Scientific method

Scientists employ a scientific method to investigate phenomena and acquire new knowledge. The method enables a way of thinking based on observable, empirical, measurable evidence, subject to the principles of reasoning and to verification by others. Scientists propose hypotheses to explain natural phenomena, and test those hypotheses with experiments. Scientists also formulate theories that encompass whole domains of inquiry, and which bind well supported hypotheses together into logically coherent wholes. The technological achievements that have changed our world have led many to conclude that the success of science stems from the methodological rules that scientists follow. As this article will show, not all philosophers and scientists accept that conclusion, and some deny that science has a genuinely methodological process at all.

Components of the scientific method

Generally accepted components of the scientific method are:

• Observation. According to most current views, no observations are wholly independent of a theory.
• Experiment An experiment is a procedure carried out under controlled conditions to discover an unknown effect, or to test or confirm a hypothesis, or to illustrate an accepted theory. Not all areas of science involve direct experimentation; for example the human genome project largely involves (highly technical) interpretation of gene sequences, but the data used were obtained by experimental investigation.
• Hypothesis Hypotheses are general statements, formulated as plausible conjectures to explain existing observations and predict future observations.
• Theory A theory includes a set of hypothesis within a logical framework.
• Prediction. A prediction is a logical deduction from a hypothesis by which the hypothesis can be tested experimentally.
• Testing A scientific theory must contain components that are empirically testable. There are two aspects of testing: confirmation and falsification.
• Causal explanation Many scientists and theorists argue that concepts of causality are not obligatory to science, but are well-defined only under particular conditions.
• Theory development There is no widely accepted method of theory acceptance or rejection.
• Skeptical open mindedness Progress in extending existing theoretical frameworks is made possible by a scientific culture that encourages challenges to existing theory, while also demanding that far-reaching conjectures are validated by exceptional evidence.

Philosophy of scientific methods

If the purpose of scientific methodology is to prescribe or expound a system of enquiry or even a code of practice for scientific behavior, then scientists seem to be able to get on very well without it. Most scientists receive no tuition in scientific method, but those who have been instructed perform no better as scientists than those who have not. Of what other branch of learning can it be said that it gives its proficients no advantage; that it need not be taught or, if taught, need not be learned? (Sir Peter Medawar)

Non-scientists often represent science as a dry, mechanical activity, involving accumulating large numbers of facts, whether by simple observations or by technologically ingenious means. Indeed, the gathering of observations is an important part of science, and technological advances in our ability to interrogate the world have played an essential part in the advance of science: we need only consider how the microscope, then the electron microscope, and now the tumnneling electron microscope and 2-photon confocal microscope have radically changed our understanding of the world. However. observations, things that we might sometimes call 'facts', are just the beginning. Thus, according to Charles Darwin (1809-1882), "science consists in grouping facts so that general laws or conclusions may be drawn from them."

But what exactly do we mean by ‘facts’? We sometimes disagree about the ‘facts’ we see around us, and some things in the world are at odds with our understanding. How much can we trust our senses to enable us to believe what we see? How do scientists ‘group’ facts? How do they choose which facts to attend to, and is it possible to do this in an objective way? And having done this, how do they draw any broader conclusions? Most importantly, how can we ever know more than we observe directly? We live in a world that is not directly understandable: we all interpret everything that we see and hear and feel, and to make sense of what our senses tell us we need to construct explanations, or formulate theories. Our explanations identify some things as important and other things as irrelevant; they lead us to pay attention to some things and not others, and they lead us to expect some things to happen and not others — they lead, in other words, to predictions.

Nothing about this is unique to science, but scientists attempt to harness these universal elements of reasoning in a consistent, systematic and rigorous manner, and in a way that minimises bias. What we call the “scientific method” is an account of how scientists gather and report observations in ways that will be understood by other scientists and accepted as valid evidence, and how they construct explanations that are consistent with the world, and that can withstand logical and experimental scrutiny and provide the foundations for further increases in understanding.

