I am someone who has one foot firmly in the twenty first century, who revels in everything that science, and in particular physics, has achieved and is achieving, and the other in the thirteenth, and who despairs of how badly philosophy has fallen since that era. This immediately strikes many people as odd. Didn't the birth of science emerge from the destruction of medieval thought?

So let us begin with the common narrative. In the beginning, there were the Babylonians and Egyptians, who began the process of thinking deeply about the natural world and mathematics. They had some fine achievements, but didn't get very far. Over on the other side of the world, the Chinese also built a strong civilisation and culture, but isolated from everyone else, also only developed up to a point and no further.

Then came the Greeks, and we start to make strong progress. Firstly, we have the great mathematicians, from Pythagoras to Euclid, who formalised the beginnings of the subject found in Babylonian and Egyptian cultures, and really established the subject as a strong intellectual discipline. Then there were the Greek philosophers, starting from Thales, who had many different schools, some of which, such as the atomists and stoics, had genuine insights. However, there was a competing school, founded by Socrates, and with Plato and Aristotle as his successors, which began to dominate, even though it was based on hugely complex and weird notions.

A few centuries later Christianity burst into the scene, and adopted Plato's and Aristotle's school of thought, and violently suppressed all others. It forced conformity to its doctrine, and all progress immediately stalled. Western Europe in particular fell into a dark age that would last until the sixteenth century. Depending on which version of the story you hear, the Arabs were either another source of stagnation or the lone bright spark in the world until they too stagnated under religious domination.

Aristotle's thought was a dead end. It dominated in medieval Europe, and led to people spending ages debating over arcane and pointless things, and writing huge books that never actually said anything, thinking that they could solve everything through logic alone.

Then a ray of hope: a non-conformist rose, whose name was Copernicus. He looked at ancient Greek texts, and saw some that suggested that the earth moved round the sun rather than the sun around a stationary earth. He developed a model of the universe that showed the Church's view wrong. But the Church opposed him, and used theology to argue against his science.

However, as more Greek and Roman texts were discovered, other people began to challenge the established view. Suddenly mankind surged forward. This period was called the Renaissance, the rebirth of Western civilisation. In the middle of it rose Galileo. Galileo almost single-handedly invented the experimental method when he dropped two balls of the tower of Pisa. He made astounding discoveries through his telescope, and confirmed Copernicus' model of the solar system. But the Church opposed him, and declared him a heretic because of his scientific beliefs, and cast him out.

At the same time, Rene Descartes developed a new, non-Aristotelian philosophy. He, and others of his period such as Galileo and Francis Bacon, decisively proved that Aristotle's thought was wrong in every regard. Although he didn't get much right himself, he opened the floodgates, and allowed new philosophers to break free of Catholic dogma. This movement was called the enlightenment, and with its empiricist and rationalist roots, launched mankind into a continual stream of progress that has not abated to this day. Inspired by these thoughts, Newton discovered calculus and his laws of motion and gravity, and then history followed its natural trajectory of progress, having broken free of the superstition of the Church. The Church's final and ultimate defeat was by Darwin in the nineteenth century, and since then only idiots and the fearful have believed in Christianity.

Something along those lines (maybe not quite as extreme as I wrote it) is believed by a great many people. I myself was taught it, and never while as antagonistic to the Church as expressed above, certainly didn't question the overall narrative. Now Galileo was certainly a great astronomer, and Newton uncovered calculus and the laws of motion, inspired by the mechanical philosophy of his time. And Descartes the philosopher (as opposed to his mathematical achievements) didn't get much right, but he did open the floodgates to a lot of equally bad philosophy. But otherwise, almost everything I wrote above concerning the times after Aristotle is false. That has been clearly and decisively shown by the historians of science.

My own realisation of this came rather suddenly. It began in the latter years as a graduate student, when I became aware that the "scientific" philosophy that inspired Newton was wholly inconsistent with modern physics. That led me to question that philosophy. Were there any alternatives? What led it to be accepted in the first place?

Secondly, I became aware that I needed to understand my Christian faith better. After a crash course on Church history and textual criticism, I turned my attention to the most important Christian writers; I singled out the Church fathers, then Augustine, then Aquinas as the most important Roman Catholic theologian, then the reformers such as Luther, Calvin and the Anglican reformers. In the middle of that process I encountered Aquinas, and his sheer force of logic blew me away. That made me more sympathetic to medieval thought. It took a bit more studies, though (particularly of Plato and Aristotle), before I considered how it might fit in with my physics. I appreciated Aquinas' approach of using the best intellectual system of his time to establish many of the truths of Christianity. I felt that something needed to be done to do a similar job, only with better premises more consistent with modern science (not realising at once that his premises required only a minimal modification to fit in line with my physics; I enjoyed Aquinas, and Aristotle, but at that time didn't fully understand them).

