Aka hormones. Hormone levels are not only influenced by external stimulii, but also by the developmental history and previous internal state of the organism.
Tracking time
In animals, there is the darkness-hormone, melatonin which then acts as a trigger for sleep. Increasing melatonin secretion frequency may trigger seasonal behavior like mating, change in coat etc..
Learning, attention, reward
The dopamine system identifies patterns in the environment. Dopamine is most secreted in anticipation of reward, rather than due to the obtainment of reward itself. Eg: If a bell following a flash of light signifies arrival of food, the dopamine neurons fire when there is a flash of light, and not upon the ring of the bell or the arrival of food.
Sometimes the dopamine system makes mistakes. Patients prescribed dopamines tend to fall to gambling addiction. Even pegions can develop superstitions (studied in behaviorist experiments).
Well-being, analgesia
Endogenous morphine (endorphine) is associated with this. It is produced in response to exercise, post-crisis stress-release, laughter.
Empathy, social trust, reciprocation
Oxytocin is deeply involved in the proximal mechanism for generating empathy, trust and reciprocation.
This is observed in the famous experiment to measure trust: A is given $10 and is given an option of transferring part of it to B, with whom it will be tripled, with the expectation that B might return some money if he feels like it.
Inhibition
Inhibitory factors include Stress, history of abuse, testosterone.
Fight or flight
Adrenaline increases blood pressure, increases blood flow to the muscles and brain in crisis situations.