So, just because, I think that it might not be a bad thing to review Patrick1000's arguments in this thread and deal with them in simplified format. If anyone would like to add to any of these, please, feel free. I'm going to try to deal only with the relatively major ones, though, myself. Or just ones that really stand out. Also, please correct me if I make mistakes, not that I likely needed to say that.
I cut off at about page 15, either way.
Argument 1: The mechanism for evolution, as he understands it, seems implausible.
Responses: 1. Given the presentation, it's been an argument from incredulity, and therefore, is not a credible argument. One can believe anything, but that says nothing about the veracity of the belief, without being able to back up the position.
2. The mechanism for evolution, as is it stands currently, has been demonstrated to work as described in numerous ways. Computer simulations, for example, are a fine way to test the process, theoretically. Paleontology and fossils do a fine job of dealing with history. DNA evidence matches expectations. The list goes on.
Given all this, it is up to the groups claiming the problems to, at the least, demonstrate what they are.
Argument 2: "Just because one can soar quite high in a hot air balloon, that does not mean one can climb on and ride the balloon to the moon" as applied to evolution.
Response: Bad analogy. While the statement is true, the comparison to evolution is not, without demonstrating some evidenced insurmountable barrier that cannot already be easily explained in terms of evolutionary theory. Until said barrier is elaborated upon, the point fails, regardless.
Argument 3: "Present your molecular evidence for birds from dinosaurs. Show us the EVIDENCE that a dinosaur became a bird over time by way of a series of random, undirected, unrelated mutations."
Response: 1. Dinwar's repeatedly pointed out Jack Horner's research and addressed this.
2. This request is disingenuous in the first place. "Show me that my straw man representation of evolution is actually the case." would be a better way to sum up this, in addition to asking for what is an impossible standard of proof. Namely, "show me that this DID happen, because showing me that it is completely logical and reasonable to assume that it happened how the experts say, for the reasons that they say it did, is not enough."
3. Random, undirected, unrelated, etc will be dealt with later.
Argument 3: Concedes that common ancestry is, by far, the more likely option, but keeps coincidence on the table as a possibility for another option.
Goes on to say that just because common ancestry is probably the case, that doesn't automatically mean that we understand how things happened.
Response: 1: Entirely correct, at the level of "possible." At the level of "probable," this is nonsense.
2. This screams "Creationist" argument from start to end.
3. The mechanism for evolution, as is it stands currently, has been demonstrated to work as described in numerous ways. Computer simulations, for example, are a fine way to test the process, theoretically. Paleontology and fossils do a fine job of dealing with history. DNA evidence matches expectations. The list goes on.
Given all this, it is neither logical nor reasonable to withhold support from modern evolutionary theory. Certainly, there is more that can be and will be learned, at this rate, and it is unlikely that evolutionary theory is complete, but the issues with it, given current evidence, are far, far smaller than would warrant accepting this as a valid argument against modern evolutionary theory.
Argument 4: Just because we don't have another naturalistic mechanism, it doesn't mean that evolution is a good mechanism and should be believed.
Response: 1. True, taken at face value. The moment, however, that you understand that it is currently the only viable theory BECAUSE of the evidence, out of many others, this breaks down, quickly.
2. A good mechanism explains the evidence. Evolution explains the evidence. Therefore, Patrick1000's premise is simply false. It's possible that there's better, but provisional acceptance should not be withheld for "maybes."
Argument 5: Cytochrome C challenged evolutionary theory. Evolutionary theory should not have been allowed to change and adapt to instances like that.
Response: It doesn't challenge modern evolutionary theory, which is what's actually in question. Neutral mutations are accounted for in modern evolutionary theory and the function that Cytochrome C performs is essential enough to the viability of an organism that changes to the functional portions of it will almost certainly have extreme negative effects on the viability of the living thing in question. That said, there was absolutely nothing about the case of Cytochrome C that actually contradicted evolutionary theory's mechanism, therefore, there was and is no reason to say that the theory could not accept novel applications of its mechanism.
Argument 6: "How can you be so confident that the evolutionary mechanism presented to you is TRUE, if you do not have the slightest idea what the mechanism is purported to create in the first place?"
