The Preface to first great critique of Kant opens with the famous statement,

Human reason has the peculiar fate in one species of its cognitions that it is burdened with questions that it cannot dismiss, since they are given to it as problems by the nature of reason itself, but which it also cannot answer, since they transcend every capacity of human reason.

The three great questions that are are irresolvable in this context are those of divinity, soul, and free will. We are left with an almost ominous question: can we define the boundaries of the organism? Is the organism a space-time entity, or do its boundaries transcend space and time? In general the questions of fact/values, freedom, ethical action, and consciousness founder in the reductionist approach of positivistic Darwinism. 

There is nothing mysterious about the limitations of Darwinian explanation: value-free science must eliminate questions of the value domain. But is this legitimate for the question of evolution? Related to this is the attempt to produce purely causal explanations of ethical behavior and its evolution. The positivist methodology of scientific reductionism, by declaring the rigid separation of facts and values, leaves us to wonder if nature itself truly respects this division in all its processes, especially those of evolutionary emergence. Sometimes the naturalistic fallacy is cited here. But how do we know that evolution doesn't process values amidst facts, this in a naturalistic fashion? 

Darwin and his successors, making natural selection the fundamental axiom of explanation, have attempted considerable ad hoc extensions of great ingenuity to make selfishness the source of morality. This dramatic play of opposites has produced some exotic attempts to 'save the paradigm' in the theories of group and kin selection. These theories are essentially logical phantoms attempting to puzzle through the paradox of making selfishness the basis for its opposite. But none of this answers to the real issue, which is to explicate, and show evidence for, the emergence of an 'ethical' agent. The issue of ethics is really one of the freedom or potential freedom to act according to an 'ought', and it is almost by definition not going to be explained by the mechanization of valuation via natural selection. This issue gives us a hint that Darwinian style explanation is wrong in principle and wildly off the mark in practice. 

 In general, a theory of ethical behavior must explicate the consciousness of an ethical agent, and produce a model of choice-based behavior. But theories of evolution cannot yet account for consciousness. To make ethical consciousness an epiphenomenon of natural selection, and to propose that it arises as an adaptation in the game of survival beggars the nature of the phenomenon itself. What’s more, this approach creates a de facto standard of ethics based on the evolutionary ‘value’ of pure selfishness.

 Thus, one of the reasons for the confusion of the Darwin debate is that the right way to do science might be the wrong way to do evolution. To be sure, there are few ways that are better as a preliminary to a more sophisticated science needed to match the phenomena under enquiry. But the strategy of explanation needs to be something better than the elimination of the problem by making it logically consistent with natural selection. That this should precipitate conflict with religion is hardly surprising, and even if we champion a secular stance toward religion, it is hard to avoid the feeling that the research program of evolutionary biology on this question is a failure step one in the midst of the great success of its expansion of our knowledge. And part of the problem is the confusion of ‘theories’ with ‘protocols of action’. How we should act is not given to us by a theory. A theory proposes a causal explanation of action, but that by definition is not a protocol of action. Action requires choice, and we could choose to act against the theory, raising questions about its claims for causality. We are stuck trying to explain the freedom to act. We could eliminate that freedom in the name of science, but then we would be stuck with a typical situation where we would ‘preach the theory’ to something who choose to defy it. That freedom to act is an obstinate given.

There is actually no mystery here: the ‘subject’(object) of evolution is complex, has a different character from that of a point mass in physics. We must reckon with the sense of meaning, consciousness, and deliberation that are, by definition, subject to contra-causal forms of explanation. The issue must be the 'evolution of the freedom' to choose between different courses of action. This would seem to apply to the case of man, or else the later stages of primate evolution, and there the point remains that mechanized explanations of ethics are not ethics. So, is ethical behavior an illusion, as strict positivism must claim? These are actually issues carefully addressed earlier in the Enlightenment, before Darwin, with such figures as Kant standing out by their careful consideration of the implications of the rise of Newtonian physics.