Yeah, philosophy of religion was relatively secular. But if it wasn't approached in that manner, then it would just be church. I think it is wise that they show both atheistic and religious philosophical positions, rather than just one side of the coin.
That is not how it is presented. It's not like they have the courage of their convictions and present atheistic philosophy as an alternative to traditional theism. They simply assume that their naturalistic assumptions are superior and pretend to be objective, which is impossible. If this were a case of them just being resolute in their ideology we could have an interesting discussion on why they think so, but sadly that is not the case.
They are trying to systematically replace traditional theism with their atheistic philosophy and I am appalled at the dishonest and deceitful tactics.
Well, yes, alleles are variations in a given gene. A change in allele frequencies need not mean a change in allele frequencies that already exist though. For example, mutation can add a new allele into the population.
Show me even one example of how this kind of a mutation has a beneficial affect on the human brain. These genes are highly conserved for a very good reason, the deleterious affects would be devastating. If science has taught us anything it's that we do not assume anything and evolution would have us assume everything with regards to our origins.
Well, the mechanism has been explained. Random mutation and natural selection are mechanisms. I am not very familiar with the transition between apes and humans, but I do have a few questions about this study (and you seem to by the guy to ask about it

)
First of all, with regards to the evolution of the human genome from that of apes, natural selection as an explanation has been rejected:
Although it is more difficult to quantify the expected contributions of selection in the ancestral population, it is clear that the effects would have to be very strong to explain the large-scale variation observed across mammalian genomes. There is tentative evidence from in-depth analysis of divergence and diversity that natural selection is not the major contributor to the large-scale patterns of genetic variability in humans.
Initial sequence of the chimpanzee genome and comparison with the human genome, Nature Sept 05
It's ironic that they have the nerve to say that Darwin's 'predictions' have been marvelously confirmed and then reject his mechanism for the actual adaptation. The truth is that they never question the assumption of a common ancestor. That is in my view, pure, undiluted bias.
Has it been demonstrated conclusively that point mutations in any one of the 18 nucleotides involved in the change from chimps to humans would be fatal? For example, has it been demonstrated that you need to have all 18 nucleotides change at the same time for the human HAR1 gene to function? Or does it function equally or better when only one nucleotide changes at a time?
What has been demonstrated is obvious. It would require that an RNA regulatory gene be almost perfectly preserved for hundreds of millions of years and then suddenly, without explanation, get 18 substitutions. How becomes a vital question and they don't make the slightest attempt at an explanation.
The excerpt from the paper you provided does not explain it. The fact that such a drastic change had to happen so quickly does not falsify evolution.
I would submit that it does and they know it. Nothing can falsify an a priori assumption and and I have no problem with that, given one unconditional point. You have to state that before you pretend to base your ideas on science. The facts have demonstrated that there is no conceivable way for this extraordinary giant leap in evolution and if they had the courage of their convictions they would admit the alternative explanation.
They never do and it's leading science down a blind alley in the dark.
It is conceivable that that mutation and natural selection could have worked to produce such a change. The onus is now on scientists (and creationists) to design a test to falsify that prediction. You have not provided enough information here to satisfactorily do so here. Maybe there are other papers that deal with that particular sequence?
There are a bunch of them, read the two provided for you and we can move on to others. Don't pretend that this has no impact of your opinion because I have done this enough to know a shred of doubt when I see one.
But I do appreciate your post. It is very interesting, and quite fun to think about. Thanks.
Very glad you found it interesting and I appreciate the exchange.
By the way, if you think that this piece of evidence is enough to falsify evolution from common descent, then perhaps we should start a new thread to discuss it? Up to you.
There have been threads in the past and their will be others. I can't really start a new thread right now since I am a little preoccupied right now. Things may change in the very near future but I can't promise anything. Be patient and I will be happy to start a thread on that very topic, God willing and the creek don't rise

.
Keep questioning and I wish you great success in your quest for the truth.
Grace and peace,
Mark