The Scientific Method

Podcast Transcript

The modern world is built on science. Today there are millions of scientists all over thew world, doing research in thousands of different fields and specializations.

All of these researchers are, to some degree, using a system that was developed over the course of centuries. A methodology that allows for the discovery of scientific truth.

It isn’t perfect, but it ushered in a scientific revolution and helped create the modern world we live in.

Learn more about the scientific method, what it is and how it developed on this episode of Everything Everywhere Daily.

The scientific method is one of humanity’s greatest achievements. Yet it isn’t really an invention, nor is it a discovery.

The scientific method is a systematic approach to understanding the natural world through observation, hypothesis formation, experimentation, and analysis. It represents humanity’s most powerful tool for generating reliable knowledge about the universe, allowing us to move beyond speculation and develop evidence-based understanding.

The scientific method isn’t perfect and it doesn’t work in every situation, more on that in a moment, but it is the best framework we have for determining the truth of things in the natural world.

Depending on what source you use, you will see five, six, or even seven steps in the scientific method. All of the various ways of describing the scientific method are pretty much the same, but with some steps combined, or some extra ones added.

For the purpose of this episode, the steps in the scientific method are

Observation
Questioning
Hypothesis building
Experimentation
Analysis
And Conclusions

To illustrate how it works, I’ll use one of the most famous cases, Alexander Fleming’s discovery of Penicillin.

In 1928, Fleming was studying the Staphylococcus bacteria, which causes infections. One day, he noticed something unusual.

A mold, later identified as Penicillium notatum, had accidentally contaminated one of his petri dishes—and the bacteria around it had been killed.

This was the first step in the scientific method: observation. Fleming had to actually take notice of what happened. This sounds trivial, but there are countless things that can easily be overlooked. In Fleming’s case, perhaps the absence of bacterial growth was pretty obvious, but it isn’t always so obvious depending on what you are doing.

The second step is also pretty simple. Fleming had to ask himself….why? Why did the bacteria die around the mold?

Maybe when the mold contaminated the sample, it was at a different temperature. Maybe it had been contaminated by an outside chemical, and it wasn’t the mold itself that killed the bacteria.

Once the question was asked, it was necessary to come up with a hypothesis. While all of the things I brought up could have been true, it wasn’t the most obvious reason.

The hypothesis that Fleming proposed was that there was something in the mold that killed off the bacteria.

The next step was to test the hypothesis with an experiment.

To test his hypothesis that the mold produced a substance capable of killing bacteria, Alexander Fleming conducted a series of experiments in which he isolated the mold from the contaminated petri dish and allowed it to grow in a controlled environment.

He then collected the fluid surrounding the mold, which he suspected contained the antibacterial substance. Fleming applied this mold extract to cultures of various harmful bacteria, including Staphylococcus, and observed that the bacteria were inhibited or destroyed in the areas where the extract was present.

He also tested the substance with other cells, such as animal cells, and found that it didn’t harm these cells.

The next step was compiling and analyzing the data he collected from his experiment.

Having gone through the data, he reached the final step and made a conclusion. There was something in the mold that killed the bacteria.

These results confirmed his hypothesis that the mold secreted a powerful antibacterial agent, which he named penicillin.

This process sounds pretty simple and common sense, yet it was something that took centuries to develop.

Ancient people did have systematized ways of learning.

Ancient China and India contributed to the development of the scientific method through their emphasis on observation, practical experimentation, and logical reasoning.

In China, advancements in fields like medicine, astronomy, and engineering were driven by careful empirical study and innovation, such as detailed records of celestial events and the invention of tools like the compass and seismograph.

Similarly, ancient Indian scholars made major contributions in mathematics, astronomy, and medicine, using systematic observation, classification, and logical analysis.

Likewise, the Babylonian and Egyptian civilizations practiced empirical observation for practical tasks like medicine and astronomy, but without formal methodology.

Early ancient civilizations in China, India, Babylon, and Egypt were not practicing the scientific method as we know it today because their approaches to understanding the world were largely based on practical experience, tradition, and spiritual or religious beliefs rather than systematic experimentation and hypothesis testing.

While they made significant observations and developed advanced technologies, their methods lacked the structured process of forming testable hypotheses, conducting controlled experiments, and analyzing results objectively. Knowledge was often passed down through authoritative texts or oral traditions, and explanations for natural phenomena were frequently tied to mythology or divine influence.

The ancient civilization that saw major advances towards the scientific method was the Greeks.

The ancient Greeks made significant advancements toward the development of the scientific method by shifting the focus of inquiry from mythological explanations to rational thought and natural causes. Philosophers like Thales and Anaximander began to propose that natural phenomena could be explained by underlying principles rather than the actions of gods.

Pythagoras introduced the idea that mathematics could reveal truths about the universe, laying the groundwork for scientific reasoning. Plato emphasized deductive reasoning and abstract ideals, although he devalued sensory experience, while his student Aristotle took a more empirical approach, advocating for careful observation, classification, and logical reasoning.

