The history of scientific method considers changes in the methodology of scientific inquiry, as distinct from the history of science itself. The development of rules for scientific reasoning has not been straightforward; scientific method has been the subject of intense and recurring debate throughout the history of science, and eminent natural philosophers and scientists have argued for the primacy of one or another approach to establishing scientific knowledge.

Rationalist explanations of nature, including atomism, appeared both in ancient Greece in the thought of Leucippus and Democritus, and in ancient India, in the Nyaya, Vaisheshika and Buddhist schools, while Charvaka materialism rejected inference as a source of knowledge in favour of an empiricism that was always subject to doubt. Aristotle pioneered scientific method in ancient Greece alongside his empirical biology and his work on logic, rejecting a purely deductive framework in favour of generalisations made from observations of nature.

Some of the most important debates in the history of scientific method center on: rationalism, especially as advocated by René Descartes; inductivism, which rose to particular prominence with Isaac Newton and his followers; and hypothetico-deductivism, which came to the fore in the early 19th century. In the late 19th and early 20th centuries, a debate over realism vs. antirealism was central to discussions of scientific method as powerful scientific theories extended beyond the realm of the observable, while in the mid-20th century some prominent philosophers argued against any universal rules of science at all.Peter Achinstein, "General Introduction" (pp. 1–5) to Science Rules: A Historical Introduction to Scientific Methods. Johns Hopkins University Press, 2004.

Early methodology Ancient Egypt and Babylonia

There are few explicit discussions of scientific methodologies in surviving records from early cultures. The most that can be inferred about the approaches to undertaking science in this period stems from descriptions of early investigations into nature, in the surviving records. An Egyptian medical textbook, the Edwin Smith papyrus, (c. 1600 BCE), applies the following components: examination, diagnosis, treatment and prognosis, to the treatment of disease, which display strong parallels to the basic empirical method of science and according to G. E. R. LloydLloyd, G. E. R. "The development of empirical research", in his Magic, Reason and Experience: Studies in the Origin and Development of Greek Science. played a significant role in the development of this methodology. The Ebers papyrus (c. 1550 BCE) also contains evidence of traditional empiricism.

By the middle of the 1st millennium BCE in Mesopotamia, Babylonian astronomy had evolved into the earliest example of a scientific astronomy, as it was "the first and highly successful attempt at giving a refined mathematical description of astronomical phenomena." According to the historian Asger Aaboe, "all subsequent varieties of scientific astronomy, in the Hellenistic world, in India, in the Islamic world, and in the West – if not indeed all subsequent endeavour in the exact sciences – depend upon Babylonian astronomy in decisive and fundamental ways."

The early Babylonians and Egyptians developed much technical knowledge, crafts, and mathematics"The cradle of mathematics is in Egypt." – Aristotle, Metaphysics, as cited on page 1 of Olaf Pedersen (1993) Early physics and astronomy: a historical introduction Cambridge: Cambridge University Press, revised edition used in practical tasks of divination, as well as a knowledge of medicine,"There each man is a leech skilled beyond all human kind; yea, for they are of the race of Paeeon." – Homer, Odyssey book IV, acknowledges the skill of the ancient Egyptians in medicine. and made lists of various kinds. While the Babylonians in particular had engaged in the earliest forms of an empirical mathematical science, with their early attempts at mathematically describing natural phenomena, they generally lacked underlying rational theories of nature.

Classical antiquity Greek-speaking ancient philosophers engaged in the earliest known forms of what is today recognized as a rational theoretical science,Yves Gingras, Peter Keating, and Camille Limoges, Du scribe au savant: Les porteurs du savoir de l'antiquité à la révolution industrielle, Presses universitaires de France, 1998. with the move towards a more rational understanding of nature which began at least since the Archaic Period (650 – 480 BCE) with the Presocratic school. Thales was the first known philosopher to use natural explanations, proclaiming that every event had a natural cause, even though he is known for saying "all things are full of gods" and sacrificed an ox when he discovered his theorem. Leucippus, went on to develop the theory of atomism – the idea that everything is composed entirely of various imperishable, indivisible elements called atoms. This was elaborated in great detail by Democritus.

Similar atomist ideas emerged independently among ancient Indian philosophers of the Nyaya, Vaisesika and Buddhist schools.Oliver Leaman, Key Concepts in Eastern Philosophy. Routledge, 1999, page 269. In particular, like the Nyaya, Vaisesika, and Buddhist schools, the Cārvāka epistemology was materialist, and skeptical enough to admit perception as the basis for unconditionally true knowledge, while cautioning that if one could only infer a truth, then one must also harbor a doubt about that truth; an inferred truth could not be unconditional.Kamal, M.M. (1998), "The Epistemology of the Carvaka Philosophy", Journal of Indian and Buddhist Studies, 46(2): pp. 13–16

Towards the middle of the 5th century BCE, some of the components of a scientific tradition were already heavily established, even before Plato, who was an important contributor to this emerging tradition, thanks to the development of deductive reasoning, as propounded by his student, Aristotle. In Protagoras (318d–f), Plato mentioned the teaching of arithmetic, astronomy and geometry in schools. The philosophical ideas of this time were mostly freed from the constraints of everyday phenomena and common sense. This denial of reality as we experience it reached an extreme in Parmenides who argued that the world is one and that change and subdivision do not exist.