I had the great fortune of studying at Merton College in Oxford. It is the college with a long history, and with the first statutes, oldest buildings, first fellows, and first endowment (not to mention the oldest stained glass windows in the chapel) is, in my completely unbiased opinion, unquestionably the oldest of the Oxford Colleges (whatever people from Balliol and University might say). During a tour of the college going into its history, I remember how a historian mentioned that Galileo was basically a plagiarist; that all his best ideas were first developed by mathematicians at Merton. I took that with a pinch of salt. But as I later dived into the history of the scientific philosophy, I discovered that, while the view was exaggerated (and certainly not giving enough credit to scholars at Paris at about the same time), it was far closer to the truth than what I learnt at school about Galileo, Copernicus and the Renaissance. Galileo did advance the work of the medieval scientists, but not nearly by as much as we were led to believe.

Modern science is distinguished from Greek science by two main things: 1) The experimentation is more rigorous; 2) the reasoning is based on mathematics rather than logic. Experimentation and observation has always been important in science, from the pre-Socratic days to the present. There has been no time when observation has been given second place to theory. But there is a difference between observation as practised by the Greeks and Arabs, and the more rigorous and detailed experimentation. While some of the Greeks (Pythagoras and Plato being the most obvious examples) believed that geometry was the key to understanding the universe, it was Aristotle's non-mathematical physics which won out, for the simple reason that it seemed to work very well, while the more mathematical physics of the other Greeks didn't.

The break between Greek science and modern science is thus in mathematics and experiment. This is, of course, where Galileo steps up: he was both a brilliant mathematician and a top-rate experimentalist; one of the few people in history to excel at both. He was the embodiment of the scientific method, and his success ensured its widespread adoption. But neither the experimental tradition nor the mathematical tradition began with Galileo. They began in the middle ages, the very period we are taught to disdain.

The mathematical tradition began in Oxford, with a group known as the Merton calculators, led by the likes of Bradwardine, Heytesbury and Swinehead. They developed most of the mathematics that Galileo would later rely on, including its application to physical systems. They basically tried to apply mathematics to every problem, especially problems in physics, including kinematics, optics, dynamics, astronomy, magnetism and what was later studied under thermodynamics. In the course of their work (and those of the same time), they developed new branches of mathematics: probability, trigonometry, the theories of exponentials and logarithms, and mechanics. They were the first to realise the importance of acceleration, and to show how instantaneous velocity could be computed. Of course, they didn't know enough mathematics, and their physics was too rudimentary to get the right answer (the same, of course, could be said even of people such as Newton and Maxwell); but that's not my point. My point is not that they finished the journey, but that they started it. They were the ones who made the key methodological jump from Greek physics to modern physics, introducing (in a primitive form) the same key premises that modern physicists use to this day while mathematically modelling the universe.

Their ideas were taken up by scholars in the University of Paris, particularly Buridan (who developed the theory of impetus, a close precursor to the concepts of inertia and momentum, to answer problems Aristotle's physics had with projectile and pendulum motion) and Oresme (who contributed to the development of the heliocentric view of the solar system, and who also introduced the use of graphs and plots and the use of coordinates). Of course, I have just mentioned a few of the scholars of the time.

I wish I could also associate the beginnings of the experimental method to Oxford as well. Two key names, early in the tradition, were from Oxford: Grosseteste and Roger Bacon (who might have been another fellow of Merton, although that's not beyond dispute; Grosseteste was a little too early for the college system). However, there are others who can also claim this crown, for example Peter of Maricourt. The Arabs also had something of an experimental tradition. Once again, these people did not lead the experimental method to complete maturity. But they were the first to insist on the necessity of careful, meticulous, experimentation as part of the study of physics. They were the first (since)to get their hands dirty and develop ideas from induction, and to test ideas against experiment. To isolate a problem into small parts, controlling each variable at a time to discover the response.

All of the names I have mentioned lived and worked at about the same time, in the early fourteenth century. They were the culmination of the scholastic tradition. These were among the first people in Western Europe (and the thus the scientific tradition that has led to contemporary physics) to seriously question Aristotle's physics. They (and contemporaries such as Richard of Wallingford) also were the first I am aware of suggested the mechanistic picture of the world. Bradwardine compared the universe as like a giant mechanical clock; Buridan talked about the universe as a great machine. They used this language as metaphors or pictures; Galileo and Descartes would later take it literally. But nonetheless, despite not being Aristotelians with regards to science, they still fully accepted his metaphysics, albeit improving on it (or making it worse) in subtle ways. Those who claim that modern science is necessarily inconsistent with scholastic philosophy have to contend with the fact that the first modern scientists were devoted schoolmen. The premises on which modern science was founded, which we take for granted, were first derived from Christian Aristotelian philosophy. Without that basis, science is without rational foundation.

