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Vol. I, Ch. 13: Of the King who did according to his will, and magnified himself above every God, and honored Mahuzzims, and regarded not the desire of women
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: Hitherto the principles of the Encratites had been rejected by the Churches; but now being refined by the Monks, and imposed not upon all men, but only upon those who would voluntarily undertake a monastic life, they began to be admired, and to overflow first the Greek Church, and then the Latin also, like a torrent. Eusebius tells us, that Constantine the great had those men in the highest veneration, who dedicated themselves wholly to the divine philosophy; and that he almost venerated the most holy company of Virgins perpetually devoted to God; being certain that the God to whom he had consecrated himself did dwell in their minds. In his time and that of his sons, this profession of a single life was propagated in Egypt by Antony, and in Syria by Hilarion; and spread so fast, that soon after the time of Julian the Apostate a third part of the Egyptians were got into the deserts of Egypt. They lived first singly in cells, then associated into cœnobia or convents; and at length came into towns, and filled the Churches with Bishops, Presbyters and Deacons. Athanasius in his younger days poured water upon the hands of his master Antony; and finding the Monks faithful to him, made many of them Bishops and Presbyters in Egypt: and these Bishops erected new Monasteries, out of which they chose Presbyters of their own cities, and sent Bishops to others. The like was done in Syria, the superstition being quickly propagated thither out of Egypt by Hilarion a disciple of Antony. Spiridion and Epiphanius of Cyprus, James of Nisibis, Cyril of Jerusalem, Eustathius of Sebastia in Armenia, Eusebius of Emisa, Titus of Bostra, Basilius of Ancyra, Acacius of Cæsarea in Palestine, Elpidius of Laodicea, Melitius and Flavian of Antioch, Theodorus of Tyre, Protogenes of Carrhæ, Acacius of Berrhæa, Theodotus of Hierapolis, Eusebius of Chalcedon, Amphilochius of Iconium, Gregory Nazianzen, Gregory Nyssen, and John Chrysostom of Constantinople, were both Bishops and Monks in the fourth century. Eustathius, Gregory Nazianzen, Gregory Nyssen, Basil, &c. had Monasteries of Clergymen in their cities, out of which Bishops were sent to other cities; who in like manner erected Monasteries there, till the Churches were supplied with Bishops out of these Monasteries.... Not long after even the Emperors commanded the Churches to choose Clergymen out of the Monasteries by this Law.

Vol. I, Ch. 13: Of the King who did according to his will, and magnified himself above every God, and honored Mahuzzims, and regarded not the desire of women
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: The Cataphrygians brought in also several other superstitions: such as were the doctrine of Ghosts, and of their punishment in Purgatory, with prayers and oblations for mitigating that punishment, as Tertullian teaches in his books De Anima and De Monogamia. They used also the sign of the cross as a charm. So Tertullian in his book de Corona militis... All these superstitions the Apostle refers to, where he saith: Now the Spirit speaketh expressly, that in the latter times some shall depart from the faith, giving heed to seducing spirits, and doctrines of devils, the Dæmons and Ghosts worshiped by the heathens, speaking lies in hypocrisy, about their apparitions, the miracles done by them, their relics, and the sign of the cross, having consciences seared with a hot iron; forbidding to marry, and commanding to abstain from meats, &c. 1 Tim. iv. 1,2,3. From the Cataphrygians these principles and practices were propagated down to posterity. For the mystery of iniquity did already work in the Apostles days in the Gnostics, continued to work very strongly in their offspring the Tatianists and Cataphrygians, and was to work till that man of sin should be revealed; whose coming is after the working of Satan, with all power and signs, and lying wonders, and all deceivableness of unrighteousness; colored over with a form of Christian godliness, but without the power thereof, 2 Thess. ii. 7-10.

