Darwinian Evolution versus Neo-Darwinian Evolution

I got a very interesting comment in a recent post in evolution from Carlos Villacorta:

hi Boscoh, I found a couple of misunderstandings of Darwin's ideas:

1. evolution by means of natural selection does not require "great dying off of the young and infirm". It simply implies a differentiated birth rate and therefore, a gradual change of the gene frequencies in the population

2. the fact that a population is growing does not stop it from evolving. A pool of polymorphic bacteria evolves while growing exponentially. So do viruses (and they do in real measurable time)

3. also note that, in order to quantify positive selection at a molecular level, you need high mutation rates (viruses) or hundreds of thousands of years of evolutionary time. But the fact that you can not detect it right now doesn't mean it is not happening anymore.

There's a lot of stuff that I'd like to unpack here, and it relates to the enormous gulf of modern biology from the biology of the 19th century. What is interesting from Carlos' comment, is that he speaks from the modern neo-Darwinian synthesis, which is a conceptually larger and more complex beast than what Darwin grappled with in the "Origin of Species". The difference is almost as great as the difference between Newtonian mechanics and relativistic physics.

Specifically, I want to emphasize the word species. It is one of the most fascinating discoveries of microbiology that the very notion of species is an incredibly fluid concept for prokaryotes. When plasmids swap genes between bacteria, there is no notion of a stable genome. Some bacteria have even an off-switch for fidelity in DNA reproduction during times of stress. As such, it has been speculated that bacteria families should not even be considered different species but some kind of supraorganism.

Even more so for viruses, which doesn't have an organism to take care of. I think Carlos uses evolution in the neo-Darwinist sense, where changes occur even for bacteria and viruses. In this case, we are far from considering the relatively simple cases of organisms, but quasi-stable organisms and naked genes. The virus is a naked piece of DNA that gets swap around. It is not so much an organism itself but closer to the mechanism of genetic exchange that occurs between bacteria.

If you read the natural selection argument in the "Origins of Species" then it's pretty clear that Darwin's argument applies to organisms with a very stable reproduction of the genetic material, in other words, a stable species.

Still, evolution can be boiled down to two steps, variability in a population AND natural selection. Now, it is essential in Darwin's theory that there is a natural degree of variation in a species for evolution to occur (re: his wonderful chapters on domesticated dogs and pigeons), but it is the culling involved in natural selection that leads to evolution, as described in the "Origin". For viruses, there is exponential growth, and hyper-variation. But this is only the first part of evolution, you also need the second part, natural selection. It is only when the virus is defeated by the immune system, when the virus is culled and the resistant strain survives, that we get the natural selection, leading to evolution of viruses. The difference with this rather abstract description and the discussion of young and adult in the "origin" is that clearly, a virus is not an organism with a life-cycle, and so one would have to warp Darwin's original arguments to make it work for viruses.

Whilst Carlos may claim I am misunderstanding evolution, it is really the misunderstanding of the neo-Darwinist synthesis of evolution, as applied to bacteria and virus (to which the notion of species is even suspect). My arguments work quite well for the evolution of species (of discrete biological organisms that self-replicate in a stable manner), which is precisely the kind of evolution discussed by Darwin in "The Origin of Species". Specifically, making an analogy with viruses, Carlos claims that we could still be evolving but that it's undetectable. Well the neo-Darwininist understanding of evolution points to genetic differences, and gene frequencies.

In contrast, the classical darwinian understanding would look at distinct physiological differences in the phenotypes, that is matched to the environment. For a good example of this, you should check out one of my favorite biology books, Jonathan Weiner's The Beak of the Finch. So in conclusion, I still claim that humans (which is a distinct species, as evidenced by the existence of a protective nucleus in our cells) have stopped evolving, but only in the Darwinian sense, meaning of course, the view expressed in the "Origin of Species".