April 9, 2013 | David F. Coppedge

The Hunt for Selection in the Genes

One might think that 154 years after Darwin’s book about it, natural selection would be empirically obvious.  The journal Nature went on a search for it in DNA.

Nature‘s piece, “Evolutionary Genomics: Detecting Selection” begins with hopes and worries:

Advances in population genetics and genome sequencing have made it possible to identify anonymous fragments of DNA that have undergone selection. This yields some evolutionary answers, and a panoply of puzzles.

Two things must be clarified before detecting natural selection.  One is that artificial selection has nothing to do with it.  Artificial selection is intelligently designed for a purpose; natural selection, by contrast, is unguided and purposeless.  Even survival fails as a purpose; it’s only a consequence of selection, not a goal of selection.   The other is that natural selection is more than variation.  To differentiate itself from creationism, natural selection has to overcome small changes within a population that creationists willingly acknowledge help an organism adapt.  Evolutionists need to demonstrate innovation, an undirected change providing new functional information.  A mutation that produces “more of the same” effects, like a change in enzyme production, does not qualify.

With that in mind, what did the Nature article find in its selection hunt?  The authors acknowledged the “awesome power of artificial selection” directed by the mind of man, such as in dog breeding, but claimed that dogs and humans have been partners in natural selection for 10,000 years in a case of “parallel evolution.”  They praised a recent paper in population genetics that “promises to revolutionize evolutionary biology, by challenging us to detect traits affected by evolution on the basis of genotype rather than an organism’s characteristics, or phenotype.”  Then they praised two other papers that “rise to this challenge and show how hypotheses about an adaptive human genotype can be tested in controlled experiments.”  Sounds impressive.  But is this something new?  What’s gone on in the past 154 years of research on natural selection?  It must not have been very revolutionary.

Together, the three papers are a wonderful intersection between genomics, population science and experimental genetics — a synergy that has tremendous potential for teaching us more about how and why organisms evolve.

Unfortunately, the evidence cited in the first paper concerns genetic changes found between wolves and domestic dogs.  Even the staunchest creationists put those two animals within the same created kind.  The genetic changes, moreover, were in the “more of the same” category – enhanced ability to digest starch, presumably from crumbs dropped from the dog owners’ tables.  Nevertheless, the authors were ecstatic that dogs and humans both produce more starch-digesting enzymes: “the same molecular mechanism has acted on similar genes in different species exposed to the same dietary pressure — a striking example of parallel evolution.

The other two papers merely found evidence of “selective sweeps” without tying the changes to phenotypic change.  “Even when causal relationships seem obvious, caution is warranted,” the authors warned, noting a case with ambiguous results.  Is detection of natural selection in human populations even possible?  “Classical genetic studies are the optimal way to establish causal relationships, but in many cases these are impossible because the appropriate populations do not exist.”  The third paper invented a “model organism” to tease out evidence of natural selection.  Its researchers concluded that a mutation in East Asians produces thicker hair and more sweat glands; they verified that effect in mice (see 2/19/13, last section).  But that’s another example of “more of the same” variation; people already had sweat glands and hair, and so did mice.

Remarkably, this article, poised to showcase the power of natural selection, ended with ignorance:

Kamberov and colleagues’ study is an exceptional example of experimental genetics, but does it provide, as the authors suggest, a general framework for assessing candidate adaptive mutations? Genetically altered mice are a powerful experimental tool, but the extent to which recent positive selection in humans acts on pathways and amino-acid residues that have been conserved across mammalian evolution is uncertain. More importantly, it is often not clear how to investigate positively selected genomic regions for which the target gene, let alone its action, is unknown. And so a major challenge for population genomics remains the construction of meaningful null hypotheses. As Charles Darwin, the best known evolutionary biologist, once said, “It is always advisable to perceive clearly our ignorance”.

So even though the paper they praised was “an exceptional example” of looking for natural selection, the authors of this article worried its conclusions are uncertain.  Worse, (“more importantly”), it’s not even clear how to look for selection in genomic regions where the action is unknown.  How does a researcher compare the findings with a null hypothesis—a baseline hypothesis that posits no effect from the cause-when “meaningful null hypotheses” are lacking?

That’s why the summary of this triumphantly-titled article spoke of “some evolutionary answers, and a panoply of puzzles.”  Even the answers, though, wouldn’t impress a creationist: no clear evidence of positive selection toward new functional information was presented.  One can only hope the authors of all these papers are following Darwin’s advice to perceive clearly their ignorance.

And they call creationists ignoramuses.  OK, show us, Darwinites.  Darwin believed people have bacteria ancestors.  All the advances beyond bacteria for every species on earth—be they wings, eyes, or brains—are supposed to be the result of natural selection.  Yet here it is, 154 years after the Origin, and evolutionists still cannot show any example in the genes bigger than starch digestion in dogs, or thicker hair and more sweat glands in certain humans (all interfertile members of the same species, Homo sapiens).  The authors admit the studies are unclear.  It’s appalling that the sole theory allowed to be presented in public school science classes is ignorant, not only of examples, but of ways to test them.  What hath evolutionary theory wrought?  A panoply of puzzles!  Schools are teaching ignorance!

If evolutionists do not perceive clearly their ignorance, those of us who do perceive it need to hold it up to their faces.  We can quote Darwin for support: “It is always advisable to perceive clearly [y]our ignorance.”

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