Religion is a poor source of morality

[TheRocketSurgeon]

But again that is all speculation on your part. I could also say that empathy is a reproductive disadvantage leaving compassionate people vulnerable to hostile groups. It is premature to say with any confidence that any particular evolved trait is primary for moral behavior and I believe there is good reason not to consider natural instinct a reliable moral guide. Virtuous action is often contrary to our natural instinct, like showing courage in the face of danger. You seemed to dismiss revulsion of deviate behavior as socially constructed problems. Could we not also say that social constructs like a sense of duty and honor contribute positively. Again socialization is neutral without reference to a higher standard of value that instinct or cultural norms.

I say this with all the respect I can muster: You appear to have completely  missed the point of what I was saying. So I'll try to do better at explaining. We evolved as small tribes of hunter-gatherers, at maximum 200 in size (we know this figure because that's the most that we can observe in still-extant H-G groups, wherever civilization hasn't finished exterminating them), and our ideas about in-group/out-group and empathy and socialization are built around this sized group's social complexity level. I will explain more, below.

However, you did raise a couple of valid objections, ones which have been met with a plethora of research and writing, and which I can understand are ideas easily misunderstood, and I will also address that. You are quite right that this is a relatively new field and that much more research needs to be done on the subject. Unfortunately, people will commonly say that if we don't know everything then we don't know anything, and that's simply not true.

Concept 1: "Empathy is a reproductive disadvantage leaving compassionate people vulnerable to hostile groups"

You're still thinking in terms of the individual against a large society. This is common to American thinking (not knocking you for it, just a fact; I too am susceptible to this line of thinking), but I'm talking about 30,000 years ago, or 150,000 years ago, generation after generation of selection for suitability to a 100-200 person tribal group. The only "hostile groups" would have been other tribes who cared nothing for this  tribe's individuals or social/moral structure. However, empathy toward one's own group would convey a massive advantage on that group, even sometimes over the individual fitness of that person to reproduce; I've described kin selection to you before, but in case you've forgotten, here's a link. The evolutionary psychology version is here, explaining altruism's evolution.

Concept 2: "It is premature to say with any confidence that any particular evolved trait is primary for moral behavior" 

I'm honestly not sure what you mean by this, exactly. Most of our behavioral traits are governed by a large number of (often competing) centers of the brain, instinctive and imprinted/accultured. We have a pretty good idea of the basis for empathy and social group operation; the problem is whose definition of "moral" we're using, since you're working from one particular social-set, and I must use the term much more broadly, such as when I say that moral behavior has been observed in animals. But let's stick to humans. We know that moral behavior is specifically tied to particular sections of the brain which, when damaged, impair moral judgment but little else. The "new synthesis" in evolutionary psychology is putting together a picture which includes the following ideas:

People are selfish, yet morally motivated. Morality is universal, yet culturally variable. Such apparent contradictions are dissolving as research from many disciplines converges on a few shared principles, including the importance of moral intuitions, the socially functional (rather than truth-seeking) nature of moral thinking, and the coevolution of moral minds with cultural practices and institutions that create diverse moral communities. I propose a fourth principle to guide future research: Morality is about more than harm and fairness. More research is needed on the collective and religious parts of the moral domain, such as loyalty, authority, and spiritual purity.

The long abstract is a bit more detailed, but you need a subscription to Science  to read the full article.

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J. Haidt suggested in a recent Review in Science (18 May 2007, p. 998) that future research on moral cognition should offer views that go beyond the sole principles of harm and fairness. In agreement with this view we propose that commonly used moral dilemmas (2–4) should be considered with respect to major stages in the evolution of human behavior.

The most primitive behavior of a single individual involves decisions motivated by ensuring his own survival. During the Pleistocene, life in small groups resulted in genetic changes influenced by culture (culture/gene co-evolution,) that led to the emergence of social instincts favoring kin or the welfare of tribe members. Finally, over the past 10,000 years, social evolution resulted in culturally shaped rules that took advantage of a psychology that had evolved to cooperate with in-group members and so expanded the benefits of social instincts to larger/anonymous social systems. At the neurobiological level, this improvement of social norms likely necessitated an adaptation of conscious/rational cerebral processes to drive functional adjustment and novel coordination with more automatic intuitive/affective mechanisms. The study of these neurobiological substrates could benefit from consideration of the evolutionary stages to better accommodate behavioral decisions according to which social group they may benefit or harm. We argue for a psychological model of decisionmaking in moral dilemmas where three neural mechanisms coexist: one very primitive that mostly favors self-interest; another more automatic intuitive/affective favoring welfare of kin/in-group members; and a third conscious/rational mechanism implementing norms that favor large groups. Consequently, moral dilemmas could be sorted according to the kind of benefit they address. Such clear-cut distinctions remain theoretical in nature since, in real-life, contextual influences have a crucial role in triggering feelings that can have a critical impact on moral judgments (e.g., empathy). However, in our opinion, this framework would help refine experimental paradigms and analyses when subtle social contextual information changes are at stake in moral and economic dilemmas.

(Emphasis mine, of course.)

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Concept 3: "I believe there is good reason not to consider natural instinct a reliable moral guide."

Yet you just tried to cite to your personal revulsion (or the common revulsion) as a moral guide. I agree with you that natural instincts are a terrible moral guide. That's why I mentioned culture and civilization. The mark of culture and civilization is an attempt to rise above our natures... however, it should be noted that part of our nature is to build cultures and establish collective moral rules of varying kinds (with some obvious ones in common, like "murder = bad").

Concept 4: "Virtuous action is often contrary to our natural instinct, like showing courage in the face of danger. You seemed to dismiss revulsion of deviate behavior as socially constructed problems. Could we not also say that social constructs like a sense of duty and honor contribute positively. Again socialization is neutral without reference to a higher standard of value that instinct or cultural norms."

I suggest you spend some time really thinking about the concept of a small group setting, and what the above researchers wrote about the three-tiered morality centers of the brain. It is precisely our evolved ability to function as a social group (tribe), showing bravery in defense of the tribe, honor in our dealings with our group, etc., which "contributed positively" enough to make us into humans! 

Similarly, revulsion toward "deviate behavior" takes on many, many guises in many cultures, and I was trying to get you to see that your particular set of revulsions is particular to your inherited culture (and tends to arise in those with high levels of inter-tribal warfare, like ancient Israel, Rome, and the Mideast). I know what you think you mean, when you say "higher standard of value", but I think it's clear that even those holy books are based on the cultures that spawned them, as a way of legitimizing a particular set of values.