Scientific methods

Scientists use active and passive observations, generalizations, hypotheses, analogy and logic to propose explanations for phenomena in the form of models and theories. Predictions from these theories, often tested by experiment, are the basis for developing new technology and further theories.

However, there is often disagreement over the various aspects of these understandings and indeed whether there exists a single 'scientific method' or a plurality of them. In philosophical circles scientific method has been the source of much controversy. Philosophers and historians of science have not only questioned the nature of scientific method, but also its supposed efficacy.

Elements of scientific method
 The essential elements of a scientific method are iterations, recursions, interleavings and orderings of the following: The element of observation includes the elements of hypothesis development, prediction, and experimental test because all of these elements are typically necessary for observation. Werner Heisenberg in a quote that he attributed to Albert Einstein many years after the fact stated [Heisenberg 1971]:
 * Characterizations (Quantifications, observations and measurements)
 * Hypotheses (theoretical, hypothetical explanations of observations and measurements)
 * Predictions (reasoning including logical deduction from hypotheses and theories)
 * Experiments (tests of all of the above)


 * It is quite wrong to try founding a theory on observable magnitudes alone. In reality the very opposite happens. It is the theory which decides what we can observe. You must appreciate that observation is a very complicated process. The phenomenon under observation produces certain events in our measuring apparatus. As a result, further processes take place in the apparatus, which eventually and by complicated paths produce sense impressions and help us to fix the effects in our consciousness. Along this whole path—from the phenomenon to its fixation in our consciousness—we must be able to tell how nature functions, must know the natural laws at least in practical terms, before we can claim to have observed anything at all. Only theory, that is, knowledge of natural laws, enables us to deduce the underlying phenomena from our sense impressions. When we claim that we can observe something new, we ought really to be saying that, although we are about to formulate new natural laws that do not agree with the old ones, we nevertheless assume that the existing laws—covering the whole path from the phenomenon to our consciousness—function in such a way that we can rely upon them and hence speak of “observation.”

Also Imre Lakatos and Thomas Kuhn had done extensive work on the '"theory laden" character of observation. Each element of scientific method is subject to peer review for possible mistakes. These activities do not describe all that scientists do (see below) but apply mostly to experimental sciences (e.g., physics, chemistry). The elements above are often taught in education1.

The scientific method is not a recipe. It requires intelligence, imagination, and creativity.

The Keystones of Science project, sponsored by the journal Science, has selected a number of scientific articles from that journal and annotated them, illustrating how different parts of each article embody the scientific method. Here is one example, showing how a group of scientists disproved a claim about lateral gene transfer in the human genome.

A linearized, pragmatical scheme of the four above points is sometimes offered as a guideline for proceeding:  The iterative cycle inherent in this step-by-step methodology goes from point 3 to 6 back to 3 again. While this scheme often taught as the basis of science, many philosophers, historians and sociologists of science (particularly Paul Feyerabend and advocates of the "strong programme") claim that it has little relation to the ways science is actually practiced.
 * 1) Define the question
 * 2) Gather information and resources
 * 3) Form hypothesis
 * 4) Perform experiment and collect data
 * 5) Analyze data
 * 6) Interpret data and draw conclusions that serve as a starting point for new hypotheses
 * 7) Publish results

DNA/example

 * [[Image:DNA icon (25x25).png]]Each element of scientific method is illustrated by an example from the discovery of the structure of DNA:
 * DNA/characterizations
 * DNA/hypotheses
 * DNA/predictions
 * DNA/experiments


 * The examples are continued in "Evaluations and iterations" with DNA/iterations. [[Image:DNA icon (25x25).png]]

Characterizations
The scientific method depends upon increasingly more sophisticated characterizations of subjects of the investigation. (The subjects can also be called lists of unsolved problems or the unknowns.) For example, Benjamin Franklin correctly characterized St. Elmo's fire as electrical in nature, but it has taken a long series of experiments and theory to establish this. While seeking the pertinent properties of the subjects, this careful thought may also entail some definitions and observations; the observations often demand careful measurements and/or counting.

The systematic, careful collection of measurements or counts of relevant quantities is often the critical difference between pseudo-sciences, such as alchemy, and a science, such as chemistry. Scientific measurements taken are usually tabulated, graphed, or mapped, and statistical manipulations, such as correlation and regression, performed on them. The measurements might be made in a controlled setting, such as a laboratory, or made on more or less inaccessible or unmanipulatable objects such as stars or human populations. The measurements often require specialized scientific instruments such as thermometers, spectroscopes, or voltmeters, and the progress of a scientific field is usually intimately tied to their invention and development.

