Uganda and other affected countries in efforts to combat malaria and contributes almost $100 million to this cause annually.

Health protection should not, however, provide an alibi for illegal use in agriculture. The European Union has granted $30 million to developing countries to strengthen infrastructures and encourage the sharing of best practices — a program singled out for praise by the World Bank.

The “ban” on DDT is and always has been one on its agricultural use; household use is perfectly allowed. Here (PDF) we find, plain as day on the 4th page, that the “WHO recommends indoor residual spraying of DDT for malaria vector control.” And there is a perfectly good reason for this partial ban: basic evolutionary logic suggests that injudicious use of a pesticide like DDT will tend to hasten the adaptation of the pests to the chemical, just as improper use of antibiotics has hastened the evolution of resistance in bacteria. And indeed this is exactly what has happened in some areas (PDF).

Saying that DDT “works” is like saying penicillin or erythromycin “works” — yeah, for a while. But if you’re not careful about it you can end up pushing your enemy to evolve faster. Like Derek Lowe says: “It’s life or death for them. Just like it is for us.”

Addendum: Tim Lambert has been covering this beat for a while, and most of my info on the subject comes by way of him. Anyone curious should read his full archives on the subject here.

Edit: I am a blithering idiot and somehow misread that as 300,000. I have no defense other than that this doesn’t seem to square with the 3 billion figure that makes the title, but then they don’t specifically say that those are deaths. This is an excellent lesson in the perils of firing off posts in a rush.

Edit the second: Aha! Now I know where I got that idea in my head. Apparently they did originally say what I thought they said, but then later changed the site after having this, er, discrepancy pointed out.

Edit the third: Lambert has more on the effectiveness of nets, which was the subject of Colby’s original post.

Anyone know the best way to get a windows .exe to run within linux? I need to pass and retrieve some variables from a .exe which has an algorithm using the Asterisk pbx system (on the same box). Thanks.

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.

Read More

I’ve developed a mild interest in East-West phylogeography in Europe in regards to human populations. In the process I stumbled onto this paper, Geographical heterogeneity of Y-chromosomal lineages in Norway. I’ve put the full PDF in the forum, here. Standard caveat, take this with a grain of salt!!! But, I’ve put some maps below that readers might find of interest.

Fig. 6. Multidimensional scaling analysis of pairwise Y-SNP based FST between 23 European countries. Data were gathered only from the geographical coordinates indicated. Map coloration is the result of algorithmic interpolation and must be interpreted appropriate skepticism.

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

Read More