ViroLIEgy 101: The Scientific Method

ViroLIEgy 101 is a series of articles meant to provide relatively short (by my standards) and concise explanations of key concepts regarding both germ “theory” and virology. I’m providing an overview on topics that are essential to the conversation that people may be confused with and have difficulty understanding, or areas that seem to be controversial when engaging in discussions with those defending the germ “theory” of disease.

Over the course of the last few years, others and I have been engaged in discussions with all kinds of people who defend germ “theory” and virology, from the everyday layman to actual scientists and virologists. One of the most stunning and alarming takeaways from many of these conversations is the outright confusion over the scientific method, a logic-based procedure that has characterized natural science since at least the 17th century and has been around for much longer. When it is brought up in these exchanges as a means to challenge the pseudoscientific (i.e. fake science) evidence presented by virologists, there is a decidedly mixed reaction. Some virologists and microbiologists, who agree that the scientific method exists while claiming that they adhere to it, demonstrate that they simply do not understand the scientific method, as was shown by plant virologist Thomas Baldwin, a.k.a. Sense Strand, in conversation as well as in the image he supplied below.

Some claim that there is no one method used by scientists, arguing that the steps that I regularly outline are my own creation or definition that I apparently pulled out of thin air. When challenged on this claim that the steps outlined are “my steps,” they either have no answer (after outlining the exact same steps that I presented):

Or they end up inadvertently admitting that the steps that I presented are, in fact, the scientific method after previously claiming that they are not:

Even some who are on the “no virus” side do not believe in and outright deny the existence of the scientific method, claiming that it is a scam by doctors who “promote a made-up definition of science based on the so-called ‘Scientific Method’” in order to con the public.

With so much confusion over what the scientific method is as well as whether or not it actually exists, I figured that it was as good a time as any to dive into the history of the establishment of the scientific method. What we will see is that these logical and rational steps not only exist as a method that was carefully molded over time into what they are today, but that these steps are crucial in determining what constitutes scientific knowledge. It will be clear why myself and others are confident in holding the evidence coming from virology (as well as other fields) to these standards. You will see that any evidence that was not derived from the scientific method is, by definition, pseudoscientific.

Defining Science and The Scientific Method

In order to properly discuss the scientific method, it is beneficial to define what exactly science is first. The word “science” actually stems from the Latin word scientia which translates to “knowledge.” Ironically for virology, it is said that the original notion in the Latin verb was most likely “to separate one thing from another, to distinguish,” which is something that virologists have a major problem doing, to the point where they literally changed the definition of “isolation.” Regardless, while science may mean knowledge, knowing something in and of itself is not science. One can know that the sky is blue, but just knowing this fact does not constitute scientific knowledge. One can be an expert in all things related to Pokémon, but that does not mean that they are a scientist. In order for the knowledge to be considered scientific, it must meet certain criteria, as pointed out by The Science Council when they decided to define science in 2009. The Science Council is a UK organization established by Royal Charter in 2003, and their principal activity, according to their Wikipedia page, is “the promotion of the advancement and dissemination of knowledge of and education in science pure and applied, for the public benefit.” According to their definition, science is defined as such:

“Science is the pursuit and application of knowledge and understanding of the natural and social world following a systematic methodology based on evidence.”

The Science Council further elaborated on their definition by outlining what this systematic methodology that makes up science entails:

Scientific methodology includes the following:

• Objective observation: Measurement and data (possibly although not necessarily using mathematics as a tool)
• Evidence
• Experiment and/or observation as benchmarks for testing hypotheses
• Induction: reasoning to establish general rules or conclusions drawn from facts or examples
• Repetition
• Critical analysis
• Verification and testing: critical exposure to scrutiny, peer review and assessment

They highlighted observation, hypothesis testing, experimentation, analysis of results, drawing conclusions, and repetition along with verification as core components of the scientific methodology. The Science Council made an effort to explain exactly what the scientific methodology is that they are referring to, and used this as a central component of their definition of what science is supposed to be. However, The Science Council is not the only one to highlight the scientific method when defining science:

