While I certainly have not worked out all of the details of the theory to my own satisfaction, I feel that there is a strong scientific basis for this idea of moral instincts. In the NY Times article by de Wall, he states:
Charles Darwin was interested in how morality fits the human-animal continuum, proposing in “The Descent of Man”: “Any animal whatever, endowed with well-marked social instincts … would inevitably acquire a moral sense or conscience, as soon as its intellectual powers had become as well developed … as in man.” ...
Fortunately, there has been a resurgence of the Darwinian view that morality grew out of the social instincts. Psychologists stress the intuitive way we arrive at moral judgments while activating emotional brain areas, and economists and anthropologists have shown humanity to be far more cooperative, altruistic, and fair than predicted by self-interest models. Similarly, the latest experiments in primatology reveal that our close relatives will do each other favors even if there’s nothing in it for themselves.
Such findings have implications for human morality. According to most philosophers, we reason ourselves towards a moral position. Even if we do not invoke God, it is still a top-down process of us formulating the principles and then imposing those on human conduct. But would it be realistic to ask people to be considerate of others if we had not already a natural inclination to be so? Would it make sense to appeal to fairness and justice in the absence of powerful reactions to their absence? Imagine the cognitive burden if every decision we took needed to be vetted against handed-down principles. Instead, I am a firm believer in the Humean position that reason is the slave of the passions. We started out with moral sentiments and intuitions, which is also where we find the greatest continuity with other primates. Rather than having developed morality from scratch, we received a huge helping hand from our background as social animals [emphasis mine].
At the same time, however, I am reluctant to call a chimpanzee a “moral being.” This is because sentiments do not suffice. We strive for a logically coherent system, and have debates about how the death penalty fits arguments for the sanctity of life, or whether an unchosen sexual orientation can be wrong. These debates are uniquely human. We have no evidence that other animals judge the appropriateness of actions that do not affect themselves. The great pioneer of morality research, the Finn Edward Westermarck, explained what makes the moral emotions special: “Moral emotions are disconnected from one’s immediate situation: they deal with good and bad at a more abstract, disinterested level.” This is what sets human morality apart: a move towards universal standards combined with an elaborate system of justification, monitoring and punishment [emphasis mine].
See the video below for de Waal's contention that there is a biological basis for the 'golden rule.'