Following this summary philosophy come the sciences proper, rising like a pyramid in successive stages, the lowest floor being occupied by natural history or experience, the second by physics, the third, which is next the peak of unity, by metaphysics.[70] The knowledge of the peak, or of the one law which binds nature together, is perhaps denied to man. Of the sciences, physics, as has been already seen, deals with the efficient and material, i.e. with the variable and transient, causes of things. But its inquiries may be directed either towards concrete bodies or towards abstract qualities. The first kind of investigation rises little above mere natural history; but the other is more important and paves the way for metaphysics. It handles the configurations and the appetites or motions of matter. The configurations, or inner structure of bodies, include dense, rare, heavy, light, hot, cold, etc., - in fact, what are elsewhere called simple natures. Motions[71] are either simple or compound, the latter being the sum of a number of the former. In physics, however, these matters are treated only as regards their material or efficient causes, and the result of inquiry into any one case gives no general rule, but only facilitates invention in some similar instance.

Metaphysics, on the other hand, treats of the formal or final cause of[72] these same substances and qualities, and results in a general rule. With regard to forms, the investigation may be directed either towards concrete bodies or towards qualities. But the forms of substances "are so perplexed and complicated, that it is either vain to inquire into them at all, or such inquiry as is possible should be put off for a time, and not entered upon till forms of a more simple nature have been rightly investigated and discussed."[73] "To inquire into the form of a lion, of an oak, or gold, nay, even of water or air, is a vain pursuit; but to inquire the form of dense, rare, hot, cold, etc., as well configurations as motions, which in treating of physic I have in great part enumerated (I call them forms of the first class), and which (like the letters of the alphabet) are not many, and yet make up and sustain the essences and forms of all substances - this, I say, it is which I am attempting, and which constitutes and defines that part of metaphysic of which we are now inquiring." Physics inquires into the same qualities, but does not push its investigations into ultimate reality or reach the more general causes.

We thus at last attain a definite conclusion with regard to forms, and it appears clear that in Bacon's belief the true function of science was the search for a few fundamental physical qualities, highly abstract and general, the combinations of which give rise to the simple natures and complex phenomena around us. His general conception of the universe may therefore be called mechanical or statical; the cause of each phenomenon is supposed to be actually contained in the phenomenon itself, and by a sufficiently accurate process could be sifted out and brought to light. As soon as the causes are known man regains his power over nature, for "whosoever knows any form, knows also the utmost possibility of superinducing that nature upon every variety of matter, and so is less restrained and tied in operation either to the basis of the matter or to the condition of the efficients."[74]

Nature thus presented itself to Bacon's mind as a huge congeries of phenomena, the manifestations of some simple and primitive qualities, which were hid from us by the complexity of the things themselves. The world was a vast labyrinth, amid the windings of which we require some clue or thread whereby we may track our way to knowledge and thence to power. This thread, the filum labyrinthi, is the new method of induction. But, as has been frequently pointed out, the new method could not be applied until facts had been observed and collected. This is an indispensable preliminary. "Man, the servant and interpreter of nature, can do and understand so much, and so much only, as he has observed in fact or in thought of the course of nature; beyond this he neither knows anything nor can do anything." The proposition that our knowledge of nature necessarily begins with observation and experience, is common to Bacon and many contemporary reformers of science, but he laid peculiar stress upon it, and gave it a new meaning.

What he really meant by observation was a competent natural history or collection of facts. "The firm foundations of a purer natural philosophy are laid in natural history."[75] "First of all we must prepare a natural and experimental history, sufficient and good; and this is the foundation of all."[76] The senses and the memory, which collect and store up facts, must be assisted; there must be a ministration of the senses and another of the memory. For not only are instances required, but these must be arranged in such a manner as not to distract or confuse the mind, i.e. tables and arrangements of instances must be constructed. In the preliminary collection the greatest care must be taken that the mind be absolutely free from preconceived ideas; nature is only to be conquered by obedience; man must be merely receptive. "All depends on keeping the eye steadily fixed upon the facts of nature, and so receiving their images simply as they are; for God forbid that we should give out a dream of our own imagination for a pattern of the world; rather may He graciously grant to us to write an apocalypse or true vision of the footsteps of the Creator imprinted on his creatures."[77] Concealed among the facts presented to sense are the causes or forms, and the problem therefore is so to analyse experience[78], so to break it up into pieces, that we shall with certainty and mechanical ease arrive at a true conclusion.

This process, which forms the essence of the new method, may in its entirety, as a ministration to the reason, be called a logic; but it differs widely from the ordinary or school logic in end, method and form. Its aim is to acquire command over nature by knowledge, and to invent new arts, whereas the old logic strove only after dialectic victories and the discovery of new arguments. In method the difference is even more fundamental. Hitherto the mode of demonstration had been by the syllogism; but the syllogism is, in many respects, an incompetent weapon. It is compelled to accept its first principles on trust from the science in which it is employed; it cannot cope with the subtlety of nature; and it is radically vitiated by being founded on hastily and inaccurately abstracted notions of things. For a syllogism consists of propositions, propositions of words, and words are the symbols of notions. Now the first step in accurate progress from sense to reason, or true philosophy, is to frame a bona notio or accurate conception of the thing; but the received logic never does this. It flies off at once from experience and particulars to the highest and most general propositions, and from these descends, by the use of middle terms, to axioms of lower generality.