The author strikes me as someone who has not read many neuroscience papers, or talked to many researchers, and only read headlines which poorly summarize neurological studies.

Let's start with the first few paragraphs, where your friend's input literally changes your perception. This could be broadly categorized as "top down processing". That is, larger ideas shape your perceptions about stimuli, rather than stimuli creating a larger idea. It's why the "playing a record backwards" fear mongering kind of worked. If you're told WHAT to listen for, you can hear it, even if you never could have come up with the sentence supposedly embedded if you listened to the audio a million times.

We find it somehow compelling to think that the brain holds the answers to the questions about, well, everything that matters to us, including art.

I'm confused, I think this is the start of the "the mind is completely separate and distinct from the brain" argument. The "limits" the author is speaking of are there, to an extent. I would argue that the "why" of experiences is left open to philosophy, rather than science. Or "what is the ideal experience", or things of that nature. But pretending that study of the organ which organizes all our sensory data has no bearing on the study of how we perceive things is really very stupid sounding, to my ears.

The author defines the "ideology" of neuroscience thusly:

Each of us, according to this ideology, is a brain in a vat of flesh and bone, or, to change the image, we are like submariners in a windowless craft (the body) afloat in a dark ocean of energy (the world). We know nothing of what there is around us except what shows up on our internal screens.

Now, neuroscience and psychology BOTH endorse a mind/body interaction. There are some interesting conditions that reflect this relationship. Capgras syndrome is a syndrome where the subject can recognize friends and family, but is convinced they are imposters. Why is this? The physiological response we have when we see someone we know/care about is absent. Normally you get a measurable increase in palm sweating (called "galvanic skin response"), your pulse may quicken. With these feelings absent, when you clearly "know" the person in front of you, leads you to jump to the conclusion that they are a fake.

Video of Capgras Syndrome

Another example is auditory judgement of an object. If you are blindfolded, and hear a pitch which sounds like it is approaching you, and asked to call out when it is halfway from its starting point to you, everyone, all subjects, will call out early. Subjects more in shape (runners, weight lifters, etc.) will still call out early, but later than their untrained peers. Men call out later than women (on average).

Neuroscience very clearly does NOT think that the mind is some closed system with a few A/V inputs from the body. It is certainly thought of as central to the system, and job critical. Not isolated.

Every thought, feeling, experience, impression, value, argument, emotion, attitude, inclination, belief, desire, and ambition is in your brain.

Well, uh, it's more fair to say that every thought, feeling, etc. is the result of your brain's actions, in response to stimuli, and in conjunction with your own physiological state (adrenaline, testosterone, estrogen are all modulatory hormones involved in mood, that are NOT produced in the brain, but rather, in your body).

Now, I'm open to other explanations grounded in fact, but people attacking the idea that the brain is LARGELY responsible for how you think and act rarely purpose a reasonable (or testable) hypothesis

And this new knowledge — of how the organization of bits of matter inside your head can be your personality, thoughts, understanding, wonderings, religious or sexual impulses -- is surely among the most exciting and important in all of science, or so it is claimed.

I'll use the "sexual impulses" as an example for why I think this concept is solid, rather than foolish, as the author thinks. In males, (and, to an extent, in females), testosterone plays a critical role in sexual desire. If you increase T, on average, a male's sex drive will go up. If you reduce T, it will go down. And if a male has his testicles removed (castration) you will see a complete elimination of T, and it pretty much renders the man asexual (I believe the Romans had castrated male servants to take care of the female royalty for this reason). NPR had a good segment on Testosterone recently, and it's worth a listen. My point being: this is a single hormone, but it completely changes (sexual) behavior, in addition to modulating things like aggression. So if you change a hormone level, it changes personality traits.

More relevant to the author's gripe with neuroscience, what happens when you are brain damaged? If it is severe enough, you are almost an entirely different person, are you not? Why? You've damaged the interpreter,the puzzle-solver, the pattern finder. It works differently (worse) now, and so do you.

But a work of art, like the meaningful world around us, is not a mere stimulus.

I've never talked to a neuroscientist who thought that the brain couldn't provide a stimulus to itself. That's basically what abstract thinking is. You are presenting your brain with memories and ideas stored in your brain, comparing them to other ideas in your brain and sometimes coming original conclusions. The life you've lived up until the point you see some painting or another could EASILY impact your preception of it, because you have DIFFERENT ideas stored in your brain, different memories, different experiences, and different bodily chemistry (within a range, but still).

For instance, seeing a cube, according to this sort of approach, is having a line drawing of a cube in your brain. And that, in turn, is supposed to explain why we consciously experience a cube when we look at a mere picture of one.

This is heinously misrepresenting human perception, but that's what happens when you try to criticize a field of science with a layman's understanding of it. Let's use visual perception as an example. There are degrees to perceiving depth and 3 dimensionality.

If I draw two stick figures, and one is large than the other, I might precieve either that one stick figure is small, and one is a giant, or that one is in the foreground, and the other is in the background. With some top down processing, maybe I can pick which of these is correct. That is me trying to make sense of simple stimulus, which I suspect was designed to be interpreted in one of these two ways.

Now, something like this:

Is a bit different.

It's not a perfect fraud, but it is carefully designed to have a recognizeable shape, and shading that closely mimics shadows on an actual, 3-dimensional object.

That's not our brain being "tricked" really. It's our brain having certain little cues that it picks up on, which tell us, in the everyday world, whether something is a drawing or whether it's really a snake. This drawing is carefully trying to tick more of those boxes than a drawing normally would.

I've already typed too much, but if anyone would like to change my mind, or talk about something later in the article, feel free: I certainly don't know everything about how the brain works, but I feel the author knows next to nothing about it. To quote hitchens, he gives me the "awful impression...of someone who hasn't read any of the arguments against your position ever. "

And to be clear, I agree that perhaps art isn't "best" studied by neuroscience ,and that it is hard to study, and extremely varied. I don't think this means that neuroscience can have nothing to say about the perception of art.