According to Merriam-Webster, science is defined as knowledge obtained through the scientific method:

knowledge or a system of knowledge covering general truths or the operation of general laws especially as obtained and tested through scientific method

Their definition of the scientific method involves observation, the formulation and testing of hypotheses, experimentation, and the collection of data:

principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses

According to Vocabulary.com, science is defined as an empirical field that utilizes the scientific method to aquire knowledge:

“Science is an “empirical” field, that is, it develops a body of knowledge by observing things and performing experiments. The meticulous process of gathering and analyzing data is called the “scientific method,” and we sometimes use science to describe the knowledge we already have.”

Their definition of the scientific method includes observation, hypothesis testing, and experimentation, and within their further breakdown of the method, they state that scientists look to explain cause and effect relationships observed in nature:

“a systematic way of investigating to test a hypothesis”

“The scientific method is a process for experimentation that is used to explore observations and answer questions.”

“Scientists use the scientific method to search for cause and effect relationships in nature”

From BiologyOnline.com, science is defined as a body of knowledge that is gained from the application of the scientific method:

A systematized body of knowledge in the form of hypotheses, theories, principles, models or laws that have been conclusively drawn from observed or verifiable facts or from experimental findings gained basically from the application of the scientific method.

Their definition of the scientific method involves investigating a phenomenon, the formulation and testing of a hypothesis, experimentation, gathering and analyzing data, and drawing conclusions:

A systematic approach to solving a problem by discovering knowledge, investigating a phenomenon, verifying and integrating previous knowledge. It follows a series of steps that evaluates the veracity or the feasibility of a prediction through research and experimentation from where the information obtained will be used as a basis in making conclusions.

The fundamental steps of scientific mA systematic approach to solving a problem by discovering knowledge, investigating a phenomenon, verifying and integrating previous knowledge. It follows a series of steps that evaluates the veracity or the feasibility of a prediction through research and experimentation from where the information obtained will be used as a basis in making conclusions.

The fundamental steps of scientific method are:

(1) Identifying the problem to solve

(2) Formulating a tentative answer or hypothesis

(3) Testing the hypothesis

(4) Gathering and analyzing data

(5) Making conclusions

Even Wikipedia understands that science requires the use of the scientific method:

Scientific research involves using the scientific method, which seeks to objectively explain the events of nature in a reproducible way.^[167]

The Wikipedia scientific method page lays out observation, creation of a hypothesis, testing through experimentation, and analyzing the results in order to accept or reject the hypothesis. They go so far as to say that these are a definitive series of steps for all scientific enterprises:

The scientific method involves careful observation coupled with rigorous scepticism, because cognitive assumptions can distort the interpretation of the observation. Scientific inquiry includes creating a hypothesis through inductive reasoning, testing it through experiments and statistical analysis, and adjusting or discarding the hypothesis based on the results.

The above mentioned are principles of the scientific method, a definitive series of steps applicable to all scientific enterprises.

Wikipedia even supplied a nifty little graphic demonstrating the scientific method.

Finally, according to Black’s Law Dictionary, considered America’s most trusted law dictionary and one of the most valuable reference tools to the legal community, the legal definition of science is knowledge that is gained through the application of a scientific method:

Knowledge that is comprised of verifiable and measurable facts that have been acquired by the application of a scientific method.

The legal definition of the scientific method is a step-by-step approach that involves identifying and defining a problem, hypothesis formation, testing the hypothesis through experimentation, gathering and interpreting the data, and repeating the process:

A step-by-step approach to solving problems. Identify and define the problem, accumulate data, formulate a hypothesis, conduct experiments to prove hypothesis, interpret results in an objective manner and repeat.

As can be seen, the scientific method is a core component of what makes up scientific knowledge. You can’t have one without the other. The steps outlined in the above definitions line up exactly with what myself and others have highlighted in our conversations with those who deny the method.