As early as the 4th century BCE, armillary spheres had been invented in China, and in the 3rd century BCE in Greece for use in astronomy; their use was promulgated thereafter, for example by § Ibn al-Haytham, and by § Tycho Brahe.

In the 3rd and 4th centuries BCE, the Greek physicians Herophilos (335–280 BCE) and Erasistratus of Chios employed experiments to further their medical research; Erasistratus at one time repeatedly weighed a caged bird, and noted its weight loss between feeding times.Barnes, Hellenistic Philosophy and Science, pp. 383–384

Aristotle Aristotle's inductive-deductive method used inductions from observations to infer general principles, deductions from those principles to check against further observations, and more cycles of induction and deduction to continue the advance of knowledge.

The Organon (Greek: , meaning "instrument, tool, organ") is the standard collection of Aristotle's six works on logic. The name Organon was given by Aristotle's followers, the Peripatetics. The order of the works is not chronological (the chronology is now difficult to determine) but was deliberately chosen by Theophrastus to constitute a well-structured system. Indeed, parts of them seem to be a scheme of a lecture on logic. The arrangement of the works was made by Andronicus of Rhodes around 40 BCE.Hammond, p. 64, "Andronicus Rhodus"

The Organon comprises the following six works: The Categories (Greek: , Latin: ) introduces Aristotle's 10-fold classification of that which exists: substance, quantity, quality, relation, place, time, situation, condition, action, and passion. On Interpretation (Greek: , Latin: ) introduces Aristotle's conception of proposition and judgment, and the various relations between affirmative, negative, universal, and particular propositions. Aristotle discusses the square of opposition or square of Apuleius in Chapter 7 and its appendix Chapter 8. Chapter 9 deals with the problem of future contingents. The Prior Analytics (Greek: , Latin: ) introduces Aristotle's syllogistic method (see term logic), argues for its correctness, and discusses inductive inference. The Posterior Analytics (Greek: , Latin: ) deals with demonstration, definition, and scientific knowledge. The Topics (Greek: , Latin: ) treats of issues in constructing valid arguments, and of inference that is probable, rather than certain. It is in this treatise that Aristotle mentions the predicables, later discussed by Porphyry and by the scholastic logicians. The Sophistical Refutations (Greek: , Latin: ) gives a treatment of logical fallacies, and provides a key link to Aristotle's work on rhetoric.

Aristotle's Metaphysics has some points of overlap with the works making up the Organon but is not traditionally considered part of it; additionally there are works on logic attributed, with varying degrees of plausibility, to Aristotle that were not known to the Peripatetics.

Aristotle has been called the founder of modern science by De Lacy O'Leary."In the days when the Arabs inherited the culture of ancient Greece, Greek thought was chiefly interested in science, Athens was replaced by Alexandria, and Hellenism had an entirely "modem "outlook. This was an attitude with which Alexandria and its scholars were directly connected, but it was by no means confined to Alexandria. It was a logical outcome of the influence of Aristotle who before all else was a patient observer of nature, and was, in fact, the founder of modern science." Ch.1, Introduction —De Lacy O'Leary (1949), How Greek Science Passed to the Arabs, London: Routledge & Kegan Paul Ltd., His demonstration method is found in Posterior Analytics. He provided another of the ingredients of scientific tradition: empiricism. For Aristotle, universal truths can be known from particular things via induction. To some extent then, Aristotle reconciles abstract thought with observation, although it would be a mistake to imply that Aristotelian science is empirical in form. Indeed, Aristotle did not accept that knowledge acquired by induction could rightly be counted as scientific knowledge. Nevertheless, induction was for him a necessary preliminary to the main business of scientific enquiry, providing the primary premises required for scientific demonstrations.

Aristotle largely ignored inductive reasoning in his treatment of scientific enquiry. To make it clear why this is so, consider this statement in the Posterior Analytics:

We suppose ourselves to possess unqualified scientific knowledge of a thing, as opposed to knowing it in the accidental way in which the sophist knows, when we think that we know the cause on which the fact depends, as the cause of that fact and of no other, and, further, that the fact could not be other than it is.

It was therefore the work of the philosopher to demonstrate universal truths and to discover their causes.See Nominalism#The problem of universals for several approaches to this goal. While induction was sufficient for discovering universals by generalization, it did not succeed in identifying causes. For this task Aristotle used the tool of deductive reasoning in the form of syllogisms. Using the syllogism, scientists could infer new universal truths from those already established.