Agents, however, are assumed and reasoned upon very successfully which, by their nature, never can be objects of perception:  such are the atoms of Chemistry and the ether of Optics.  But the severer methodologists regard them with suspicion:  Mill was never completely convinced about the ether; the defining of which has been found very difficult.  He was willing, however, to make the most of the evidence that has been adduced as indicating a certain property of it distinct from those by which it transmits radiation, namely, mechanical inertia, whereby it has been supposed to retard the career of the heavenly bodies, as shown especially by the history of Encke’s comet.  This comet returned sooner than it should, as calculated from the usual data; the difference was ascribed to the influence of a resisting medium in reducing the extent of its orbit; and such a medium may be the ether.  If this conjecture (now of less credit) should gain acceptance, the ether might be regarded as a vera causa (that is, a condition whose existence may be proved independently of the phenomena it was intended to explain), in spite of its being excluded by its nature from the sphere of direct perception.  However, science is not a way of perceiving things, but essentially a way of thinking about them.  It starts, indeed, from perception and returns to it, and its thinking is controlled by the analogies of perception.  Atoms and ether are thought about as if they could be seen or felt, not as noumena; and if still successful in connecting and explaining perceptions, and free from contradiction, they will stand as hypotheses on that ground.

On the other hand, a great many agents, once assumed in order to explain phenomena, have since been explained away.  Of course, a fact can never be ‘explained away’:  the phrase is properly applicable to the fate of erroneous hypotheses, when, not only are they disproved, but others are established in their places.  Of the Aristotelian spheres, which were supposed to support and translate sun, moon and planets, no trace has ever been found:  they would have been very much in the way of the comets.  Phlogiston, again, an agent much in favour with the earlier Chemists, was found, Whewell tells us, when their theories were tested by exact weighing, to be not merely non-existent but a minus quantity; that is to say, it required the assumption of its absolute lightness “so that it diminished the weight of the compounds into which it entered.”  These agents, then, the spheres and phlogiston, have been explained away, and instead of them we have the laws of motion and oxygen.

(2) Whether the hypothetical agent be perceptible or not, it cannot be established as a cause, nor can a supposed law of such an agent be accepted as sufficient to the given inquiry, unless it is adequate to account for the effects which it is called upon to explain, at least so far as it pretends to explain them. The general truth of this is sufficiently obvious, since to explain the facts is the purpose of an hypothesis; and we have seen that Newton gave up his hypothesis that the moon was a falling body, as long as he was unable to show that the amount of its deflection from a tangent (or fall) in a given time, was exactly what it should be, if the Moon was controlled by the same force as falling bodies on the Earth.