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The computer analogy is doing a lot of heavy lifting here, but it's carrying more weight than it can bear. Yes, if you take a soldering iron to your CPU, you'll break it. But the reason we know computers are deterministic isn't because we can point to individual transistors and say "this one controls the mouse cursor." It's because we built them from the ground up with deterministic principles, and we can trace the logical flow from input to output through layers of abstraction.
Compare that to any more tangled, yet mechanistic naturally occurring phenomena, and you can see that just knowing the fundamental or even statistical laws governing a complex process doesn't give us the ability to make surgical changes. We can predict the weather several days out with significant accuracy, yet our ability to change it to our benefit is limited.
The brain is not a tool we built. The brain is a three-pound lump of evolved, self-organizing, wet, squishy, recursively layered technology that we woke up inside of. We are not engineers with a schematic, I'd say we're closer to archaeologists who have discovered an alien supercomputer of terrifying complexity, with no instruction manual and no "off" switch.
The universe, biology, or natural selection, was under no selection pressure to make the brain legible to itself. You can look at our attempts at making evolutionary algorithms, and see how the outputs often appear chaotic, but still work.
Consider even LLMs. The basic units, neurons? Not a big deal. Simple linear algebra. Even the attention mechanism isn't too complicated. Yet run the whole ensemble through enormous amounts of data, and we find ourselves consistently befuddled by how the fuck the whole thing works. And yet we understand it perfectly fine on a micro level! Or consider the inevitable buildup of spaghetti code, turning something as deterministic (let's not get into race-conditions and all that, but in general) as code into something headache inducing at best.
And LLMs were built by humans. To be legible to humans. Neuroscience has a far more uphill struggle.
And yet we've made considerable progress. We're well past the sheer crudeness of lobotomies or hits on the head.
fMRI studies can predict with reasonable accuracy which of several choices a person will make seconds before they're consciously aware of the decision. We've got functional BCIs. We can interpret dreams, we can take a literal snapshot of your mind's eye. We can use deep brain stimulation or optogentics to flip individual neurons or neural circuits with reproducible and consistent effects.
As for "determinism of the gaps". What?
Two hundred years ago, the "gap" was the entire brain. The mind was a total mystery. Now, we can point to specific neural circuits involved in decision-making, emotion, and perception. We've moved from "an imbalance of humors causes melancholy" to "stimulating the subgenual cingulate can alleviate depressive symptoms." We've gone from believing seizures were demonic possession to understanding them as uncontrolled electrical storms in the cortex. The gaps where a non-material explanation can hide are shrinking daily. The vector of scientific progress seems to be pointing firmly in one direction. At this point, there's little but wishful thinking behind vain hopes that just maybe, mechanistic interpretation might fail on the next rung of the ladder.
I am frankly flabbergasted that anyone could come away with the opposite takeaway. It's akin to claiming that progress from Newton's laws to the Standard Model has somehow left us in more ontological and epistemic confusion. It has the same chutzpah as a homeopath telling me that modern medicine is a failure because we were wrong about the aetiogenesis of gastric ulcers.
Citation needed? I mean, what's so non-deterministic about the advances I mentioned? What exactly do you think are the "non-deterministic" techniques that work?
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