In 1661, Robert Boyle, called the father of modern chemistry, defined an element as a substance that cannot be further decomposed. He distinguished an element from both a mixture, which is easily separable, and a compound, which is not easily separable. He used an air pump he developed and a glass jar to create a confined vacuum space for experiments to find the properties of heat, light, and sound. He noted that burning objects such as candles and coal, when placed in the receiver of his air pump, went out after a time although air was still present. He opined that animals were dependent upon a fresh supply of air to live. He studied the relationship between the volume, density, and pressure of air and gases. He proved by experiment that the volume of a gas at a constant temperature varies in inverse proportion to the pressure applied to the gas. Since gas is compressible, he opined that gases must be composed of discrete particles separated by void, and also that basic physical properties were due to motions of particles, or atoms, which was an ancient Greek conjecture. This cast doubt on the long-held belief that everything was composed from four basic elements: air, water, fire, and earth. Boyle's laboratory at Oxford was denounced by the Oxford clergy as destroying religion. In 1679, the steam pressure cooker was invented by Denis Papin from France. He invented the atmospheric engine in 1690.

Robert Hooke helped Boyle build his air pump. Hooke was thirteen when his father, a minister, died. Hooke was a genius with innate mechanical skill and was an able mathematician. He applied a spiral spring to regulate the balance of watches. A lord financed him as a Gresham lecturer of geometry for 50 pounds a year. In 1666, he used a pendulum to measure the force of gravity and showed that the center of gravity of the earth and moon is a point describing an ellipse around the sun. In 1667, he explained the twinkling of the stars by irregular atmospheric refractions. He formulated the theory that light is composed of pulses. Hooke's Law states that the amount an elastic body such as a spring stretches out of shape is in direct proportion to the force acting on it: its tension. He invented the odometer, a wheel to measure distances. He constructed an arithmetical machine. He invented the universal joint, which can move in many angles. His book of drawings of microscopic animals is a classic. He proposed that fossils can be used as a source of information about the earth's history. Hooke became rich from his inventions, but this was not known until his death, when thousands of pounds were found in his iron chest.

In 1668, Wallis postulated the correct theory of impacts of inelastic bodies, based on the principle of conservation of momentum. In 1685, he introduced the first graphical representation of complex numbers.

Royal astronomer and genius Edmond Halley, the son of a soap maker, studied tides, magnetism, and the paths of comets and stars. He went on voyages to study the heavens from different positions, thereby laying the foundations of physical geography. He showed that the stars change in position in relation to each other. With Newton's help, he calculated the orbit of a comet he saw in 1682 to be elliptical rather than parabolic and then proved it was the same comet that had appeared in 1531 and 1607, indicating it's regularity; it was then named "Halley's comet". However, the Church of England still embraced the idea that comets and eclipses were evidence of God's wrath. Greenwich Observatory was built in 1675. Halley used a barometer to measure the density of the atmosphere and related its readings to elevations into the atmosphere and to weather. He determined that the cause of the tropical trade winds was the sun warming the tropical air at the equator, causing it to rise and move north as it was replaced by cooler air from the north. This body of air was deflected by the rotation of the earth. He illustrated the tropical winds with the first meteorological map. He made a descent in a diving bell, which was used to try to reach wrecked treasure ships. He studied fossils and perceived them as remnants of living beings that had died long ago, and imagined a succession of living things. Halley surveyed the tides and coasts of the British Channel for the king in 1701.

In 1675, apothecary Nicolas Lemery divided substances into mineral, vegetable, and animal. He wrote a dictionary of pharmaceuticals.

John Ray and Francis Willoughby were friends who traveled together to study plants and animals respectively. John Ray started the science of zoology with his edition of Francis Willoughby's "Ornithology" on birds and his own "History of Fishes". He also attempted the first scientific classification of animals in his "Synopsis of Quadrupeds". Ray compared anatomies and experimented on movements of plants and the ascent of sap. He knew that fossils were remnants of old animals. Ray first suggested the concept of species in classification of animals and plants. He opined that the goodness and wisdom of God was shown not only by the usefulness of animals to man's uses as taught by the church, but also by the adaptation of animals to their own lives and surroundings. The vast array and dispersal of animals found by world explorers all over the world cast doubt on the biblical story of Noah putting two of every kind of animal on an ark. The science of botany began with Ray's "History of Plants" and the researches of Robert Morrison, who was Charles' physician and keeper of his gardens.

Nicholaus Steno, a Danish physician, diagrammed six levels of stratification on the earth's surface and demonstrated in 1669 that layers of strata of rock are always deposited with the oldest layers on the bottom and the youngest layers on the top. This began the science of geology. He argued that shifts in the earth's strata caused the formation of mountains. He identified fossils as ancient creatures. The idea that fossils were remnants of dead animals existing before man conflicted with the religious idea that Adam's fall began sin and caused death. The idea from fossils that existing species of animals were modifications of predecessor animals conflicted with the religious belief that Noah's ark had preserved all the varieties of animals. John Aubrey described Stonehenge, thus founding prehistoric archaeology. He thought it to be a Druid temple.

The telescope and compound microscope, which has an objective lens and an eyepiece lens for producing a wide range of magnifications, were further developed. The cellular basis of life was discovered and described by Robert Hooke. Nehemia Grew, the son of a grammar school master who became a physician, observed and drew plant anatomy, including leaves, flowers, fruits, seeds, ovules, pollen grains, and stamens. He was the first to observe the existence of plant sexuality. Italian Marcello Malpighi, a physician, used the new compound microscope to study human skin, spleen, kidneys, and liver and also compared the livers of several types of animals. He discovered capillaries linking the arterial and venous circulation in the lungs. Dutchman Anton van Leeuwenhock, a cloth manufacturer who made microscopes to inspect the quality of cloth, turned them to use in understanding the life cycles of mites, lice, and fleas. He correctly described human blood cells. When he found what he described as tiny animals (bacteria, protozoa, and rotifers), he sent clear descriptions of them to the Royal Society in London as proof against the theory of spontaneous generation, which held that lower forms of life could arise from nonliving matter. This started the science of bacteriology. With the discovery of the egg in the female reproductive system, the status of women was lifted.

Physician Thomas Willis, son of a farmer, dissected brains of men and animals to study the anatomical relations of nerves and arteries. Excess urine had been associated with a wasting disease. Willis identified diabetes mellitus with excess of urine that was sweet. Physician Thomas Sydenham, son of a gentleman, observed epidemic diseases of London over successive years, thus founding epidemiology. He also furthered clinical medicine by emphasizing detailed observations of patients and maintaining accurate records. He wrote a treatise on gout and identified scarlet fever. He introduced a cooling method of treating smallpox. But he still relied on the big three treatments: bloodletting, purging, and sweating. Bloodletting was to draw off bad blood so that it could be replaced by a better fluid. Another treatment used was cupping, whereby a vacuum was created by heated glass cups to draw blood to the surface of the skin. John Locke performed one of the first successful operations draining a kind of abscess of a man's liver. It was common for people who felt ill to take a laxative and rest at home.

In 1690, physicians opened the first dispensaries, which gave treatment and medicine together, to take business away from their rivals: the apothecaries. London's apothecaries were released in 1694 from jury service and service as constable, scavenger, or other parish or ward office because it was necessary that they be available to attend the sick at all times. Peruvian bark which had quinine as its alkaloid had been introduced as a proven cure for the ague, a fever with chills usually due to malaria, in 1653. The English ceased to believe in holy wells, but went to spas such as Bath for treatment of disease.