So was there a "dark age" in Europe? Yes, but much briefer than most people believe. The fall of Rome was a catastrophe for Western Europe. The reasons for that fall are very familiar to us: increasingly over-centralised, inward-looking and bureaucratic government; an inability to control national borders, letting in hordes of migrants who wanted the riches of Rome but not Roman culture, little appreciating that those riches were built from the traditional virtues encouraged by Roman culture, so as the culture diminished so did those riches; breakdown in family and sexual morality; internal dissension, rebellion and power grabs for a weak throne; and finally military conquest by barbarians.

The problem was that the academic language of the ancient world was Greek. The Western Roman Empire spoke Latin, as well as some local languages. The collapse of the economy meant that people were more focussed on survival than education. The Greek language became unknown, and with it almost all the philosophical, mathematical and scientific texts, baring those few which were originally written in Latin, or which had been translated into Latin (I should here mention Boethius, the last great philosopher of the Roman world, who did much of that translating as a last-ditch, and only partially successful, attempt to save civilisation: he could not prevent the fall, but his work was instrumental in the rebirth). Only the Church, in particular the monasteries, remained as a centre of learning.

Next came the raids and invasions: first the Vandals and Goths, then the Saxons and Angles, then the Scandinavians and Arabs. None of these had an intellectual tradition (though the Arabs temporarily absorbed one from the Persians and Byzantines, before more fundamentalist Islam pushed it back down). Eventually Europe was converted back to Christianity; the invaders assimilated; the Arab conquests forced back to the Pyrenees. Society settled down. In the eighth and ninth centuries, finally, the first schools were founded, encouraged by figures such as Alfred the Great and Charlemagne. Small, local, affairs at first, they gradually grew and merged together into the medieval universities. They started with nothing but a few scraps of Plato, Augustine, Boethius, Aristotle's logic and ethics, and Euclid's mathematics. Within two hundred years, they had turned that into a thriving intellectual culture. Then, translations started to arrive into Europe of Aristotle's writings and his commentators, and of the Islamic merger of Greek and Indian mathematics. This caused turmoil; Aristotle's work was not immediately accepted by everyone. But enough people took the works of the Macedonian and his commentators, and perfected them. There were dissensions between different schools depending on how much of Aristotle was to be accepted, and in which direction he should be improved upon; Albert Magnus, Scotus, Aquinas, Ockham, Anselm are the leading names of this period, each with different philosophies, some realist, and others nominalist. They challenged the classical writers, thought through the consequences, improved on them (in some cases) or made them worse (in others).

There was free intellectual inquiry. Atheists often look at the Church, and say that it states "believe this dogma," like a straight-jacket. There have been a few occasions in history when that has been true; but they are the exception. The Church is not afraid of intellectual inquiry, for She is convinced that all truth ultimately leads to God and His revelation in Jesus. And so She encourages and sponsors it, believing that the best answer to bad ideas leading away from God are better ideas with a closer grasp of the Truth. Church doctrine is not accepted in an arbitrary way; it is accepted because Christians believe that it is what the evidence, including the evidence which atheists dismiss out of hand or aren't aware of, points to. The Christians of the period came to accept Aristotle's philosophy because it made better sense of the world than any rival system, not because of any Church dogma. They accepted Church doctrine because both the evidence of reason and the evidence of observation (which is ultimately what revelation is) points to it as being true.

And that the Church was the midwife of science was crucial. Science rests on various premises: that the universe is regular and understandable; that it is rational; that the same experiment repeated will give the same result; that the laws of physics are universal, eternal, and cover everything material; that we can think of a single unified laws of physics in the first place; that the material universe is distinct from God and that its evolution arises from secondary causes which can be expressed without direct reference to God but follow from the nature of the beings as established by God; that the laws can be understood in terms of material properties without having to invoke an individual god or spirit for each phenomena. All of these ideas seem like second nature to us; they are not. Most of humanity throughout history would have regarded ideas such as this as ludicrous. They are derived from Jewish/Christian theology, in particular the belief that God conserves and sustains the physical world in such a way that He respects the created nature and powers of beings and so that the regularities we study in physics are a description of God's regular act of conservation. Only Jewish/Christian theology provides a basis all of these ideas together. Atheism presupposes them, but cannot justify them.

