Alchemy and the Problems of Modern Science

How our biases and expectations keep shaping our results

The 16th century was a turbulent time for Europe. With Luther’s reformation and Henry’s separation of the English from the Catholic Church (the original Brexit, if you will), the hold Rome had on Europe for a thousand years was starting to dissipate, and with it the force that had held all the different powers of the continent in check.

The Copernican evolution was likewise underfoot. Humankind’s place in the universe and relationship with the universe was being renegotiated, and new modes of inquiry into the world were being discovered.

The original Doctor Faustus

John Dee. Ashmolean Museum / Public domain

One of the time’s most colorful and influential figures was John Dee: as a mathematician, navigator, spy, magician, alchemist, and counselor to Queen Elizabeth of England, Dee was of lasting influence in a number of ways. Maybe his biggest political contribution was to convince Queen Elizabeth to build a naval fleet, and to develop a plan to reconquer the whole world and institute a framework based on a modernized, Protestant form of Christianity.

Following Elizabeth’s execution of Dee’s plan, the Catholic Spanish fleet vanquished at the shores of Britain in 1588, and the British would rule the oceans of the world for over three centuries to come. 350 years later, Dee’s vision had become a reality: the sun would never set over the British Empire, and the United States of America, a nation much in the spirit of Dee, was emerging as the dominant world power.

At the same time, Dee was also an important mathematician, political theorist, and proto-scientist, and his intellectual heritage influenced Francis Bacon and the founding of the Royal Society, the oldest national scientific institution, in 1660. Nevertheless, Dee is not as well-known today as other Renaissance men such as Da Vinci, Leibniz, or Descartes. The political situation of England in the Dee’s lifetime, swinging back and forth between Catholicism and Protestantism, was difficult to navigate. Shifiting alliances and monarchs made Dee already lose much of his reputation while still alive, but in many ways, he is disregarded today because of his involvement in alchemy, magic, and the summoning of spirits.

And so his most well-known influence on our culture might actually not come from his intellectual heritage, but from being the inspiration for Marlowe’s Doctor Faustus, written in 1588, a subject that was later to be picked up again by Goethe in his world-famous classic.

The medieval alchemical sorcerer with crystal ball and stern glance is depicted as a perversion of the insatiable thirst of mankind to delve into the darkest arts to acquire knowledge…while at the same time coming across to our modern mind as a pseudoscientific fool.

In retrospect, alchemy, astrology and other forms of magic nowadays have a bad reputation in the scientific community: they come across as silly, ridiculous, originating from the strange ideas of an ancient, pre-scientific world. We think that are not worth considering anymore. But I think this view of alchemy is a bit too one-dimensional: Alchemy persisted far into the 18th century, and was still highly influential at the beginnings of what we now consider to be the modern scientific period.

The heritage of alchemy

The Alchemist in Search of the Philosopher’s Stone, Joseph Wright of Derby / Public domain

“Why were so many clever people turning out such illegitimate results?”
Leif Nelson

When we look at the past, we often run the risk of projecting the present on it, with our hindsight bias making it seem like it would have been obvious to us all along had we just been there.

Alchemy was primarily concerned with the transmutation of base metals into noble metals. Its most famous enterprise was the creation of the philosopher’s stone. And as we now have come to realize, from the perspective of atomic physics, alchemy rested on nonsensical systemic assumptions, and the existence of a philosopher’s stone would have to violate a lot of the fundamental laws of physics.

But the scientific spirit was still present in many alchemists in an early form, and many of them genuinely believed in the validity of what they were doing. In alchemy hides the germ of a protoscience that would later become the modern scientific method. And in conjunction with the rediscovery of Hermeticism and Neoplatonism during the Renaissance, some of its ideas about personal transformation and individual paths to self-realization would, through the Rosicrucian and Freemasonic sects, pave the way to a proto-individualist ideology, sparking the French and American revolution whose ideals so define our modern world.

Alchemy made it clear that just by doing things the regular way, you could find just about anything.
E.J. Wagenmaker

I think there is an important lesson to be learned from alchemy. It shows us that many good and promising ideas (namely that you could run experiments to figure the world out, and that the world was to be understood through observation), combined with the wrong methods, can lead many intelligent, creative people, and even the most brilliant minds of their periods genuinely interested in acquiring knowledge, to keep running experiments and finding results that appear absolutely nonsensical from our point of view.

“Something was deeply wrong with the way alchemists designed their experiments and reported their results.”
E.J. Wagenmaker

Not only Dee, but Isaac Newton spent most of his time on alchemy, trying to summon spirits and transmute lead into gold. As Sean Carroll says, if he focused on physics, he might have been famous. Paracelsus (the man with the coolest, most medieval name of all time: Philippus Aureolus Theophrastus Bombastus von Hohenheim), considered one of the fathers of a scientific approach to modern medicine and toxicology (and the guys who reintroduced opium to Western Europe), likewise spent much of his life on alchemy and divinations of questionable validity.

