Views of logic: theism vs atheism part 3

In a previous post, I noted that while atheists claim that theists simply choose to "ignore" the laws of logic and physics when they choose, it's actually the other way around.  Unless you decide to suspend the laws of physics and logic when you wish, you must actually come to the conclusion that the universe had a Personal First Cause outside of space and time.

This was all in response to a comment by an atheist that I saw reposted on the pleaseconvinceme blog.  But there was something else about that post that got me riled up.  The original post said:

Theists imagine anything is possible simply because they have an imagination that can dream up anything they want. Atheists realize that isn't the case.

What I find especially interesting about that statement is that I am actually frustrated by this tactic coming from the atheist camp, not the theist camp.  This is especially obvious when you study the naturalistic theory of evolution as an explanation for everything.  For example, one of the issues I noted last time was with the charge from atheists that the belief in God that runs rampant within our species is simply a product of evolutionary history.  The thought is that, at a previous point in our species, the belief in a god or gods gave those believers some selective advantage.  So now, even though that's not necessarily giving anyone a selective reproductive advantage anymore, it's something that has been imprinted in our species from our evolutionary history.  That's actually become a working theory nowadays.  The problem is there is zero evidence of this.  It's an example of "as long as you can imagine it and it's consistent with naturalistic evolution, it's accepted as true".

Another example of this particular problem is where did our morals come from?  Well, clearly (since there is no god), our morals do not come from a transcendent source.  They must have been at one time given us an evolutionary advantage over the other humans who did not have those morals.  Nowadays, since we are a "social species", morals are in place in our genes so that we contribute to the greater good of our whole species.  The evidence for this is as abundant as for the above example.  That is to say, it is completely absent. But it's an explanation that is consistent with the naturalistic evolutionary paradigm, so it's taken as a given now that someone thought of it.

Of course, the most classic example of, "as long as I can imagine it, it must be true" is Darwin's "warm little pond".  In regards to theories of the origin of life, Darwin said in a famous letter to one of his colleagues that he could imagine a warm little pond where life got started.  This idea alone gave rise to the entire hypothesis of a prebiotic soup that was supposedly present on the early earth, from which life arose. It wasn't long before this idea, for which there was zero evidentiary support, became scientific dogma.  The idea of a prebiotic soup became so prevalent that nowadays everyone "knows" that's where life came from.  Very, very interesting how these things happen.

Evolutionary morals

OK, so maybe very few people really believe in moral relativism.  After all, you can get to some pretty crazy conclusions from it.  So what do the majority of people believe about morals?  Besides those that adopt an absolute moral system (ie, from Christianity and other possibly transcendent sources), many people nowadays will adopt something I call evolutionary morals (for lack of a better term).

Those that claim this point of view will often say that this belief system is different from complete moral relativism, in that their morals are grounded in an objective system: the greater good of humanity.

The belief system goes like this (I think).  Humans evolved as a societal species.  We make relationships with each other, and we make social contracts, etc.  These things were selected for as we evolved. Therefore, evolution has preserved in us a natural tendency to do things that promote the good of the human race as a whole.

In this way, morals develop.  There are things that are definitely bad for the human race, as a whole, such as killing another human without justification.  That's why murder is wrong in almost all societies.  In fact, any moral can be defined this way: as long as it's good for society as a whole, then it's morally right.  Anything that's bad for society is morally wrong.  Thus, an absolute standard exists.

If anyone out there can explain this point of view better, or if you have one that's similar to this but there are important differences, please speak up.

What if genomes of organisms didn't appear related?

In my opinion, one of the more compelling lines of evidence for evolution is that we can sequence the genomes of any living organism nowadays, and what we've found is a striking similarity among organisms. For example, and oft-quoted number is that the genomes of humans and chimpanzees are 99% similar. Pretty good evidence for common descent, is it not?

And by the way, this isn't exactly a new thing; it isn't just with the dawning of the post-genomic era that this line of evidence was put forth. There was a seminal study by I-forget-who back in I-forget-which-year where a graduate student was determining the primary sequence of some proteins in different organisms. She was attempting to show that these proteins were different in different organisms, and was dismayed to find that there was striking similarity. Her advisor being very wise (as advisors usually are), quickly saw the high-impact factor of such a find: this was concrete evidence for common descent!

Anyway, back to my main point. Is this similarity in genes and proteins and whole genomes compelling evidence for common descent? Or is there a way to explain it from a "God-created-it" standpoint? After all, if you're a creationist, you may not have to explain the mechanism by which genomes became related, but you do have to explain why God would do it that way.

One of the counter arguments is that God used a common design template when creating organisms, and only modified this template in small ways to account for the different purposes that He had for the different organisms. After all, there's no need to reinvent the wheel. In essence, this is arguing that God designs life in the same way that engineers design machines they build.

This argument doesn't really sit well with me. It's not that I don't think God would design life in the same way engineers design machines. To the contrary, I am convinced that He would, or perhaps more appropriately, we design machines in the same manner that God designs life. No, I am uncomfortable with this argument mostly because it's too hand waving. It doesn't have any real substance to it.

I prefer to put forth a counter argument from the basis of the question: What if God had done it another way? That is, what if genomes of organisms didn't appear related?