A much simplified review: classical conditioning is Pavlov, and operant conditioning is Skinner. In the first case, an initially neutral (i.e. affectively meaningless) stimulus is paired closely with an "unconditioned" (i.e. intrinsically meaningful) stimulus often and consistently enough that it becomes meaningful even in isolation. Unless a dog is temperamentally nervous, she is unlikely to have any strong primary response to the sound of a bell. Unless she is sick, full, or finicky, however, she will almost invariably respond to the presence of food, by salivating, pricking her ears, widening her eyes, etc. As Pavlov discovered, if the sound of a bell is repeatedly paired with the arrival of food, it will soon provoke many of the same reflexive responses that food does, even in food's absence. (These responses will often extinguish if the association is not periodically maintained -- though threatening associations are more resilient than positive ones -- but there are interesting and somewhat counterintuitive laws governing the effectual timing of that maintenance. More on that another day.)
Operant conditioning involves willed (or, if you won't go so far, voluntary) behavior. In this case, some specific action by the animal repeatedly and consistently provokes a change in her environment; if that change is meaningful to the animal, she will alter her behavior accordingly. Thus the Skinner box: rat presses lever, food pellet arrives, rat presses lever again with same result, and rat soon becomes a lever-pressing fiend. A fat lever-pressing fiend. Time to add a complication, in the form of a "green" light: only when the light is on will food pellets be available at press of lever. When the light is off, the rat can press for all she's worth but press in vain. The rat soon stops pressing the lever in the absence of light.
At what point (if any) in that sequence does analysis enter in? At what point does a rat or dog or human begin to perceive "coincidence" (the predictable proximity of two previously unrelated things or events) as a relationship of cause and effect? And is that perception most potent (most behavior-altering) at a conscious or unconscious level?
Even in the case of the planet's Great Brains (i.e. humans), it appears that the unconscious gets there first and most decisively. "Gut feelings" whisper to the frontal cortex the conclusions that older, deeper structures have already drawn -- and in many cases already prompted our bodies to act upon. Gerd Gigerenzer has done some incisive research into this dynamic, and his book Gut Feelings: The Intelligence of the Unconscious is one of the best introductions I've found. I'd also highly recommend Timothy Wilson's Strangers to Ourselves: Discovering the Adaptive Unconscious, which beautifully assimilates contemporary research with earlier descriptions of the relationship between conscious and unconscious thought. But among books written for the lay reader, Antonio Damasio's Descartes' Error: Emotions, Reason, and the Human Brain remains the most coherent (if necessarily speculative) revision of the "top-down" model of human decision making that I've read, and it's a good place to go if you're ready to dig into the physiological bases of cognition (insofar as these are intelligible to us, which isn't yet very far). His "somatic marker" hypothesis turns the idea that the consciously reasoning mind is in command of the lowly body pretty much literally on its head.
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