I’m following your objections and listened to Jon Perry, who strongly disagrees with Noble, so… Coyne’s characterization of Noble was nevertheless off base.
Yes and no with respct to what is of interest… the point was that HIV insertions appeared random at first, but turned out to be non-random.
There are fuzzy boundaries here, but I would look at a virus as closer to an adapted structure (or system).
HIV insertions are random with respect to fitness.
How you look at things is a subjective opinion which isn’t part of science. That’s not to say your worldview is unimportant, but science is a bit picky when it comes to data. Again, this gets to the heart of one of the problems with EES. It appears to more about semantics, rhetoric, aesthetics, and emotions than it is about data and science. This is probably why EES has made more headway among the general public than it has in the scientific community.
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Are they random with respect to the fitness of the virus?
In my naive view, I would see a difference with presence of feedback mechanisms. Or a system which displays adaptability would be distinct from how a collection of water particles act in a gravitational field.
Yes.
The only feedback is natural selection. What determines if a genetic change is deleterious, neutral, or beneficial is relative reproductive success.
To be clear, HIV is a poor choice if we are talking about evolution of species because there are no endogenous copies of HIV that I am aware of. In other words, HIV insertions occur in somatic cells and are not heritable. Obviously, functional HIV insertions in CD4 cells are very harmful to the carrier, resulting in loss of CD4 immune cells and subsequent death if not treated. HIV has also evolved resistance (through standard evolutionary mechanisms) to some HIV drugs. It is also worth mentioning that there are pre-existing mutations in the human population that confer resistance to HIV infection.
Added in edit:
A better model might be koala bears who are currently experiencing a retroviral germline invasion of their genomes in real time. From my reading, the endogenized viral insertions look to be deleterious as a whole. In fact, some worry this retroviral invasion may lead to extinction in most populations of koala bears.
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I would argue that they are still random, with respect to fitness, but also because they are not determined.
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They probably are, but even if they’re not (that is, if the virus can choose better spots in the host genome for its own success), that has nothing to do with the role of random mutations in evolution. HIV insertions are not mutation in the virus’s genome: they’re something it does to another organism. HIV itself evolves just like everything else: by random mutations in its own genome.
With two exceptions that I can think of (*), all adaptive evolution occurs through mutations that are random with respect to fitness, mutations that are subsequently filtered by natural selection. If Noble gets that, then he’s right but he’s not saying anything fundamental about evolution. If he claims otherwise, then he’s wrong, whatever somebody on Youtube says about him.
(*) The two exceptions are the previously mentioned CRISPR mechanism, which has no long term effect on bacterial evolution, and intentional human genetic engineering.
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This is a very surprising turn in the discussion. No one that I can tell is claiming the virus makes a choice, but it does insert itself into the genome in a way that is advantageous to its survival. So that means it is a non-random behavior of the virus.
No one is claiming behavior is random, nor is the theory of evolution built on the concept of behavior being random. In fact, the theory can treat behaviors as alleles that are faithfully inherited by offspring and can be modeled through population genetics. Organisms acting in a way that increases their survival is a foundational concept of the the theory of evolution, and has been for over a hundred years. What you are essentially describing is adaptation.
This is yet another example of why EES has lost the plot. They seem to be arguing against a strawman version of the theory.
What are you talking about? HIV showing purpose was a point raised by a Neo-Darwinist.
In what way is HIV “showing purpose”? Is a river flowing into the ocean showing purpose?
The activity of HIV is deterministic. Viruses that don’t insert into the genome don’t reproduce, so we don’t see them. They disappear. The ones that do insert into a genome and reproduce are the ones we see, and continue to see. How is that purpose? I don’t see how you can describe the actions of non-conscious viruses as having purpose.