Measurements demand the use of operational definitions of relevant quantities. That is, a scientific quantity is described or defined by how it is measured, as opposed to some more vague, inexact or "idealized" definition. For example, electrical current, measured in Amperes, may be operationally defined in terms of the mass of silver deposited in a certain time on an electrode in an electrochemical device that is described in some detail. The operational definition of a thing often relies on comparisons with standards: the operational definition of "mass" ultimately relies on the use of an artifact, such as a certain kilogram of platinum kept in a laboratory in France.

The scientific definition of a term sometimes differs substantially from their natural language usage. For example, mass and weight are often used interchangeably in common discourse, but have distinct meanings in physics. Scientific quantities are often characterized by their units of measure which can later be described in terms of conventional physical units when communicating the work.

Measurements in scientific work are also usually accompanied by estimates of their uncertainty. The uncertainty is often estimated by making repeated measurements of the desired quantity. Uncertainties may also be calculated by consideration of the uncertainties of the individual underlying quantities that are used. Counts of things, such as the number of people in a nation at a particular time, may also have an uncertainty due to limitations of the method used. Counts may only represent a sample of desired quantities, with an uncertainty that depends upon the sampling method used and the number of samples taken.

New theories sometimes arise upon realizing that certain terms had not previously been sufficiently clearly defined. For example, Albert Einstein's first paper on relativity begins by defining simultaneity and the means for determining length. These ideas were skipped over by Isaac Newton with, "I do not define time, space, place and motion, as being well known to all." Einstein's paper then demonstrates that they (viz., absolute time and length independent of motion) were approximations. Francis Crick cautions us that when characterizing a subject, however, it can be premature to define something when it remains ill-understood. In Crick's study of consciousness, he actually found it easier to study awareness in the visual system, rather than to study Free Will, for example. His cautionary example was the gene; the gene was much more poorly understood before Watson and Crick's pioneering discovery of the structure of DNA; it would have been counterproductive to spend much time on the definition of the gene, before them.


 * Francis Crick (1994), The Astonishing Hypothesis ISBN 0-684-19431-7 p.20

The precession of Mercury
The characterization element can require extended and extensive study, even centuries. It took thousands of years of measurements, from the Chaldean, Indian, Persian, Greek, Arabic and European astronomers, to record the motion of planet Earth. Newton was able to condense these measurements into consequences of his laws of motion. But the perihelion of the planet Mercury's orbit exhibits a precession which is not fully explained by Newton's laws of motion. The observed difference for Mercury's precession, between Newtonian theory and relativistic theory (approximately 43 arc-seconds per century), was one of the things that occurred to Einstein as a possible early test of his theory of General Relativity.

DNA/characterizations

 * [[Image:DNA icon (25x25).png]]The history of the discovery of the structure of DNA is a classic example of the elements of scientific method: in 1950 it was known that genetic inheritance had a mathematical description, starting with the studies of Gregor Mendel. But the mechanism of the gene was unclear. Researchers in Bragg's laboratory at Cambridge University made X-ray diffraction pictures of various molecules, starting with crystals of salt, and proceeding to more complicated substances. Using clues which were painstakingly assembled over the course of decades, beginning with its chemical composition, it was determined that it should be possible to characterize the physical structure of DNA, and the X-ray images would be the vehicle. [[Image:DNA icon (25x25).png]]

Hypotheses development
A hypothesis is a suggested description of the subject.

Normally hypotheses have the form of a mathematical model. Sometimes, but not always, they can also be formulated as existential statements, stating that some particular instance of the phenomenon being studied has some characteristic and causal explanations, which have the general form of universal statements, stating that every instance of the phenomenon has a particular characteristic.

Scientists are free to use whatever they can &#8212; their own creativity, ideas from other fields, induction, systematic guessing, Bayesian inference, etc. &#8212; to imagine possible explanations for a phenomenon under study. The history of science is filled with stories of scientists claiming a "flash of inspiration", or a hunch, which then motivated them to look for evidence to support or refute their idea. Michael Polanyi made such creativity the centrepiece of his discussion of methodology.

Karl Popper, following others, has argued that a hypothesis must be falsifiable, and that a proposition or theory cannot be called scientific if it does not admit the possibility of being shown false. It must at least in principle be possible to make an observation that would show the proposition to be false, even if that observation had not yet been made.

In general scientists tend to look for theories that are "elegant" or "beautiful". In contrast to the usual English use of these terms, they here refer to a theory in accordance with the known facts, which is nevertheless relatively simple and easy to handle. If a model is mathematically too complicated, it is hard to deduce any prediction. Note that 'simplicity' may be perceived differently by different individuals and cultures.