Vol. I, Ch. 13: Of the King who did according to his will, and magnified himself above every God, and honored Mahuzzims, and regarded not the desire of women
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: For though some stop was put to the Cataphrygian Christianity, by Provincial Councils, till the fourth century; yet the Roman Emperors then turning Christians, and great multitudes of heathens coming over in outward profession, these found the Cataphrygian Christianity more suitable to their old principles, of placing religion in outward forms and ceremonies, holy-days, and doctrines of Ghosts, than the religion of the sincere Christians: wherefore they readily sided with the Cataphrygian Christians, and established that Christianity before the end of the fourth century. By this means those of understanding, after they had been persecuted by the heathen Emperors in the three first centuries, and were holpen with a little help, by the conversion of Constantine the great and his sons to the Christian religion, fell under new persecutions, to purge them from the dissemblers, and to make them white, even to the time of the end.

Philosophiae Naturalis Principia Mathematica (1687), Scholium Generale (1713; 1726)
Context: This Being governs all things, not as the soul of the world, but as Lord over all: And on account of his dominion he is wont to be called Lord God παντοκρáτωρ or Universal Ruler. For God is a relative word, and has a respect to servants; and Deity is the dominion of God, not over his own body, as those imagine who fancy God to be the soul of the world, but over servants. The supreme God is a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: These are titles which have no respect to servants. The word God usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God; a true, supreme or imaginary dominion makes a true, supreme or imaginary God. And from his true dominion it follows, that the true God is a Living, Intelligent and Powerful Being; and from his other perfections, that he is Supreme or most Perfect. He is Eternal and Infinite, Omnipotent and Omniscient; that is, his duration reaches from Eternity to Eternity; his presence from Infinity to Infinity; he governs all things, and knows all things that are or can be done. He is not Eternity or Infinity, but Eternal and Infinite; he is not Duration or Space, but he endures and is present. He endures for ever, and is every where present; and by existing always and every where, he constitutes Duration and Space. Since every particle of Space is always, and every indivisible moment of Duration is every where, certainly the Maker and Lord of all things cannot be never and no where. Every soul that has perception is, though in different times and in different organs of sense and motion, still the same indivisible person. There are given successive parts in duration, co-existant parts in space, but neither the one nor the other in the person of a man, or his thinking principle; and much less can they be found in the thinking substance of God. Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. God is the same God, always and every where. He is omnipresent, not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. 'Tis allowed by all that the supreme God exists necessarily; and by the same necessity he exists always and every where. Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure, and can therefore neither be seen, nor heard, nor touched; nor ought to be worshipped under the representation of any corporeal thing. We have ideas of his attributes, but what the real substance of any thing is, we know not. In bodies we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the favours; but their inward substances are not to be known, either by our senses, or by any reflex act of our minds; much less then have we any idea of the substance of God. We know him only by his most wise and excellent contrivances of things, and final causes; we admire him for his perfections; but we reverence and adore him on account of his dominion. For we adore him as his servants; and a God without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. All that diversity of natural things which we find, suited to different times and places, could arise from nothing but the ideas and will of a Being necessarily existing. But by way of allegory, God is said to see, to speak, to laugh, to love, to hate, to desire, to give, to receive, to rejoice, to be angry, to fight, to frame, to work, to build. For all our notions of God are taken from the ways of mankind, by a certain similitude which, though not perfect, has some likeness however. And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy.

Vol. I, Ch. 11: Of the Times of the Birth and Passion of Christ
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: Thus have we in the Gospels of Matthew and John all things told in due order, from the beginning of John's preaching to the death of Christ, and the years distinguished from one another by such essential characters that they cannot be mistaken. The second Passover is distinguished from the first, by the interposition of John's imprisonment. The third is distinguished from the second, by a double character: first, by the interposition of the feast to which Christ went up, Mat. viii. 19. Luke ix. 57. and secondly, by the distance of time from the beginning of Christ's preaching: for the second was in the beginning of his preaching, and the third so long after, that before it came Christ said, from the days of John the Baptist until now, &c. and upbraided the cities of Galilee for their not repenting at his preaching, and mighty works done in all that time. The fourth is distinguished from the third, by the mission of the twelve from Christ to preach in the cities of Judea in all the interval. The fifth is distinguished from all the former by the twelve's being returned from preaching, and continuing with Christ during all the interval, between the fourth and fifth, and by the passion and other infallible characters.

