An obvious example would be the supplanting of geocentrism by heliocentric theory.
But to get back to Darwin's evolution theory, the main problem seems to be that it really has no method to explain complex systems. Its evolution is linear, local, and historical and focuses on species (and that mainly through the lens of "survival fitness" for "reproductive success" — how reductive can you get!), not on individual biological organisms as complexes of functions (which imply non-linearity, non-locality, and purpose). Which they obviously are.
Further, Darwinism seems to function wholly within the Newtonian paradigm, with its emphasis on mechanism and material bodies. What research into complexity is beginning to show, however, is that complex systems are not inherently mechanical, and an immaterial element — information — is present in their composition.
I came across a notable paper the other day, by Donald C. Mikulecky — Robert Rosen: The Well Posed Question and Its Answer — Why Are Organisms Different from Machines?. The following excerpt addresses our present question as follows:
What is a complex system and why is a complex system different from a machine?I find this "stuff" so fascinating, freedumb2003! Truly exciting. Liberating!
A complex system falls outside the formalism called the Newtonian Paradigm. That is not to say that complex systems cannot be seen as machines for limited kinds of analysis. This is, in fact, what traditional science does. Using [mathematician Robert] Rosen's general characteristics to separate the two kinds of objects, we see that complex systems contain semantic aspects [meaning of a communication] which cannot be reduced to syntax [the grammar or parts of speech of a communication]. Therefore they are not simulatable even though, when viewed as machines, the machine model is simulatable. They have no largest model from which all other models can be derived. This is simply because complex systems, by their very nature, require multiple distinct ways of interacting with them to capture their qualities. Their models are now distinct. Analytic models, which are expressed mathematically as direct products of quotient spaces are no longer equivalent to synthetic models which are built up from disjoint pieces as direct sums. Using this formulation every synthetic model is an analytic model, but there are analytic models which are not synthetic models. In other words, these analytic models are not reducible to disjoint sets of parts. This is a most profound distinction and requires some elaboration, for in it lies the essence of the failure of reductionism. In the machine, each model analytic or synthetic, is formulated in terms of the material parts of the system. Thus any model will be reducible and can be reconstructed from its parts.This is not the case in a complex system. There are certain key models which are formulated in an entirely different way. These models are made up of functional components which do not map to the material parts in any one to one manner. The functional component itself is totally dependent on the context of the whole system and has no meaning outside that context. This is why reducing the system to its material parts loses information irreversibly. This is a cornerstone to the overall discovery Rosen made. It captures a real difference between complexity and reductionism which no other approach seems to have been able to formulate. This distinction makes it impossible to confuse computer models with complex systems. It also explains how there can be real "objective" aspects of a complex system that are to be considered along with the material parts, but which have a totally different character [i.e., they are immaterial].... [emphasis added]
If you have the time and interest, please do take a look — and let me know what you think?
Thank you so very much for your excellent essay/post freedumb2003!
I wonder how his system of analysis of the difference between a complex system and a machine would distinguish between a lit candle and an unlit one? (Not trying to be snarky; I'm really curious about that.)
If you disassemble a candle, you can presumably reassemble it, and it remains unchanged.
However, if you disassemble a lit candle, you may "extinguish" an ineffable property of the candle that cannot be reassembled readily.
Thank you so very much for all your insights, dearest sister in Christ!