let's see if she reads it...
Agent Smith: I tried to classify your species and I realized that you aren’t actually mammals. Every mammal on this planet instinctively develops a natural equilibrium with its surrounding environment, but you humans do not. You move to an area and you multiply, and multiply until every natural resource is consumed. The only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus.
Sarah: That's incorrect; viruses do adapt to their environment.
Me: No they don't, their environment adapts to them.
When there isn't enough to eat in an area, many higher species will cease reproducing; that is the instinctive equilibrium which (as the movie points out) humans for some reason do not have.
A common argument for pathogens adapting to their environment is that of the spirochetal bacterium Treponema Pallidum, which causes syphilis. Previously, this disease was very deadly, and caused very large and very odorous sores to cover the body. Oddly, it also evolved as an STD. This created a problem; who among you wants to have sex with a very stinky, very sick person covered in oozing sores? So the bacteria "evolved" (so say those who believe in a strictly Darwinian approach) to be less deadly, and less obvious. In much the same way, HIV is "evolving" to be less dangerous than it initially was - because it too is adapting to it's environment.
On a Darwinian level however, I disagree; it is not the virus or bacteria that is adapting, it is the environment that is adapting. "But those that do still reproduce were able to do so because they adapted to how the environment changed" some would reply.
No.
As a species, humans have become more and more physically attractive, more intelligent, stronger, etc. Why? Because (at least, until the last few decades) those traits are selected for, as an improvement. It is an active selection. Mendel bred for short stems, purple flowers, etc. The plants didn't adapt to that particular environment - they merely reproduced in the way the environment (Mendel) allowed them to reproduce. This works in the Darwinian model as well however. In such a system, changes are reactive - the change has to first exist, for it to then be more "fit." The selected trait doesn't just "appear" - it is selected for.
The alternative is something which has been called Molecular Evolution, something all life undergoes, but for which less complex organisms are much more dependent upon for change. This style of evolution is neutral; it is not driven by the selection of traits that are better suited for the environment, it is instead proactive - changes occur before they are needed. Changes that aren't needed at all occur as well.
The difference may seem worthless, moot; I, obviously, disagree. To say a bacteria or virus becomes less virulent because it is adapting to it's environment is to ascribe to such pathogens a form of intelligence of which it is not capable.
Instead, the different model answers the problem; under stress, molecules will change (which isn't itself evolution yet) in chaotic, sometimes dramatic, ways. What was Treponema Pallidum before it became the disease that killed people in just a few days? Who knows, maybe someone in North America spilled some tanning solution on a bacteria-covered hide, and it just happened to undergo a dramatic evolution. Impossible to say, but it is important to note that it didn't just become syphilis overnight; it started as something much weaker. Any Darwinian-evolution based argument for why it would become less strong is likewise an argument for why it would have never become that strong in the first place, as it would suggest the bacteria was spreading with it's effects becoming worse, within some population that didn't mind extremely stinky oozing sores in their sexual partners.
Instead, back to Molecular Evolution - under stress, "things happen." I admit I'm not a geneticist, nor even a biologist, but I have my elementary understanding of such things and I do know that there is substantial evidence to cellular stress causing changes in how proteins behave, which could in turn change the genetics that cell passes on. Further, the "stability" of this code...the resistance to this Molecular Evolution taking place rapidly and frequently...is by necessity something that becomes stronger (the stability) the more evolved an organism becomes. This is especially true for those organisms that reproduce via meiosis versus organisms like viruses and bacteria, which are agamogenetic. The reason is that dramatic and unstable genetic mutation in higher organisms would create offspring that could possibly be no longer compatible with other offspring from what had otherwise been the same species in the prior generation, a generation that had undergone some large amount of stress of some sort (plague, starvation, etc). Such offspring could be far more suited for the environment perhaps, but if they cannot reproduce - since they require a second organism like enough that their gametes can combine - than such traits are worthless. The genetic stability itself then is the most highly selected-for trait, all other traits being secondary to it.
At this point it is either less clear, or more clear, why I think ascribing to viruses the idea that they are themselves adapting to their environment is not something I'm comfortable with. They change, but they are always changing. In more complex organisms, those changes occur because of the "survival of the fittest" (or, more appropriately, "survival of the most well adapted"). In lesser organisms, that makes no sense - again, the virility of syphilis was a bell curve, not something that just appeared out of the blue killing people. It was obviously less virulent to the people who gave it to the Europeans before they brought it back to their homeland, but that is itself an argument that the environment is changing for such organisms, not that the organisms are changing for the environment.
So why did is HIV becoming less virulent, assuming it is as she said? Who knows - perhaps because the immune system is stronger in homo sapiens (especially caucasoids) than it was in whatever primate HIV came from? And this extra stress (from the immune system) affected the genetic material of the virus itself? I cannot say. However, logic would dictate that some such mechanism for change is what is causing the change, and logic would also dictate that the transmission of viruses benefits greatly by having almost no genetic stability at all.
What does this mean then? Imagine a world that is created by a god-being, and is instantly fully populated with all sorts of flora and fauna. One way this particular fictional environment can be classified is with a matrix that has as rows: agamogenesis and meiosis. As columns, it has: very stable genetics, very unstable genetics.
It would be little wonder that those meiotic organisms with very unstable genetics would be unable to reproduce for long, and would be gone in a few generations. It should also, however, be obvious that those agamogenetic organisms with very stable genetics would also be gone - assuming the host organisms have any decent immune system (and if not, they'd still be gone, having taken their hosts with them).
Neither event would be because of evolution. Instead, the events themselves would never happen in the first place (short of divine cause), because Darwinian evolution itself would not allow it.
So, the point? Viruses do not adapt, they change. Some of these changes are more synergistic with the environment - sure. Some of these changes are also potentially because of things the environment is doing to the virus. Consider the possibility of proteins within the host cells that have as their duty the job of causing chaos (recombination with something, or...???) to push a virus to the extreme where it hopefully does little more than kill the one cell it is in, or causes it to no longer be able to reproduce, or...? Who knows. For every virus mutation that survives and thrives, how many billions died? We have no way of knowing at all. Yet it is not the "fittest" that survive, nor the most well-adapted, because the virus fails if it survives at all. It, in the matrix, is by necessity very unstable, and thus is only successful if it does not pass on itself at all - if it does not, at all, survive. Finally, some of the changes are merely lateral - change for change, due the abstract trait "changes often" being selected for, versus an concrete trait of some sort being selected for.
The field is far too infant, and I believe in my wife's ability to improve it far too much, to assume such things as Darwinian evolution as a major mechanism for change. Mendel's genetics do not apply here. Darwin's theories are moot. Change merely occurs - in seeming chaos. Not adaptation - change for the sake of change. Change where even the less fit can survive, and perhaps flourish, just fine. After all, since meiosis is not occurring, it is irrelevant to 2 different variants of a virus that they are different; viruses are "me" and "not me." Weaker, stronger, it matters little. There is no Darwinian Evolution, no adaptation.
So concludes this insight into my very non-edumacated view of evolution in viruses.