Arithmetica Universalis (1707), p.232

Arithmetica Universalis (1707), p.248

Anecdote reported by Dr. Robert Smith, late Master of Trinity College, to his student Richard Watson, as something that Newton expressed when he was writing his Commentary On Daniel. In Watson's Apology for the Bible. London 8vo. (1806), p. 57

Philosophiae Naturalis Principia Mathematica (1687), Scholium Generale (1713; 1726)
Context: This Being governs all things, not as the soul of the world, but as Lord over all: And on account of his dominion he is wont to be called Lord God παντοκρáτωρ or Universal Ruler. For God is a relative word, and has a respect to servants; and Deity is the dominion of God, not over his own body, as those imagine who fancy God to be the soul of the world, but over servants. The supreme God is a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: These are titles which have no respect to servants. The word God usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God; a true, supreme or imaginary dominion makes a true, supreme or imaginary God. And from his true dominion it follows, that the true God is a Living, Intelligent and Powerful Being; and from his other perfections, that he is Supreme or most Perfect. He is Eternal and Infinite, Omnipotent and Omniscient; that is, his duration reaches from Eternity to Eternity; his presence from Infinity to Infinity; he governs all things, and knows all things that are or can be done. He is not Eternity or Infinity, but Eternal and Infinite; he is not Duration or Space, but he endures and is present. He endures for ever, and is every where present; and by existing always and every where, he constitutes Duration and Space. Since every particle of Space is always, and every indivisible moment of Duration is every where, certainly the Maker and Lord of all things cannot be never and no where. Every soul that has perception is, though in different times and in different organs of sense and motion, still the same indivisible person. There are given successive parts in duration, co-existant parts in space, but neither the one nor the other in the person of a man, or his thinking principle; and much less can they be found in the thinking substance of God. Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. God is the same God, always and every where. He is omnipresent, not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. 'Tis allowed by all that the supreme God exists necessarily; and by the same necessity he exists always and every where. Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure, and can therefore neither be seen, nor heard, nor touched; nor ought to be worshipped under the representation of any corporeal thing. We have ideas of his attributes, but what the real substance of any thing is, we know not. In bodies we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the favours; but their inward substances are not to be known, either by our senses, or by any reflex act of our minds; much less then have we any idea of the substance of God. We know him only by his most wise and excellent contrivances of things, and final causes; we admire him for his perfections; but we reverence and adore him on account of his dominion. For we adore him as his servants; and a God without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. All that diversity of natural things which we find, suited to different times and places, could arise from nothing but the ideas and will of a Being necessarily existing. But by way of allegory, God is said to see, to speak, to laugh, to love, to hate, to desire, to give, to receive, to rejoice, to be angry, to fight, to frame, to work, to build. For all our notions of God are taken from the ways of mankind, by a certain similitude which, though not perfect, has some likeness however. And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy.

Vol. I, Ch. 2: Of the Prophetic Language
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: When a man is taken in a mystical sense, his qualities are often signified by his actions, and by the circumstances of things about him. So a Ruler is signified by his riding on a beast; a Warrior and Conqueror, by his having a sword and bow; a potent man, by his gigantic stature; a Judge, by weights and measures... the affliction or persecution which a people suffers in laboring to bring forth a new kingdom, by the pain of a woman in labor to bring forth a man-child; the dissolution of a body politic or ecclesiastic, by the death of a man or beast; and the revival of a dissolved dominion, by the resurrection of the dead.

Vol. I, Ch. 7: Of the Eleventh Horn of Daniel's Fourth Beast
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: Now Daniel, considered the horns, and behold there came up among them another horn, before whom there were three of the first horns plucked up by the roots; and behold in this horn were eyes like the eyes of a man, and a mouth speaking great things,—and his look was more stout than his fellows,—and the same horn made war with the saints, and prevailed against them... and speak great words against the most High, and wear out the saints, and think to change times and laws... By its eyes it was a Seer; and by its mouth speaking great things and changing times and laws, it was a Prophet as well as a King. And such a Seer, a Prophet and a King, is the Church of Rome. A Seer, Επισκοπος, is a Bishop in the literal sense of the word; and this Church claims the universal Bishopric. With his mouth he gives laws to kings and nations as an Oracle; and pretends to Infallibility, and that his dictates are binding to the whole world; which is to be a Prophet in the highest degree.