DNA/hypotheses

 * [[Image:DNA icon (25x25).png]]Linus Pauling proposed that DNA was a triple helix. Francis Crick and James Watson learned of Pauling's hypothesis, understood that Pauling was wrong and realized that Pauling would soon realize his mistake.  So the race was on to figure out the correct structure.  Except that Pauling did not realize at the time that he was in a race!  [[Image:DNA icon (25x25).png]]

Predictions from the hypotheses
Any useful hypothesis will enable predictions, by reasoning including deductive reasoning.

It might predict the outcome of an experiment in a laboratory setting or the observation of a phenomenon in nature. The prediction can also be statistical and only talk about probabilities.

It is essential that the outcome be currently unknown. Only in this case does the eventuation increase the probability that the hypothesis be true. If the outcome is already known, it's called a consequence and should have already been considered while formulating the hypothesis.

If the predictions are not accessible by observation or experience, the hypothesis is not yet useful for the method, and must wait for others who might come afterward, and perhaps rekindle its line of reasoning. For example, a new technology or theory might make the necessary experiments feasible.

Halley's comet
The classic example was Edmund Halley's prediction of the year of return of Halley's comet which returned after his death.

General Relativity
Einstein's theory of General Relativity makes several specific predictions about the observable structure of space-time, such as a prediction that light bends in a gravitational field and that the amount of bending depends in a precise way on the strength of that gravitational field. Arthur Eddington's observations made during a 1919 solar eclipse supported General Relativity rather than Newtonian gravitation.

DNA/predictions

 * [[Image:DNA icon (25x25).png]]When Watson and Crick hypothesized that DNA was a double helix, Francis Crick predicted that an X-ray diffraction image of DNA would show an X-shape. Also in their first paper they predicted that the double helix structure that they discovered would prove important in biology writing "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material." [[Image:DNA icon (25x25).png]]

Experiments
Once predictions are made, they can be tested by experiments. If test results contradict predictions, then the hypotheses are called into question and explanations may be sought. Sometimes experiments are conducted incorrectly and are at fault. If the results confirm the predictions, then the hypotheses are considered likely to be correct but might still be wrong and are subject to further testing.

Depending on the predictions, the experiments can have different shapes. It could be a classical experiment in a laboratory setting, a double-blind study or an archeological excavation. Even taking a plane from New York to Paris is an experiment which tests the aerodynamical hypotheses used for constructing the plane.

Scientists assume an attitude of openness and accountability on the part of those conducting an experiment. Detailed recordkeeping is essential, to aid in recording and reporting on the experimental results, and providing evidence of the effectiveness and integrity of the procedure. They will also assist in reproducing the experimental results. This tradition can be seen in the work of Hipparchus (190 BCE - 120 BCE), when determining a value for the precession of the Earth over 2100 years ago, and 1000 years before Al-Batani.

DNA/experiments

 * [[Image:DNA icon (25x25).png]] Before proposing their model Watson and Crick had previously seen x-ray diffraction images by Rosalind Franklin, Maurice Wilkins, and Raymond Gosling. However, they later reported that Franklin initially rebuffed their suggestion that DNA might be a double helix. Franklin had immediately spotted flaws in the initial hypotheses about the structure of DNA by Watson and Crick.  The X-shape in X-ray images helped confirm the helical structure of DNA. [[Image:DNA icon (25x25).png]]

Testing and improvements
The scientific process is iterative. At any stage it is possible that some consideration will lead the scientist to repeat an earlier part of the process. Failure to develop an interesting hypothesis may lead a scientist to re-define the subject they are considering. Failure of a hypothesis to produce interesting and testable predictions may lead to reconsideration of the hypothesis or of the definition of the subject. Failure of the experiment to produce interesting results may lead the scientist to reconsidering the experimental method, the hypothesis or the definition of the subject.

Other scientists may start their own research and enter the process at any stage. They might adopt the characterization and formulate their own hypothesis, or they might adopt the hypothesis and deduce their own predictions. Often the experiment is not done by the person who made the prediction and the characterization is based on experiments done by someone else. Published results of experiments can also serve as a hypothesis predicting their own reproducibility.

