Investigating
The main ideas and procedures about how the natural world should be investigated were established by about 1450-1500 . However, at this time physics, the main driver of finding out about how the world works, had not yet defined its fundamental units of thought. Its individual branches were a scattered collection. 
Sound was much occupied with a semi- mystical arithmetic of music. Magnetism, in spite of the stimulus of navigation, was in abeyance.  Electricity was confined to a few mysterious observations on amber and the like. Heat was, in the main, part and parcel of alchemy. Like biology, optics and mechanics interested the great artists. To us, their optics is little more than geometry—than perspective. But then both perspective and anatomical accuracy were part of the new phase of artistic naturalism which was setting in, with men like Botticelli (1444- 1510), Durer (1471-1528), and Leonardo da Vinci. Such phases are recurrent in the history of art and are commonly associated in discussions of the subject with that very consultation of nature which is one side of the scientific spirit. 
The geometrical side of perspective was studied by a series of artists, Brunelleschi (1379- 1446), Leonardo, Alberti, and Durer; and this study had important effects in mathematics and physics.
The geometry of refraction already had a long, if intermittent, history : from Ptolemy's experiments, through Ibn-al- Haitham (965-1020) on the refraction of lenses and of the atmosphere, to Roger Bacon's project for a telescope (c. 1250), By 1300 convex spectacles were spreading, especially from the Venetian glass-works, but concave ones were not common until the middle of the 16th century, and were even then were rare, highly valued objects.
There was, however, some physical, and physiological, optics as well. Leonardo studied the eye, though he thought the liquid centre portion was the main image maker. But the old view that vision is a matter of tentacles coming out of, as well as of light entering, the eye had still not lost its dominance.
For their movement-studies artists called in the science of mechanics. But they did little to advance it. Leonardo's work, being unpublished, produced little effect. In spite of the classical texts of Vitruvlus, Hero, and Ctesibius, established theory ended with statics. In dynamics perpetual motion was still sought after, " gravity " and " levity " still made things seek their "natural" places, and the naive point of view held sway that force is needed to keep up a uniform motion. It was otherwise with practice as opposed to theory. Many early clock mechanisms are remarkably well-balanced in their action, though without the pendulum their accuracy could only be low. With the growth of trade, however, punctuality began to be demanded in other matters than religion. The Renaissance metal workers achieved a virtuoso's skill with mechanical toys; and when jointed-metal work was going out for armour, the great surgeon Ambroise Pare found a new niche for it in the manufacture of artificial limbs (c. 1560). Thus craftsmanship was ready to pick up applications of mechanical theory in the 15th century.
In chemistry there was not yet a body of exact ideas, but an alchemical literature and an oral tradition of craft knowledge. There were balances and weights of considerable accuracy. The chemical crafts already made and used in some quantity the fundamental reagents, such as sulphuric and nitric acids. Distillation had been, practised from the 11th or 12th century. The distillation of spirits became a considerable trade in the 16th century. The German mining and metallurgy of the 16th century were already old. Italian glass dated from at least the 12th century, and by the end of the 16th had reached an artistic climax. Gunpowder was already an industry, though gun barrels were still very crude. Drugs were a chief article of long- distance trade, and were responsible for a great diffusion of chemical technique. Toxicology, though little understood, was much practised. Like the chemical weapons of to-day, it contributed its quota to the tradition of chemical skill. In all this, much future chemical knowledge was implicit, but a major deficiency was the lack of clear conceptions of the nature of gases and of experimental technique for handling them. But this was itself only an aspect of a deeper deficiency of ideas: the concept of the physical, of bodily materiality as we understand it, was lacking. Ideas were still, for the speculative mind, more real than material things. Science awaited th idea of a material something existing independently of the observer and underlying, essentially unchanged, the transformation and varieties of matter, such as fusion, solution, chemical reaction. But in fact this idea only began to grow definite in the 17th century.  It did not mature until the early 19th century. Without it, in those early days, men were helpless: helpless in physiology; helpless in physics. Without it, optics and astronomy all through the 16th century were largely exercises in geometry. Heat was not a branch of physics but a chemical element; while the alchemists made what seem to us gross confusions of material substances and abstractions or qualities such as colour. Thus, the ability to make a substance look like gold seemed to them at least an approach to actual transmutation. At the opposite extreme, they held that, whatever the appearances, each firing or distillation refines away more of a thing's external "dross" or "accidents" and brings us nearer its quintessence or "soul," which is the elixir of life or the philosopher's stone.
The Greeks, having analysed the world into the fiery, the liquid, the earthy, and so on, did not use these as mere convenient abstractions, but rather treated individual substances as particular cases of these underlying realities. The alchemists identified the realities with particular material substances: sulphur, mercury, and salt respectively. Nor was this mere verbiage. They gave such symbolic correspondences practical effect. That between the planets and the chemical elements constituted a connection of alchemy with astrology.  When one dealt with a metal, its planet had to be in the proper position. The conjunction of fire and water among the elements was correlated by Renaissance geologists with the fact that volcanoes are always near the sea. The conjunction of fire and sulphur was connected by Paracelsus with the preparation of the very "fiery" substance, ether, with the aid of sulphuric acid. It was long before men found anything better than such apparently not unpromising starts ; and they only did so after decisive advances had been made in physics.
The service of all the centuries of alchemy was that of trying all the possible permutations and combinations of all the substances known, mineral, vegetable, "spiritual," "aerial", of clearing away those which did not interact, and of slowly fixing attention on the less accidental features of those which did.  Three individuals of note soon after 1500 were were trying to free chemistry from mysticism and to bring it into touch with those craft-sources from which it was to draw such wealth. Paracelsus (c. 1493-1541) was perhaps a typical Renaissance braggart. It has still to be proved that he knew of hydrogen as such; while it was another, Valerius Cordus (1515-44), who gave the first non- mystical account of the sulphuric preparation, of ether. But Paracelsus was also a lifelong voyager in search of facts, with a hot tongue in his head for the pomposities of contemporary scholarship and medicine. Agricola (1490-1555) a metallurgist was a much quieter figure, a collector of information and specimens, a genuine practising expert in his subject, an exemplar of the scientific virtue of sobriety.
Paracelsus, who was more a doctor than a chemist, was one of the first to insist that the body must be viewed as primarily chemical. He favoured mercury and other mineral drugs at the expense of the vegetable decoctions of the time. In fact, like Agricola, he was a keen mineralogist, and had glimmerings of the ideas which later developed into geology; such as that of the succession of the rocks. But a few solitary voices were not enough. In the 16th century a new burst of religious fanaticism flooded Western Europe.   It was after these men, that isolation swallowed up the science of chemistry.
Nevertheless, from the above account it is clear that the major procedures for investigating the workings of nature had been defined as ‘observing’, ‘taking apart’, ‘transforming’, ‘reasoning with numbers’, and theorising. With regard to theorising, science still needed abstractions narrow enough to make predictions which are disprovable, if false, by experiment.