D'Souza outlines his argument in this way (from Part I):
Unlike material objects and all other living creatures, we humans inhabit two domains: the way things are, and the way things ought to be. In other words, we are moral animals who recognize that just as there are natural laws that govern every object in the universe, there are also moral laws that govern the behavior of one special set of objects in the universe, namely us. While the universe is externally moved by "facts," we are internally moved also by "values." Yet these values defy natural and scientific explanation, because the laws of nature, as discovered by science, concern only the way things are and not the way they ought to be. Moreover, the essence of morality is to curtail and contradict the powerful engine of human self-interest, giving morality an undeniable anti-evolutionary thrust. So how do we explain the existence of moral values that stand athwart our animal nature? The presupposition of cosmic justice, achieved not in this life but in another life beyond the grave, is by far the best and in some respects the only explanation. This presupposition fully explains why humans continue to espouse goodness and justice even when the world is evil and unjust.
One sentence in the middle is the most contentious, and unsurprisingly is the part D'Souza spends the most effort on: the idea that "morality [has] an undeniable anti-evolutionary thrust." Let us see if this idea has any merit.
The first argument raised in its defense is this (from Part II):
So if we are mere evolutionary primates, how to account for morality as a central and universal feature of our nature? Why would morality develop among creatures obsessively bent on survival and reproduction?... Darwin argued that "although a high standard of morality gives but a slight or no advantage to each individual man and his children over the other men of the same tribe, yet . . . an advancement in the standard of morality will rtainly give an immense advantage to one tribe over another." Darwin’s point is that a tribe of virtuous patriots, with each of its members willing to make sacrifices for the group, would prove more successful and thus be favored by natural selection over a tribe of self-serving individuals.
But as biologists now recognize, the argument has a fatal flaw. The question we have to ask is how a tribe of individuals would become self-sacrificing in the first place. Imagine a tribe where, for instance, many people shared their food with others or volunteered to defend the tribe from external attack. Now what would be the fate of individual cheaters who benefited from this arrangement but hoarded their own food and themselves refused to volunteer to fight? Clearly these scoundrels would have the best deal of all. In other words, cheaters could easily become free riders, benefiting from the sacrifices of others but making no sacrifices themselves, and they would be more likely to survive than their more altruistic fellow tribesmen.
D'Souza says this is a "fatal flaw" and dismisses it without further consideration. I think he should not be so quick on the draw, though. The most obvious rejoinder is that altruistic tribes do not suffer cheaters lightly: they punish them severely, by exile or death. The development of altruism need not have the same genetic basis as the development of punishment, but clearly the combination of the two is powerful. Once this combination, which we might dub "enforced altruism", develops, it would quickly outperform selfish tribes.
Note that this does not say that all members of the tribe are forced to act altruistically (which is not really altruism). What it says is that some individuals express the altruistic trait, and that those who do not either fake it or get punished. (A few probably cheat and manage to escape punishment, of course. But now we are down to arguments over numbers: the conditions under which enforced altruism proves genetically successful depend on the ratio of altruists to cheaters, and of undetected to detected cheaters.)
Another argument for the evolution of altruism is based on the idea that individuals can be thought of as "survival machines — robot vehicles blindly programmed to preserve the selfish molecules known as genes," in the words of Richard Dawkins. In D'Souza's words:
This idea helps us understand why certain insects, birds, and animals endanger their own welfare to promote that of their fellow creatures. Vervet monkeys and prairie dogs, for instance, give warning calls that signal approaching predators, sometimes at the cost of becoming the target of those predators. Why would they risk their lives in this way? Kin selection holds that it is because they are genetically related to those they are helping. So there is an evolutionary payoff: The risk-takers are maximizing not their individual chance for survival but the chance for their genes to make it into future generations. From the gene’s point of view, helping one’s kin is simply a form of helping oneself.
But of course kin selection is a very limited explanation, in that it only accounts for why animals and people behave altruistically toward relatives. In life, however, humans and even some animals behave that way toward innumerable others who don’t share their genes.
It's worth pausing at this point to mention that this last bit is a major stolen base. All of us share the vast majority of our genes; only a tiny residue of genetic difference separates Swedes from Australian aborigines. So the selfish gene hypothesis could easily explain all altruism among humans.
But of course kin selection is a very limited explanation, in that it only accounts for why animals and people behave altruistically toward relatives. In life, however, humans and even some animals behave that way toward innumerable others who don’t share their genes. Robert Trivers argued that this is because of "reciprocal altruism." A better term would be reciprocal bargaining: What Trivers means is that creatures behave generously toward others in the expectation that they will get something in return....
Even reciprocal altruism, however, cannot explain the good things that we do that offer no actual return. A fellow gets up to give his seat on the bus to an 80-year-old woman. No, she isn’t grandma, nor is it reasonable to say that he’s doing it so that next week she will give him her seat. So neither kin selection nor reciprocal altruism provides any solution in this case....
