KP: Thanks for your patience. You have been over this territory many times before, I am sure, but something basic is dividing us, and, with your help, I want to see exactly what it is. So, please do bear with me. I doubt that we will agree, having been disagreeing for forty years now, but at least I, for one, hope to finally see EXACTLY where we disagree.
No, I do not think that the physical includes the mental at the "basic" level. At the basic level it is just quarks and leptons doing what they do without any teleology or guidance. However we know that some ensembles of quarks and leptons can run fade routes, sing arias, and dance Swan Lake. Fade routes, arias, and choreography are not physical things. They are abstract patterns of movement or sound that can have innumerable distinct physical realizations. The physics of quarks and leptons makes no reference to football, music, or dance, and nothing in that physics entails such an ability, and no one would expect that it would. However, we know it as a plain and non-mysterious fact, that various functional capacities only emerge with certain types of structural organization. There is no enigmatic "woo woo" emergence involved. It is simply a matter of (physical) form enabling function.
Innumerable examples abound. Merely having a protein with the chemical sequence of amino acid of an enzyme does not make that molecule an enzyme. It is only when it has folded into a particular functional three-dimensional shape that it is able to do the job of catalysis. At the basic level of quarks and leptons, there are no enzymes. At the far more complex level of folded proteins there are enzymes. Similarly, digestion is a function of the digestive system and the circulation of the blood is a function of the circulatory system. Digestive systems and circulatory systems are physical systems made of quarks and leptons that, at the basic level, cannot digest food or circulate the blood, but most definitely can when incomprehensibly great numbers of them are organized in very complex ways.
Therefore you must admit as a plain, commonplace, and undeniable fact that as things are organized they can acquire functions and capabilities of an entirely different sort than those evinced by their fundamental constituents. Again, quarks cannot do ballroom dance but Fred Astaire and Ginger Rogers most definitely could. I guess then, what I need to know is why mental performances, in principle, cannot be among the capacities that vast ensembles of quarks and leptons can acquire when they are organized into brains. You need to tell me plainly why not. My cat can think. She can even do modus ponens. She often knows that if she does A I will do B, so she does A to get me to do B. Dammit, that is as good as my freshmen can often do! Are you saying that my cat's brain is not up to it? Sorry, I do not mean to sound flippant, but if you admit that a brain (a cat's or a human's) is up to modus ponens, then everything else follows. Using my brain to understand, say, the Axiom of Choice is just around the corner.
VR: Well, this is the fallacy of composition objection, that says that organization makes it possible for things which are not x by themselves are x in combination. But if it's ensembles of quarks, et al, then the governing laws are the laws governing quarks. Are you prepared to say a higher level of organization introduces new laws into physics?
It is true that if none of the bricks in a wall are six feet in height, the wall can be nonetheless. But in this case, it adds up. The brick-facts add up to close the question of the height of the wall. Going from the physical to the mental, the physical facts don't add up to mental-state facts. The underdetermine the mental. That is what Quine was getting at with the indeterminacy of translation, what Davidson was getting at when the attacked psychophysical laws, what is going on in Kripke with plus and quus.
There are four things that don't add up from the physical to the mental.
One of them is a first person perspective. If something has a first person perspective it affects what it does. If Trump doesn't know who he is, he might watch the news and think the President should be impeached. If he knows who he is, this will happen when hell freezes over. Yet how would science describe what Trump comes to know. "I am Donald Trump" is false for you and me (thank you Jesus!), "Donald Trump is Donald Trump" is a tautology that couldn't possible change anyone's behavior, so what is this truth, exactly?
The second is purpose. If the base level is purposeless, how do you get purpose at another level. You might get something that serves the purposes of a mind, but how can it have a purpose its parts don't have, especially if the laws governing the purposeless parts determine motions without purpose. (And quantum randomness is, well, quantum randomness).
The third is intentionality. How does that work? How the state of a set of particles be about an eternal object, or a nonexistent object. What you have is a set of particles in space, time, and causal connection. Add up the nonintentional facts all day, and you won't see an intentional fact. Given the physical, a person's thought could be about a rabbit, about undetatched rabbit parts, or about nothing at all, since the "person" could actually be a zombie without real mental states. Nothing follows logically from the state of the physical.
The fourth thing that is necessarily missing at the bottom level is normativity. Nothing happens at that level because it ought to happen. We were discussing earlier in this thread the idea that it seems pretty critical to an ethical theory that people are capable of doing some things because it's their duty. But, in that last analysis, everything that happens in the world happens, according to materialism, because of what happens at the basic level. Therefore, in the last analysis, no one ever does anything because it's their duty. They do it because of the state of the physical world.
And on materialism, the "thinghood" of the brain is questionable. Consciousness has a unity to it, but while we attribute a unity to the brain, in reality the "brain" is just a bunch of parts we CALL a brain. The real entities are the basic particles, the brain is just a bunch.
If a brain is literally what a brain is supposed to be on physicalism, a bunch of particles, then it is NOT up to modus ponens. Different parts do different steps, so what makes it modus ponens? If something provides a perspective, then, sure, even a computer can do modus ponens. But only considered as an extension of the mental states of its programmers, and only as a product of intelligent design.