I suspect this reads Aquinas through the lens of nominalism. Here's a commentary on the natural and supernatural in Aquinas:
"At any rate, in Aquinas's thought, "nature" refers to human nature as it concretely exists, that is, as already integrated within the context of grace but as formally considered independently of what revelation teaches of that context. Viewed from that perspective, nature possesses a transcendent openness to grace and, some Thomists would claim, a desiderium naturale toward fulfillment in grace. Sixteenth-century theologians, however, tended to take the natura pura to be a full reality in its own right. On the basis of Aristotle's principle concerning the proportion of ends to means, they declared this nature incapable of any supernatural desire of God. Their theological dualism was complete but remained hidden behind a traditional terminology--"natural" and "supernatural--whose meaning it subverted. In Aquinas, the term supernatural does not refer to a new order of being added to nature but to the means for attaining the one final end for which the power of nature alone does not suffice. He calls God agens supernaturalis to distinguish the order of the Creator from that of creation(in which nature and grace appear together). Nature thereby becomes the effect of a supernatural agent."
-Louis Dupre, Passage to Modernity
I have been thinking about this post a little more. I know I am not qualified to attempt to develop such a cosmology, it is plainly beyond my abilities. But I will foolheartedly offer these observations; before anyone makes mince-meat of me I only ask that you be quick and merciful...
I am generally more inclined to dig into political philosophy, where although we are dealing with intangibles, they are intangibles with a fairly ready connection back to the material world. Philosophy as applied to the nature of God and the Universe is of a different sort. In this case we are using Philosophy as a tool to see beyond the limits of our knowledge. In this case the connections back to known territory are a little more tenuous.
Of course, to see beyond the limits of our knowledge, we first have to know what the limits of our knowledge are.
In the case of God, we have scripture, and we have our own personal experiences with him. We tend to ignore the latter when putting together a philosophical position because it doesn't lend itself to use as direct evidence in developing an argument. But inevitably it will inform everything else, and provide the silent underpinnings, and this is not wrong. If we are developing a philosophy of God it has to take into account the real God as we know him or its just a pointless exercise.
At least in the case of the Universe, which has a material component, there is also material knowledge, and the possibility of further material knowledge. You are dealing with the melding of a number of different scientific disciplines, and in this case "philosophy" ought not to go beyond the known realm without at least a tip of the hat to what is "known"... or at least, thought to be known. That means our budding young cosmologist needs at least a metaphorical grasp of physics, and astronomy, and the life sciences. Someone attempting such a thing without trying to include what is known is only going to be made a fool the next time some grad student flips on his electron microscope. So to speak.
By which I mean to say that while its wise to approach the known sciences with a healthy skepticism, it is a mistake to ignore what is known when it creates problems in our dogmatic presuppositions. No one here would do that, but I have met people who would...
The next thing is that the purpose of such a philosophy must be to describe the world as it, in fact, is. This is why I prefer political philosophy where I get to worry about how it ought to be... but in the kind of study we are discussing here the actual nature of creation must harmonize with our philosophical model. We can't worry if the model we develop crosses some line that sets off alarms somewhere. We aren't trying to prove or disprove Plato, or Dualism, or anything else. A fair proportion of the physics text writers aren't Christians, but we won't let that bother us either, truth is truth, and it is where you find it.
The article that kicked off this thread points out the incompleteness, and the inapplicability of the dualist model in some cases, or even many cases. The medievalists used that way of arriving at a solution but we aren't required to, obviously. If as a metaphor for what we see we use some of their thinking in a particular case, we are tipping our hat to the old guys but we are not enslaved to them. Similarly we are often surprised at how much some of the Greeks seem to have gotten right. But we aren't persuaded because they are Greek, we are impressed that they seem to agree with us 3000 years before we graduated high school. Or at least I am.
My point, which I have tortured nearly to death, is that an attempt to accomplish a new philosophy coming from a Christian perspective will not be an explicit refutation of anything necessarily. It should simply start from what we know, or think we know, matched up against what we believe, or think we believe, and go from there chiseling and polishing the pieces until they fit. Sort of.
An honest effort to do that will bring out the peanut gallery to accuse you of some kind of heresy, I promise you, but I won't do it. I'll give it an honest reading, and if I can understand it, an honest argument. Some of the smarter people here may have to explain it to me first, though.
Hm. I just saw this, from a Web search, LL. Are you still around? If so, what do you mean by the term, “biblical prolegomena?”