For many, the scientific approach begins with an attitude of skepticism %mdash a willingness to question accepted beliefs, expressed by René Descartes in 1637 as a determination "never to accept anything for true which I did not clearly know to be such". The English philosopher Francis Bacon (1561-1626), often described as the pioneer of the modern scientific method, proposed that scientists should "empty their minds" of self-evident truths and, by observation and experimentation, should draw general conclusions by a process known as induction. Bacon described many of the commonly accepted principles of scientific method, but recognised that to interpret nature, something more than observation and reason is needed:

...the universe to the eye of the human understanding is framed like a labyrinth, presenting as it does on every side so many ambiguities of way, such deceitful resemblances of objects and signs, natures so irregular in their lines and so knotted and entangled. ... No excellence of wit, no repetition of chance experiments, can overcome such difficulties as these. Our steps must be guided by a clue...

The 'something more' that is needed comes from imagination and intuition, guided by reason and understanding. Scientists make ambitious 'leaps' to envisage possible explanations that make sense of what we see. Classically, the scientific method has thus been broken into basic facets that start with observations of nature and how it behaves and then making a prediction about how it might behave under different circumstance. Scientists propose a hypothesis and, by experiments test it by eliminating any plausible alternatives in a process of falsification. Other scientists join in the process of hypothesis testing, while at the same time developing new hypotheses that seek to explain more and more, thereby building a foundation of knowledge that they call science. However all of this is guided by theory — a framework of accepted knowledge and understanding that guides our choice of questions to ask, guides our choices about how to go about answering those question, and guides our interpretation of the results of those experiments. This theoretical framework that captures what we think we already know, is what provides the clues to know more. When we are mistaken in what we think we know however, everything that we build on those foundations becomes unsafe, and when a new theory emerges much of what we thought we had learned has to be interpreted afresh. New theories are therefore embraced only with reluctance, only as a last resort, because of the inevitable disruption that entails

Hypotheses and theories

The man of science must work with method. Science is built up of facts, as a house is built of stones; but an accumulation of facts is no more a science than a heap of stones is a house.Henri Poincaré

The philosopher Karl Popper (1902-1994), in The Logic of Scientific Discovery argued that the 'Baconian' process of induction - of gathering facts, considering them, and inferring general laws - is logically unsound, as many mutually inconsistent hypotheses might be consistent with any given facts. Rather, Popper argued that the good scientist begins with a bold speculation, a hypothesis, from which he logically deduces predictions that can be tested by experiments. Experiments are not designed to confirm or verify the hypothesis, quite the contrary, they are designed to test the hypothesis, by attempting to disprove it. He argued that this 'hypothetico-deductive' method was the only sound way by which science makes progress. Popper concluded that for a proposition to be considered scientific, it must, at least in principle, be possible to make an observation that would show it to be false. Otherwise, the proposition has, as Popper put it, no connection with the real world.

Popper's views were in marked contrast to those of his contemporary, Thomas Kuhn (1922-1996). Kuhn's own book The Structure of Scientific Revolutions was as influential as Popper's, but its message was very different. Kuhn analysed 'scientific revolutions' — times in the history of science when one dominant theory was replaced by another, such as the replacement of Ptolemy's geocentric model of the Universe with the Copernican heliocentric model, and the replacement of Newtonian laws of motion with Einstein's theory of Relativity. While in many respects, Popper seemed to be asserting his rules for 'good science', Kuhn considered himself to be reporting what scientists actually did, but he believed that, as they were so successful, probably there was merit in what they did. Kuhn concluded that falsifiability had played almost no role in scientific revolutions. He argued that scientists working in a field resist the alternative interpretations of 'outsiders', and tenaciously defend their world view by continually elaborating their shared theory; "normal science often suppresses fundamental novelties because they are necessarily subversive of its basic commitments".

According to Kuhn, most progress is made in a scientific field when one theory is dominant. Progress occurs by the "puzzle solving" of scientists who are not trying to challenge the accepted theory, but are trying to extend its scope and explanatory power, bringing theory and fact into closer agreement by a "strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education".

