Nick Wade in The New York Times has a piece out titled Still Evolving, Human Genes Tell New Story, based on a paper published today in PLOS, A Map of Recent Positive Selection in the Human Genome. This paper is an extension of the research project that emerges out of the International HapMap Project. In short the HapMap is an assay of ~300 individuals from 3 populations, European Americans from Utah, ethnic Yorubas from Nigeria, and a collection of Japanese and Chinese. What can a few hundred individuals tell you? A lot.
Wade's piece is a soft landing survey of the major points. His forthcoming book, Before the Dawn, which would have more aptly been titled Still Evolving, elaborates on many of the points he brings up in in the piece. I won't scoop my own book review, but this article is simply an appetizer for what you'll find in Before the Dawn...the title hints at another popularization of scientific genealogy, but within the text there's a lot more stuff about functional genomics than phylogenetics.
But, on to the paper...where the real meat is.
How:
The authors are basically using the three test populations as guinea pigs. Prior to the molecular era geneticists had to assay visible traits, the kink of a wing, a particular coat coloration, etc. In regards to humans pedigree analysis was about all there was. That all changed with the molecular revolution, as researchers began to have access to the informational guts of our genetics. Today, in the "postgenomic era" masses of direct sequence data can be massaged by computational algorithms to scry the information we desire.
In this paper the authors are basically looking for signs of selection. Contrary to popular imagination selection, the motive engine behind evolution, is still happening, and it is happening with our own species. Selection occurs via differential fitness correlated with heritable variation. Variation is still around, as is differential fitness. The only question might be whether the variation is heritable...and I think reasonable people can agree that to some extent it is, variation is not totally uncorrelated with your genetic inheritance. While previous research tended to focus on zooming in on a candidate gene upon which we know selection occurred because of phenotypic variation we see around us (e.g., malarial resistence or lactose tolerance), the paper above assays the genome and attempts to detect tell-tale eddies in the sea of neutral genetic variation.
Much of the genome is operationally neutral in its variation (pseudogenes, introns, etc.). Substitutions on a locus, a gene, from one allele to another are random and have no fitness implication. As Motoo Kimura showed this implies that the substitution rate is only proportional to the mutation rate (larger populations have weaker drift, but more mutations, smaller populations are the inverse). Additionally, recombination across the chromosomes in diploid organisms breaks apart synteny between alleles on the same sequence of the genome. With a few parameters like this, rates of recombination and neutral substitution, you can formulate a basic null hypothesis and computational models which allow you to test for deviations from expectation.
And this is what the authors did in the paper. Basically, if you have a genome which is a flux of alleles moving from 0 to 100% in frequency you will have variation as different loci are in different states of polymorphism. Additionally, recombination, even if heterogeneous in its rate (as the authors assume, and is empirically attested), will break apart assocations between loci across a the genome so that you eventually attain linkage equilibrium. But the null hypothesis doesn't always hold, and this is evidence for selection. Sometimes genes are functionally constrained so powerful selection homogenizes a region of the genome so that no change is allowed. Sometimes you have a situation where two alleles exist at high frequency, and this could be some sort of balancing selection where heterozygotes are more fit than homozygotes.
Voight et al., the PLOS paper, examine instances of selection happening now. In other words, the statistical test they use, which detects regions of "long haplotypes," that is, homogeneity that hasn't been disrupted on a region of the genome by recombination because selection has been too recent, is looking for current linkage disequilibrium regions. What is likely happening is that an allele is being selected for so strongly that it is dragging along other portions of the genome along with it. Over time recombination should break apart these associations, but until then you see evidence for selection via these long homogenized blocks. The statistical test used in the paper doesn't pinpoint those regions where fixation is nearly complete so that you can't discern the eddie of the long haplotype stranded in the middle of neutral variation.
What:
Wade's article covers most of the big points. But I'll go over it again.
1) Selection happens, and its happening. The whole idea that humans stopped evolving, that we are outside of God's evolutionary plan, is bunk. There is human variation to attest to selection, from skin color to variations in nutritional metabolism, to disease tolerances. The fact that not all of the regions of the genome detected by this group are at fixation suggests that selection continues (or did until recently, unless you believe in the ubiquity of balancing selection, in which case I have a bridge to sell you). Additionally, the test likely missed genes which are just now rising in frequency due to selection.
2) The time period in terms of "recent" is in the 10,000 to present range. This is a big window, and the paper is sketchy about giving too precise of a handle because they really used some back-of-the-envelope numbers. It seems they want to give you a taste for the character of selection that is reshaping the genome. Wade's article does point to one reality which is salient: the increase in population due to agriculture was really a rock that hit the human genome.