Vol. I, Ch. 13: Of the King who did according to his will, and magnified himself above every God, and honored Mahuzzims, and regarded not the desire of women
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: In the first ages of the Christian religion the Christians of every city were governed by a Council of Presbyters, and the President of the Council was the Bishop of the city. The Bishop and Presbyters of one city meddled not with the affairs of another city, except by admonitory letters or messages. Nor did the Bishops of several cities meet together in Council before the time of the Emperor Commodus: for they could not meet together without the leave of the Roman governors of the Provinces. But in the days of that Emperor they began to meet in Provincial Councils, by the leave of the governors; first in Asia, in opposition to the Cataphrygian Heresy, and soon after in other places and upon other occasions. The Bishop of the chief city, or Metropolis of the Roman Province, was usually made President of the Council; and hence came the authority of Metropolitan Bishops above that of other Bishops within the same Province. Hence also it was that the Bishop of Rome in Cyprian's days called himself the Bishop of Bishops. As soon as the Empire became Christian, the Roman Emperors began to call general Councils out of all the Provinces of the Empire; and by prescribing to them what points they should consider, and influencing them by their interest and power, they set up what party they pleased. Hereby the Greek Empire, upon the division of the Roman Empire into the Greek and Latin Empires, became the King who, in matters of religion, did according to his will; and, in legislature, exalted and magnified himself above every God: and at length, by the seventh general Council, established the worship of the images and souls of dead men, here called Mahuzzims.

Vol. I, Ch. 4: Of the vision of the four Beasts
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: The fourth Beast was the empire which succeeded that of the Greeks, and this was the Roman. This beast was exceeding dreadful and terrible, and had great iron teeth, and devoured and brake in pieces, and stamped the residue with its feet; and such was the Roman empire. It was larger, stronger, and more formidable and lasting than any of the former.... it became greater and more terrible than any of the three former Beasts. This Empire continued in its greatness till the reign of Theodosius the great; and then brake into ten kingdoms, represented by the ten horns of this Beast; and continued in a broken form, till the Ancient of days sat in a throne like fiery flame, and the judgment was set, and the books were opened, and the Beast was slain and his body destroyed, and given to the burning flames; and one like the son of man came with the clouds of heaven, and came to the Ancient of days, and received dominion over all nations, and judgment was given to the saints of the most high, and the time came that they possessed the kingdom.

Vol. I, Ch. 12: Of the Prophecy of the Scripture of Truth
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: In the same year that Antiochus by the command of the Romans retired out of Egypt, and set up the worship of the Greeks in Judea; the Romans conquered the kingdom of Macedon, the fundamental kingdom of the Empire of the Greeks, and reduced it into a Roman Province; and thereby began to put an end to the reign of Daniel's third Beast. This is thus expressed by Daniel. And after him Arms, that is the Romans, shall stand up. As ממלך signifies after the King, Dan. xi. 8; so ממנו may signify after him. Arms are every where in this Prophecy of Daniel put for the military power of a kingdom: and they stand up when they conquer and grow powerful. Hitherto Daniel described the actions of the Kings of the North and South; but upon the conquest of Macedon by the Romans, he left off describing the actions of the Greeks, and began to describe those of the Romans in Greece. They conquered Macedon, Illyricum and Epirus, in the year of Nabonassar 580. 35 years after, by the last will and testament of Attalus the last King of Pergamus, they inherited that rich and flourishing kingdom, that is, all Asia westward of mount Taurus; 69 years after they conquered the kingdom of Syria, and reduced it into a Province, and 34 years after they did the like to Egypt. By all these steps the Roman Arms stood up over the Greeks: and after 95 years more, by making war upon the Jews, they polluted the sanctuary of strength, and took away the daily sacrifice, and then placed the abomination of desolation. For this abomination was placed after the days of Christ, Math. xxiv. 15. In the 16th year of the Emperor Adrian, A. C. 132, they placed this abomination by building a Temple to Jupiter Capitolinus, where the Temple of God in Jerusalem had stood. Thereupon the Jews under the conduct of Barchochab rose up in arms against the Romans, and in the war had 50 cities demolished, 985 of their best towns destroyed, and 580,000 men slain by the sword; and in the end of the war, A. C. 136, were banished Judea upon pain of death, and thenceforward the land remained desolate of its old inhabitants.