The scientific method in practice

While philosophers and scientists may disagree among themselves and between themselves about whether there is a general "scientific method" and if so exactly what it involves, in any given field there are always some practices that are accepted as scientific good practice and others that are not. When scientists give expert evidence in Courts of Law, their evidence is given particular weight, reflecting the respect that is given to good scientific practice. In 1993, in the extremely influential Daubert v. Merrell Dow Pharmaceuticals decision, the U.S. Supreme Court accorded a special status to 'The Scientific Method', in ruling that "… to qualify as 'scientific knowledge' an inference or assertion must be derived by the scientific method. Proposed testimony must be supported by appropriate validation - i.e., 'good grounds', based on what is known." The Court also stated that "A new theory or explanation must generally survive a period of testing, review, and refinement before achieving scientific acceptance. This process does not merely reflect the scientific method, it is the scientific method."

The UK Research Charity Cancer Research UK gives an outline of the scientific method, as practised by their scientists [5]. The quotes that follow are from this outline

Hypotheses

[Scientists] start by making an educated guess about what they think the answer might be, based on all the available evidence they have. This is known as forming an hypothesis.

A hypothesis is a proposed explanation of a phenomenon. It may be an “inspired guess”, a “bold speculation”, embedded in current understanding yet going beyond that to assert something that we do not know for sure as a way of explaining something not otherwise accounted for. Most importantly, a scientific hypothesis is something that has consequences, it leads to predictions and these can be tested by experiments. If the predictions prove wrong, the hypothesis is discarded, otherwise it is put to further test. If it resists determined attempts to disprove it, then it might come to be accepted, at least for the moment, as 'true'.

Scientists use many different means to generate hypotheses, including their own creative imagination, ideas from other fields, and by induction. Charles Sanders Peirce (1939-1914) described the incipient stages of inquiry, instigated by the "irritation of doubt" to venture a plausible guess, as abductive reasoning. The history of science is full of stories of scientists claiming a "flash of inspiration" which motivated them. One of the best known is Kekule's account that the structure of benzene came to him in a dream, in which rows of atoms wound like serpents before him; one of the serpents seized its own tail and "the form whirled mockingly before my eyes. I came awake like a flash of lightning. This time also I spent the remainder of the night working out the consequences of the hypothesis".

Experiments and observations

Researchers carry out carefully designed studies, often known as experiments, to test their hypothesis. They collect and record detailed information from the studies. They look carefully at the results to work out if their hypothesis is right or wrong…

For example, several predictions can be derived from Einstein's theory of General Relativity. One prediction was that light will appear to 'bend' in a gravitational field by an amount that depends on the strength of the field. Arthur Eddington (1882-1994) devised experiments to test this prediction; his observations, made during a solar eclipse in 1919, supported General Relativity rather than the older Newtonian theory.

An experiment is a procedure carried out under controlled conditions. Not all areas of science involve direct experimentation; for example the human genome project largely involves (highly technical) interpretation of gene sequences, but the data were obtained by experimental investigation. Equally, not all experiments are designed to test hypotheses; some, for example, extend our knowledge by making more detailed observations of known phenomena, or by exploring new or unexplained phenomena more fully.

Werner Heisenberg, in a quote that he attributed to Albert Einstein, stressed how observations depend upon the theories that are held at the time they are made "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."

For Karl Popper, theory was profoundly important in science; a theory encompasses the preconceptions by which the world is viewed, and defines what we choose to study, and how we study it and understand it. He recognised that theories are not discarded lightly, and a theory might be retained long after it has been shown to be inconsistent with many known facts (anomalies). However, the recognition of anomalies drives scientists to adjust the theory, and if the anomalies continue to accumulate, will drive them to develop alternative theories.

Popper proposed that a theory should be judged by the extent to which it inspires testable hypotheses. While theories always contain many elements that are not falsifiable, Popper argued that these should be kept to a minimum. However, scientists also seek theories that are "elegant"; a theory should yield clear, simple explanations of complex phenomena, that are intellectually satisfying in appearing to be logically coherent, rich in content, and involving no miracles or other supernatural devices.

