CM, I've explained this to you in depth before, but if time doesn't necessarily exist outside of our universe, than our universe doesn't necessarily need a cause or creator any more than God would. Causality only applies within the universe.
"This is the guy who entitled one of his books - 'The selfish gene'. What a horrible example of dogmatism triumphing over objectivity. He probably set the Public Understanding of Science back around a decade with this one move."
Have you read the book? He's actually very careful to make it clear that he's anthropomorphizing genes for the sake of simplicity but that one must always check to see that they are not overstepping the boundaries of the analogy. I think the title is quite appropriate, and that it does an excellent job of explaining evolution. I myself read it when I was about 8 and had no trouble understanding it even then. I wish he had stuck to teaching evolution and hadn't moved on to this atheist stuff because he was extremely good at what he did, which was writing science for the layman. I can't think of a more qualified person to hold that chair.
Re: 1) You can't expect to find a single gene that makes someone more altruistic... there's a whole host of human behaviour built to lubricate co-operation. There's a great deal known already about the physiology surrounding these behaviours, such as the hormones involved in trust, and the brain areas responsible for moral judgement. It is not farfetched to say that genes have a role to play in the development of these faculties, and just because we have not pinpointed the genes responsible *yet* does not make the hypothesis unscientific or implausible. The gaps are hardly large enough to justify shoehorning God into the equation.
Re: 2) Uh, actually there's a very simple way to define fitness... and that's by reproductive success, because that's how selection works. Yes, this means that a celibate Nobel prize winner or Olympic athlete is less evolutionarily fit than the trailer park Mom with six kids. In addition, you cannot separate the population into such groups, because natural selection works on the allele frequency and it works in parallel, not on one advantage at a time. It is more probable that over time the population gets stronger, more resistant to malaria, and more efficient at digestion if the costs of such adaptation are outweighed by their benefits.
Re: 3) No, that is no true. It is only "pure" altruism, in the sense that one individual sacrifices its reproductive success to increase another's, that can only exist amongst kin groups. But evolution doesn't act upon the individual, but on the gene pool, so this is perfectly possible. Reciprocal altruism doesn't require one individual to sacrifice for anothers benefit, but rather there is a mutual benefit involved, so you do not need to be related to someone to engage in reciprocal altruism. Reciprocity doesn't just extend beyond immediate kin, but extends beyond species. Humans and dogs share a reciprocal relationships, and there are many great examples of symbiotic relationships in nature. On the contrary, this doesn't legitimize racism, but makes it completely irrational as it creates artificial and arbitrary dividers on what is in reality a continuum. In addition, it creates a much stronger case for the ethical treatment of intelligent animals.
Regarding your conclusions, for one, I believe that morals are derived from human society and not from any higher power or authority. This is not nearly the same as believing that rape is not always immoral, and I'm a little annoyed that you would try to pose it as such. Just because morals aren't derived from an authority does not mean that they are inconsistent... Frankly, I find the idea of a morality derived from authority to be little in the way of morality at all. What sort of morality is it if you don't kill people because you'll get an eternity of pleasure and if you do commit murder you'll be disobeying the edict of an omnipotent deity that will bring upon you the punishment of eternal damnation. I don't call that free will, I call that bribery and threat; its coercion.
Additionally, I do not believe that pure altruism does not, or cannot exist. People do not actually carry out any direct accounting when determining the fairness of a deal, nor do they engage purely in direct reciprocal relationships. This is because the faculties involved are inexact and qualitative; there is more feeling than calculating going on, and it is a result of our evolutionary legacy. It is just that these faculties combined tend to give, on average, a form of reciprocal altruism between nonrelated members of premodern society. It is apparent that society and culture have a significant role to play in the development of a human being, and there is no reason to believe that a society could not make someone more, or even less, altruistic. In the long term, if pure altruism is not met in kind by pure altruism, then it cannot be sustained in the gene pool to the extent by which it is governed by genes. However, this is on evolutionary time scales, and we, as individuals, do not live on evolutionary time scales. It is up to you how you choose to conduct your relationships with the people around you, and it will be them that judge you, not God or natural selection.