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.
It is important to observe the limitations to this canon. In the first place, it says that, unless adequate to explain the facts in question, an hypothesis cannot be 'established'; but, for all that, such an hypothesis may be a very promising one, not to be hastily rejected, since it may take a very long time fully to verify an hypothesis. Some facts may not be obtainable that are necessary to show the connection of others: as, for example, the hypothesis that all species of animals have arisen from earlier ones by some process of gradual change, can be only imperfectly verified by collecting the fossil remains of extinct species, because immense depths and expanses of fossiliferous strata have been destroyed. Or, again, the general state of culture may be such as to prevent men from tracing the consequences of an hypothesis; for which reason, apparently, the doctrine that the Sun is the centre of our planetary system remained a discredited hypothesis for 2000 years. This should instruct us not to regard an hypothesis as necessarily erroneous or illegitimate merely because we cannot yet see how it works out: but neither can we in such a case regard it as established, unless we take somebody's word for it.
Secondly, the canon says that an hypothesis is not established, unless it accounts for the phenomena so far as it professes to. But it implies a complete misunderstanding to assail a doctrine for not explaining what lies beyond its scope. Thus, it is no objection to a theory of the origin of species, that it does not explain the origin of life: it does not profess to. For the same reason, it is no objection to the theory of Natural Selection, that it does not account for the variations which selection presupposes. But such objections might be perfectly fair against a general doctrine of Evolution.
An interesting case in Wallace's Darwinism (chap. x.) will illustrate the importance of attending to the exact conditions of an hypothesis. He says that in those groups of "birds that need protection from enemies," "when the male is brightly coloured and the female sits exposed on the nest, she is always less brilliant and generally of quite sober and protective hues"; and his hypothesis is, that these sober hues have been acquired or preserved by Natural Selection, because it is important to the family that the sitting bird should be inconspicuous. Now to this it might be objected that in some birds both sexes are brilliant or conspicuous; but the answer is that the female of such species does not sit exposed on the nest; for the nests are either domed over, or made in a hole; so that the sitting bird does not need protective colouring. If it be objected, again, that some sober-coloured birds build domed nests, it may be replied that the proposition 'All conspicuously coloured birds are concealed in the nest,' is not to be converted simply into 'All birds that sit concealed in the nest are conspicuously coloured.' In the cases alleged the domed nests are a protection against the weather, and the sober colouring is a general protection to the bird, which inhabits an open country. It may be urged, however, that jays, crows, and magpies are conspicuous birds, and yet build open nests: but these are aggressive birds, not needing protection from enemies. Finally, there are cases, it must be confessed, in which the female is more brilliant than the male, and which yet have open nests. Yes: but then the male sits upon the eggs, and the female is stronger and more pugnacious!
Thus every objection is shown to imply some inattention to the conditions of the hypothesis; and in each case it may be said, exceptio probat regulam—the exception tests the rule. (Of course, the usual translation "proves the rule," in the restricted modern sense of "prove," is absurd.) That is to say, it appears on examination: (1) that the alleged exception is not really one, and (2) that it stands in such relation to the rule as to confirm it. For to all the above objections it is replied that, granting the phenomenon in question (special protective colouring for the female) to be absent, the alleged cause (need of protection) is also absent; so that the proof is, by means of the objections, extended, from being one by the method of Agreement, into one by the Double Method.
Thirdly, an hypothesis originally intended to account for the whole of a phenomenon and failing to do so, though it cannot be established in that sense, may nevertheless contain an essential part of the explanation. The Neptunian Hypothesis in Geology, was an attempt to explain the formation of the Earth's outer crust, as having been deposited from an universal ocean of mud. In the progress of the science other causes, seismic, fluvial and atmospheric, have been found necessary in order to complete the theory of the history of the Earth's crust; but it remains true that the stratified rocks, and some that have lost their stratified character, were originally deposited under water. Inadequacy, therefore, is not a reason for entirely rejecting an hypothesis or treating it as illegitimate.
(3) Granting that the hypothetical cause is real and adequate, the investigation is not complete. Agreement with the facts is a very persuasive circumstance, the more so the more extensive the agreement, especially if no exceptions are known. Still, if this is all that can be said in favour of an hypothesis, it amounts to proof at most by the method of Agreement; it does not exclude the possibility of vicarious causes; and if the hypothesis proposes a new agent that cannot be directly observed, an equally plausible hypothesis about another imagined agent may perhaps be invented.
According to Whewell, it is a strong mark of the truth of an hypothesis when it agrees with distinct inductions concerning different classes of facts, and he calls this the 'Consilience of Inductions,' because they jump together in the unity of the hypothesis. It is particularly convincing when this consilience takes place easily and naturally without necessitating the mending and tinkering of the hypothesis; and he cites the Theory of Gravitation and the Undulatory Theory of Light as the most conspicuous examples of such ever-victorious hypotheses. Thus, gravitation explains the fall of bodies on the Earth, and the orbits of the planets and their satellites; it applies to the tides, the comets, the double stars, and gives consistency to the Nebular Hypothesis, whence flow important geological inferences; and all this without any need of amendment. Nevertheless, Mill, with his rigorous sense of duty, points out, that an induction is merely a proposition concerning many facts, and that a consilience of inductions is merely a multiplication of the facts explained; and that, therefore, if the proof is merely Agreement in each case, there can be no more in the totality; the possibility of vicarious causes is not precluded; and the hypothesis may, after all, describe an accidental circumstance.