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Without God, a natural morality has no foundation. This is because in nature we find all kinds of behaviours that we would be unwilling to regard as morally good: we find animals that lay their eggs in the living bodies of other animals, we find animals that eat their young, we find animals that do a variety of unpleasant and disgusting things in order to survive and proliferate. How can we assume that the sub-set of behaviours that human beings engage in is morally superior to the behaviour of a prying mantis or a pig? Only if we assume, like Thomas Aquinus, the existence of a transcendent being who, for whatever reason, favours our species, can we explain our moral superiority to others and regard morality as being 'in nature'.
Otherwise, as TGS argues, any biological impulsion will need to be scrutinized in the light of ethical principles that are not themselves given biologically. Acquinus held that humans use reason in order to understand the natural commands of God; even if we assume that morality is natural, we cannot simply taken it as given. Without Acquinus's God to invest nature with morality, we cannot even make the assumption.
Morality is, and probably always will be, ultimately undecidable. The hope that there might be a natural set of rules or principles is only viable in a world in which transcendence is possible. In a world completely governed by scientific principles there is no bed-rock upon which to build the one true moral system.
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