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.

There was more bathing because private homes in towns now had indoor baths. The public baths came into disuse.

For childbirth, only rich women were attended by physicians. Most physicians used talismen such as the eagle stone at deliveries. Caesarian section almost always led to the death of the mother. Midwives were licensed by the church and could baptize babies. Jane Sharp wrote "The Midwives Book" with anatomical illustrations.

Women over thirty had fewer children and the last child born was at an earlier age than before. This was in part due to birth control such as coitus-interruptus, long breast-feeding of a current child and/or the taboo against sex if the wife was still breast-feeding. Rich women often employed wet-nurses to breast- feed their babies. Babies seldom thrived, or even survived, without out a regular supply of breast milk.

John Locke, an Oxford don, physician, and son of an attorney, expressed a view that the monarchy was not based on divine right, but rather on a contractual relationship with the people, who were reasonable, free, and equal by nature. This idea was first adopted by revolutionists and then became accepted as orthodoxy. Also, he articulated the right of resistance, the supremacy of legislative assemblies, and the responsibility of rulers to answer to their subjects. He theorized that men turn to forming a civil government when there is a need to protect accumulated property from some unreasonable men. This, along with the protection of life and liberty, was the primary function of government, before royal pleasure, national pride, or foreign conquest. He wrote theories on the interaction of supply, demand, interest rates, rents, coinage, and foreign exchange rates. He believed that interest rates should be the natural ones determined by market forces rather than by the legislature, especially if there was an attempt to lower interest rates below their natural rate, which was not only undesirable but easily circumvented. He thought that attempting to legislate contrary to natural economic laws, e.g. prices, was doomed to failure from unexpected consequences. He agreed with most mercantilists that by maintaining a large inflow of precious metals through consistent export of surpluses in foreign trade would lead to low interest rates, increased trade, increased capital stock, high employment, and high prices, and therefore a healthy economy and enrichment of the nation.