“We could see that even a rigorous scientist could cart himself to crazy-land, just by following the rules of the road.”
Daniel Engber

Newton’s alchemical heritage is not much talked about, and John Dee is likewise largely ignored by many writers of the history of science. But this lesson: that the framework matters, and that our assumptions about the world can strongly shape the outcomes of the results of our experiments, is still, as we will shortly see, absolutely relevant to this day.

The advent of modern science

Roger Bacon, who was much indebted to Dee’s work, can be credited for formalizing the framework of modern empirical science. He tried to overcome the secrecy and shadow language of Hermeticism and alchemy, and create a more objective, evidence-based science.

Houghton Library / Public domain

The title page of his Novum Organum depicts a ship sailing past two pillars representing ancient Greek knowledge, which, in combination with the scholastic tradition, had held Europe locked in a state of epistemological stasis for millennia. It was setting course towards an infinite ocean of knowledge if only mankind would follow the methods of empirical science.

Bacon finally brought more clarity into empirical science, and his methods have changed the world in more ways than anyone can count. After Robert Boyle introduced Bacon’s principles in a chemical environment, they slowly but surely lead to the modern chemical revolutions and the decline of alchemy.

But at the same time, it remains difficult to come to robust conclusions about the world. The genius of Dee, Newton, and Paracelsus shows that the framework is which these conclusions are made matters and that even the most innovative thinkers can come across as ridiculous in hindsight: every single generation has in some way thought they had figured the world out, and in retrospect, they were never even close.

Daryl Bem shows that extrasensory perception is real

“I gathered data to show how my point would be made. I used data as a point of persuasion, and I never really worried about,‘Will this replicate or will this not?”
Daryl Bem

Let’s jump 400 years into the future.

All of the quotes I used in the paragraph on alchemy weren’t in fact about alchemy but rather were taken from this article about a psychology paper published by Daryl Bem in 2011 in the leading psychology journal Journal of Personality and Social Psychology.

Bem made it clear that just by doing things the regular way, you could find just about anything.
E.J. Wagenmaker

In the paper, Daryl Bem claimed to have shown that Extrasensory Perception (ESP) is real. According to Bem: “Well, extrasensory perception, also called ESP, is when you can perceive things that are not immediately available in space or time. So, for example, when you can perceive something on the other side of the world, or in a different room, or something that hasn’t happened yet.”

“We could see that even a rigorous scientist could cart himself to crazy-land, just by following the rules of the road.”
Daniel Engber

He showed this by rigorously testing his hypothesis for ten years. He had a large sample size of 1000 participants. He had significant results in eight of ten studies. He published his findings in a leading psychology journal.

The question here is not if ESP is real or not, or if Daryl Bem is an idiot. It’s pretty clear that he isn’t. Knowing how controversial his findings would be, he used large sample sizes and only the most conventional statistical methods to evaluate his hypothesis.

“Bem’s 10-year investigation, his nine experiments, his thousand subjects — all of it would have to be taken seriously. He’d shown, with more rigor than anyone ever had before,that it might be possible to see into the future. Bem knew his research would not convince the die-hard skeptics. But he also knew it couldn’t be ignored.”

Is Science Broken?

Psychologists were faced with a dilemma: Bem’s case gave them two bad and irreconcilable options to choose from. Either accept the improbable conclusion that people could sense the future and objects beyond their sensory perception. Or that there was something else going on.

“Something is deeply wrong with the way experimental psychologists design their studies and report their statistical results.”
E.J. Wagenmaker

The controversy surrounding Bem can in part be credited for bringing about the replication crisis in modern psychology, casting shadows of doubt on even textbook findings such as social priming. The crisis now extends to many other fields as well.

In my article on the Insignificance of Significance Testing, I looked at the influence bad statistical methods can have on the validity of experiments, how they have played their part in causing the reproducibility crisis, and why some of these flawed statistical methods are crying out for reform.

I’m not trying to discredit science and its statistical methods. It is the best we have, and in many cases, it is working brilliantly.

But scientists remain human, and our human brains are optimized to construct narratives about the world based on incomplete facts (as I go into more detail in my article on cognitive biases and AI explainability). There are hundreds of biases floating around in our ape brains. We are not natural-born scientists or critical thinkers, and in every individual, hundreds of interests compete, most of which we’re not even consciously aware of.

In science, it’s not only about individuals being smart and coming up with great ideas. The systems we build and the language in which we communicate are crucial for the success of the scientific enterprise. They keep our biases in check, and they help us collectively sort good ideas from bad ones.

Alchemists weren’t stupid. But because the framework in which they operated was flawed, the results they obtained were flawed as well.

And so it remains as crucial as to keep on updating the scientific framework, to stay humble in the face of our biases, in the face of what we don’t know. To keep looking at the past with more respect and humility: because we should realize that people from the future might look at us in the same way.

About the Author

Manuel Brenner studied Physics at the University of Heidelberg and is now pursuing his PhD in Theoretical Neuroscience at the Central Institute for Mental Health in Mannheim at the intersection between AI, Neuroscience and Mental Health. He is head of Content Creation for ACIT, for which he hosts the ACIT Science Podcast. He is interested in music, photography, chess, meditation, cooking, and many other things. Connect with him on LinkedIn at

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