Theory of Evolution

I saw an interesting documentary on a local national station a few days ago. I believe it was called "The War on Evolution"; it detailed the "Intelligent Design" movements' "assault" on evolution and its attempts to have intelligent design taught in classrooms as an alternative theory. This led to a few faculty members of a highschool somewhere in fucktown USA to vote to start teaching this theory in schools; this prompted several parents to sue the school and was taken to the supreme court, I believe. In the end, the judge ruled that "intelligent design" was not a scientific theory but the application of religious teaching, which is barred from public schools. "Intelligent Design" is a movement which attempts to clarify its difference from "Creationism" (ie, that life was created by God); they promptly leave out references to a specific creator and simply argue that the machinations of life are so complex that some sort of intelligence must have been responsible for its development. Funny part is, though, "intelligent design" theorists are almost exclusively devout religious people.

That's no coincidence. The Intelligent Design nonsense was specifically engineered to serve as a trojan horse for religious belief. In fact, one of the original ID texts, Of Pandas and People, is just a young-earth creationist text with the specifically Christian material excised and 'creationist' replaced with 'intelligent design proponent. Google 'cdesign proponentsist' for more information.

Anyway, I thought it very interesting, and I thought the arguements of both the evolutionists and intelligent designists were good.

Pseudo-scientific charlatans always try to make their fallacies and lies sound believable to the lay observer. I don't mean to insult you, but you can't possibly know very much about biology if you thought the arguments advanced by the ID crowd very convincing.

EVOLUTION: Essentially, in laymens terms, evolution is a process where the DNA code of all living things mutates slightly from generation to generation, prompted by changes in external environmental conditions and needs. This process of "random mutation" eventually splits species' genetically from one another; those species that have achieved mutation beneficial to their environment prosper, while mutations leading to deficiencies in adaption lead to extinction.

Not quite right. Strictly speaking, biological evolution is the change in the gene pool over time. There are a host of related concepts that need to be understood in order to properly grasp evolution, primarily the modern synthesis, the fusion of Darwinian natural selection and Mendelian genetics. You can't say that the "random mutation" is what leads to speciation events, as selection forces play the major role there.

The second part of the arguement was the claim by some mathematician

William Dembski most likely.

that mathematically, the process of randomized mutation could not have accomplished such a variety in the complexities of life as we see it today -- even over a billion years. He argued that the rate of mutation and evolution we have viewed over the past several hundreds of years of scientific analysis have shown that even over the course of a billion years, life could not have evolved into its various forms by a generation-to-generation random mutation.

Otherwise known as the 'argument from personal incredulity': "Well, I can't figure it out, so it must not have happened."

What's my take on this? Well, the intelligent design arguement is compelling, but has some loopholes. For one, in the case of the flagellan, it is quite possible that the mechanics for the device were evolved gradually without removing entirely certain parts. Rather than 10 ball-bearing like devices, earlier models may have had 4 or 5; the appendage could have manifested itself from a simple growth that generation-by-generation was used for locomotion.

You are right here. In addition exaptation (co-option of characteristics for other purposes) plays a role; a simplified form of some trait may not perform its current function, but it may have historically served some other function. I believe that the mentioned bacterial flagellum is homologous to the bubonic plague virus cell injection mechanism.

Mathematically, science has in the past decades that the mutation responsible for evolution can at times become drastically accelerated; case in point, humanity, over the past several hundred years, has seen a huge increase in average height; this is in part due to the increase in proteins and dietary intake, but rather than being the direct cause, that formed the fuel which, genetically, was used to increase our size.

I do not think that this has much to do with evolution. Like longer lifespans, it is more related to better nutrition and medicine.

I am still "on the fence", as it were; scientifically, neither theory has been proven beyond a shadow of a doubt, as both rely on methods of analysis that do not exist; time travel, or the ability to analyse something over the course of hundreds of thousands of years to qualitatively and quantitatively assess its evolutionary patterns.

Not true. This requires a little more in-depth explanation.
The idea of evolution/common descent as a modern scientific theory first arose when people started travelling the world and digging shit up a couple hundred years ago. They found fossils: preserved remains (including skeletons) of animals and plants, a great many of which did not exist anymore. Then some people noticed that some of the extinct animals, while definitely distinct, still bore notable resemblances to each other. Some of them, in fact, could be arranged so as to suggest a progression of animals whose features slowly changed such that the more recent creatures more closely resembled the modern forms. Given this, evolution and common descent are reasonable inferences.
Many people latched onto this idea of gradual change of forms over time in its early days. The trouble was, nobody was particularly sure how exactly they changed. Then one day Charles Darwin was wandering through the Galapagos when he noticed some finches. Specifically, he noticed that the finches on the different islands had differently shaped beaks and stuff, and furthermore that each variety of finch possessed features suited to its own island. An idea occurred to him: within every generation, there is great variation between individuals. Surely, he reasoned, some individuals will be better suited to survival and reproduction than others. Those individuals, therefore, will survive and reproduce more often than the others, meaning that the traits conducive to survival and reproduction will be more prevalent in the succeeding generations. This effect, over time, could lead to drastic changes in the forms of creatures.
Darwin returned home and spent the next few decades gathering evidence for and refining his theory. Then he published The Origin of Species, and evolution took the world by storm. Within fifty years, the vast majority of biologists had come to accept it on its merits. Mendel's theory of genetics gave a viable system of heredity that complemented and helped better explain natural selection.
By the fifties, geographic as well as paleontological evidence supported evolution. As an example consider the genus Homo. The earliest Homo fossils were found in southern and central Africa or thereabouts. Later Homo species are found in northern Africa as well, later species in the Middle East, and then Homo sapiens emerged, which is found all over the world.
Then along came molecular biology. You have, I imagine, heard the claim that the DNA of humans and chimpanzees is 98% identical (the number may actually vary due to conflicting definitions of 'identical', I believe). Forgetting that, the fact that all life has DNA at all (except for like, retroviruses and shit) is extremely strong evidence of common descent. Then when you do bring phylogenetics into the mix, evolution and common descent can no more be seriously argued against than the fact of gravity can be. DNA analysis reveals phylogenies supported by all the paleontological evidence. No time travel required. There's really not much more to say.

