As I was thinking about the problems of trying to reduce ideas to a molecular form, the entire thing looks massively far fetched to me, in thinking about what I've read on the topic, it seems ever more far fetched. Since the brawl, discussed below, came up over the alleged existence of "empathy" as a product of natural selection, in its modern form, that would mean that those ideas were inherited as behaviors through natural selection.
In terms of materialist dogma, they would almost certainly have to be coded in proteins that were the product of specific "empathy genes" that were what was inherited. But that is quite a problem, in itself. Do proteins of sufficient complexity form as quickly as we have new ideas? And, once one is formed, how does its form become modified to represent a new, twist, as it were, in the idea? Every step between vague consideration and final "proof" of an idea involves myriad different ideas, if that soup of thoughts can realistically be divided into ideas. [In editing this the idea that that division of continuous thinking into discreet ideas isn't exactly a certain and non-problematic act, I don't think it can honestly be done. Is every fraction of a second during which an idea exists in our experience, in our mind but is not formed represented by its specific molecule?]
I briefly searched for time ranges for the production and folding of proteins to see if those have been estimated and haven't found much to go on, though what I have found would lead me to think that the idea, just on the basis of the time it would take to form an "idea protein" and for it to go through the rapid and extraordinarily unpredictable modifications that our ideas take in our most direct experience.*
When you start cogitating on an idea, you never know what you're going to put into it in terms of additional information, speculations, hunches, personal predilections and preferences (many of those not consciously included or even admitted to), things you'll take up and reject, sometimes reconsidering those rejections and putting them, often in modified form, themselves, back into the process. How does the gene, coded to produce a specific type of protein, deal with all of that? And how does it know how to edit out the bad content from the good? Our ideas, we aren't born with them, if there is one thing we can know with absolute confidence that is the case. They aren't formed automatically and unrelated to our own volition, they are frequently the process of intentional effort, for varying motives, honest curiosity, dishonest motivations. And that brings us to the quality of the product. Some ideas are developed in an effort to find the truth, some with the intention of deceiving other people to rob them or use them or to enable the liar to get away with something.
Ideas aren't the simple, definite entities that the breezy materialist presentation of them as the neat packets of genetic heritability insists they are. They are as varied as the indices of all of the books in all of human history times some enormous number that could, plausibly, be infinity. And that is just what we can safely say about human ideas, internal human experience and conception of the universe. About that of other species, we aren't really even that definite about. The only thing we can know about that is that human beings have never experienced life as a member of any other individual of another species in any other genus, family, order class, phylum, or even, possibly kingdom or domain has experienced. Everything said about that is human speculation, based on the consultation of human experience of being a human being with our individual experience.
If the range of possible human ideas exceeds the physical capacity of our physical constituents to form the appropriate molecules in which the materialist would imprison thoughts by one or more than one, then the theory that our consciousness is the mere product of chemistry and physics becomes massively implausible.
And that is just considering the matter on the materialists' own terms. When something other than a material basis of consciousness is considered to be possible, anything the materialist can come up with could merely be a physical artifact of something that is motivated by something entirely different, something that can't fit into their hermetically sealed maze for particles to move around in. Given the problems with the materialists' belief on its most basic terms, its wild difference from my own experience of thinking, I find an immaterial consciousness that is unlike physical matter, operating on other than physical laws and which is able to interact with physical matter in ways more subtle and unlike those things science deals with entirely more plausible. Throwing the words "natural selection" into the gap of scientific knowledge of consciousness seems to me to make the effort less instead of more plausible.
* Here is a post from the somewhat less dogmatic atheist, Larry Moran, on what was known about one stage of protein production, folding, and the many problem of just that process. And I doubt it's anything like a final word on that topic.
Update: The more I think about this the more obvious it is that that our consciousness, our thoughts, our ideas cannot be the product of material causation. We talk about all of those things as if we really can define any of them. The assertion that we know what an idea consists of, as if it were a definite thing that comes into being and has a definite form and character is merely pretense. There isn't anything that constitutes a final entity that is an "idea". Ideas are constantly changing and are developed on an individual basis. Every idea is always contingent, it is always in the process of development, there is no way to fix an idea as final and unchanging. There would be no means of applying such an idea to novel situations if that were the case. The new application would have to alter the idea.
Pretend that there is such a thing as an idea that assumes a final form. If it is represented in a final form by a specific molecule or physical structure then it would have to have been derived from an extraordinary number of previous, related ideas, which would have had to exist as entities discrete enough to have also had a physical basis. The final form would have to develop from the incomplete form. But thoughts don't exist as static entities fixed in some Platonic form, they exist in time and in the ever changing, ever fluctuating conditions of our minds.
If the molecules of the final "idea" are formed of the ruins of the previous molecules that they supersede, where does the memory of those previous states reside?
Nope, I think the idea that our minds are the mere expression of molecules and physical structures is not credible. It isn't molecules all the way down because there is no "thing" to be comprised of those molecules and, anyway, where are the molecules? Our brains would have to be full of them in order to account for that idea and they would have to each be significantly different from the others in order to constitute a different idea.
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