3) Some of the detected regions were already well known. For example, the lactose tolerance region in Europeans, ADH in Asians. Seeing as how the Neolithic Revolution increased population sizes and resulted in a radically alterted lifestyle it is no surprise that genes which control metabolization of our foods changed a lot. Additionally, pathogen resistence was a big issue as packing into unsanitary villages became the norm (many viral infections can't survive at the low densities of pre-agricultural peoples). Several genes related to skin color show evidence of recent selection in Europeans. There was the expected (to my mind) changes found in bone morphogenesis genes, agricultural populations exhibit a more gracile skull form and delictate dentition, the result of universal selective forces that arise out of transition to particular cereals as primary foostuffs. Finally, genes that effect brain and cognitive development are under recent selection, suggesting that behavior and personality might be traits which evolution has reshaped since settled agricultural life. It certainly seems plausible that denser life would result in different personality traits being selected for.
4) Variation is real, and selection is stochastic. Here the skin color data is illustrative. Northwest and Northeast Eurasians are both fair skinned, but their genes differ. Europeans seem to be selected for paleness on particular loci where East Asians are not, while on MC1R they exhibit extreme polymoprhism, in contrast to East Asians who seem subject to recent selection. My point is that phenotype is not that different, but it reaches its end state via an alternative path. Selection on a certain set of genes may allow one to attain the given phenoptype, and that might free other loci from selective constraint. The recent evolution of blondes paper hints at this insofar as MC1R was putatively left free to respond to sexual selection because Europeans were already fixed on other loci for pale skin.
5) Selective sweeps are powerful enough to be transregional. The lactose tolerance gene is a case in point, though it seems that the frequency increased first and is highest for adult milk digestion in Northern Europeans, the capacity is present in other Eurasian populations. This is not because Europeans expanded and filled western Eurasia, it is because the gene spread via selective pressures. Sweeps and linkage disequilibrium shared between populations is evidence of powerful genetic forces that undergird our genomes. The probability of fixation of a new positive mutation is 2s, where s is the selection coefficient, so deme-to-deme migration could result in wildfire spread of new traits (each introduction via intermarriage can be modeled as a mutation).
6) A few hundred individuals from 3 populations. Do you really think this is the end? Cheap genomics I hear your siren song! We live in the age of Kepler. The Principia has yet to be unveiled...and the sweet low hanging fruit beckons.
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I wonder about the method used to distinguish selction from genetic variations related to other forces. How well established is it?
"Contrary to popular imagination selection, the motive engine behind evolution, is still happening . . ."
I noticed this line being taken up in the Times piece, too. I'm not so sure this is as prevalent a misconception as the author seems to assume. The findings are interesting, but I don't think the populace at large is going to have to rethink their assumptions about life. This is a field I think about quite a lot, and I can't say I really had an opinion on this matter.
While everyone wants their research to overturn popular misconceptions or to reveal "dangerous" truths, scientists don't get to very often, because by an large people just don't care about what scientists are working on. If they hold incorrect beliefs, they are usually quite casually held, and most reasonable people withhold judgement in research areas that are more or less nascent.
Someone wrote about Dennett, I believe: the point of scholarship isn't to be dangerous or provoking, it's to be right. And the two things have nothing to do with each other. Falling in love with provocativeness is exactly what went wrong with a lot of social and cultural theory. Scientists ought to take heed of that.
I'm not so sure this is as prevalent a misconception as the author seems to assume.
1) when i was a kid in the intermontate west most of my creationist friends (this was about 80% of my friends) asked me "how come we aren't evolving now?"
2) there is a common misconception that evolution works very slowly. i know, because i talk to non-scientists regularly and they are shocked at the relatively recent patina of malarial resistance of lactose tolerance.
3) you aren't the test of the "man on the street." to some extent, the people i talk to aren't the test for that either. most people don't think about evolution. but, of those lay persons who do think about evolution there are many misconceptions. two of the common ones are that "punctuated equilibrium" has overturned "darwinism" (thanks to sj gould's copious output) and that humans are outside of evolution (thanks to a host of assorted of social science biases, and evo psych's emphasis on the pleistocene).
4) the point that scientists work in areas that most people "dont care about" is well taken. most people don't care about solid state physics, though that is a very important area of research. but, talking about evolution in the current political climate, that seems a absurdly contrarian point of view. at least verbally, if not deeply, people do care about evolutionary theory (my emph.). for people who reject speciation and are even turning on microevolution (if they only know the vaguest outlines of what these are in any case) the idea that humans are themselves animals subject to natural selection can be rather offensive. you can see this in conservative religious references to r. lewontin to "debunk" evolutionary psychology as they engage in is/ought fallacies.