The steps of the scientific method are clearly not our own creation. They are not a scam or a con used to deceive the public. Nature.com even shared the exact same steps when defining science and stated that “Any field of study which adheres to this process is considered science,” and that by using the scientific method, “a proper characterization and by extension, definition, of science can be made.” Thus, it can easily be said that without adhering to these steps and gaining evidence using this methodology, the knowledge acquired is not scientific.

The History of The Scientific Method

Now that we have a definition for what constitutes scientific knowledge and we can see that adherence to the scientific method is essential to aquiring this knowledge, this leaves us with the question as to where exactly these steps that make up the scientific method actually came from. Let’s take a brief look at the documented history to find out exactly how this methodology was established.

According to the 2019 paper Perspective: Dimensions of the scientific method by clinical professor of biological science and researcher Eberhard O. Voit, the roots of the scientific method stretch all of the way back to ancient Greece with the work of Aristotle and Herophilus in the 3rd century. Aristotle was considered the first to define and conduct empirical studies with concrete evidence, purpose, and logic. This framework of empirical study based on logic and reason established by the Greeks was expanded upon by the Arabs with the work of Avicenna and Alhazen (also known as al-Haytham) around 1,000 AD, who developed meticulous methods of experimentation utilizing “controlled scientific testing in order to verify theoretical hypotheses and substantiate inductive conjectures.” The English philosophers Robert Grosseteste and Roger Bacon contributed to the expansion of the scientific method in the Middle Ages around 1200-1250 AD by promoting “the conception of science as the inductive study of nature, based on and tested by experiment.” However, according to many researchers, the scientific method, as we know it today, was crystallized around the 17th and 18th century with the work of English philosopher and statesman Sir Francis Bacon and French philosopher and scientist Rene Descartes, both of whom strove for objectivity based upon observations rather than preconceived ideas and superstitions:

“This scientific method has deep roots going back to Aristotle and Herophilus (approximately 300 BC), Avicenna and Alhazen (approximately 1,000 AD), Grosseteste and Robert Bacon (approximately 1,250 AD), and many others, but solidified and crystallized into the gold standard of quality research during the 17th and 18th centuries [1–7]. In particular, Sir Francis Bacon (1561–1626) and René Descartes (1596–1650) are often considered the founders of the scientific method, because they insisted on careful, systematic observations of high quality, rather than metaphysical speculations that were en vogue among the scholars of the time [1, 8]. In contrast to their peers, they strove for objectivity and insisted that observations, rather than an investigator’s preconceived ideas or superstitions, should be the basis for formulating a research idea [7, 9].”

Even though many credit Aristotle with setting the foundation for the empirical scientific method while recognizing Francis Bacon and Rene Descartes for solidifying it, the work of the Arab scientists, particularly Ibn al-Haytham, is where the steps that resemble the modern version of the scientific method were first established. Al-Haytham was known for being a mathematician and astronomer who made significant advances in the field of optics. He is considered the architect of the scientific method due to his detailed writings of his own procedures, focusing on the importance of observation and experimentation. In the paper Al-Haytham the man of experience. First steps in the science of vision, author Rosanna Gorini stated that the majority of the historians consider al-Haytham as the one who pioneered the modern scientific method. With his writings, al-Haytham established experiments as the standard of proof in the field as his investigations were based on evidence obtained through experimentation rather than on abstract theories. He wanted to ensure that his experiments were systematic and repeatable. The steps attributed to al-Haytham’s method include:

1. Observation of the natural world
2. Stating a definite problem
3. Formulating a robust hypothesis
4. Test the hypothesis through experimentation
5. Assess and analyze the results
6. Interpret the data and draw conclusions
7. Publish the findings