Some biologists concede that evolution is at a loss here. "Altruism toward strangers," writes biologist Ernst Mayr, "is a behavior not supported by natural selection." Still, some diehard champions of evolution do try to accommodate such behavior within their evolutionary framework. Their best attempt is to argue that seemingly disinterested altruism toward strangers has a well-hidden personal motive. Essentially it is performed in order to enhance one’s social reputation.
Again, though, there are easy responses to what D'Souza characterizes as intractable problems. First, as already mentioned, all humans are kin. Given a random gene in a random human being, the odds are extremely good that that gene also exists in any other human. Second, the description of reciprocal altruism is too limited. While we may not expect that particular individual to reciprocate, we are members of a social species. A fellow who gives up his seat on the bus may expect that someone else will give him a seat when he is 80. The best way to perpetuate the social behavior of "giving up bus seats to the elderly" is to practice them. This is a different and more subtle argument than the simplistic one of enhancing one's personal reputation.
But all these responses are not really necessary, because D'Souza's arguments are weakened by his insistance that every instance of altruism have a genetic basis. Nowhere in evolutionary theory is it required that genes evolve unerring behavior. Many insects are fooled by flowers into "mating" with them; D'Souza would presumably argue that this behavior could not have evolved because insects that were not fooled would outcompete the others. But in reality, it's just not worth it not to be fooled: the cost of being fooled is low. Similarly, the survival cost of giving up one's seat on a bus is low. Some of his other examples (e.g., "assisting AID victims in Africa") are better, but note how few people engage in these forms of altruism.
He also ignores the fact that humans have brains. Once a capacity for altruism (even just kin altruism) and a capacity for abstract thought have both evolved, it is not a stretch to infer that those capacities might start to be connected. Human evolution is not only a genetic story, but also a social one. This is obvious to anyone who has raised children: in their state of nature, they are not particular moral. A young child will lie, steal and cheat if he can get away with it. It is only through normative socialization that these tendencies are curbed; clearly they are learned, not genetic. (This is not to say that genetic tendencies toward moral behavior are stronger in some than others. But no one is born a saint any more than they are born an NBA All-Star.)
One other point D'Souza makes about morality (in Part III) is this:
All evolutionary attempts to explain morality ultimately miss the point. They seek to explain morality, but even at their best what they explain is not morality at all. Imagine a shopkeeper who routinely increases his profits by cheating his customers. So smoothly does he do this that he is never exposed and his reputation remains unimpeached. Even though the man is successful in the game of survival, if he has a conscience it will be nagging at him from the inside. It may not be strong enough to make him change his ways, but it will at least make him feel bad and perhaps ultimately despise himself. Now where have our evolutionary explanations accounted for morality in this sense?
The argument here is that evolutionary explanations for morality reduce it to just a greater form of self-interest, and that this cannot be explaining by a "nagging conscience." But this is far from clear. Why couldn't the mechanism for inducing altruistic behavior be a mental tug that we call a "conscience"? D'Souza seems to imagine that evolution must express self-interest by a little red devil in our minds encouraging us to act deviously. But consider hunger, a sense that we can hopefully agree developed via evolution. When we are hungry, we are not induced to merely ape the motions of others who are eating. Rather, we feel sensations akin to pain, which we have learned we can assuage by actually eating. Similarly, our conscience is our mental conduit for feeling our moral sense, and it is expressed by a sort of pain when we do not act appropriately. Our conscience is designed to be triggered by things which even D'Souza would recognize as being in our gene's self-interest but, being an imperfect mechanism, is sometimes triggered by things which are not. This should not be any more surprising than the discovery that we sometimes eat unhealthy things.
Having made his various points about evolution, D'Souza hits us with his conclusion:
Now let’s make the supposition that there is cosmic justice after death and ask, Does this help to explain the great mystery of human morality? It seems clear that it does. Humans recognize that there is no ultimate goodness and justice in this world, but they continue to uphold those ideals.
By now it should be obvious why I think this is flawed: the premise - that human morality is mysterious and has no otherwise good explanation - is not reasonable. Human morality can be explained perfectly well by evolutionary means; D'Souza does them a disservice by his overly-simplistic explication of them.
Full disclosure: even if I did not think evolution provided a good explanation for human morality, it would take more than D'Souza's argument to convince me of the existence of an afterlife in which we are judged for our actions in this life. His argument makes the common error of confusing metaphysics with science. What evolution can predict is a scientific question: it can be tested, verified or found wanting, modified and tested again, etc. Such is the scientific method. His hypothesis, however, is untestable, and his argument, metaphysical. It requires us to assume at a minimum that there is no physical explanation for morality. As a somewhat silly example: suppose humans did not evolve from primates at all, but - as in 2001: A Space Odyssey - were created by aliens, who inserted some moral sense in our genetic code. That is certainly an alternative explanation for the origin of morality, and it does not require us to posit an alternative universe to which we are connected (by no means detectable to science). It would require us to posit alien genetically engineers with an interest in humanity, but it strikes me at least as an open question which hypothesis is the more unlikely. In the meantime, the evolutionary explanation seems to work better than most.