Vol. I, Ch. 11: Of the Times of the Birth and Passion of Christ
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: John therefore baptized two summers, and Christ preached three. The first summer John preached to make himself known, in order to give testimony to Christ. Then, after Christ came to his baptism and was made known to him, he baptized another summer, to make Christ known by his testimony; and Christ also baptized the same summer, to make himself the more known: and by reason of John's testimony there came more to Christ's baptism than to John's. The winter following John was imprisoned; and now his course being at an end, Christ entered upon his proper office of preaching in the cities. In the beginning of his preaching he completed the number of the twelve Apostles, and instructed them all the first year in order to send them abroad. Before the end of this year, his fame by his preaching and miracles was so far spread abroad, that the Jews at the Passover following consulted how to kill him. In the second year of his preaching, it being no longer safe for him to converse openly in Judea, he sent the twelve to preach in all their cities: and in the end of the year they returned to him, and told him all they had done. All the last year the twelve continued with him to be instructed more perfectly, in order to their preaching to all nations after his death. And upon the news of John's death, being afraid of Herod as well as of the Jews, he walked this year more secretly than before; frequenting deserts, and spending the last half of the year in Judea, without the dominions of Herod.

Vol. I, Ch. 13: Of the King who did according to his will, and magnified himself above every God, and honored Mahuzzims, and regarded not the desire of women
Observations upon the Prophecies of Daniel, and the Apocalypse of St. John (1733)
Context: Hitherto the principles of the Encratites had been rejected by the Churches; but now being refined by the Monks, and imposed not upon all men, but only upon those who would voluntarily undertake a monastic life, they began to be admired, and to overflow first the Greek Church, and then the Latin also, like a torrent. Eusebius tells us, that Constantine the great had those men in the highest veneration, who dedicated themselves wholly to the divine philosophy; and that he almost venerated the most holy company of Virgins perpetually devoted to God; being certain that the God to whom he had consecrated himself did dwell in their minds. In his time and that of his sons, this profession of a single life was propagated in Egypt by Antony, and in Syria by Hilarion; and spread so fast, that soon after the time of Julian the Apostate a third part of the Egyptians were got into the deserts of Egypt. They lived first singly in cells, then associated into cœnobia or convents; and at length came into towns, and filled the Churches with Bishops, Presbyters and Deacons. Athanasius in his younger days poured water upon the hands of his master Antony; and finding the Monks faithful to him, made many of them Bishops and Presbyters in Egypt: and these Bishops erected new Monasteries, out of which they chose Presbyters of their own cities, and sent Bishops to others. The like was done in Syria, the superstition being quickly propagated thither out of Egypt by Hilarion a disciple of Antony. Spiridion and Epiphanius of Cyprus, James of Nisibis, Cyril of Jerusalem, Eustathius of Sebastia in Armenia, Eusebius of Emisa, Titus of Bostra, Basilius of Ancyra, Acacius of Cæsarea in Palestine, Elpidius of Laodicea, Melitius and Flavian of Antioch, Theodorus of Tyre, Protogenes of Carrhæ, Acacius of Berrhæa, Theodotus of Hierapolis, Eusebius of Chalcedon, Amphilochius of Iconium, Gregory Nazianzen, Gregory Nyssen, and John Chrysostom of Constantinople, were both Bishops and Monks in the fourth century. Eustathius, Gregory Nazianzen, Gregory Nyssen, Basil, &c. had Monasteries of Clergymen in their cities, out of which Bishops were sent to other cities; who in like manner erected Monasteries there, till the Churches were supplied with Bishops out of these Monasteries.... Not long after even the Emperors commanded the Churches to choose Clergymen out of the Monasteries by this Law.