I am not understanding (most of what you wrote, but, specifically) about lactose tolerance.
Razib confused me further with
"recent patina of malarial resistance of lactose tolerance."
Is that phrase just missing a comma after "resistance"?
More generally: Are you (and the paper you are reviewing) saying that lactose TOLERANCE is a recent development and therefore lactose INtolerance is the prior, general, condition?
That confuses me for two reasons: 1) Isn't human milk a lactose? How would the species have survived in that case? And 2) I thoughr that lactose INtolerance was a trait of Ashkenazy Jews and that (generally) the rest of Europe didn't have that problem.
karl,
adult lactose digestion is a derived character. that is, only a minority of adult humans can metabolize lactose comfortably. of course, this ability is partly environmental, people seem to be able to tolerate milk as adults given enough conditioning...but this is not the ancestral trait. follow this link and you will see % for populations, note that the numbers will differ according to source, but the rank order remains the same.
the most recent genetic research suggests that the positive selection for lactose tolerance was initiated in northern europe around 10,000 years ago. it spread to other populations after that time, more or less. some african nilotic groups are also lactose tolerant as adults, but it seems that the alleles are different than those in eurasians, in other words, a separate mutational source.
though i tend to shy from "eurocentric" canards, but the terminology of this term is actually a peculiar form of bias. northern europeans, assuming they were species typical on this trait were quite surprised to find that many peoples (most) are not lactose tolerant as adults. this has caused serious problems, as when powdered milk was given to famine victims in parts of africa where it just induced stomach ailments, or the milk that the federal gov. gave native american tribes as part of nutritional subsidies.
"how come we aren't evolving now"
I've always believed that we humans are evolving, gradually becoming more and more intelligent. How did we wind up as intelligent as we are in the first place? Obviously, there's been some kind of intense selection for the gradual raising of intelligence throughout our evolution.
Our hunter-gather ancestors must have been intensely selecting for IQ, on the basis of who employed the best hunting/war strategies, weapons, etc. US defense statistics have reported that those with high IQ's hit their targets significantly more often when using weaponry. Even in every primitive society around the globe, it is those with the highest IQ's that are on top of their social hierarchies, & are most respected, i believe. "Primitive" peoples respect intelligence & make those with the highest IQ's among themselves their chieftains/ religious leaders/presidents.
This would seem to show an innate human bias in trusting, accepting and respecting the authority of the more intelligent, right? Is there any eveidence to suggest the opposite, that humans don't respect high IQ individuals more highly? Doesn't status in almost every society, industrial & non-industrial correlate very closely with what westerners associate with higher IQ?
In most societies, higher IQ seems to *increase* fitness and survivability, whereas low IQ reduces it.
I also tend to believe that those with the best access to education, those who place the most emphasis on education, & those already on top of status hierarchies will probably evolve higher intelligence more quickly than the rest of humanity, as the selection for it will be much greater.
I'm still wondering whether i'm correct that humans have an innate tendency to respect, even revere, individuals with high IQ's above those with average or low IQ's. I do realize that freethought wasn't encouraged for most of humanity's history, so it's not clear to me.
I'm still wondering whether i'm correct that humans have an innate tendency to respect, even revere, individuals with high IQ's above those with average or low IQ's.
heh. did you attend an american high school?
btw, it is a truism that traits which exhibit a normal distribution have ambivalent fitness implications. otherwise all the loci would have fixed and the trait would become a genetic insteand of a heritable one. to use a non-cognitive example, consider the range in height. tall males tend to often be prized mates for females cross-culturally, but they also have higher metabolic needs, perhaps reducing their fitness in many environments where nutritional intake is stochastic. additionally, there are health issues relating to males who are much above 6'5. anyway, the point is that various counterposing selective vectors are probably maintaining the normal distribution of male height even though we "know" that tall me are the desired mates for females (there is the possibility that preference for short females results in a sort of balancing selection).
Yes, i did attend an american high school. But, American culture is unlike other cultures in that a particular disdain for intellectualism has arisen here. This(spite for intellectualism) isn't the case anywhere outside the western world, is it?
This(spite for intellectualism) isn't the case anywhere outside the western world, is it?
interesting question. call out to international readers....
I used to teach a class which included some history of urban development, and I used to ask studnets whether there were cars in the 18th century. About 20% didn't know or got it wrong. Your "how come we aren't evolving now?" question is an appeal to historcial myopia, I think. These folks don't believe in *any* processes ocurring on a scale greater than their everyday experiential one.
