Sunday, January 27, 2013

Natural Selection is Dead. Long Live Evolution.

Lecture: Evolution in Four Dimensions

Click the image for an excellent talk by Eva Jablonka, in which she describes provocative new findings in epigenetics and animal behavior. The findings move natural selection farther toward the periphery of evolutionary theory. Phenotypes, as they differetiate during evolution, seem to self-organize, as do the differentiating cells in a developing organism. My contention is that evolution and development resemble one another because they are two appearances of the same process, which is development.

If one could lay Darwin's concept of natural selection next to the current model of evolution, one would have a hard time finding much in common between them. Outside of the vaguest generalization of the evolutionary process, captured in Darwin's phrase, "Descent with modification," nothing much of the original formulation survives to contribute to the current model, the so-called Extended Synthesis.

Epigenetics, niche construction, phenotypic plasticity and other intriguing new developments in bioscience sit at the center of that synthesis and throw into question the foundations of the Darwinian model. Despite evolution theory's provisional character, however, the fossils record descent’s modifications, and they taunt us: What during descent accounts for these modifications?

The conventional answer is natural selection, which is the assertion that random phenotypic variation, which bestows "fitness advantages" disproportionately to particular individuals of a given species in a local population relative to their cohorts, accounts for differential reproductive success among those individuals. Because they enjoy greater reproductive success, the favored individuals disproportionately influence the gene distributions of subsequent generations. The shifting gene distributions account for macroevolutionary change. That's the general idea.

If we were satisfied to say that differences in reproductive success among individuals are taken to be the cause of gene distributions observed in subsequent generations, then we would have a noncontroversial theory of evolution. But that would be not so much a theory as just a description of what is observed.

If we want to explain what is observed and take differential reproductive success among individuals of a species in a local population to be in itself an effect, then we need to look for that effect's cause. Natural selection in fact can't be that cause, because it is merely a restatement of the effect that it is supposed to explain.

A longstanding criticism of natural selection theory is that it is tautological, an exercise in circular reasoning, because what constitutes a fitness advantage can be supposed only after reproductive success is evaluated. Moreover, even after differences in reproductive success (the effect) are sorted out, and genetic causes supposed, those supposed causes cannot be teased apart from mere environmental contingencies, at least not in the wild, where evolution actually occurs. And this is despite the formulations of the discipline of population genetics, which claims to distinguish between causal mechanisms (natural selection vs. genetic drift) based on ranges and thresholds within statistical distributions of genes and traits. Labeling distribution ranges doesn't explain anything.

The role of contingency takes center stage in the critique of natural selection theory that Jerry Fodor and Massimo Piatelli-Palmarini offer. In "What Darwin Got Wrong," they argue against natural selection playing a significant role in the modifications that occur during descent and offer instead the mechanism of natural history, which is just whatever happens, the contingent interplay of endogenous and exogenous factors. Directionless and extemporaneous, evolution lurches, plods, this way and that, a concatenation of occurances and nothing more that can be approached systematically. Natural history, they remind us, "is just one damned thing after another. This should seem, on reflection, unsurprising, since, to repeat, natural history is a species of history, and history is itself just one damned thing after another." Shit happens, and that's how phenotypes get to be how they get to be, say these guys.

 Theirs is not a theory, they explain, because there are no theories of history, natural or otherwise. There are descriptive narratives. Theories describe what had to happen, but nothing in history or evolution had to happen, or at least not as it did, as seen through natural history. Fodor and Piatelli-Palmarini seem to conclude that the new developments in the bioscience that marginalize natural selection as a cause of evolution fail to constellate into any recognizable pattern. They conclude that evolution just isn't the kind of thing that lets itself be explained by scientific laws. Contingencies rule.

But, new developments in biological science do fall into a recognizable pattern. Evolution looks like a process of development more than it does anything else. Below are described four recent discoveries that reveal the mechanisms of development to be also the mechanisms of evolution. Evolution is regulated by developmental mechanisms, because it is a developmental process.