"Hypothesis explaining the Properties of Light" (1675)
Context: Were I to assume an hypothesis, it should be this, if propounded more generally, so as not to assume what light is further than that it is something or other capable of exciting vibrations of the ether. First, it is to be assumed that there is an ethereal medium, much of the same constitution as air, but far rarer, subtiller, and more strongly elastic.... In the second place, it is to be supposed that the ether is a vibrating medium, like air, only the vibrations much more swift and minute; those of air made by a man's ordinary voice succeeding at more than half a foot or a foot distance, but those of ether at a less distance than the hundredth-thousandth part of an inch. And as in air the vibrations are some larger than others, but yet all equally swift... so I suppose the ethereal vibrations differ in bigness but not in swiftness.... In the fourth place, therefore, I suppose that light is neither ether nor its vibrating motion, but something of a different kind propagated from lucid bodies. They that will may suppose it an aggregate of various peripatetic qualities. Others may suppose it multitudes of unimaginable small and swift corpuscles of various sizes springing from shining bodies at great distances one after the other, but yet without any sensible interval of time.... To avoid dispute and make this hypothesis general, let every man here take his fancy; only whatever light be, I would suppose it consists of successive rays differing from one another in contingent circumstances, as bigness, force, or vigour, like as the sands on the shore... and, further, I would suppose it diverse from the vibrations of the ether.... Fifthly, it is to be supposed that light and ether mutually act upon one another.... æthereal vibrations are therefore the best means by which such a subtile agent as light can shake the gross particles of solid bodies to heat them.

Query 28 : Are not all Hypotheses erroneous in which Light is supposed to consist of Pression or Motion propagated through a fluid medium?
Opticks (1704)
Context: To make way for the regular and lasting Motions of the Planets and Comets, it's necessary to empty the Heavens of all Matter, except perhaps some very thin Vapours, Steams or Effluvia, arising from the Atmospheres of the Earth, Planets and Comets, and from such an exceedingly rare Æthereal Medium … A dense Fluid can be of no use for explaining the Phænomena of Nature, the Motions of the Planets and Comets being better explain'd without it. It serves only to disturb and retard the Motions of those great Bodies, and make the frame of Nature languish: And in the Pores of Bodies, it serves only to stop the vibrating Motions of their Parts, wherein their Heat and Activity consists. And as it is of no use, and hinders the Operations of Nature, and makes her languish, so there is no evidence for its Existence, and therefore it ought to be rejected. And if it be rejected, the Hypotheses that Light consists in Pression or Motion propagated through such a Medium, are rejected with it.
And for rejecting such a Medium, we have the authority of those the oldest and most celebrated philosophers of ancient Greece and Phoenicia, who made a vacuum and atoms and the gravity of atoms the first principles of their philosophy, tacitly attributing Gravity to some other Cause than dense Matter. Later Philosophers banish the Consideration of such a Cause out of natural Philosophy, feigning Hypotheses for explaining all things mechanically, and referring other Causes to Metaphysicks: Whereas the main Business of natural Philosophy is to argue from Phenomena without feigning Hypotheses, and to deduce Causes from Effects, till we come to the very first Cause, which certainly is not mechanical.

Query 31 : Have not the small particles of bodies certain powers, virtues, or forces, by which they act at a distance, not only upon the rays of light for reflecting, refracting, and inflecting them, but also upon one another for producing a great part of the Phenomena of nature? <br/> How these Attractions may be perform'd, I do not here consider. What I call Attraction may be perform'd by impulse, or by some other means unknown to me. I use that Word here to signify only in general any Force by which Bodies tend towards one another, whatsoever be the Cause. For we must learn from the Phaenomena of Nature what Bodies attract one another, and what are the Laws and Properties of the attraction, before we enquire the Cause by which the Attraction is perform'd, The Attractions of Gravity, Magnetism and Electricity, react to very sensible distances, and so have been observed by vulgar Eyes, and there may be others which reach to so small distances as hitherto escape observation; and perhaps electrical Attraction may react to such small distances, even without being excited by Friction
Opticks (1704)
Context: It seems probable to me that God, in the beginning, formed matter in solid, massy, hard, impenetrable, moveable particles, of such sizes and figures, and with such other properties, and in such proportions to space, as most conduced to the end for which He formed 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 had 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.<!-- Book III, Part I, pp.375-376 http://books.google.com/books?id=XXu4AkRVBBoC