Light
Light had long been supposed to be made of particles. Isaac Newton, and before him many of the Classical Greeks, was convinced it was so, but his light-is-particles account was overturned by evidence in favor of a wave theory of light suggested most notably in the early 1800s by Thomas Young, an English physician. Light as waves neatly explained the observed diffraction and interference of light when, to the contrary, the light-as-a-particle theory did not. The wave interpretation of light was widely held to be unassailably correct for most of the 19th century. Around the turn of the century, however, observations were made that a wave theory of light could not explain. This new set of observations could be accounted for by Max Planck's quantum theory (including the photoelectric effect and Brownian motion&mdash;both from Albert Einstein), but not by a wave theory of light, nor by a particle theory.

DNA/iterations

 * [[Image:DNA icon (25x25).png]] After considerable fruitless experimentation, being discouraged by their superior from continuing, and numerous false starts, Watson and Crick were able to infer the essential structure of DNA by concrete modelling of the physical shapes of the nucleotides which comprise it. They were guided by the bond lengths which had been deduced by Linus Pauling and the X-ray diffraction images of Rosalind Franklin. [[Image:DNA icon (25x25).png]]

Confirmations
Science is a social enterprise, and scientific work tends to be accepted by the community when it has been confirmed. Crucially, experimental and theoretical results must be reproduced by others within the science community. Researchers have given their lives for this vision; Georg Wilhelm Richmann was killed by ball lightning to his forehead (1753) when attempting to replicate the 1752 kite experiment of Benjamin Franklin.

Scope and goals
Scientific method can be applied to anything within the range of our experiences. As long as something has an effect on our lives, we can formulate theories and try to predict what this effect might be. The effect itself is an experiment, testing whether our theory was right.

People use scientific methods all the time. They have theories about devices and make predictions how those will react to their actions. If a device does not work as expected, the experiment may disprove their theory. If they adjust their theory, they are applying scientific methods; if they nevertheless stick to their theory because of nonscientific reasons, they are not.

Scientific method does not aim to give an ultimate answer. Its iterative and recursive nature implies that it will never come to an end, so any answer it gives is provisional. Hence it cannot prove or verify anything in a strong sense. However, if a theory passed many experimental tests without being disproved, it is usually considered superior to any theory that has not yet been put to a test.

Scientific communities
Frequently the scientific method is not employed by a single person, but by several people cooperating directly or indirectly. Such cooperation can be regarded as one of the defining elements of a scientific community. Various techniques have been developed to ensure the integrity of the scientific method within such an environment.

Peer review evaluations
Scientific journals use a process of peer review, in which scientists' manuscripts are submitted by editors of scientific journals to (usually one to three) fellow (usually anonymous) scientists familiar with the field for evaluation. The referees may or may not recommend publication, publication with suggested modifications, or, sometimes, publication in another journal. This serves to keep the scientific literature free of unscientific or crackpot work, helps to cut down on obvious errors, and generally otherwise improve the quality of the scientific literature. Work announced in the popular press before going through this process is generally frowned upon. Sometimes peer review inhibits the circulation of unorthodox work, and at other times may be too permissive. The peer review process is not always successful, but has been very widely adopted by the scientific community.

Reproduction and record-keeping
Sometimes experimenters may make systematic errors during their experiments, or (in rare cases) deliberately falsify their results. Consequently, it is a common practice for other scientists to attempt to repeat the experiments in order to duplicate the results, thus further validating the hypothesis.

As a result, experimenters are expected to maintain detailed records of their experimental procedures, in order to provide evidence of the effectiveness and integrity of the procedure and assist in reproduction. These procedural records may also assist in the conception of new experiments to test the hypothesis, and may prove useful to engineers who might examine the potential practical applications of a discovery.

Note that it is not possible for a scientist to record everything that took place in an experiment. He must select the facts he believes to be relevant to the experiment and report them. This may lead, unavoidably, to problems later if some supposedly irrelevant feature is questions. For example, Heinrich Hertz did not report the size of the room used to test Maxwell's equations, which later turned out to account for a small deviation in the results. The problem is that parts of the theory itself need to be assumed in order to select and report the experimental conditions. The observations are sometimes hence described as being 'theory-laden'.

History
The development of the scientific method is inseparable from the history of science itself. Although documents from even before 1000 BC exists that describe methods resembling that of the scientific method, it wasn't until the advent of the culture of Ancient Greece that the first elements of the scientific method were well established. The crystallization of the scientific method took place with the rise of modern physical sciences, in the 17th and 18th centuries. In his work Novum Organum--a reference to Aristotle's Organon--Francis Bacon outlined a new system of logic to improve upon the old philosophical process of syllogism. These writings were critical in the historical development of the scientific method.

Philosophical issues
The study of a scientific method is distinct from the practice of science and is more a part of the philosophy, history and sociology of science than of science. While such studies have limited direct impact on day-to-day scientific practice, they have a vital role in justifying and defending the scientific approach.