To test the general social imaginary, we'd probably best look to science fiction. How many far-future sci-fi stories have humans significantly evolve (w/o civilization collapsing or similar spur to selection)? May be a tough question to answer since most sci-fi seems to posit some such grand environmental change.
But anyhow, I can attest to BOTH ideas being pretty current(we've stopped evolution because practically everyone lives to reproduce/ we're definitely evolving (getting taller, more sociable, whatever) and even we're devolving because the less fit reproduce more than the fit).
I think freeing EP from the pleistocene paradigm may be one of the most welcome effects of this research should it come to be generally accepted. The Panksepps already have pointed out instances where EP researchers have sought out pleistocene origins for traits that probably go back way farther than that. Now this. It begins to look as if much of this field was getting a bit ahead of itself.
Much as Gould pointed out years ago.
And Punctuated Eq is definitely a great example of provacativeness wining out over care in presentation, with continuing negative consequences.
To test the general social imaginary, we'd probably best look to science fiction. How many far-future sci-fi stories have humans significantly evolve
when i have seen science fiction authors asked about they almost always admit that if they made human beings as different as they will likely be the books wouldn't sell because no one would be able to relate to them. basically, most of science fiction, even hard sf, is basically about contemporary people in far future environments. some of the more avante guarde stuff that incorporates cybernetics, info-tech and bioengineering is really hard to follow because of the cognitive overhead in taking into account the various parameters which differ in the far future.
"we're devolving because the less fit reproduce more than the fit"
I've given this some thought, & i've come to the conclusion that it may or may not be true.
In many parts of American society, it does seem to be true. But, on a global scale, think of the situations that the low IQ and poor are very often in - parents selling their children to brothels, disasters, disease, war.
High IQ(meaning high education & high social standing almost everywhere in the world) almost ensures greater protection from disastors of all kinds, lower infant mortality, less risky life behaviors, etc.
So even if the low IQ do reproduce more, do they *survive* more? Civilization *must* continue, because those who are civilized live better lives & survive more, thus ensuring that rationalism survives forever. And even if the world were completely swamped with the low IQ masses, it would still be the cognitive elite who would run things, figuring out solutions, deciding who lived & who died, right?
Besides, human evolution is like an algorithm where intelligence & the intelligent & rational must survive. There's no going back into the dark ages now. I don't believe that that could ever happen. Rationalism is pretty much here to stay, as are those who value it, the cognitive elite.
We have to realize that it is the high IQ who determine and have ultimate control of *everything on this globe*, do they not? I'm beginning to see this idea of the stupids winning out over the smarties as hogwash. seriously.
I'm wondering right now which is more evolutionarily stable, superstition or rationalism?
Could the dark ages really return? Could rationalism one day lose out to superstition or savagery? I tend to see rationalism as more stable. When humanity reaches a certain minimum IQ, say 125, would rationalism then be inevitable? Do humans have compartmentalize their minds, so that someone with the IQ of a physics professor could be superstitious. I suppose culture also plays a role, but then, IQ shapes culture.
Razib, what is your take on this? Could the age of magic & superstition ever return to western society, without an external ideological imposition? Are we rationalists here to stay, because we are rational?
Razib, what is your take on this? Could the age of magic & superstition ever return to western society....
yes.
"yes"
I apologize for that. I forgot to consider that many americans are already superstitious types who use magic as their everyday explanations for life's events.
But assuming a society that was thoroughly & completely populated by intellectual rationalists, could a reversion to pre-modern-style superstition be possible?
But assuming a society that was thoroughly & completely populated by intellectual rationalists, could a reversion to pre-modern-style superstition be possible?
ah, is this a fever dream? :) and even 'intellectual rationalists' have other aspects of their personality that could destabilize an established order. passion holds rationality on a short leash.
"passions hold rationality on a short leash"
Well, yes, reason as in slave to the passions. But in the reasonable & rational people, doesn't/wouldn't reason always take precedence over the passions?
Do you believe that in high IQ people, it is only the IQ component that makes the big difference? Does personality have a wide variance among the high IQ, such that someone with a towering IQ could possess the personality traits associated with those of low IQ delinquent?
The whole "reason as slave to the passions" idea seems to suggest that while IQ can make you a nobel prize winner, these 'other aspects' of their personality' can remain that of the savage.
One question/comment, which is off topic, but i don't know where else i would inquire?
In the US Armed Forces, what do they do with enlistees who have super-high IQ's? Are they among the infantry too?
Or, would they be required/assigned to accept some special position if their IQ were university-professor level?