Response: Non sequitur. These two things are not related in such a way as to make this a valid argument.
Argument 7:
Finally, God would be dead once and for all......
Just in case you didn't notice Dinwar, were the fossil record to actually provide solid proof that the conventional(UNDIRECTED, UNINTENTIONAL) biochemical mechanism of evolution was a FACT, God would POOF!, no longer be a possibility, let alone a fact, proven out of existence she would finally be, once and for all. The fossils, "proving" the molecular mechanism, would prove that God never was, as there never was INTENTION.
Response: 1. Irrelevant. Implications about whether God exists have nothing to do with whether evolution theory is correct.
2. Dramatically and incorrectly characterizing issues makes for blatantly bad arguments. God could not "POOF" if it never existed. God could not be a fact, if it never existed.
3. "Solid proof" strongly suggests basic misunderstandings of science, in general. Science disproves. Science does not prove.
4. Only a very limited subsection of versions of deities are directly contradicted by evolutionary theory. The versions of the Christian God upheld by most Christians are not contradicted, contrary to Patrick1000's and a number of Creationist's claims.
5. Undirected and unintentional are dealt with later, given how common the claims are.
Argument 8:
There may be some wholly natural, heretofore unrecognized "biologic variable"(not related to God in any sense) generating, being responsible for, the dynamic of intention/direction/purpose in the development/evolution of living systems.
Could we have "non random mutations" without a God, without an external director?
Response: 1. Without either evidence for this, nor a demonstrated issue without this, there is no reason to accept this to be the case.
2. Proposing "psychic DNA" as Dinwar put it, rests on a number of unscientific and potentially untestable assumptions.
Litany of claims, which I left out numerous arguments that deal with them. "Evolution is...
"Random mutations" - No. Mutations can be considered to be random, but that's just one of a number of mechanisms that form evolutionary theory. Natural selection, which is another extremely important mechanism in evolutionary theory, is not random.
"Unrelated mutations" - Yes. That said, each of Patrick1000's usages were part of an argument from incredulity.
"Purposeless" - Depends on the form of purpose. The purpose of evolutionary theory is to explain the evidence gathered, form conclusions based on that, and make predictions, based on those conclusions. So far, those conclusions have been upheld.
Asking what the purpose of evolution is, is similar to asking what the purpose of gravity is. Blind speculation in an attempt to answer what may very well be an irrelevant question.
In the sense it's being used? Creationist nonsense. "What's the purpose of life?" Neither evolutionary theory nor science in general ever claimed to answer that question, beyond a mechanistic level.
"Undirected" - No. Natural selection counts just fine for direction.
In the sense that it's being used? Either Creationist nonsense or general nonsense.
"Unintentional" - Sorta, yes for a nonstandard usage of unintentional. Specifically, intention is utterly and completely irrelevant to evolutionary theory. It says absolutely nothing for or against intentionality. Nor can it, really. It can demonstrate that specific forms that the intention might take are highly unlikely, when combined with other fields, but that's about it.
"Not testable" - Every new piece of evidence tests the theory, given science. Every. Single. One. A number of examples of ways to test and falsify evolutionary theory were given in the thread and can easily be found elsewhere. Note: Creationist claim.
"Not falsifiable" - See "Not testable."
"Not scientific" - No real evidence was given to back up this claim. See "Not testable" for summary.
"Starkly anti-theistic" - No. Evolutionary theory is atheistic, in the sense that all science is atheistic, namely, "without God or god(s)." God is not part of the equation for lots of excellent reasons. Given that God is not part of the equation, science is not and CANNOT be either theistic or anti-theistic. Any and all arguments that say otherwise are wrong, to the point that they could never be right.
As an aside, excessively frequent cases of resorting to God as somehow relevant, the prevalence of logic and claims that only really make sense to make if one's working from a Christian Creationist's worldview, Creationist tactics, even with the concessions, quotes like "the gospel of conventional neo-Darwinism," praise for ID, and so on all point very strongly to Patrick1000 being either a Creationist troll or parrot. This may not be true, granted, but is highly likely. Just in case anyone else hadn't come to that conclusion on their own.