All these things being consider'd, it seems probable to me, that God in the Beginning form'd Matter in solid, massy, hard, impenetrable Particles, of such Sizes and Figures, and with such other Properties, and in such Proportion to Space, as most conduced to the End for which he form'd them; and that these primitive Particles being Solids, are incomparably harder than any porous Bodies compounded of them; even so very hard, as never to wear or break in pieces; no ordinary Power being able to divide what God himself made one in the first Creation. While the Particles continue entire, they may compose Bodies of one and the same Nature and Texture in all Ages: But should they wear away, or break in pieces, the Nature of Things depending on them, would be changed. Water and Earth, composed of old worn Particles and Fragments of Particles, would not be of the same Nature and Texture now, with Water and Earth composed of entire Particles in the Beginning. And therefore, that Nature may be lasting, the Changes of corporeal Things are to be placed only in the various Separations and new Associations and Motions of these permanent Particles; compound Bodies being apt to break, not in the midst of solid Particles, but where those Particles are laid together, and only touch in a few Points.
It seems to me farther, that these Particles have not only a Vis inertiae, accompanied with such passive Laws of Motion as naturally result from the Force, but also that they are moved by certain active Principles, such as is that of Gravity, and that which causes Fermentation, and the Cohesion of Bodies. These Principles I consider, not as occult Qualities, supposed to result from the specifick Forms of Things, but as general Laws of Nature, by which the Things themselves are form'd; their Truth appearing to us by Phaenomena, though their Causes be not yet discover'd. For these are manifest Qualities, and their Causes only are occult. And the Aristotelians gave the Name of occult Qualities only as they supposed to lie hid in Bodies, and to be the unknown Causes of manifest Effects: Such as would be the Causes of Gravity, and of magnetick and electrick Attractions, and of Fermentations, if we should suppose that these Forces or Actions arose from Qualities unknown to us, and uncapable of being discovered and made manifest. Such occult Qualities put a stop to the Improvement of natural Philosophy, and therefore of late Years have been rejected. To tell us that every Species of Things is endow'd with an occult specifick Quality by which it acts and produces manifest Effects, is to tell us nothing: But to derive two or three general Principles of Motion from Phaenomena, and afterwards to tell us how the Properties and Actions of all corporeal Things follow from those manifest Principles, would be a very great step in Philosophy, though the Causes of those Principles were not yet discover'd: And therefore I scruple not to propose the Principles of Motion above-mention'd, they being of very general Extent, and leave their Causes to be found out.
Now by the help of these Principles, all material Things seem to have been composed of the hard and solid Particles above-mention'd, variously associated in the first Creation by the Counsel of an intelligent Agent. For it became him who created them to set them in order. And if he did so, it's unphilosophical to seek for any other Origin of the World, or to pretend that it might arise out of a Chaos by the mere Laws of Nature; though being once form'd, it may continue by those Laws for many Ages. For while Comets move in very excentrick Orbs in all manner of Positions, blind Fate could never make all the Planets move one and the same way in Orbs concentrick, some inconsiderable Irregularities excepted, which may have risen from the mutual Actions of Comets and Planets upon one another, and which will be apt to increase, till this System wants a Reformation. Such a wonderful Uniformity in the Planetary System must be allowed the Effect of Choice. And so must the Uniformity in the Bodies of Animals, they having generally a right and a left side shaped alike, and on either side of their Bodies two Legs behind, and either two Arms, or two Legs, or two Wings before upon their Shoulders, and between their Shoulders a Neck running down into a Back-bone, and a Head upon it; and in the Head two Ears, two Eyes, a Nose, a Mouth, and a Tongue, alike situated. Also the first Contrivance of those very artificial Parts of Animals, the Eyes, Ears, Brain, Muscles, Heart, Lungs, Midriff, Glands, Larynx, Hands, Wings, swimming Bladders, natural Spectacles, and other Organs of Sense and Motion; and the Instinct of Brutes and Insects, can be the effect of nothing else than the Wisdom and Skill of a powerful ever-living Agent, who being in all Places, is more able by his Will to move the Bodies within his boundless uniform Sensorium, and thereby to form and reform the Parts of our own Bodies. And yet we are not to consider the World as the Body of God, or the several Parts thereof, as the Parts of God. He is an uniform Being, void of Organs, Members or Parts, and they are his Creatures subordinate to him, and subservient to his Will; and he is no more of the Species of Things carried through the Organs of Sense into the place of its Sensation, where it perceives them by means of its immediate Presence, without the Intervention of any third thing. The Organs of Sense are not for enabling the Soul to perceive the Species of Things in its Sensorium, but only for conveying them thither; and God has no need of such Organs, he being every where present to the Things themselves. And since Space is divisible in infinitum, and Matter is not necessarily in all places, it may be also allow'd that God is able to create Particles of Matter of several Sizes and Figures, and in several Proportions to Space, and perhaps of different Densities and Forces, and thereby to vary the Laws of Nature, and make Worlds of several sort in several Parts of the Universe. At least, I see nothing of Contradiction in all this.
As in Mathematicks, so in Natural Philosophy, the Investigation of difficult Things by the Method of Analysis, ought ever to precede the Method of Composition. This Analysis consists in making Experiments and Observations, and in drawing general Conclusions from them by Induction, and admitting of no Objections against the Conclusions, but such as are taken from Experiments, or other certain Truths. For Hypotheses are not to be regarded in experimental Philosophy. And although the arguing from Experiments and Observations by Induction be no Demonstration of general Conclusions; yet it is the best way of arguing which the Nature of Things admits of, and may be looked upon as so much the stronger, by how much the Induction is more general. And if no Exception occur from Phaenomena, the Conclusion may be pronounced generally. But if at any time afterwards any Exception shall occur from Experiments, it may then begin to be pronounced with such Exceptions as occur. By this way of Analysis we may proceed from Compounds to Ingredients, and from Motions to the Forces producing them; and in general, from Effects to their Causes, and from particular Causes to more general ones, till the Argument end in the most general. This is the Method of Analysis: And the Synthesis consists in assuming the Causes discover'd, and establish'd as Principles, and by them explaining the Phaenomena proceeding from them, and proving the Explanations.
In the two first Books of these Opticks, I proceeded by this Analysis to discover and prove the original Differences of the Rays of Light in respect of Refrangibility, Reflexibility, and Colour, and their alternate Fits of easy Reflexion and easy Transmission, and the Properties of Bodies , both opake and pellucid, on which their Reflexions and Colours depend. And these Discoveries being proved, may be assumed in the Method of Composition for explaining the Phaenomena arising from them: An Instance of which Method I gave in the End of the first Book. In this third Book I have only begun the Analysis of what remains to be discover'd about Light and its Effects upon the Frame of Nature, hinting several things about it, and leaving the Hints to be examin'd and improv'd by the farther Experiments and Observations of such as are inquisitive. And if natural Philosophy in all its Parts, by pursuing this Method, shall at length be perfected, the Bounds of Moral Philosophy will be also enlarged. For so far as we can know by natural Philosophy what is the first Cause, what Power he has over us, and what Benefits we receive from him, so far our Duty towards him, as well as that towards one another, will appear to us by the Light of Nature. And no doubt, if the Worship of false Gods had not blinded the Heathen, their moral Philosophy would have gone farther than to the four Cardinal Virtues; and instead of teaching the Transmigration of Souls, and to worship the Sun and Moon, and dead Heroes, they would have taught us to worship our true Author and Benefactor, as their Ancestors did under the Government of Noah and his Sons before they corrupted themselves.