As can be seen, the core concepts that make up what we know of as the scientific method today were being utilized by al-Haytham around 1,000 AD. Due to the excellence of his scientific method utilized some 500 years before the “Scientific Revolution,” al-Haytham has become known as “the first scientist” by some historians, with his great influence on science extending well beyond the Arab world. Roger Bacon, who was one of the earliest European proponents of the scientific method, was inspired by the writings of al-Haytham in his own work about 200 years later. Bacon wanted to confirm the findings of Aristotle, whose work he was teaching to his students at the time. By utilizing the methods of al-Haytham, whom Bacon knew about thoroughly to the point where he intended his Perspectiva (part V of his Opus Maius) to be an interpretation of al-Haytham’s theory, Bacon discovered that many of the Greek philosopher Aristotle’s findings were actually incorrect. His version of al-Haytham’s scientific method involved four crucial steps:

• Observation
• Hypothesis
• Experiment
• Verification

The work produced by Roger Bacon earned him the nickname of “Britain’s first scientist,” and there is evidence that he strongly influenced Sir Francis Bacon (not related) a few hundred years later when the scientific method was said to be codified during the “Scientific Revolution” of the 17th and 18th centuries. Francis Bacon contributed to solidifying the scientific method within the field by emphasizing and promoting the inductive process, relying on both observation and experimentation to form a conclusion. His method utilized experiments to manipulate nature in order to attempt to prove the hypotheses wrong. As an example, Francis Bacon argued that, in order to prove that disease developed due to external causes, healthy people needed to be exposed to the variables individually so that it could be determined if any of them were a potential cause. He insisted that this must be confirmed through repeated experimentation. We know that this is an area that has regularly refuted virology:

“For example, in order to test the idea that sickness came from external causes, Bacon argued that scientists should expose healthy people to outside influences such as coldness, wetness, or other sick people to discover if any of these external variables resulted in more people getting sick. Knowing that many different causes for sickness might be missed by humans who are unable or unwilling to perceive them, Bacon insisted that experiments must be consistently repeated before truth can be known: a scientist must show that patients exposed to a specific variable more frequently got sick again, and again, and again.”

Francis Bacon and the Scientific Revolution

Eberhard Voit noted that the traditional scientific method was further established throughout this period by the work of researchers such as Rene Descartes (importance of deduction), Sir Isaac Newton (incorporated both induction and deduction), Karl Popper (the concept of falsifiability), and many others, and that their work throughout the centuries cemented the scientific method into what it is today; a method that is ultimately based upon formulating and testing hypotheses from observations. From the results of these tests, a deduction is made regarding whether the hypothesis is presumably true or false. Voit pointed out that, while it is often presented in discrete steps, the scientific method should be seen as a form of critical thinking that is subject to review and independent validation. The scientific method is very influential and has proven valuable in prescribing valid experimentation and affecting the way we attempt to understand nature. He stated that the scientific method has become “deeply ingrained in the scientific psyche, and it is now taught as early as middle school in order to teach students valid means of discovery.” Even though various researchers influenced the method along the way, the “conceptual scaffold remained essentially unchanged.” This method has since guided research studies, fundamentally influencing the thoughts on the process of scientific discovery to the point that nonadherence to the scientific method is seen as “lacking in rigor,” leading to irreproducible and irreplicable results.

Breaking Down The Scientific Method

Now that we have established the core steps of the scientific method, let’s examine them in more detail. In the Blinded by Pseudoscience article that I wrote a year ago, I went through the main steps of the scientific method and provided descriptions for each that I am sharing here. The article goes into more detail on how virology is unable to adhere to the scientific method and how it is, in fact, pseudoscience, so I recommend checking it out for further details.

1. Observe a Natural Phenomenon

This may be the most controversial of the core steps as people try to argue over what is considered a phenomenon. However, there should be no confusion when we define the word as it is most commonly understood; a phenomenon is an observable fact or event. A natural phenomenon is an observable fact or event that occurs in nature that is not man-made nor influenced or manufactured by human engineering or intervention. The cause or explanation of this observation is in question which leads one to start to investigate the matter scientifically in order to provide an explanation. Observing a natural phenomenon is usually done through the senses either by sight, sound, taste, touch, and smell. However, some phenomena are unable to be detected directly through the senses and require enhancement through the aid of technology such as microscopes, telescopes, stethoscopes, etc. Some examples of natural phenomena which are not man-made include lightning/thunder, volcanic eruptions, weather, decomposition, earthquakes, fire, etc. It is through the observation of the phenomenon that the necessary questions are asked in order to move into the next step in the process, forming a hypothesis.