Peer review

…Once they have completed their study, the researchers write up their results and conclusions. And they try to publish them as a paper in a scientific journal. Before the work can be published, it must be checked by a number of independent researchers who are experts in a relevant field. This process is called ‘peer review’, and involves scrutinising the research to see if there are any flaws that invalidate the results…

The main way of disseminating scientific information is through the peer-reviewed scientific literature. This is a vast array of academic journals that was once mainly restricted to the libraries of Universities and research institutes, but these are now mostly available on-line through the internet, and often they are freely available. There are many thousands of these journals, some of which are managed and owned by scientific societies, others by commercial publishers. In general, scientific journals publish just a small proportion of the manuscripts submitted to them, and only after a process of peer review and revision. An article published in the peer-reviewed literature that describes the outcome of a series of experiments is known as a 'scientific paper'. Over their careers, many scientists may publish more than a hundred such papers, but even for the most successful scientists very few of their papers have a major, lasting influence. Some scientists have achieved wide acclaim despite publishing very few papers, because of the exceptional importance of those few. One measure of the influence of a paper is how often it is 'cited' — referenced in other scientific papers. As most scientific papers include references to about 30 other papers, an average paper will eventually accrue about 30 'citations'. Fred Sanger, twice winner of the Nobel Prize for Chemistry (in 1958 and in 1980) published about 70 papers in his whole career; 30 of these have been cited more than 100 times each, and four of them more than 1000 times each.

Manuscripts submitted for publication in scientific journals are normally sent by the editor to (usually one to three) other scientists for evaluation. These 'expert referees' advise the editor about the suitability of the paper for publication in the journal. They also report, usually anonymously, on its strengths and weaknesses, pointing out any errors or omissions that they noticed and offering suggestions for how the paper might be improved by revision or by further experiments. With this advice, the editor might reject the paper or decide that it might be acceptable if appropriately revised.

Peer review has been widely adopted by the scientific community, but has weaknesses. In particular, it is easier to publish data that are consistent with a generally accepted theory than data that contradict it. This helps to ensure the stability of the accepted theory, but it also means that the appearance of the extent to which a current theory is supported by evidence might be misleading - boosted by a poorly scrutinised supportive work while protected against ctiticism. The biologist Lynn Margulis encountered great difficulty in publishing her theory that the eukaryotic cell is a symbiotic union of primitive prokaryotic cells. In 1966, she wrote a theoretical paper entitled The Origin of Mitosing Cells; it was "rejected by about fifteen scientific journals," as Margulis recalled. Finally accepted by The Journal of Theoretical Biology, it is now considered a landmark in modern endosymbiotic theory. In 1995, Richard Dawkins said, "I greatly admire Lynn Margulis's sheer courage and stamina in sticking by the endosymbiosis theory, and carrying it through from being an unorthodoxy to an orthodoxy."

The scientific literature

…If the study is found to be good enough, the findings are published and acknowledged by the wider scientific community…

Peter Medawar (1915-1987), Nobel laureate in Physiology and Medicine, in his article “Is the scientific paper a fraud?” argued that the scientific paper in its orthodox form embodies "a totally mistaken conception, even a travesty, of the nature of scientific thought." In scientific papers, the results of an experiment are interpreted only at the end, in the discussion section, giving the impression that those conclusions are drawn by induction or deduction from the reported evidence. However, explains Medawar, it is the expectations that a scientist begins with that provide the incentive for the experiments, determine their nature, and determine which observations are relevant and which are not. Only in the light of these initial expectations do the activities described in a paper have any meaning at all. The expectation, the original hypothesis, according to Medawar, is not the product of inductive reasoning but of inspiration, educated guesswork.

Confirmation

…But, it isn’t enough to prove a hypothesis once. Other researchers must also be able to repeat the study and produce the same results, if the hypothesis is to remain valid…

Sometimes scientists make errors in the design, execution or analysis of their experiments, so it is common for other scientists to try to repeat experiments, especially when the results were surprising . Accordingly, scientists keep detailed records of their experiments, to provide evidence of their effectiveness and integrity and assist in reproduction, and generally in publishing their work it is considered essential that they describe their methods in sufficient detail to allow themm to be repeated by others. However, a scientist cannot record everything about an experiment; he (or she) reports what he believes to be relevant. This can cause problems if some supposedly irrelevant feature is questioned, but the accepted theory itself often defines what a scientist expects to be relevant. For example, Sidney Ringer's experiments with isolated frog hearts first led him to declare that the heart could continue to beat if kept in a simple saline solution. However, he later discovered that the solution had been made up not with distilled water but with London tap water, which contained a significant amount of dissolved calcium carbonate. He retracted his first reports, and is now known as the scientist who demonstrated the importance of calcium for the contractile activity of the heart.