1. Conservation of DNA 
The cells that make up a body share a common genotype, the one that they inherit from the zygote from which they all descend, even though the descendant cells are of distinct types, each functioning in its distinct way: skin cells, muscle cells, nerve cells, liver cells, and so on--very different phenotypically but sharing the same genotype. They don't evolve from the zygote by natural selection. They develop from it, retaining its genotype despite themselves displaying vast phenotypic variation. We now know that this same relationship between conserved DNA and phenotypic diversity also characterizes evolution. Some researchers propose that science adopt the concept of a universal genome, the genotype of biology per se. This proposal grows from the discovery that genomes vary only slightly among species comapared to the vast variation among phenotypes. DNA, it turns out, is highly conserved across generations of organisms, from ancestral to descendant species. There is nothing in the dramatic diversity of species phenotypes that would have indicated the paucity of variation among the various species' genomes. READ MORE
In Development and in Evolution,
DNA is Highly Conserved.
2. Epigenetic regulatory networks 
How is it that highly conserved DNA can produce so many variant phenotypes, in development and in evolution? It is because genes are not the whole story. DNA sports an entourage of attendants whose job it is to regulate genetic expression, essentially to turn genes on and off as needed. The mechanisms of DNA regulation are called epigenetic mechanisms, and they take various forms, the simplest of which is methylation, the attachment of a methyl group to DNA to regulate local genetic expression. Epigenetic regulatory mechanisms control which genes get expressed and which repressed during the various stages of an organism's life cycle. In this way, a single genotype can produce a variety of cellular phenotypes and stabilize them so that they breed true, so that, for exmaple, a liver cell gives rise to more liver cells and not to undifferentiated cells that resemble the original zygote. Now, it turns out that epigenetic mechanisms also regulate the expression of species phenotypes from the universal genome and stabilize the phenotypes so that they breed true, so that, for example, frogs give rise to more frogs and not to ancestral forms. READ MORE
In development and in evolution,
epigenetic mechanisms originate and stabilize phenotypes.
3. Niche construction 
 Traditionally, evolution theory saw the natural world as a bunch of of ecological keyholes, called niches, into which the various organisms fit, more or less, according to their adaptedness. It's remarkable that this view held on for so long, given that one can observe how handily all kinds of organisms modify their surroundings to suit their needs. These days researchers recognize niche construction as foundational to evolution. But what happens to natural selection theory when environments are the effect of phenotypic causes? The whole thing blows up, and something like Ptolemaic epicycles are invoked to preserve the paradigm. In the context of development, phenotypes also construct their niches. Differentiating cells release chemicals called morphogens which spread through the developing body and regulate cellular differentiation according to concentration gradients. In this way the cells construct their niches in the developing body, chemically. Phenotypes and environments shape each other. READ MORE.
In development and in evolution,
differentiating phenotypes condition their environments to make them more hospitable. Living entities construct their niches.
4. Genetic pre-adaptation
The zygote contains the full complement of genes needed for all of the cell types into which its descendants will differentiate. Early generations of cells in a developing organism carry genes that are "pre-adapted" to the needs of future generations. That is, in its genotype the zygote carries genes pre-adapted to the needs of skin, muscle, liver, etc. cells. It turns out that the story of evolution is chock full of instances of ancestral species harboring genes that are pre-adapted to the needs of descendant species. As ongoing genomic studies unearth more and more examples of such pre-adaptations handed down from ancestral to descendant species, the orthodox view becomes less and less aligned with the empirical data. READ MORE.
In development and in evolution,
ancestors carry genes for features and functions that their descendants will need.
Evolution and development are distinguishable only by their spatial and temporal scales. Evolution just is an instance of development. This interpretation poses a question: "What kind of creature is developing?"

The star larvae hypothesis answers: "On a clear day, you can see an instance of the type overhead. On a clear night, you can see many instances."

I invite Eva Jablonka and the other contributors to "Evolution, The Extended Synthesis" to evaluate the case that evolution operates by mechanisms already known to regulate development and to acknowledge that evolution looks more like an instance of development than it looks like anything else.

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