> If the tools can't crack a system we built and fully documented, our inability to simulate brains just means we're ignorant, not that substrate is magic

Nobody said the substrate is magic. Just that it isn't understood. Plenty of CS folks have also been trying to simulate a brain. We haven't figured it out. The same logic that tells you the neuroscientific model is broken at some level should inform that the brains-as-computers model is similarly deficient.

> Pointing at "multidimensional electrochemical complexity" is just phlogiston with better vocabulary

Sorry, have you figured out how to simulate a brain?

Multidimensional because you have more than one signalling chemical. Electrochemical because you can't just watch what the electrons are doing.

> Name something specific transformers can't do?

That what can't do. A neuron? A neurotransmitter-receptor system? We literally can't simulate these systems beyond toy models. We don't even know what the essential parts are--can you safely lump together N neutransmitter molecules? What's N? We're still discovering new ion channels?!