You wrote:
Since the days of Newton, science has ignored formal and final cause with the assumption that everything in the universe is a machine that can be understood by material and efficient causes....The "presupposition" that the universe "ought" to be understood as a machine obviously limits the scientific search to machine-like characteristics from the get-go.And their presupposition has been wildly successful for centuries because, with the notable exception of living things, the rest of the universe can be understood as a machine.
Evidently, the scientists always considered biology to be a “special case” – minor in comparison to the rest of the universe – and not really worth their time. The machine presupposition works well in physics and chemistry, so it’s just a matter of time before they can explain life as a machine, too.
The Newtonian paradigm has been so successful that by now, most people believe that physics (including mechanics of course) is THE universal descriptor of the laws of the universe, and biology — as you noted — is just a fairly "rare" and thus uninteresting case. Biology is simply assumed to reduce to the physical laws.
On that very assumption, though, biology hits the wall.
Notice that Darwin's Theory of Evolution is not a theory of biology, per se. It is only a theory of speciation. It takes the biology "for granted," and then purports to explain how it speciates.
A much more interesting proposal has been surfacing in recent times, however — the idea that biology is the basic, "more general law" of the universe, and physics is a special case of it.
It seems to me that a science that purports to be a "life science" ought to get a bit more serious about the question, What is life itself? That is, what constitutes "biology?" This is not to ask how do biological organisms change — this is to ask, What is it that makes them biological organisms — living systems — in the first place?
To me, this is the greatest question for 21st-century science. And it is clear that the Newtonian Paradigm cannot answer it. Since Darwin's theory rests on that, it has no answers either.
Here's an excerpt from Robert Rosen's working notes that sheds light on the issues of self-imposed "scientific limitations" WRT to inquiry into biological nature — in a delightfully humorous way:
WHY DO PEOPLE HATE SCIENCE SO MUCH?Thank you ever so much for writing, dearest sister in Christ!a. IT'S REMOTE. (hence, limited away from what is concrete and near).
b. IT PERTAINS, AT BEST, TO ONLY ONE WAY OF KNOWING. (hence, limited away from what is inaccessible to that way of knowing).
c. IT'S RESPONSIBLE FOR OUR PRESENT PROBLEMS; PROBLEMS WHICH CAN ONLY GET WORSE AS SCIENCE PROGRESSES. (hence, limited away from the roots of those problems, limited away from solving those problems; indeed, a cause of those very problems; making the world increasingly worse as it advances).
Re (b): Hutchins felt that scientists were in fact insufferable; arrogant and impudent; confusing reality with objectivity, facts with understanding or principle. Remember his remarks about the Great Conversation. He held that the real question was "what should I do now?" "What should we do now, why should we do these things?" The Great Conversation was, he felt, about politics and religion.
What I am trying to argue is that science is characterized by what it is about, not by any method or way of knowing. Something becomes scientific not by means of a particular way of knowing, or of doing, but by what it is about. It is about truth. It is about finding the consequents of hypotheses: IF a, then what? IF b, why b?
Is A true? (observation).
If A is true, what else is true? (prediction).
Why is A true? (causality).Pretty benign. In this context, a "limitation" of science, would be something like: (a) an inherent inability to tell whether A is true or not; (b) an inherent inability to find out what A implies; (c) an inability to find out what implies A....
If not A, then what? If B, then why B and not C?
On that very assumption, though, biology hits the wall.
And of course I very strongly agree that the big science question this century ought to be what life "is" not simply what it looks like.