Hi
As a professional biologist I spent ten years researching cell-level biophysical processes, and have the doctorate and the t-shirt to prove it. Putting my cards on the table straight off, I should say that I am most assuredly not a young-earth creationist
Nevertheless, I know enough about the scientific method to see why it doesn't
automatically apply very well to `deep issues'. In my opinion, the problem with turning our scientific method to something like the origin of life is not that we don't have the right scientific process, but that we don't have the right
epistemology.
Here is an example. As scientists, one of the things we seek from our theories is falsifiability. But we don't usually stop to wonder
why falsifiability is desirable. To most scientists, it's just too obvious to worry about. But I think that the real reason we insist on falsifiability is that it sort of works. We turn the scientific method to a great many
similar problems, and we develop an idea of the probability of falsifiability that a theory must have to be considered worthwhile alongside other theories relating to problems in the same domain.
Where the origin of life is concerned, there simply aren't any problems in the same domain. It is a unique (we assume) problem. So when somebody says, for example, finding human remains alongside trilobites would falsify the theory of evolution -- yes it would; but so what? Does the environment provide us with sufficient opportunities for falsification that non-falsification is epistemelogically meaningful? How would we know one way or the other?
There is a similar problem with predictive power -- we assume that a sound theory will allow us to make predictions about future observations, but we don't have a clear way of judging how many predictions, how often, are required to validate the theory?
None of this is much of a problem when we do day-to-day science, because we develop an intuitive understanding of the epistemelogical power of our theories by considering the success or failure of theories in the same problem domain. Where there are no problems in the same domain, our ability to do this is weakened. What is required, I submit, is not a different scientific method, or even (Heaven forbid) a non-scientific method, but a deeper investigation of the whether our assumptions about the scientific method stand up in the face of unique problems.
For what it's worth, although I'm not much of a supporter of the Intelligent Design movement myself, it isn't really a criticism to say that it `focuses on minutiae'. Modern biology as a discipline is concerned with minuitiae. Minuitiae is where it's at right now. It is commonly thought that the real challenge -- if there is one -- to the neo-Darwinian model of evolution is to explain how (say) complex structures like the mammalian eye arise. But the processes that go on inside the cell nucleus are of such staggering complexity that they make the eye look like Lego model.
I should also point out also that `irreducible complexity' of the flagellum is still very much a live issue. Arguments that the flagellum has a functional precursor in the type-III secretory system (TTSS) have proven to be ill-founded -- it now seems that the TTSS is derived from the flagellum rather than the other way about.
But I doubt that this is a good place to discuss, say, irreducible complexity -- it's just too technical for a general readership to take much of an interest in, in my opinion.
Best wishes
MadBear