As we yawn and open our eyes in the morning, the brain stem sends little puffs of nitric oxide to another part of the brain, the thalamus, which then directs it elsewhere.

Like a computer booting up its operating system before running more complicated programs, nitric oxide triggers certain functions that set the stage for more complex brain operations, according to a new study.

In these first moments of the day, sensory information floods the system — the bright sunlight coming through the curtains, the time on the screeching alarm clock — and all of it needs to be processed and organized, so the brain can understand its surroundings and begin to perform more complex tasks.

“The thinking part of the brain is applying a sort of stencil to the information coming in, and what the nitric oxide is doing is allowing more refinement of that stencil,” says Dwayne Godwin, an associate professor at Wake Forest University and lead author of the study, which was funded by the National Eye Institute .

The little two-atom molecule, it seems, is partly responsible for our ability to perceive whatever it is we’re sensing.

The finding, published last week in the journal Neuroscience, changes the way scientists understand nitric oxide’s role in the brain, and it also has them rethinking the function of the thalamus, where the chemical is released.

The thalamus was thought to be a fairly primitive structure, sort of a gate that could either open and allow sensory information to stream into the cerebral cortex, the most highly functioning part of the brain, or cut off the flow entirely.

Godwin says the new research shows it’s more accurate to think of the thalamus not as a gate but as a club bouncer, one who doesn’t simply allow a huge rush of people to go in or no one at all, but picks and chooses whom to let in and out.

“Instead of vision being a process going straight from eye to cortex, it’s more of a loop,” Godwin explained. “This constitutes a new role for the thalamus in directing, not just modulating.”

While this study is the first to identify nitric oxide’s role in the thalamus, it was already known to have an important, if somewhat different function elsewhere in the body.