Statistics

…If the initial study was carried out using a small number of samples or people, larger studies are also needed. This is to make sure the hypothesis remains valid for bigger group and isn't due to chance variation…

Statistical analysis is a standard part of hypothesis testing in many areas of science. This formalises the criteria for disproof by allowing statements of the form: "If our hypothesis is true, the chance of getting the results that we observed is (say) only 1 in 20 or less (P < 0.05); therefore the hypothesis is probably wrong, and so we reject it. For instance, we might predict that a given chemical will produce a certain effect. However what we often test is not this, but the complementary null hypothesis - that the chemical will have no effect[6]. The reason is that, if our original hypothesis is vague about how big an effect to expect, then we cannot disprove it, as we can't exclude the possibility that the effect is smaller than we can measure. However, we can disprove the null hypothesis (by showing an effect). Ideally, we choose hypotheses that give precise predictions, but this is often unrealistic. In medicine for example, we might expect a new drug to be effective in a particular condition from our understanding of its mechanism of action. Even so, we might not know how big an effect to expect because of many uncertainties - how many people will be resistant to the drug? for example, and how quickly will tolerance to the drug develop in people who respond well?

This is not hypothesis testing in Popper's sense, because the original hypothesis is not put at any hazard of disproof. Verification of this type is something that Popper considered to be, at best, weak corroborative evidence, partly because it is impossible to measure the degree of support that such evidence provides.

In the 18th century, Thomas Bayes proved a result, now known as Bayes' theorem, that, in some interpretations, provides a formal method for revising beliefs in the light of new evidence. It has been argued that Bayesian statistics can be used to provide a statistical basis for support by induction, and some areas of science use these approaches. Bayesian statistics measures how the probability that a hypothesis is true changes as a result of observations, but depends on assigning initial a priori values to the probabilities of alternative outcomes of an experiment. This approach is not always tenable because of the difficulty of assigning these a priori probabilities in any meaningful way.

Progress in science

…Over time, scientific opinion can change. This is because new technologies can allow us to re-examine old questions in greater detail.

Kuhn argued that scientific opinion does not change easily in fundamental things. In particular, one theory or world view is replaced by another not because many scientists are "converted" to the new world view. Instead, a new theory begins as an unfashionable alternative that is often derided, but gains adherents as its advantages become apparent to new scientists entering the field, while the adherents of the old view fight a 'rear guard action' to defend it. Barbara McClintock's work on regulatory elements that control gene expression won her the Nobel Prize in Physiology or Medicine in 1983, but in 1953 she had decided to stop trying to publish detailed accounts of her work, because of the puzzlement and hostility of her peers. In 1973 she wrote:

"Over the years I have found that it is difficult if not impossible to bring to consciousness of another person the nature of his tacit assumptions when, by some special experiences, I have been made aware of them. ...One must await the right time for conceptual change"

Kuhn focused attention on the unexplainable phenomena as the key to scientific revolutions, which he termed, "paradigm shifts." One example reported in The Structure of Scientific Revolutions dates back to the time of Ptolemy in ancient Egypt. The improvements in astronomical observation, and the accumulation of more data during that time required more and more elaborate explanations to reconcile the earth-centric paradigm at the time with observation. By the time of Copernicus, so much evidence had accumulated suggesting that the sun was in fact the center of the solar system, the whole infrastructure of theories broke down, leading the way to acceptance of a new world picture. New observations about natural phenomena continue to lead to such revolutions in biology, plate tectonics, particle physics, and many other branches of science.

