Conditioned reflexes are automatic responses that are learned rather than naturally occurring. They occur when a previously neutral stimulus is paired with an unconditioned stimulus, leading to a conditioned response.
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This is something that naturally and automatically triggers a response without any learning needed. For example, food is an unconditioned stimulus for a hungry animal.
This is previously neutral but becomes meaningful after being paired with an unconditioned stimulus. In our analogy, the whistle becomes a conditioned stimulus after pairing it with the command to sit.
A neutral stimulus does not trigger any particular response until it's associated with an unconditioned stimulus. The whistle was initially a neutral stimulus for your dog.