Late Medieval Europe was not only a period of great philosophical, mathematical and scientific advance; it was also a period of great technological advance. It was quite possibly the fastest time of technological advance before the industrial revolution and the agricultural and transport revolution before it. (Maybe it has some competitors from ancient China, Korea or Japan; I am not sure of that, but I can't think of any other possible rivals that achieved so much in such a short period of time.) But didn't the industrial revolution achieve more? Perhaps, but by building on the innovation of medieval and then Renaissance Europe (plus a few imported from China). The point is that progress often starts slow, and then accelerates as it builds. When was the start of Western European dominance in technology (which continues to this day, since cultures such as the North Americans, the Chinese, Koreans and Japanese have adopted the methods that made Europe great to move ahead of Europe)? When did people start to show an inventive spirit, informed by science, to make lives easier? When did the mindset that we could use technology to overcome the forces and seasons of nature first arise? Again, we have to turn to medieval Europe, and Christian scholasticism.

So why do we have such a low view of Medieval Europe? The answer in part lies in what killed Bradwardine. He died of the plague; as did one third of the population: more in the great European university cities. Equally, European society was ravaged by wars; the hundred years war; the war of the Roses, and others. Between a third and a half of the population died; no economy can survive that. Once again, for a short time, survival became more important than education. Many of the best minds were taken by the plague. Perhaps more important was the decline in pre-university education. People no longer arrived at the medieval university ready for its difficult but rigorous syllabus. The teachers didn't So the heirs to that great generation were lesser men. They taught from the textbooks of people such as Aquinas, Buridan and Swineshead, but didn't understand them.

It was these scholars, those two generations between the black death and the Renaissance, who tried to teach the great minds of the Renaissance (pre-university education having now recovered). Of course they were dissatisfied with it, finding concepts such as form, force and substance ill-defined. It wasn't the fault of the concepts, but of the teachers. But the renaissance scholars criticisms of and prejudices against scholastic philosophy passed down from them to their successors, and continued to be parroted until the mid-twentieth century, with few people checking to see if their presentations of scholastic philosophy were accurate. Galileo rescued the scholastic mathematics and physics, by not acknowledging his sources, but was just as disdainful of the rest of the philosophy.

Of course, none of the Renaissance criticisms of scholastic philosophy (which are the same as many atheists use today) stand up to criticism. Mostly they are obviously wrong, based on either misrepresentations of what the scholastic philosophers taught, or simple errors of fact, and can be dismissed immediately. As one particularly prominent example, the renaissance writers and their successors defined final causality as purpose or design, while for Aristotelians it is closer to tendency towards a goal; it does not immediately imply mental activity. They again mis-defined and misunderstood other key concepts such as form. To anyone knowledgeable of medieval philosophy, it is clear that it is vastly superior and more rigorous than anything that arose in the Renaissance period or later. The only objection raised against scholasticism that counts for anything was the claim that it is inconsistent with the emerging mechanical physics. I am not sure if that claim is true -- the caricatures of scholastic philosophy commonly cited are inconsistent with mechanical physics, but it is not so obvious when we consider the real thing (although the mechanical philosophy of the early modern period is certainly a better fit with mechanical physics than the scholastic philosophy). But in any case, the claim is irrelevant, because we now know that mechanical physics is wrong. Almost all of the premises of the mechanical philosophy are directly refuted by contemporary quantum physics. All of the "scientific" arguments which were used to question scholasticism were based on a drastically incorrect understanding of physics. The question is not whether scholastic philosophy matches Newton's physics, but whether it is consistent and can explain quantum physics. And my claim is that, when properly understood, it does an exceptionally good, if not quite perfect, job. The very parts of mechanical physics which were used to question scholastic philosophy were the very parts of it which were undermined in the quantum revolution.

And this is particularly bad news for atheists. Most atheists have many misconceptions, and their parroting of the flawed renaissance and early modern dismissal of scholastic philosophy looms large among them; and the general historical ignorance that I see in most atheist writings (believing the popular myths without evidence; indeed often contrary to the evidence). Modern atheism is built on the assumptions of the mechanical philosophy, in particular that there are laws of physics which operate independently of God. If scholastic philosophy is back on the table, in particular if its version of causality is the only version on the table, which I believe is the case, and if the doctrine of potentiality and actuality is accurate, which is, I think, implied by the quantum physics superposition principle, then the classical proofs of God's existence and attributes are looking pretty strong again (if they were ever weak).