Alternative views

The success of science, as measured by the technological achievements that have changed our world, have led many to conclude that this success is because of the methodological rules that scientists follow. However, not all philosophers accept this conclusion; for example, Paul Feyerabend (1924-1994) denied that science is genuinely a methodological process. In his book Against Method he argued that scientific progress is not the result of applying any particular rules. Instead, he concluded almost that 'anything goes', in that for any particular 'rule' there are abundant examples of successful science that have proceeded in a way that seems to contradict it. To Feyeraband, there is no real difference between science and other areas of human activity characterised by reasoned thought. A similar sentiment was expressed by T.H. Huxley in 1863: "The method of scientific investigation is nothing but the expression of the necessary mode or working of the human mind. It is simply the mode at which all phenomena are reasoned about, rendered precise and exact."

Some scientists focus their activity on making precise and detailed observations of a phenomenon, gathering data, organizing it in sensible ways, making it accessible to other scientists. We do not disqualify those scientists as ‘scientists’ on the grounds they do not employ a scientific method. Other scientists might use their observational data to generate testable hypotheses to disconfirm or not, and other scientists might test those hypotheses by experiment, and others try to reproduce the findings. That illustrates an instance of the scientific method in action realized by the combined effort of two or more scientists working with different methods, not necessarily in one generation. Regardless of the hopefully rational approach each scientist employs in her 'scientific method', however, none can leave their biases and passions outside their mind. Sometimes biases and passions contribute the advancement of science. The scientific method is the endeavor of humans, prone to error for many reasons, prone to creative insights by nature. But scientists agree on the need for verifiable knowledge, and they cannot suppress the emergence of novel perspectives and paradigms.

In his 1958 book, Personal Knowledge, the chemist and philosopher Michael Polanyi (1891-1976) criticized the view that the scientific method is purely objective and generates objective knowledge. Polanyi considered this to be a misunderstanding of the scientific method, and argued that scientists do and must follow personal passions in appraising facts and in choosing which questions to investigate. He concluded that a structure of liberty is essential for the advancement of science -- that the freedom to pursue science for its own sake is a prerequisite for the production of knowledge.

The changing nature of science

Charles Darwin was an amateur scientist, a man of independent means and broad ranging interests who worked to satisfy his own curiosity. In the 20th century science became largely professionalised, conducted increasingly by specialised experts employed in Universities or research institutes, and increasingly governed by the priorities of funding bodies, which in turn have become increasingly influenced by the political priorities of the Governments that are the source of the funding for research.

The 'lone scientist' is now a rare animal; most science is now a collaborative enterprise, often conducted in large teams where each member of the team supplies a specific area of specialised expertise. Most of Frederick Sanger's scientific papers, published between 1945 and 1980, were either authored by him alone or with just one other co-author. This is now very unusual in the Life Sciences, where most papers have several authors and many have ten or more.

Increasingly, scientists work towards specified ambitous goals; a prime example of this being the Human Genome Project, a research program involving hundreds of laboratories across many countries directed at sequencing the entire human genome [7]. This 13-year project, coordinated by the U.S. Department of Energy and the National Institutes of Health, was completed in 2003.

Thus the 20th century saw a transition from curiosity-driven research to hypothesis-driven research and then to goal-directed research, accompanied by major changes in the sociology of the scientific community.

See also

• Discourse on Method
• History of scientific method
• Thomas Kuhn
• Karl Popper
• Pseudoscience
• Reductionism
• René Descartes
• Scientific misconduct

External links

• The Keystones of Science project, sponsored by the journal Science Science has selected a number of scientific articles from that journal and annotated them, illustrating how different parts embody the scientific method. Here is an annotated example of the scientific method example
• 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
• Using the scientific method for designing science fair projects from Science Made Simple
• Scientific Revolution from the Internet History Sourcebooks Project
• Carnap R (1950) Empiricism, Semantics, and Ontology Revue Internationale de Philosophie 4:20-40.
• Carnap R (1966) Theories and Nonobservablesfrom Philosophical Foundations of Physics
• Achinstein P (editor) (2004) Science Rules: A Historical Introduction to Scientific Methods The Johns Hopkins University Press, