Speaking as a biologist as well . . . it's interesting discussion as to whether protective response and fight vs. flight are innate or learned, but there are truths that go a little deeper than cultural perspective. Everyone blinks when something is blown into the eyes. Everyone responds when another entity makes contact or displays an intent to make contact. Our task is to identify the subtleties of Atemi and utilize the elicited responses to supplement the techniques. My brother and I--about 270 lbs. and 200 lbs. respectively--have been studying a range of martial arts and full contact sparring for many years. We have relatively solid centers. When we began studying Aikido, we used to crank on each other's joints to make the techniques work. Then we started really getting into Atemi, strong thrusts to the face or abdomen, rapid shots to the groin or other parts of the body, and it made the techniques very effective.
Then we finally got a little older and smartened up a bit.
Now, the Atemi is little more than snapping the fingers in uke's face. A quick blow--but with the breath--to the eyes. (Onions for lunch help immensely!)
Atemi is subtle and does not need to make contact. It depends upon how involved Nage becomes with Uke's spirit and ki. Less connection, harder Atemi; more connection, more subtle Atemi.
We all go through the "does-this-really-work, daito-ryu-to-make-it-stronger" phase, and we know that Atemi is 98% of Aikido. But if your Atemi is slamming, breaking, bruising, bloodying, then you're doing 98% boxing.
Make a funny face. Fart. Flap your elbows like a chicken. Does it elicit a response from Uke that may facilitate a resolution to the situation? If so, then you have performed your Atemiwaza.