erv

Super awesome review of viral quasispecies and what they mean, historically and currently:

Unfinished stories on viral quasispecies and Darwinian views of evolution.

They touch on so many good points, I could write about this review for a week! But just read it, cause I think you all can access it for free :P

One point I love: Quasispecies are like A Wrinkle in Time, connecting the origin of life to modern day viruses:

(on the origin of the quasispecies concept) First, there was the interaction between ideas from different fields of science such as physical chemistry and biological evolution. Second, there was the discovery that the concept of organizing genetic information in the form of quasispecies had relevance far beyond the idea of the origin of life. It was as though a time loop had joined microscopic and macroscopic knowledge together in our view of the world and established a link between the remote-in-time origin of life and current concepts about the genetic organization of RNA viruses.

Also, quasispecies give us a real-world framework by which we can test evolutionary/information theory concepts that were previously theoretical:

The addition of aspects arising from information theory complemented the theoretical framework. A multidimensional hypercube (cubes within cubes, as in a Russian nesting doll) served as a "space" for the theoretical representation of all the possible variants in a viral sequence. An important property of the space, referred to as a sequence space, is that all the variant sequences of a virus can be theoretically represented according to their kinship relation to the remaining variants. This framework served as a support for representing the fitness of each variant sequence in the sequence space (the fitness space) and for visualizing the correlation between fitness space and the distribution of the variants.

... Thus, several classic genetic principles applied to the evolution of the biological species, such as the Red Queen hypothesis, Muller Ratchet theory, and competitive exclusion, held up to experimentation and proved useful in viral quasispecies analysis. In contrast, experimental findings showed that the classic genetic concepts of wild type and mutant may not be applicable to molecular viral elements and that the idea of individuality does not relate to single, replicative RNA molecules but instead must be viewed in terms of a "clan" or quasispecies.

Theyve got a huge section on random mutation, fitness, and antiviral resistance, which several Creationists need to read.

And, a pretty funny commentary on the development of antivirals:

A drug reaches the last phases of development because it is predicted to have a reasonably good chance of being effective. Nonetheless, these predictions can fail when unexpected viral mutations that confer on the virus the ability to evade treatment develop. This outcome is so frequent that it raises the question of why scientists have been surprised again and again for decades by this "strange" phenomenon, instead of being surprised by the lack of flexibility of our concepts.

...There is enough experimental work to propose that at the RNA self-replication level, the "resistant" mutation is no more accidental than the "norm".

...Despite the fact that the concept of quasispecies was initially developed as a deterministic theory, chance is an essential element in all of these theories, conferring plasticity on the systems described.

EXACTLY! This is a point I have really tried to drive home on ERV:

The moral of this story, children, is that HIV-1 does NOT need to 'evolve' resistance to all the drugs in HAART therapy. The drug resistance mutations are already there, in every patient, for no reason at all. Just chance. Its just a matter of how fit those resistant viruses are, and they do regain fitness over time. In some unfortunate patients, their quasispecies contains viruses that are resistant and very fit-- you must change their drug regime immediately.

Random mutations, chance, are what a quasispecies is all about. The fact there are variants within a quasispecies that are resistant to any drug you happen to think up is 100% totally normal. Its not 'miraculous' or 'proof of a Designer' any more than water freezing at 32 F.

Thats just what quasispecies do. Thats just what water does. Its chemistry, not magic.

Fantastic review of quasispecies-- You all should read it :)