Evolutionary science has worked in the context of metaphysical materialism since the time of Darwin. Darwin himself did not. Darwinism as detailed by Charles Darwin maintained a primary role for mind and postulated mental evolution.
https://en.wikibooks.org/wiki/The_Descent_of_Man/Chapter_III
The modern synthesis of evolution did not embrace Darwin's field observations and believed in only the chemistry of genes. Current evolutionary scholars are looking at a large gap in the amount and capability of the chemicals of encoded genes to be casual to the extent of observed hereditary behavior. (citations available on request)
This writer asserts that the information sciences are more germane than chemisrty in addressing observed behaviors in living things by understanding biological information processing. This field is exploding in use and is termed Bioinformatics. Bioinformatics can objectively address the measurable variables of mental activity and how mental capabilities are inherited. Further, the role of mentation and biological information processing can support pathways for an active causal agency in biological evolution itself. (see Darwin in the Genome - by Lynn Caporale)
The thought-experiment, which went unappreciated, was to point out the fact that epigenetic markers are not causal in terms of chemistry turning into codons, David points this out. Error-correction systems erase them. However, there are messages received and instructions that persist through information leaking into the DNA/RNA/Ribosome natural language. Birds can inherit a fear of man in a single generation. That fear can persit for many generation as instinct unless different instructions enter the "conversation". The markers are semantic notation, not a mechanism.
Through the processes of transcription, translation and cybernetic feedback, these markers encode meaningful information into the system through linguistic means as a natural language. I am aware that this flies in the face of what many people have been taught (wrongly), but it predicts a means detailing field observations of how living species adapt and evolve. The "markers" carry messages from the environment as detected by living things from their personal, social and species context) to the evolving genome and while organic chemistry is the channel - the functionality is in information processing about fitness in the future.
My next point would how this works and can be measured - but without speaking to an understanding of mutual information in action I should stop.
Thank you, Stephen, for your effort in trying to express your ideas in more understandable English. However, while the English is clearer, some of the underlying concepts are still, to me at least, sketchy. You say that epigenetic markers aren't causal. Well, in the end, neither might DNA sequences be
causal; rather than their
causing this or that phenotypic trait, they may rather be the
appearance to our perception (or its extension through instruments and/or logical constructions) of phenotypic traits at a fine level of granularity.
When we look at phenomenality, the habit of reductionism tends to put causation at the lowest level possible: e.g. we explain why the sky appears blue by talking about scattering effects occurring at the level of atoms and molecules, and thereby think we have explained the phenomenon. But what if the sky appears blue for some as yet dimly understood reason, and at the level of our perception/its extensions, we are imposing a causative narrative of "atoms and molecules"?
Rather than science discovering new mechanisms, it might be in the business of constructing
consistent narratives. The fact that these narratives at some point always break down (however useful they might be within a certain range) could be flagging to us to the possibility that causation isn't bottom-up, but rather top-down. If that is so, the amazing thing is that the narratives appear so consistent over their effective range: good enough for us to be able to create hi-tech products, for example.
The temptation to assert scientists have their world view largely correct is almost irresistible: but in the end it could be merely an
appearance of correctness, and entails us constructing insoluble "problems" such as the hard problem of consciousness (see Bernardo Kastrup's paper
here), or the fact that relativity and Quantum theories are incompatible. These "problems", in the end, may be semantic artifacts of the way that scientists tend to think that the physical is fundamental rather than consciousness.
Now I don't know if any of that relates to what you are saying, and I'm still unsure what you mean when you say that
mutual information is important. One of the reasons is that it's an area that seems to be shrouded in much mathematical rubric, and I'm not by any stretch of the imagination a mathematician, making it very difficult for me to get a handle on it. You insist that I have that understanding before you are willing to go further, and so it appears that we are at an impasse. Hence your understanding remains with you, and I still, essentially, have only the vaguest clue what you're saying. If you want to engage in meaningful communication, for me you would need to be less elliptical, I'm afraid.