No - it would be anachronistic if you did, which is a large part of my point. But take the account of the Tabernacle, in which there is a conscious echo in Bezalel and Oholiab, filled with God’s Spirit to make the tabernacle, with God creating his cosmic temple in Gen 1 (see Greg Beale on this).
Amongst other things, they were responsible for the design and casting of the bronze furnishings of the temple, such as the laver. Later, Hiram did castings on a much grander scale for Solomon’s Temple - remember the two large pillars Boaz and Jachin. Today, such metalwork would be regarded as engineering, and the decorative work as “art” - but then it was just artisanship.
But the point is that all those “making” analogies, authorised by Scripture, still treat creation as an “artifact”, recognising that we will intuit that it is more than that. (In my last post I should also have added that the “speech” analogy, as well as being a royal image, also covers the bard, weaving organic worlds of imagination that can change how we see things: there’s a closer analogy).
Paley, I think, gets a bad deal nowadays - most critics haven’t read him (I reviewed him [here](http://potiphar.jongarvey.co.uk/2012/01/04/natural-theology-paley-and-darwin/ .) For a start, although he begins with his watch analogy, and deals with biology according to the mechanical anatomy of the time, he also deals with astronomy, the nature of the elements and (as I mention in my piece) fine tuning of laws, such as the inverse square law. But he was doing apologetics with the concepts of his time, as you rightly say:
Bacon and Descartes championed “the mechanical philosophy”, right? And as you say, Boyle was its chief prophet. You can’t get more mechanistic than that. Descartes regarded animals as mere automata, directly leading to the interest in mechanical automata in Paley’s own century. He responded to people where they were at the time.
But that mechanistic view has, surely, only continued in our time in the molecular biology conception of life. Biology has seen organisms as molecular machines - and the whole evolutionary concept of altering the parts of living things piecemeal through mutation of the manufacturing program (DNA) is a wholly mechanical, engineering concept. So it is not surprising that ID as an apologetics movement should begin there, as Paley began with his watch.
The very label “Intelligent Design” was a direct reaction to the prevalent idea of evolution as “design without intelligence” in the Blind Watchmaker. In fact, though, I’ve seen more questioning of such metaphors by ID writers (and those they champion such as the systems biologists and structuralists) than I have in the EC community.
And that includes a number of writers espousing A_T philosophy, including Vincent Torley, Michael Chaberek and others. I believe you’re right that to get a more rounded conception we have to go back to Aristotle and Plato. Before Bacon and Co, the world was seen not as a machine, but more like an holistic being - and of course, organisms were substantial forms, created as understood by Aquinas) not as disparate parts but as integrated wholes.
It’s the congruence of that with the biblical concept of creation, and the recognition of the deeply integrated nature of living things, that has helped a resurgence in A_T kinds of thinking amongst philosophers like Ed Feser and Tom Nagel, physicists like Heisenberg and Hump poster Ian Thompson, and biologists in fields like systems biology and physiology (such as Denis Noble).
In theology, N T Wright has sharply summed it up as a worldview conflict between one currently dominant ancient philsopohy - Epicureanism - and the more biblical, slightly less ancient philosophies that included final and formal causation in their schemes (which seem essential if we are to escape from narrowly mechanistic views).
But as I’ve been saying in the beginnings of my theology of nature series on The Hump, if one wants to go in that direction, something will have to give in ones approach to biological science, which is currently completely Epicurean.
Specifically, if orgainsms are not machines, but substantial forms, is piecemeal evolution a plausible mechanism to explain their transformations?