1.2: Scientific Method - The Practice of Science

Let’s focus here on the essentials of the scientific method originally inspired by Robert Boyle, and then on how science is practiced today. Scientific method is one or another standardized protocol for observing, asking questions about, and investigating natural phenomena. Its simplest expressions are look/listen, infer, and test your inference.

According to the Oxford English Dictionary, all scientific practice relies on the systematic observation, measurement, and experiment, and the formulation, testing and modification ofhypotheses.Here is the scientific method as you might read it a typical science textbook:

• Read the science of others and observe natural phenomena on your own.
• Infer and state a hypothesis (explanation) based on logic and reason.
• Hypotheses are declarative sentences that sound like fact but aren’t! Good hypotheses are testable predictions, easily turned in to if/then statements or yes-or-no questions.
• Design experiments to test the hypothesis: results must be measurable evidence for or against the hypothesis.
• Perform that experiment and then observe, measure, collect data, and test for statistical validity (where applicable). Then, repeat the experiment.
• Consider how your data supports or does not support your hypothesis and then integrate your experimental results with earlier hypotheses and prior knowledge.
• Finally, publish (i.e., make public) your experiments, results and conclusions. In this way, shared data and experimental methods can be evaluated (and repeated) by other scientists.

We’ll return to the scientific method and how it is practiced shortly.

So, what are scientific hypotheses, theories and laws and how do they fit into the scientific method? A scientific hypothesis, as suggested above, is an inference, and educated guess about what might be going on based on evidence and logic. A hypothesis is a declarative sentence, for example “The Sun revolves around the Earth”. This hypothesis was stated by Aristotle(among others)! Remember, a good hypothesis can be easily turned into a yes-or-no question, in this case “Does the sun revolve around the Earth?” By its nature, such yes-or-no questions can be answered (i.e., a good hypothesis can be tested) by gathering more evidence by observation and experiment. When Aristotle’s hypothesis was finally tested by the observations and measurements of Nicolaus Copernicus, Galileo Galilei and others, it proved to be false! But you knew that, didn’t you?

Contrary to what many people think, a scientific theory is not a guess, neither an educated nor an uneducated one.Rather, a theory is a statement well supported by experimental evidence and widely accepted by the scientific community. Nevertheless, theories are not ‘facts’. Scientists know that theories are subject to further test and modification and may even be overturned. Even scientific laws can be questioned. Astrophysicists actively test otherwise universally accepted physical laws, occasionally threatening to modify them. In biology, Mendel’s Law of Independent Assortment shouldn’t even be called a law. Indeed, it was not factual as he stated it, or for that matter when he stated it. Check the Mendelian Genetics section of an introductory textbook to see how chromosomal crossing over violates this law, and a history of science book to see what happens when observations or experimental results are inexplicable or as we might say today, ‘too far out’.

On the other hand, one of the most enduring and tested biological theories is Darwin’s Theory of Evolution. While some of Darwin’s notions have been modified over time, the theory holds. The modifications have only strengthened our understanding that biological diversity is the result of natural selection. For commentary on the evolutionary underpinnings of biology, check out Dobzhansky T (1973, Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach. 35:125-129), and Gould, S.J. (2002,The Structure of Evolutionary Theory. Boston, Harvard University Press). Or, check out some of Darwin’s own work at Origin of Species. Do you think that Darwin’s Theory of Evolution by natural selection should be promoted to a law? To sum up, a Wikipedia entry states that the goal of a scientific inquiry is to obtain knowledge in the form of testable explanations (hypotheses) that can predict the results of future experiments. This allows scientists to gain an understanding of reality, and later use that understanding to intervene in its causal mechanisms (such as to cure disease). The better a hypothesis is at making predictions, the more useful it is. In the last analysis, think of hypotheses as educated guesses and think of theories and/or laws not as proofs of anything,but as one or more experimentally supported hypothesis that everyone agrees should serve as guide posts to help us evaluate new observations and hypotheses.

But do not making the mistake of placing hypotheses at the low end of a hierarchy of ideas. They are in fact are the bread and butter of the scientific enterprise. Good ones are testable and should predict either/or results of well-designed experiments.Those results (observations, experimental data) should support or nullify the hypotheses being tested. In either case, scientific data generates conclusions that inevitably lead to new hypotheses whose predictive value will also be tested. If you get the impression that scientific discovery is a cyclic process, that’s the point! Exploring scientific questions reveals more questions than answers!