2. Alternative Hypothesis

The hypothesis is the foundation of the scientific method. It is an educated guess as to a possible explanation for what has caused the observed phenomenon. In order to have a valid hypothesis, there are two crucial elements that must be defined from the very start. These are the independent and dependent variables. The independent variable (IV) is the presumed cause of the effect that was observed. The IV must actually exist and be able to be varied and manipulated throughout experimentation to see what affects it may have, if any. It cannot be the end-result of the experiment. The dependent variable (DV), on the other hand, is the effect that was observed and that the researcher is looking to identify the root cause for. Unlike the IV, the DV cannot be directly manipulated as it is entirely dependent upon the manipulation of the IV.

Once both variables are identified, a hypothesis can be formulated. This is written as an if-then statement and drawn up as a possible explanation as to what may happen to be discovered upon experimentation. An example would look like this:

“If I water my plant every day, then it will grow.”

In this example, the water is the IV while the growth rate of the plant is the DV. Along with these variables, there are other factors that must be identified as well, known as control variables. These are the factors that may influence the outcome of the experiment. In our example, these could include the amount of sunlight, the type of soil, the time of day, the temperature, the weather, indoor or outdoor environment, etc. Control variables must be accounted for and must remain unchanged throughout the course of the experiment. This is to ensure that any effect attributed to the IV was actually a result of the IV alone and not due to other confounding factors.

3. Null Hypothesis

An absolutely essential component of the hypothesis is that it must be falsifiable, meaning that it can be proven wrong. This is why one must also be able to establish a null hypothesis, which assumes that there is no relationship between the IV and DV. In other words, it is the exact opposite of the alternate hypothesis. Using our earlier example, it would be written simply as such:

“If I water my plant every day, it will not grow (or it may grow less or may die).”

It is this very concept of falsifiability that is a hallmark of true science. If one is repeatedly unable to falsify the alternate hypothesis, this is a very strong indicator that the results are indeed valid scientifically.

4. Test/Experiment

It is at this stage where the real heart of science takes place. In order for the knowledge gained to be considered scientific, the hypothesis must be testable through experimentation. This is where the hypothesis will either be proven or disproven in regard to the causal relationship between the IV and the DV. The experiment must focus on only changing one variable at a time and must be repeated numerous times. The main experiment will coincide with control experiments to ensure that the hypothesized results are only seen with the experimental group. In order to be considered a success, the expected results must not be seen in the control group and must be reproduced more than once.

Going back to our water and plant example, we could plant seeds in two identical pots with the same soil. We would need to figure out how much water we want to use and then water our experimental pot daily while our control pot receives water once a week. As the plants grow, the height of each plant would be measured to see if the amount of water had any effect on the growth of the plant.

5. Analyze the Observation/Data

After experimenting, the data is collected and ready for analysis in order to confirm or reject the hypothesis. This is rather self-explanatory. In our plant scenario, the heights would be measured to see what kind of difference may have been noticed. Did the experimental plant grow faster? Or perhaps daily watering resulted in over-watering and the death of the plant. How did the results compare with the control? Which plant fared better overall? Once completed, the experiments can be run again, if validated, in order to see if the results are repeatable and reproducible.

6. Validate/Invalidate Hypothesis

This is another self-explanatory step. Either the experiment produced the intended result, thus confirming the alternative hypothesis, or it did not, thus confirming the null hypothesis. If it did not confirm the alternative hypothesis, then it is back to the drawing board to either come up with a new hypothesis and/or examine the variables which may have impacted the experimental results.

