Perceptions may be compared with hypotheses in science. The methods of acquiring scientific knowledge provide a working paradigm for investigating processes of perception. Much as the information channels of instruments, such as radio telescopes, transmit signals which are processed according to various assumptions to give useful data, so neural signals are processed to give data for perception. To understand perception, the signal codes and the stored knowledge or assumptions used for deriving perceptual hypotheses must be discovered. Systematic perceptual errors are important clues for appreciating signal channel limitations, and for discovering hypothesis-generating procedures. Although this distinction between ‘physiological’ and ‘cognitive’ aspects of perception may be logically clear, it is in practice surprisingly difficult to establish which are responsible even for clearly established phenomena such as the classical distortion illusions. Experimental results are presented, aimed at distinguishing between and discovering what happens when there is mismatch with the neural signal channel, and when neural signals are processed inappropriately for the current situation. This leads us to make some distinctions between perceptual and scientific hypotheses, which raise in a new form the problem: What are ‘objects’?