A word about well-designed experiments. Erwin Schrödinger (winner of a Nobel Prize in physics in 1933) once proposed a thought experiment. He wanted his audience to understand the requirements of scientific investigation but gained a fame (and notoriety) far beyond the world of theoretical physics. Perhaps you have heard of his cat! Considered a founding father of quantum physics, he recognized that adherence to scientific method is not strict and that we can (and should) occasionally violate adherence to the dictates of scientific method. In the now popular story of Schrödinger’s Cat, Schrödinger stated that if you sealed a cat in a box with a toxic substance, how could you know if the cat was alive or dead unless you open the box. Wearing his philosopher’s hat (yes, he had one!), he postulated that until you open the box, the cat is both “dead and alive”. That is, until the box was opened, the cat was in a sense, neither dead nor alive, but both! Often presented as little more than an amusing puzzle, Schrödinger was in fact illustrating that there were two alternate hypotheses: (1) the cat exposed to toxin survived, or (2) the cat exposed to toxin died. Note that either hypothesis is a declarative sentence, and that either could be tested. Just open the box!

In a twist however, Schrödinger added that by opening the box, the investigator would become a factor in the experiment. For example, let’s say (for the sake of argument) that you find a dead cat in the box. Is it possible that instead of dying from a poison, the cat was scared to death by your act of opening the box? Or that the toxin made the cat more likely to die off right but was not lethal by itself? How then to determine whether it was the toxin or your action that killed the cat? This made the puzzle even more beguiling, and to the many laypersons, his greatest scientific contribution! But to a scientist, the solution to the puzzle just means that a scientist must take all possible outcomes of the experiment into account, including the actions of the experimenter, ensuring sound experimental design with all necessary controls. The bottom line—and often the reason that scientific manuscripts suffer negative peer review—is the absence, or inadequacy of control experiments. See more about Schrödinger’s cat at A Cat Video.

CHALLENGE

Assume that Schrödinger's cat is found dead when the box was opened. Suggest some controls for the experiment to eliminate an alternative to the hypothesis that it was the toxin that caused the death?

1.2.1 The Method as It Is Really Practiced!

If you become a scientist, you may find that adherence to the ‘rules’ of scientific method are honored as much in the breach as in their rigorous observance. An understanding of those rules, or more appropriately principles of scientific method guide prudent investigators to balance personal bias against the leaps of intuition that successful science requires. Deviations from protocol are allowed!

I think that we would all acknowledge that the actual practice of science by would be considered a success by almost any measure. Science is a way of knowing the world around us through constant test, confirmation, and rejection that ultimately reveals new knowledge,integrating that knowledge into our worldview.

An element often missing but integral to any scientific method is that doing science is collaborative. Less than a century ago, many scientists worked alone. Again, Gregor Mendel is an example, and his work was not appreciated until decades after he published it. In this day and age, most publications have two or more coauthors who contribute to a study. And the inherent collaborative nature of science doesn’t end with the investigators in a study. In fact, when a paper (or a research grant for that matter) is submitted for consideration, other scientists are recruited to evaluate the quality of hypotheses, lines of experimentation, experimental design and soundness of any conclusions reported in a manuscript.This peer review of fellow scientists is part and parcel of good scientific investigation.

CHALLENGE

Since laws, theories, and hypothesis are each stated as declarative sentences and thus sound like facts, articulate the difference between them in your own words.

1.2.2 Logic and the Origins of the Scientific Method

The scientist, defined as a both observer and investigator of natural phenomena, is only a few centuries old. Long before that, philosophers developed formal rules of deductive and inferential logic to try and understand nature, humanity’s relationship to nature, and the relationship of humans to each other. We owe to those philosophers the logical basis of the scientific enterprise.They came up with the rules and systems of deductive and inductive logic now integral to the practice of science. Scientific method grew from those beginnings, along with increasing empirical observation and experimentation. We recognize these origins when we award the Ph.D. (Doctor of Philosophy), our highest academic degree! We are now going to learn about the life of cells, their structure and function, and their classification or grouping based on those structures and functions. Everything we know about life comes from applying the principles of scientific method to our intuition. For a bemused take on how scientists think, check out The Pleasure of Finding Things Out: The Best Short Works of Richard Feynman (1999,New York, Harper Collins).

CHALLENGE

The article at (How to Defend Against Science Deniers) has a clear point of view, (i.e., it takes sides!). The author feels that defending valid science by offering up the scientific method (i.e., how science is done) is flawed because it invites rebuttal. Summarize his argument, list some take-home messages you feel are important, and why... either because you agree or because you disagree with them.