And there are some things in this world which continue to boggle my mind, and make me question either the legitimacy or the power of evolution. A few years ago I watched a documentary on North American life and one of the animals "interviewed" was a mollusk native in some rivers in the US.

This mollusk was peculiar in that its reproductive cycle depended on jettisoning its offspring -- thousands of them -- into the mouth and gills of salmon and trout populations living in the river. There the offspring would clamp down on the gills and draw sustenance, until they got older and dropped off.

To facilitate this transfer, this mollusk evolved a little appendage of its tissue which it stuck out of its shell. This appendage was made to look exactly like a minnow; with everything from backfins, to matching colour and spot patterns, to little fake eyes, to a little fake mouth that opened and closed, just like minnows. This would draw their nursery fish in, who would attempt to eat the minnow, only to have a cloud of tiny little clams sprayed into their faces.

So how did this creature, which has neither ears or a nose or any sort of intelligence and no understanding of its surroundings, develop such an exact replica in order to lure fish in for its reproductive cycle?

How, genetically, did its DNA "know" to evolve such an appendage? Was it really a process of genetical mutation over the course of millions of years, whereby "successful" mutations would lead to fruition whereas "unsuccessful" mutations would lead to a mollusk incapable of drawing fish in to plant its young, and thus die out? If so, what did the mollusk do before it evolved this appendage? Surely the species survived without it at some point, and if so, how did they die out? Did something in the environment change to prompt the development, something that negated the ability of non-appendaged mollusks to die out?

Perhaps the mollusk used to reproduce by a different method, and one day one was born with an odd, amorphous growth sticking out of it (not at all implausible). A single nursery fish mistook it for food and tried to eat it just as the mollusk was releasing its offspring. There would now exist a population of mollusks who were marginally more succesful at reproducing than the rest were. Within this population, those mollusks more succesfully able to disguise themselves as food would be produce more offspring, so even the tiniest difference that made this growth better resemble a minnow would be an advantage - be it a small spot that could be mistaken for an eye, or a change in the shape to give the appearance of fins. Given that, it is inevitable that it should eventually come to closely resemble an actual fish.
That right there is an entirely plausible story. Without molecular evidence to back it up, it is largely worthless (and probably untrue), but I think I have proved my point re: the ability of evolution to create novel features.
When you find yourself doubting the likelihood of some trait arising through purely natural means, all you need to do is remember Orgel's second rule: evolution is cleverer than you are.

Minor terminology niggle: 'gene pool' refers to the aggregate of all genomes for a specified population. Therefore any individual being born changes the composition of the gene pool, and yes, this single act does qualify as 'evolution'.

To answer your question: initially, favourable mutations would have been confined to a single area. As the variety of creature with the new trait outperformed the others, it would eventually lead to their extinction in that area. The mutation would spread to other areas through migration/inter-population breeding. A deer that belongs to one group might get lost one day, meet up with another group and join it, introducing the traits of its original population. Or else the mutated variety becomes so successful that its original home can no longer sustain the exploding population, so there is a tendency to migrate outwards into new areas, displacing the animals already living there. And yes, it is certain that all modern mollusks bearing this faux-minnow trait are direct descendants of a single ancestral mollusk of a species that did not bear it, an individual that had some primitive form of the trait. Consider that the most recent common ancestor of all humans, who every living human is a direct descendant of, lived only around three to five thousand years ago (I think?).

If there is a barrier to reproduction between two populations, and one of them develops an advantageous new trait, then of course they will evolve in different directions. Consider the example of Indian and African elephants. Looking at a map, it's easy to see how an initial population in, say, the north of Africa (maybe? I don't know where elephants originated) could have migrated to India over time. However, since crossing the Middle East is not the easiest trek, nor the shortest, it is not likely to happen often, leaving ancestral populations of elephants in India and Africa genetically isolated from each other. They then proceeded to evolve in separate directions, each accumulating different sets of mutations, and today they are different species, unable to reproduce with each other to create fertile offspring.

[FONT=Arial]I believe you're looking to have a discussion over abiogenesis, not evolution. Theistic evolutionists are aplenty.
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Although ID might at first glance appear to bear some resemblance to theistic evolution, it differs in that ID proponents ('IDiots' in those sections of the internet dedicated to combatting pseudoscience) claim that there is positive evidence of intelligent interference in the evolution of life. Theistic evolutionists just say "God guided evolution in the direction of intelligent life" or "God gave early hominids a soul" or somesuch nonsense. A theistic evolutionist will probably not claim that God personally constructed bacterial flagella and stuck them on bacteria.

And RNK: it occurs to me (actually it occurred to someone else and I just remembered reading about it a while ago) that an excellent metaphor for biological evolution is the evolution of language. Consider some individual in England who can trace her ancestry back through English families to a thousand years ago. Now she speaks the same language as her parents, doesn't she? And they speak the same language as their parents, who speak the same language as their parents, and so on back for a millennium. But a thousand years ago, people in England were speaking Old English, a completely different language to Modern English (find a copy of the original text of Beowulf if you don't believe that!). If someone were to speak to this girl in Old English, she would have no clue at all what was being said, and yet she can claim an unbroken line of descent from people who spoke it every day. What happened is that gradual changes in the language built up over time, the successful changes eventually becoming present over the entire countryside.