We find ourselves in a world that is not directly understandable. We find that we sometimes disagree with others as to the facts of the things we see in the world around us, and we find that there are things in the world that sometimes are at odds with our present understanding. The scientific method attempts to provide a way in which we can reach agreement and understanding. A perfect scientific method would work in such a way that rational application of the method would always result in agreement and understanding; a perfect method would be algorithmic, and so not leave any room for rational agents to disagree. As with all philosophical topics, the search has been neither straightforward nor simple.Logical Positivist, empiricist, falsificationist, and other theories have claimed to give a definitive account of the logic of science, but each has in turn been criticised.

Considerations such as these led Feyerabend to deny that science is an entirely rational process. In his book Against Method he argues that scientific progress is not the result of applying any particular method. In essence, he says that "anything goes", by which he meant that for any specific methodology or norm of science, successful science has been done in violation of it. Criticisms such as his led to a rise in the study of the scientific enterprise as a social phenomena. However the sociology of science may also be incapable of accounting for the success of the scientific enterprise.

Adherence to a Scientific Method is often used to discern scientific disciplines from non-scientific ones. That is method is used as the criterion for demarcation between science and non-science. If it is not possible to articulate a definitive method, then it may also not be possible to articulate a definition of science, and distinguish between science and pseudoscience, between scientists and non-scientists.

The scientific method is nevertheless often held up as a model for rational thinking. For example, Carl Sagan, in his book The Demon-Haunted World, argues that we should use a scientific method as a tool for skeptical thinking, in order to identify and reject those movements which misrepresent science - pseudoscience or quackery. Many authors have suggested that we would benefit from applying the scientific method to other areas. At its extreme, the application of scientific methods outside of science leads to dogmatic scientism.

Scientific method and the practice of science
The primary constraints on contemporary western science are: It has not always been like this: in the old days of the "gentleman scientist" funding (and to a lesser extent publication) were far weaker constraints.
 * Publication, i.e. Peer review
 * Resources (mostly, funding)

Both of these constraints indirectly bring in a scientific method &mdash; work that too obviously violates the constraints will be difficult to publish and difficult to get funded. Journals do not require submitted papers to conform to anything more specific than "good scientific practice" and this is mostly enforced by peer review. Originality, importance and interest are more important - see for example the author guidelines for Nature.

Criticisms (see Critical theory) of these restraints are that they are so nebulous in definition (e.g. "good scientific practice") and open to ideological, or even political, manipulation apart from a rigorous practice of a scientific method, that they often serve to censor rather than promote scientific discovery. Apparent censorship through refusal to publish ideas unpopular with mainstream scientists (unpopular because of ideological reasons and/or because they seem to contradict long held scientific theories) has soured the popular perception of scientists as being neutral or seekers of truth and often denigrated popular perception of science as a whole.

Formal approaches
Inferential statistics and computational learning theory are concerned with setting out rigorous statistical resp. algorithmic frameworks for induction, or at least practically effective ones. For a near-optimal method in the sense of computable predictions in the context of algorithmic information theory, see the speed prior.

Quotations

 * "The scientific approach to the examination of phenomena is a defense against the pure emotion of fear." Tom Stoppard, Rosencrantz & Guildenstern Are Dead (1967, page 17 in Grove edition)

Historical references to scientific method

 * W. Stanley Jevons, 1874, 1877. The Principles of Science, 786pp., index. Reprinted by Dover, 1958, with a forward by Ernst Nagel.
 * Francis Bacon 1620. Novum Organum (The New Organon).
 * Werner Heisenberg. Physics and Beyond: Encounters and Conversations translated by A. J. Pomerans (Harper & Row, New York, 1971), pp. 63–64.

Bacon's original work described many of the accepted principles, underscoring the importance of Theory, empirical results, data gathering, experiment, and independent corroboration.

Science treatments

 * An Introduction to Science: Scientific Thinking and a scientific method by Steven D. Schafersman.
 * Introduction to a scientific method
 * Theory-ladenness by Paul Newall at The Galilean Library
 * Scientific Method
 * Analysis and Synthesis: On Scientific Method based on a study by Bernhard Riemann From the Swedish Morphological Society

Alternative scientific treatments

 * The Myth of a scientific method by Dr. Terry Halwes (A respectful essay making the point that scientists actually use a variety of methods that cannot be easily reduced to a single coherent methodology.)
 * The Test Case As A Scientific Experiment] (An article that compares the scientific method and software testing)

Religious treatments

 * Scientific Method in Religious Practice

Humor

 * Updated Scientific Method

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