You might say optogenetics renders the workings of the brain more transparent, except that would steal the thunder of the thing Deisseroth developed next. It’s a technology known as Clarity, and it makes it possible to take brains (or other organs) donated for research and drain them of opaque materials, like lipids, and replace them with a transparent “hydrogel” that preserves the intricate structure of the organ. Clarity lets scientists study the brain in three-dimensional detail: local circuit wiring, neuronal connections, subcellular structures, and the chemical interplay of neurotransmitters can all be revealed. It’s a big opening for psychiatrists like Deisseroth who have long wondered: to what extent are autism, depression, and other mental disorders rooted in (or themselves the causes of) abnormal wiring or patterns of connectivity in the brain?

Deisseroth’s patients are like many of the big questions he’s trying to answer: they don’t lend themselves to easy answers or simple explanations. In his office he tells me that he’s only accepting patients with depression or autism so he can focus on those conditions more intently. While scientists have identified genes associated with both disorders, and some therapies work to certain extents in certain people, variations in individual expression are vast. There’s no easy way to diagnose them, no lab test or scan. There’s more that we don’t know than what we do know. Every patient Deisseroth encounters is like a cipher, a lengthy hangman of consonants. A different kind of examination, or perspective, is required to even attempt to treat them.

To get inside their heads, Deisseroth needs to understand their stories. He is a devoted reader (attributed in part to a childhood hardly marked by television) and a fiction writer, and he inspects patients’ minds the way a reader inspects a protagonist’s. He is very sensitive about how his patients deal with, and comprehend, their own symptoms.

For instance:

One time, several years after he began seeing Pablo, Deisseroth asked Pablo why he avoided eye contact. Deisseroth asked him if he felt shy. Pablo said he didn’t. Deisseroth asked if he made Pablo feel uncomfortable. Pablo denied that as well. Eventually, Pablo revealed that when talking or explaining something, maintaining eye contact and then having to process his listener’s reactions amounted to an overwhelming added task to juggle. “It felt like too much stimulus for him,” Deisseroth said.

Social interaction is such a hard thing for humans to master — it requires a certain rhythm, anticipation of another’s moves, execution of one’s own. “It’s like a dance,” Deisseroth says. His mention of rhythm reminded me of Pablo’s laugh: Pablo tended to inject laughter before he said something funny, rather than in time with it. That’s a little different from laughing at one’s own jokes (which I am an expert at, I’m afraid); instead it seemed as though Pablo anticipated a humorous reaction, ideally, from what he’d say, and then rushed to it. Like shuffling the sequence of expected events, Deisseroth noted.

That set off a spark of insight in Deisseroth. Pablo’s lack of eye contact fit with the information-overload theory, previously suggested by UCSF’s John Rubenstein, that individuals with autism feel their speech disrupted by extra sensory and processing information. And that took Deisseroth back to the bench. In 2011 Nature published a study out of Deisseroth’s lab that showed ordinary mice can be made to develop autism-type behavioral deficiencies by stimulating certain nerve cells. Then last year, Deisseroth’s lab went further. Lab members conducted two experiments on hyperactive mice using optogenetics: in the first, they used light to stimulate an inhibitory neuron in the prefrontal cortex. In the second, the lab used light to dampen an excitatory neuron. Both experiments resulted in less hyperactive, more sociable mice who spent as much time schmoozing new mice as controls.

Deisseroth intends to further investigate neural circuits implicated in autism. Last November, his lab published a paper in Cell on the brain’s mechanism for attention. After witnessing how various neurons speak to one other during a behavioral state, Deisseroth discovered that circuits that modulate brain behavior do not perform in a binary fashion (either “on” or “off”). Instead they have a sort of gradualism, secreting molecules that render excitatory or inhibitory firing more likely or less likely depending on environment. Little by little, this kind of work is demystifying why people with autism have issues with sensory integration issues and sociability. It’s also a step toward understanding the mechanisms of different states of consciousness.