There Is No Science Without The Scientific Method

“Scientific knowledge can only advance when all scientists systematically use the same process to discover and disseminate new information. The advantage of all scientific research using the Scientific Method is that the experiments are repeatable by anyone, anywhere.”

https://extension.unr.edu/publication.aspx?PubID=4239

The image above is from the U.S. National Science Foundation (NSF) which was established by Congress in 1950 as “an independent federal agency that supports science and engineering in all 50 states and U.S. territories.” In the document that the image is obtained from, the NSF states that the scientific method is “a series of steps that a scientist follows to analyze and answer a question about a specific observation.” As can be seen, the steps that are listed include observation, the formulation of a hypothesis, testing through experimentation, examining the data, and forming a conclusion. The National Institute of Environmental Health Sciences, a part of the NIH, states that “a good scientist learns about the world by using the scientific method” and that “all fields of science use the scientific method as a framework to make observations, gather data, and draw conclusions.” It goes on to lay out the steps of the scientific method such as forming a hypothesis, testing it through experimentation, analyzing the results, and reporting conclusions. The National Institute for Standards and Technology (NIST), another governmental agency, states that the scientific method is the “systematic pursuit of knowledge involving the recognition and definition of a problem; the collection of data through observation and experimentation; analysis of the data; the formulation, evaluation and testing of hypotheses; and, where possible, the selection of a final hypothesis.” We can find many other sources (examples here, here, here, and here) that all list the same steps as the NSF, the NIH, and the NIST as these steps are the core of scientific method, and they allow one to logically and rigorously test hypotheses in an unbiased fashion in order to obtain scientific knowledge. Without adherence to the steps of the scientific method, and without the ability to establish a falsifiable hypothesis based upon observed natural phenomenon that is capable of being tested experimentally, the evidence and knowledge gained are considered to be pseudoscience by definition.

According to Oxford Languages, pseudoscience is defined as such:

a collection of beliefs or practices mistakenly regarded as being based on scientific method.

According to BiologyOnline.com:

Any body of knowledge, methodology, belief, or practice purported to be scientific but which fails to comply with the scientific method, lacks supporting evidence, or cannot be tested in practice or in principle.

According to TechTarget.com:

Pseudoscience is a proposition, a finding or a system of explanation that is presented as science but that lacks the essential rigor of the scientific method.

According to Study.com:

Pseudosciences often appear to be a genuine science, but they do not follow the scientific method.

And once again, even Wikipedia understands that without the scientific method, it isn’t science:

Pseudoscience consists of statements, beliefs, or practices that claim to be both scientific and factual but are incompatible with the scientific method.

As scientific knowledge must be aquired through the adherence to the steps of the scientific method, perhaps this is why many scientists and virologists try so hard to deny the scientific method, even to the point of claiming that it doesn’t exist or that it is a scam used to con the public. Perhaps they realize that the steps actually conflict with the results of their own work and beliefs. Perhaps, upon realizing that the scientific method does exist, they come to the understanding that the work that they produced may not be scientific at all, and that, instead of practicing science, they have been engaged in pseudoscience all along. Perhaps, upon this realization, they go up against their own cognitive dissonance, which frightens and angers them.

Had these scientists and virologists understood and adhered to the scientific method, we wouldn’t have a situation where most published scientific research findings are false, and we wouldn’t be stuck in a reproducibility and replication crisis with no end in sight. Had the scientific method been followed, the repeatedly disproven and falsified germ hypothesis would have never been elevated to a “scientific theory,” and the entire field of virology would have remained within the realm of fantasy and pure imagination right where it belongs. Instead, we find ourselves in a world that has largely misplaced and disregarded its method for determining true scientific knowledge, which has led to the mistaken belief that pseudoscience is science, and a generation of scientists and virologists, along with the laymen who listen to them, that can’t tell the difference.

This article originally appeared on ViroLIEgy’s Antiviral Substack.