Specifically, as evolgen points out the acceleration paper was focused on adaptive evolution, the subset of allele frequency changes driven predominantly by the force of natural selection. What's the rest? Read the post.
Why does this matter? Evolution is a science, and in science this sort of pedantic precision in definition, terminology and meaning matters a great deal because it is embedded in a contingent system. One of the most frustrating things about the necessity of the rearguard action against Creationists is that the "controversy" swamps this reality, that evolution is a science which is the process of refinement and change due to theoretical & empirical developments. Instead evolution is only discussed in the broadest generalities, which is an insight with might spark the imagination in the 19th century, but is now simply a background assumption which serves as the framework for the real action. Books such as this one are a necessary evil. Why evil? Because the time invested in the production of that prose could have been time devoted to research and (alas) grant writing.
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When normal people talk about evolution they are thinking phenotype, not DNA.
Do you foresee a day when we will be past all this? I mean, will, for instance, four years of an Obama or Clinton lend itself -- through policy changes and a better attitude toward science -- to muffling the ID/creationists, or would either, as president, exacerbate their bellicose rancor?
How much trouble do you think we're in? (Personally, I fear that we are in intractable trouble, culturally.)
In the name of transparency: I am considering writing a blog entry of some length regarding science, religion and our cultural woes here in America, and I might quote you (along with others). As a person with a moderate education and an understanding that there is a huge amount I don't know regarding science and evolution, I am nonetheless adamantly pro-science because it is rational, unafraid of inquiry, and open to all.
I've located 90% of the problem right there.
Not only is the PNAS paper about adaptive genetic evolution as opposed to genetic evolution, it must be evolution mainly in genetic variants of pretty small effect. There is a very low upper bound on mutations that are both beneficial and of moderate or large effect, and as genetic evolution becomes more rapid it must pass a point at which it is increasingly reflective of smaller effect variants.
Consistent with that, there is no acceleration in overall morphological evolution over the past 2 million years (or 50,000 years, or 5,000 years). Maybe in a few isolated characters.
Isn't increased evidence of selection partly an artifact of expanding population size because stochasticity is less important the larger the population?
Also, the larger the population and the faster its expansion, the less intense selection needs to be for a given degree of selection-determined differential allele frequency. (Right?) That is, these reflect, for instance, having 5 offspring as opposed to 4 rather than, say, pre-reproductive morality. And that is congruent with smaller phenoypic effect of these allelic variants.
No, it concerns mutations with large effects on fitness, ~3-4% on up. Probably larger than that, allowing for geographical substructure. They're the only ones that can go from a single copy to tens of percent across a subcontinent during the Holocene. Such big improvements are possible because the switch to agriculture and dense, disease-ridden hierarchical societies was such a drastic change. Eventually, you'd expect the rate of adaptation to slow down as we got closer to the new optimum, but it's not clear that has happened yet. New beneficial mutations were still emerging and beginning sweeps as recently as 3k years ago. And of course environmental change continues. Then again, some of these changes may have slowed down, either because we are close to the optimum or because the world has changed so dramatically in the last couple of centuries. For example smallpox resistance doesn't increase fitness at all nowadays. Knock wood.
There _is_ an acceleration in morphological evolution over that period. The change per unit time is much faster than in the deep past. Brain size is down 10% over the last 30k years or so, for example, and skeletons are a lot less robust then even 12k years ago.
Increased population size made a lot of slightly-deleterious mutations visible to selection that hadn't been before, when populations were small, but the word is _slightly_. The mutations in that class have selective disadvantages well under a tenth of a percent - that means that their frequency has hardly changed over the Holocene. Not enough time.
Lastly: about smaller amounts of selection being sufficient to make significant differences in allele frequency in large, expanding populations: nope.
Personally, I'm more interested in the kind of evolution that does things, as opposed to the kind that doesn't, but tastes differ. The kind that causes phenotypic change appears to have accelerated enormously in humans.
"...it must be evolution mainly in genetic variants of pretty small effect. There is a very low upper bound on mutations that are both beneficial and of moderate or large effect, and as genetic evolution becomes more rapid it must pass a point at which it is increasingly reflective of smaller effect variants."
What is your reasoning? I know of yeast culture adaptation experiments that show modest adaptation and an exponential decrease in effect size with time. However microbial populations in the wild are far less limited when developing resistance. (Larger populations or gene sharing within the microbial community?)
Unlike the laboratory yeast experiments, the human population has grown so fast, expanded into so many different climates, and experienced so many cultural changes that I wouldn't expect the human genome to be close to any local adaptation peak.
My intuition is that for some traits your statement, "evolution mainly in genetic variants of pretty small effect", is right. Here is a prior comment that explains my reasoning:
How many different types of mutation/trait relationships exist? These types should have different adaptive landscapes. Here are some example types:
Constrained by physical laws: Improves one trait but at a cost. (E.g., brain size vs. metabolic cost.)
Balanced: Improves one trait, harms a different trait. Balance point is determined by environment. (E.g., vitamin D production vs. UV protection.) In some cases if the traits are sufficiently important then the traits may eventually de-couple.
Unconstrained: For rapid adaptation to the environment, the trait is relatively free to change without affecting other traits. (E.g., some immune system genes. Skeletal adaptations such as jaw or tooth structure.)
Network constraints: The trait depends on a complex regulatory gene network, metabolic pathway, or peripheral nerve-brain-hormone feedback control. Many other traits are affected by the same systems. The trait will depend on hundreds or thousands of "nodes" and hundreds of other traits are likewise affected. The biological system has evolved to be robust and canalized. Trait values are constrained by multiple, redundant feedback controls. Genetic variation is often masked, not obviously appearing in the phenotype. Some highly connected or highly important nodes are severely constrained, conserved for hundreds of millions of years.
I find the network constraints type most interesting. Suppose having more intelligence increases fitness. There are potentially thousands of mutations that could increase intelligence. But a mutation of large effect might well disrupt other important traits. Instead I'd expect to see a long series of mutations of modest effect that slowly push the network in a direction that increases the desirable trait. Now consider the recent paper on accelerated human adaptation and imagine large numbers of mutations of modest effect arising and sweeping local populations. What does this suggest with regard to DNA variants associated with intelligence variance? Or groups that have a mental abilities, personalities, and behaviors shaped by different environments for thousands of years? (Gene flow between groups will have mitigated this process somewhat.)
gcochran: I should have specified that by "small effect" I mean phenotypic effect, and indirectly selective effect. All else being equal the larger the phenotypic effect the greater the intensity of positive or negative selection, and the greater the likelihood of the mutation being deleterious.
Reduction in brain size and skeletal robusticity is certainly interesting. Although the energetic significance is fairly clear, the functional significance of recent brain morphology change is not, nor do we understand the genetic-development mechanisms.
Fly: Right, depending on how modularized or integrated (networked) gene actions are, selection for a few genes can pull a lot of other genes along with it.
"the greater the intensity of positive or negative selection"
Should have wrote "the greater the positive or negative selective effect."