Evolutionary materialism, which is the mainstream view of much of the modern world, supposes that living things arose as a consequence of the spontaneous reaction of certain kinds of molecular substances, which, when combined under particular circumstances, will give rise to primitive life forms, after which Darwinian principles kick and life begins to evolve (although the details are still regarded as very unclear and even contentious.)
While I am convinced of the fact of evolution, I have never accepted the materialist account because I don't think it is complete. I don't believe that matter itself, on the molecular or atomic level, acts. It doesn't do anything - at least, not anything which cannot be described by the laws of physics and chemistry. And I don't believe the laws of physics and chemistry describe the nature of living beings, nor provide any philosophical basis for the very high degree of order which even the simplest of life forms exhibit, let alone life forms such as humans. In other words, I am not a reductionist; I don't believe that the level of complexity which is exemplified by living things arises solely as a consequence of forces that can be understood on the level of chemistry and physics. Something else is at work, or at least, there must be an explanation that works at a different level; however I don't wish to depict this in terms of the action of a deity. So this is not an argument for the existence of God. But I have never felt that the materialist account comes to terms with the ontological difference between living and non-living things; in my experience, materialists are obliged to deny this difference, a denial which seems implausible to me, but which is fundamental to materialism.
The obvious question that this raises is, what is the nature of the power which causes things to come into existence? Am I positing 'spirit', as opposed to, and in distinction from, 'matter', in the sense that a dualist would?
One difficulty presented by this arises from the fact that the act of thought itself can only proceed either in relation to objects or things, or by the logical operations of mathematics and reasoning. Consequently if you think about 'spirit', then you will generally think of it as something, some fine material essence or substance - something which is distributed everywhere, but which we can't see. I am sure this is the very kind of notion of spirit - as a 'geist' or 'ghost' - that has been rejected by modern naturalism. This is similar to the notion of the 'ghost in the machine', which was used as an argument against Cartesian dualism.
I don't believe there is any such thing as spirit conceived in such terms either. But in saying this, I am not denying the reality of what has been spoken of as 'spirit' or 'being-as-such'. I am simply denying the possibility of thinking about it objectively. I think that what has been described as 'Spirit' can be thought of as 'the universal potentiality for things to come into being' (among other meanings). In other words, the nature of the universe is such that, given the appropriate combinations of circumstances, it will spontaneously give rise to living beings. However, this does not mean that matter itself 'acts' or causes anything to come into existence. Nor does it mean that 'Spirit' is any kind of essence distributed throughout the Universe; to conceive of it on those terms is to put it on the same level as matter. (The question in regards to the nature of 'spirit' ought never never to be posed in terms of 'what', but in terms of 'who'1.) It is more that there is an inherent tendency for evolution latent within the fabric of the Universe. It could be described as inherent, implicit, or unmanifested; but were it not real, nothing would come to be. It precedes existence, and while it does not in itself exist, in the manner that material things exist, it is that which causes anything to exist. (In this view, evolution is a result, not a cause - specifically, the result of this inherent tendency for conscious life to evolve.)
This could be seen as being suggested by the idea of the 'anthropic principle' which observes that the causes and conditions which give rise to living beings are attributes of the very nature of the universe itself, and had they been slightly different, no life forms would be able to exist. So these very attributes and characteristics characterise the nature of the Universe, which is such that, given the correct circumstances, living beings will evolve within it. In this understanding, the Universe has just those properties and attributes which will inevitably give rise to conscious living beings. (See also 'Just Six Numbers' which discusses universal mathematical constants that underpin nature.)
As a consequence of these regularities, the Universe is lawful. Nature exhibits regularities which we are able to describe and summarize as formulae or scientific laws. Such regularities reflect the very deep structure of nature itself, as expressed in the classic essay, The Unreasonable Effectiveness of Mathematics in the Natural Sciences by Eugene Wigner. And surely the intuition of the deep relationship between mathematically expressible laws and the fabric of the cosmos is an attribute of the Pythagorean philosophy, without which neither Western philosophy nor mathematical physics could have developed.
Furthermore, this internal logic, as logos, is the reason why anything works. It is the basis of ratio, of harmony, of proportion and even of reason itself (because A, then B). But this can never been seen directly, only in the way it manifests, again, because it is implicit or given, rather than explicit or consequential. But as empiricism only considers the 'manifest realm', trying to explain the basis of reason on the basis of what appears in the manifest realm is like looking into the electronic circuitry of a television to locate the characters in the television show.
They are not there.
So my feeling is that the latent intelligence of the world is not the attribute or characteristic of any kind of fine material substance, stuff, or thing, conceived in the way that modern natural science would conceive it. If we have to conceive of it at all, it is much more like the inherent tendency of certain types of things to form, or to form along certain lines, which is an expression of the inherent logic, or logos, of the nature of reality itself.
And, of course, we ourselves are an expression of that, even a particular outcome of it; in fact, as 'the rational animal', we are uniquely able to appreciate this fact, in our realm of existence. Of course, this view is rather Hegelian, but Hegel himself was an inheritor of the Pythagorean tradition. (Also perhaps similar in meaning to Simon Conway Morris' 'Life's Solution'.)
1. 'Substance is that which is always a subject, never a predicate' ~ Kelly Ross, Meaning and the Problem of Universals