But in the reasonable & rational people, doesn't/wouldn't reason always take precedence over the passions?
no, i doubt it. behavior is not deterministic, it is probabilistic. let me illustrate what i'm saying with a thought experiment.
imagine a circumstance where you are very hungry, and you have no money. imagine you have a gun. now, you make a choice to shoplift, and the clerk catches you. what do you do?
i think the probability that someone who has an IQ of 80 will shoot the clerk is far higher than someone who has an IQ of 120. why? i don't think it is because the person who has an IQ of 120 is innately more "moral," but, they are more rational actors. they know very well that the cost vs. benefit calculus is pretty dumb, and they do the sums. but, that doesn't mean that in all circumstances will the person who has an IQ of 120 not shoot the clerk, and that person who has an IQ of 80 shoot the clerk. in fact, in the vast majority of circumstances the person who has an IQ of 80 probably wouldn't shoot the clerk (though one wonders what sort of person would take a gun into a minimarket!).
Does personality have a wide variance among the high IQ, such that someone with a towering IQ could possess the personality traits associated with those of low IQ delinquent?
yes. think of it like CPU, a faster computer can be malicious more effectively. the nazi leadership were rather bright.
The whole "reason as slave to the passions" idea seems to suggest that while IQ can make you a nobel prize winner, these 'other aspects' of their personality' can remain that of the savage.
i am convinced by the CTY study that the benefits of IQ are roughly monotonic, but other personality factors can really help. eg., james watson was not really that brilliant, but he was socially smart and conniving and he hitched himself to francis crick, a real brilliance.
At least among a sample of university students (so, selected for above-avg IQ), IQ correlated +0.43 with Objective Openness in personality. "Objective" Openness refers to openness to ideas, actions, & values (not necessarily to aesthetics, fantasy, or feelings). Read more here (pdf).
"yes. think of it like CPU, a faster computer can be malicious more effectively. the nazi leadership were rather bright."
Definitely.
Intelligence is dangerous in that it can allow the generation of virtually unlimited options, even when these concern the gruesome in nature. Think of what the Japanese soldiers were capable of in the Nanking Massacre. I used to be interested in the massacre at Nanking &, when i researched, there seemed to be a never ending variety of gruesome acts(e.g, hanging by the tongue) perpetrated . These Japanese soldiers, being Japanese, were probably pretty bright as well. If these soldiers had had low IQ's, there might just have been somewhat less variability in the cruelty, due an absence of 'cruel creativity'. Intelligence can come in handy for cruelty.
Razib,
by the way, do you know what the US Armed Forces does with super-high IQ individuals?
Will they ever consider someone 'too bright' to fight? Where do they place those above a certain high-IQ ceiling?
by the way, do you know what the US Armed Forces does with super-high IQ individuals?
Will they ever consider someone 'too bright' to fight? Where do they place those above a certain high-IQ ceiling?
staff. i believe they also train these people to do specialized tests, eg., complex engineering on nuclear subs. i knew people who were enlistees prior to going to college and their scores on standardized tests determined their grades, ergo, perks, privs & responsibilites.
basically, most of science fiction, even hard sf, is basically about contemporary people in far future environments. some of the more avante guarde stuff that incorporates cybernetics, info-tech and bioengineering is really hard to follow because of the cognitive overhead in taking into account the various parameters which differ in the far future.
Hmmm. Hadn't considered how much the conventional mechanisms of fiction (e.g. identification) would restrain the speculation here.
I guess the question would have to be: does this fiction seem to assume evolution as well as technology as an agent of change?
Perhaps we just aren't as interested in reading about ontologically different people in different situations (frame of reference for identificiation way too shaky to work?) as reading about similar people in different situations?
Perhaps we just aren't as interested in reading about ontologically different people in different situations (frame of reference for identificiation way too shaky to work?) as reading about similar people in different situations?
yep. larry niven explicitly stated that he "knew" that his far future depicted in mote in god's eye was unrealistic and that the humans were pretty conventional, but he also stated that you simply wouldn't have paid attention plot and characters if the setting was so novel and exotic as to assault you constantly.
over the last decade hard science fiction is taking biological evolution more seriously, but i think part of the relative neglect of biology was a function of the fact that most hard sf writers were from physical science backgrounds. but over all, i think being modern & embedded in novel technology is easier to "relate" to than being an alien physiologically. the stories that tend to be most appealing are mildly counterintuitive, novel enough to attract and stimulate, but grounded enough not to confuse.
Look at the SAT scores of freshman entering the military schools. They're on a par with the Ivy League.
For a smart guy with an engineering point of view, a bit of macho, and conservative or centrist politics, a military academy might well e best choice, and not just because it's almost the only free education you can get.
ummm....Dune?
;)
and Ringworld.