The concept of freedom, behind that of free will, is indispensable for the proper discourse of secularism itself, with its defense of freedom and autonomy. We can proceed in an indirect way by looking at the historical phenomenon of freedom with or without the far more elusive proof of the existence of 'free will'.

Freedom evolving It is not necessary to assume the existence of free will to posit an ‘evolution of freedom’, since the evolving system might show ‘evolving toward’ rather than ‘result achieved’.  Any such system will provoke a paradoxical question, What causes freedom? This question was directly addressed by Kant. We must distinguish the macro and micro aspects of ‘freedom  evolving’, a strange complication that will in fact lead to the solution of the problem.  And it might be the case that as observers looking backward we are still short of the final stage.  So we need not assume ‘free will’ as yet in the observer, able to document earlier stages of evolution.

We can adopt a double strategy, simply introducing an 'idea of freedom' as an extra axiom, to be used for empirical study of the history of freedom, and/or creating an explicitly dualistic model that learns to live with a contradiction. We will also have still another tactic, a surrogate for 'free will', which we will call 'self-consciousness', which can be taken with chameleon neutrality as either in the causal category, or in the freedom category. 

But Kant's thinking enforces a severe discipline of the limits of our knowledge on these questions, and, this being the case, we can see that while the affirmation of a thesis on divinity is taken as metaphysical, its negation is destined to suffer a similar fate. We can see at once that, if Kant is right, then the theory of natural selection, the spearhead of much secular thought in a post-religious mode, is forced into a task that it cannot fulfill. 

As we proceed to examine history in the light of evolution we might, since our task is a fairly straightforward one of demonstrating an empirical pattern, restrain explicit assumptions on all three of these assumptions. Kant's first critique can be approached in many ways, one of them being simply the question of the 'antinomies' that infest our processes of reason. The classic Third Antinomy expresses the problematic of evolution and ethics directly:

Kant’s Third Antinomy The crux of the contradiction pervading evolutionary and ethical ideas is posed in the classic ‘Dialectic ’ of Kant’s first Critique. “Causality according to laws of nature is not the only kind of causality from which the phenomenon of the world can be derived. It is necessary, in order to explain them, to assume a causality through freedom.” Its antithesis is: “There is no freedom: everything in the world takes place solely in accordance with laws of nature.”

These antinomies are posed in the form of a debate whose thesis and antithesis are both established by logical argumentation, provoking a dilemma that can only be resolved by a transformation of our basic perspective on space, time, and the representation of them in our commonsense perspectives. But if we take the simple duality of the statement of the antinomy directly as given in the starting point of observation and reflection we can see that our questions about evolution and ethics are simply variant confusions of Kant's dialectic. That the question ‘What causes freedom’ suffers ‘logical collapse’ requiring a new language is no final objection to this approach. Our difficulty with the depiction of the evolutionary agent rises from the way in which we take the antithesis given by Kant as the sole mode of explanation. It is entirely problematical to be bringing in two forms of causality, but the dilemma is there, that we cannot reduce the potential of freedom to the level of causality and produce an account of evolutionary ethics. That this issue should prove the clue to any theory of evolution as such will become clear as we proceed. 

One of the earliest stages of the confusion over evolution lay in the conflict with the outstanding 'Nature Philosophy', especially the Hegelian version that was influential at the beginning of the nineteenth century. This reaction to the great foundation created by Kant has obscured his contribution, which is very well adapted to the needs of science. The sudden collapse of this tide of idealism, so visible in the generation of Feuerbach and Marx, left its mark on evolutionary thought as it absorbed the influences of Comte and the new positivism. But even as it embraced this rejection of metaphysics Darwin's theory of natural selection unwittingly adopted a metaphysical stance of its own. This springs from the totalizing character of the theory, which is required to reduce all organismic phenomena to scenarios of adaptation. That is not a realistic research project.

Transcendental idealism Lost in the progression of modern philosophy, next to the emergence of positivism, is the Kantian tour de force, transcendental idealism, a unique hybrid (with a misleading terminology) of causality/freedom issues, and easily taken as a superset of standard scientific thinking. The ‘positivism done right’ allows us to restate, if not fully solve, the issues of human action and scientific law in a workable form.

Despite the endless theological controversies over evolution, Darwinists, by and large, with important exceptions, tend in fact to adopt a proper stance on the issue of divinity. Darwin's theory merely wishes to explore the naturalistic implications of evolution without ad hoc theistic explanations. This is not a commitment to atheism, or some claim to have disproved the existence of god, but simply the perception that the data of evolution strongly suggest a naturalistic interpretation. And this approach has proven fruitful indeed. However, it is true that many Darwinists attempt to extend this formulation to use natural selection as argument in favor of hard claims on theistic issues. This is not in itself illegitimate but, by and large, simply creates a new metaphysical myth, and an egregious ambition that simply provokes the dialectic ad infinitum that we see in the history of Darwinism.

Questions of soul are the real nemesis of Darwinism. These are the most insidious, because materialism overwhelmingly tends to the negation of the soul idea. This should not be confused with the 'soul beliefs' espoused by monotheists. Such beliefs are as open to challenge as any religious doctrine, in a secular age. But this is tantamount to a declaration of the non-existence of soul, crossing the tripwire of metaphysical claims.

Buddhism/Hinduism The ambiguity of the term ‘soul’ is highlighted in the religions of the Indic stream where the object of religion is to transcend the ‘soul’ taken as an envelope of natural man, an aspect of his self within nature. Soul is an aspect of nature, although beyond our immediate psychological introspection.

The question of 'soul' is very provocative, and it is more fruitful simply to think in terms of the organism, and its definition. Is the organism a purely space-time entity, or does it have a complex dimensionality? This issue is especially vexacious because it suggests that we cannot properly observe the organism at all. But this then preempts any theory in closed form. We might consider the bare minimum issue here, the distinction of computer and computer program, to see that such issues resemble those of mathematical Platonism, for example.