Maybe I am misunderstanding the terms we are using. Allow me to articulate what I think the valuable line of inquiry is here, and then maybe you can identify what I am missing philosophically, because I'm still not sure exactly what that is, even after reading your comment.
In my thinking, a reductionist thought process goes something like this: we observe oxidation of the hydrogen sulfide in mud, even when there are no apparent electron acceptors in the immediate vicinity. We then identify bacterial filaments which appear to allow electron transport from the reducing agent to the electron acceptor. Furthermore, we will then attempt to isolate the bacteria making up the filaments, and then attempt to identify what structures they synthesize to allow this feat.
And a few follow up questions to your comment: what do you think population dynamics have to do with the current phenomenon, or was that more a related thought? When you talk about "destination states," are you insinuating that there is some design occurring, or that we can observe states in the state space that seem to be stable, and that random walks tend to end up in those stable states? If it is the latter, I totally agree, and I don't see how that is outside of the purview of science as traditionally practiced. It might be an interpretation or model for how the parts of a system fit together, but an attempt at synthesis is basically in the conclusions section of any paper ever written in biology. So I guess it boils down to the same question I posed earlier: how exactly are scientists failing to describe natural phenomena?