Paul L. LaClair’s post is here.  His comments are in blue

Paul,

“That the universe as we know it had a beginning does not mean that we understand the origins of that universe in the only context we know, which is space-time, beyond saying that a Big Bang appears to have occurred; in other words, we still have no idea why it happened that way.”

You are side stepping the argument I made, by trying to add additional conditions that were not part of the argument. I did not claim that we understood the origins. Again the argument I made is a simple deductive argument (technically a disjunctive syllogism). The only way to refute it is to show that the logic is invalid, or that one of the premises is false. If the premises are true, and I believe they are, and the logic is valid, which it is; then the conclusion must be sound.

Still, you have pretty much supported my argument, if “in the only context we know” is the natural world. Then any other means would be the “non-natural explanation” of the argument.

Granted there may be some other option that we have no evidence for or understanding of, but in that case, who is the one that is relying strictly on the evidence, and who is the one ignoring the evidence because it points to something that their worldview says cannot exist?

“In no way does anything we know suggest that consciousness predated matter, which is theism’s seminal claim.”

Again my argument said nothing about consciousness. This is the classic straw man fallacy. Change the argument to something you think you can more easily refute.

“On the contrary, everything we know about consciousness says that it is the product of an organic (material) brain.”

You already mentioned this, and I already addressed this point by pointing out how irrational such a line of reasoning is, but you have yet to reply to my objections. In case you missed it, here are my comments from an earlier post:

As for your views on consciousness, this is a classic example of the problems with the bias of naturalism. You basically have claimed that only natural answers are permissible, and then claim as support for this view that the only explanations we currently have for consciousness are natural. Do you not see the glaring logical fallacy in this? Frankly we know very little about consciousness, and there are some very significant questions such as the nature of Free Will that remain unanswered.

“The naturalist does not assume that ‘theirs is the only set of assumptions that allows for the advances of science.’”

Ok. That just means that the naturalists I was referring to did not understand naturalism in the same way you do. I raised that point because this was the common objection made by naturalists in the past to the claim I made that “There is nothing that makes the naturalists assumptions inherently better or worse.”

“[The naturalist] merely observes that scientific method is the only reliable means by which science had advanced,”

Something I would agree with, though if taken rigorously it becomes circular.

“and draws the logical conclusion from that: there is no reason to engage in wishful thinking about a god or gods, since this thinking has not led to any scientific advance but on the contrary has tended to retard scientific progress.”

There are several problems with this statement. The first is the phrase “wishful thinking about a god or gods.” I see two ways to take this phase. If taken literally, I would agree that we should not engage in wishful thinking about god or gods. Thus this would result in a statement that I, and probably most theist, could actually agree with. However I suspect that this was not your intent and that instead, you were simply using the phrase, “wishful thinking” as a way to denigrate theistic thought. If so this is slanting and hardly makes for a rational argument.

“since this thinking has not led to any scientific advance but on the contrary has tended to retard scientific progress.”

Assuming “wishful thinking” was a reference to all theistic thought, (and if not I apologize in advance) then you are again repeating old arguments that I have already addressed, but which you have ignored. As I pointed out the last time you used this line of argument:

[This] is simply wrong and either ignorant of the history of science, or at the very least highly selective in it view of history. It also assumes a unity in the concept of “theological framework” which simply does not exist. There are in fact a variety of theological frameworks. While some are “affirmatively harmful” not all are.

But to expand on this a bit further, there is a reason that science developed in Western Europe when it did. Classical thought certainly played a role, but so did the Judeo-Christian world view of a world created by a rational God, a rational God that created a universe that could be figured out using reason. One can certainly argue that such a view is not required for science, but this does not change the history that it did play a key role in what actually happened. This can be seen in Kepler, who after discovering his laws of planetary motion wrote, “O God, I am thinking thy thoughts after thee.”

The supposed conflicts between science and religion have been greatly exaggerated, and in some cases even invented. There is no inherent conflict between them unless science is taken as a description for all reality, and at the same time restricts itself only to the natural world, i.e., the naturalist world view. So I can fully understand why you think there is a conflict, but the conflict you see stems not from anything in science, but rather is just an expression of your worldview imposed on science.

I would argue that naturalism is somewhat harmful to science because of its naturalistic bias. In fact I see no inherent difference between theists trying to ban certain lines of inquiry because it disagrees with their understanding of reality, and naturalist trying to ban certain lines of inquiry because it disagrees with their understanding of reality. Yet the naturalists I have talked to in the past have condemn the former while supporting the latter.