Joined: April 2006
Allen MacNeill, here:
Vis-a-vis the list of "evolutionary mechanisms" at my blog (http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html):
Actually, the list is intended mostly as a compendium of all of the major mechanisms known that cause phenotypic variation in populations. As Darwin first pointed out, evolution by natural selection has three prerequisites:
1) Variety: there must be real differences between individuals in a population;
2) Heredity: some of these variations must be heritable. Darwin said from parents to offspring (i.e. "vertical" heredity), but recent analyses indicate that "horizontal" heredity (via transformation, viral transduction, and some neo-Lamarkian processes – see Jablonka & Lam/2007/Evolution in Four Dimensions) are also valid mechanisms of heredity; and
3) Fecundity: individuals must reproduce, generally at a rate that exceeds replacement. Given these three prerequisites, the following outcome is virtually inevitable:
4) Non-random, unequal survival and reproduction – what Darwin called "natural selection."
The list at my blog was mostly concerned with the first of the prerequisites listed above; that is, the sources of variation between individuals in populations. As I pointed out in my blog, creationists (including IDers) generally refer to the theory of evolution (ToE) as consisting entirely of "random mutation and natural selection" (RM & NS). What my blog post was intended to illustrate was that neither of these are the case. Random mutation (defined the way most creationists define it, as single nucleotide point mutations in DNA) is only one (and not the most important) mechanism for producing variation within populations. There are at least 46 more, and each can be further subdivided into different, but related mechanisms.
Furthermore, natural selection isn't the only outcome of the three prerequisites. As any good evolutionary biologist knows, there are at least two other major processes – sexual selection (which some evolutionary biologists, including myself, consider to be functionally separate from simple natural selection) and random genetic drift (a la Sewall Wright). This leaves out other less common processes, such as meiotic drive, which also qualify as outcomes of the three prerequisites, but occur under more restricted circumstances.
Vis-a-vis "nested hierarchies":
It is the case that a general in an army cannot himself be a "nested hierarchy", but that is a logically trivial point. It is also the case that an army is clearly a nested hierarchy, and that a general commanding an army is part of that hierarchy, just like the pope is part of the nested hierarchy of the Roman Catholic church (from whence we originally got the term "hierarchy", by the way; the pope is the "hierophant" of the catholic "hierarchy").
Biological systems are perhaps the most obvious and paradigmatic examples of nested hierarchies in the natural world. However, they are not "perfect" nested hierarchies, at least at the level of gene sequences, as there is apparently a lot of pretty promiscuous horizontal gene transfer going on, even between kingdoms (e.g. bacteria and animals, even humans), which as Ford Doolittle has pointed out makes a single-rooted "tree of life" quite implausible.
Personally, I like to refer to life on Earth as the "mangrove of life", as there was apparently a lot of diversity fairly early one, with lots of horizontal gene transfer, followed by a "constriction" within the multicellular eukaryotes (probably as a result of the complexities of meiotic cell division), followed by another radiation into the four kingdoms (Protoctista, Fungi, Plantae, and Animalia).