Recordkeeping, Writing,
& Data Analysis


Microscope studies

Flagella experiment
Laboratory math
Blood fractionation
Gel electrophoresis
Protein gel analysis
Concepts/ theory
Keeping a lab notebook
Writing research papers
Dimensions & units
Using figures (graphs)
Examples of graphs
Experimental error
Representing error
Applying statistics
Principles of microscopy

Solutions & dilutions
Protein assays
Fractionation & centrifugation
Radioisotopes and detection

Fact, Hypothesis, and Theory

Basic research is what I am doing when I don't know what I am doing. --- Wernher von Braun

This web page is part of a very small collection of essays on concepts related to the scientific method and to specific laboratory studies.

The following quote, supposedly describing the scientific method, comes from an article in the Houston Chronicle (Barlow, J. Science fiction not just in films. Jan 7, 1996, p. 1D, 8D.).

It starts with a scientific theory. That's how all science starts. Next you gather evidence to support that theory, publish the results, and let other scientists in the same area of study try their best to pick holes in your conclusions. If most everybody agrees, the theory is proven, and we make changes based on the conclusions.
Oops. The point of the article was that many costly decisions, especially environmental decisions, have been based upon 'junk' science. Typically, someone announces a conclusion prematurely, the media pick up the story, and federal agencies, the public, or Congress act on the decision by banning this or that, tightening regulations, or creating new more restrictive laws. Later, after the damage is done, it turns out the claims were false or greatly exaggerated.

Although the article made a good point, it was written with an anti-environmentalist slant, and I didn't entirely agree with the sentiment. But, so what? Everyone is entitled to an opinion. What was unforgivable was that the author's description of the scientific method was completely twisted around, yet it very likely reflects the view many people have of how science is conducted.

"It starts with scientific theory. That's how all science starts."

Oh, I hope not. This would be science in reverse. A theory has to have a basis, in fact, it must have a very strong basis. A theory is a scientifically acceptable principle that is offered to explain a vast body of facts, and is supported by an overwhelming body of evidence. You can't have a theory before you have the evidence. Science starts out with observations - facts that are not generally disputed. For example, the sky is blue; grass is green; birds migrate south for the winter and find their way to specific locations; the high temperature at the airport yesterday was 52 degrees. Accumulate enough facts and you can ask and perhaps answer a general question (why is the sky blue, or the grass green? How do birds know where to go? What makes the weather change?).

The author was probably using the lay person's definition of a theory, as in speculation, conjecture, or maybe even a legitimate hypothesis.

"Next you gather evidence to support that theory, publish the results, and let other scientists in the same area of study try their best to pick holes in your conclusions."
Yes, you are going to need evidence. But what makes you so special, that you know the evidence will support your position? Are you blessed with special powers that enable you to know, in advance, that all of the evidence will support your position? Ascientist does not ask what you can do to prove your 'theory' correct. To get answers, a scientist makes observations and/or conducts an experiment. She might start with a testable question or a testable statement. If she poses a testable statement it is a hypothesis. However the initial question is worded it had better be an objective one (see How not to do science). The next step is to test the statement or question by observation and/or experimentation. When sufficient questions have been answered, and there is at least some consensus that the answers are correct, a model can be formulated. A model isn't a theory, however; it is an explanation that is based on facts, makes sense, and can be tested and refined.

Sometimes more than one model is proposed to explain a set of observations. For example, a generation or so ago scientists were asking how mitochondria transfer energy from a system of electron transport to the universal energy-carrying molecule ATP. Since virtually all eukaryotic cells rely on mitochondria to provide usable energy, this was an important question. Three models, all fact-based, were in the running. They were the chemical intermediate model, the conformational change model, and the chemiosmotic model. There were high stakes, in fact, Peter Mitchell, who proposed the last model, was awarded the Nobel Prize for his work in that area. The chemiosmotic model was eventually supported by a vast amount of evidence, and became theory.

"If most everybody agrees, the theory is proven, and we make changes based on the conclusions."
In the nineteenth century most everyone agreed that velocity equals distance divided by time, and that physical dimensions were invariant. Of course they did. No one had ever reported exceptions to those rules. They were part of Newtonian physical theory. Were the principles of Newtonian physics 'proven?' I doubt that the physics of the universe has changed since the nineteenth century. Because classical Newtonian physics was found to be inconsistent with established facts, clearly the theory behind Newton's laws was never proven in the first place. The modern theory of special relativity holds that the speed of light in a vacuum is invariant. That principle was never proven either - it is simply consistent with every physical observation that scientists have made to date.

You can prove concepts in mathematics, because you can see every detail of logic from the first fundamental assumptions. In trying to understand nature, we can be quite sure about an explanation, but until we see every single detail, we can't say that there are no exceptions to current theory, and it just takes one exception to change a theory. For that matter, we can never know that we have seen every detail (particle physicists theorize that it is impossible to ever see all the details).

Human curiosity drives our attempts to understand the workings of nature. Presenting theories without evidence, twisting evidence to make it support one's personal view of nature, and declaring a human theory to be 'proven' are simply examples of human arrogance.

If an elderly but distinguished scientist says that something is possible he is almost certainly right, but if he
says that it is impossible he is very probably wrong. --- Arthur C. Clarke

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Created by David R. Caprette (caprette@rice.edu), Rice University Dates