Aristotle’s method of systematic inquiry and emphasis on cause-and-effect relationships brought science closer to a structured method of investigation, even if it still lacked experimentation in the modern sense. Overall, the Greeks contributed foundational ideas about logic, evidence, and the pursuit of knowledge through reason—core elements that would later evolve into the scientific method.

In most episodes, when I’m talking about the development of something, I usually talk about the Romans after the Greeks. However, in this case, the Romans did absolutely nothing in this department.

The group that really took up the mantle of the Greeks was the Muslim scholars during the Islamic Golden Age.

During the Islamic Golden Age, Muslim scholars made crucial advancements toward the development of the scientific method by emphasizing observation, experimentation, and critical thinking in their pursuit of knowledge.

Building on the works of the Greeks and other ancient civilizations, they translated and preserved classical texts while also improving and challenging them through original research. Scholars like Ibn al-Haytham played a pivotal role in shaping experimental science; in his work Book of Optics, he outlined a systematic approach that involved observation, forming hypotheses, testing through controlled experiments, and drawing conclusions—closely resembling the modern scientific method.

Muslim thinkers also stressed the importance of skepticism and verification, insisting that conclusions should be based on evidence rather than tradition or authority. Fields such as medicine, astronomy, chemistry, and mathematics flourished as scholars conducted detailed experiments, recorded their findings meticulously, and developed theories grounded in empirical observation. Their approach marked a shift from purely philosophical reasoning to a methodical, evidence-based investigation of the natural world.

During this period in Europe, scholars such as Roger Bacon emphasized the importance of empirical observation and experimentation, arguing that knowledge should be derived from experience rather than solely from accepted authorities. Universities emerged as centers of learning where logic and debate were practiced, helping to refine methods of reasoning and analysis. While experimentation was still limited and often intertwined with religious beliefs, the period saw a growing emphasis on critical thinking, systematic observation, and the questioning of established ideas.

During the Scientific Revolution, which spanned the 16th to 17th centuries, the scientific method underwent a major transformation as thinkers began to reject reliance on tradition and authority in favor of direct observation, experimentation, and logical reasoning.

Francis Bacon promoted inductive reasoning, encouraging scientists to gather data through careful observation and build general theories from specific facts. René Descartes, on the other hand, emphasized deductive reasoning and mathematical logic as a path to certain knowledge.

Moving into the 19th and 20th centuries, some philosophers of science began to think about the scientific method more explicitly.

Karl Popper and Thomas Kuhn made influential contributions to the philosophy of science by offering different perspectives on how scientific knowledge progresses and how the scientific method operates.

Karl Popper emphasized the importance of falsifiability—the idea that for a theory to be scientific, it must be testable and able to be proven wrong. He argued that science advances not by confirming hypotheses, but by rigorously attempting to refute them.

According to Popper, a good scientific theory makes bold predictions and stands up to repeated attempts at falsification, which strengthens its credibility.

In contrast, Thomas Kuhn introduced the concept of paradigm shifts in his work The Structure of Scientific Revolutions. He argued that science does not progress in a steady, cumulative way but rather through periods of normal science followed by revolutionary changes. During normal science, researchers work within an accepted framework or “paradigm.”

When enough anomalies build up that the current paradigm can’t explain, a scientific revolution occurs, and a new paradigm replaces the old one. Kuhn’s view challenged the idea of linear scientific progress and highlighted the role of social and historical context in shaping scientific discovery.

Together, Popper and Kuhn expanded our understanding of how science works—not just through experiments and data, but through philosophical and cultural processes as well.

Earlier in the episode, I mentioned that you can’t always use the textbook version of the scientific method. You might be wondering, why not?

It has to do with the ability to do experiments.

In fields like astronomy, you can’t really do experiments. You can make observations and create hypotheses, but it isn’t possible to conduct experiments.

If you have a hypothesis on the formation of galaxies, you can’t go and make a galaxy to test your hypothesis. The only thing you can do is make more observations to see if they fit your hypothesis, or to see if they falsify your hypothesis.

The reason why astronomers want bigger and bigger telescopes is that they want to push the limit of what type of observations are possible.

Sometimes experiments aren’t possible due to ethics, budget, or logistics. When evidence is gathered in the field of nutrition, there usually aren’t controlled experiments conducted, although they sometimes are.

They usually conduct epidemiological studies where they survey a large number of people. The problem with these studies is that they rely on statistics to glean information out of the data, and at that point, your conclusion will result on what statistical analysis you run and how you interpret it.

Another thing which is often added as a requirement is replicability. It isn’t enough for one scientist to conduct an experiment; it is necessary for everyone to be able to repeat the same experiment and get the same results.

This has been a huge problem in many fields, particularly in fields that study humans, such as psychology and medicine, where many studies simply cannot be replicated by anyone else.

Most people think that when a research paper is submitted to a journal, the process of peer review checks to see if an experiment works…and that is not at all what peer review does.

In some fields, the inability to replicate experiments has been dubbed The Replication crisis.

Problems with peer review, academic publishing, and the Replication crisis will be addressed in future episodes.

The scientific method isn’t a hyper-strict checklist that is followed on every scientific enquiry. Rather, it is more a way of thinking that allows you approach scientific enquiry in such a way to increase the odds that when you find something to be true, it is in fact actually true.