The Problem with Evolutionary Theory
The Theory of Evolution is quite robust in the sense that natural selection is seen to take place on fairly short time scales among bacteria and slightly longer timescales among British moths and the like. However, when one ponders the implications of the theory of evolution, it is hard not to disagree with the opinions of the "Neodarwinists", who believe that all the variety in life today has been brought about by the process of natural selection alone. This is because natural selection is in itself a somewhat destructive process, weeding most mutants out of a population and leaving those who by random chance or Fate have developed a trait which makes them more fit. Organisms aren't, however, going to randomly develop a fully-formed wing. Such an appendage would require quite a lot of random mutations over a long period of time. So would a smaller but perhaps even more profound change such as a feather. However, the troubling thing about such an innovation is the fact that the wing itself would be of no evolutionary advantage to the creature until it enabled flight. You could imagine a stunted wing which allowed short hops from branch to branch as an evolutionary advantage, much like the skin flap of a flying squirrel, but still the advantages of a stunted wing which requires modification of a working foreleg structure would almost certainly be selected against.
The reason I am talking about this is because a famous scientist, Lynn Margulis, came to speak at our weekly geosciences talk the Thursday before last. She is famous mostly for being the one who suggested that various organelles of the cell (chloroplasts, mitochondria) were actually formerly independent organisms, and were incorporated into the cells of other organisms as a result of a close symbiosis, when two organisms work together closely for the benefit of both (when two organisms live and work closely together for the benefit of only one, this is called parasitism, and it's often to the detriment of the other). In keeping with this theory, Dr. Margulis also believes that most of what has driven evolution forward is the incorporation of other organisms' genomes (mostly viral and bacterial) into larger organisms, with the wholesale adoption of their characteristics. Naturally, this is a much easier way to make sudden changes than if all of the innovation necessary for a major change had to be created by a random series of mutations. Instead, an organism can in a sense "try out" a new set of genes while living in symbiosis with another. If there is a good fit and both benefit from the living arrangement, the larger organism can begin facilitating the reproduction of the smaller one (or the smaller one can just attach its reproduction process to that of the larger) and slowly over time they can become one organism.
Dr. Margulis explains this with a series of examples. First she shows a video of a bacterium that is motile because of a large number of cilia. Some are short, energetic cilia and others are long, whip-like cilia. She then reveals that each of these cilia is an organism by itself, with the short cilia being a part of one species and the long cilia a part of another. All of these organisms work together to make the larger cell motile. This is a clear example of the type of symbiosis that could eventually lead to a more complex organism. She goes on to describe a kind of fly that functions well with a certain type of bacteria to help it digest its food. The bacteria's genome is not part of the fly's genome, but it when it lays its eggs the fly secretes a juice over them at the same time which is concentrated in this bacteria. When the new flies emerge from the eggs, they ingest the slime and the bacteria colonize immediately. Thus the flies are never without the needed bacteria to properly digest their food. A more extreme example of this is when they were examining the chromosome of another organism and they discovered that what appeared to be the end of the chromosome was in fact a complete bacterial genome attached to the chromosome. Thus it appears as if the bacteria joined its genome to the end of its host's chromosome, and thus when the host replicated, the bacteria replicated as well, taking advantage of the host's infrastructure. This is similar to viruses who use host cell infrastructure as a factory for making new viruses, except in this case the replication process is non-invasive.
This theory could explain somewhat complex evolutionary leaps, like the evolution of eyes. While it seems far-fetched that an organism could randomly mutate in a way that would make one part of it sensitive to light, it is fairly reasonable that a small, light-sensitive bacterium could exist, which would provide an advantage to a larger organism should it work cooperatively with it.
This theory has been gaining some ground since the 1980s, when people began to find other complete bacterial genomes hidden within larger organism genomes, but the idea that this kind of process is what drives evolution is still largely rejected by the community as a whole. Curiously, the reason for some of their inertia may be tied to issues completely unrelated to science at all. That is, the community preceives itself to be under attack from various religious groups, who say that natural selection cannot sufficiently explain the variation in life today. Scientists have responded to these groups with what can only be described as a mix of disdain, exasperation, and more recently, rancor. Because of their intellectual disdain for the people who are asking the questions, and the agenda driving the questioners, the scientists have formed a united front against them which strives to discredit the questions instead of answering them.
The truth is, natural selection the way we define it now is not a panacea for all the problems in evolutionary science. The way the scientific community blindly and pugnaciously defends their Neodarwinist canon is not so very different from the behavior of some of the religious groups they are arguing with. If the scientific community wants my respect, they must adhere to their own self-stated principles and remain an open, questioning group which is never satisfied to defend doctrines but strives always to test and reformulate them into something more correct. But to say "remain" suggests that they have ever been that way, which they never have been. Starting before Copernicus and encompassing Galileo, Keplar, Alfred Wegener and the Theory of Plate Tectonics, and almost every other great breakthrough in the history of science, the innovators have had to face down the immovability and intolerance of the scientific community. So maybe the neodarwinists aren't so new.
Dr. Margulis' theory may not be correct. The real answer may lie somewhere between that of the neodarwinists and the proponents of symbiosis-driven evolution, or it could be something different completely (I think the wing, for example, requires innovation in evolutionary thinking to explain). But to throw that statement out there and leave it like that is the biggest evasion of all. We must continue to challenge and test different ideas, continue to pursue end-member hypotheses until we discover exactly what it means to say that the real answer is "a combination of the two".
And until the scientific community starts doing that in earnest, they will continue to piss me off.
I yield the floor to NuTang[Ranor].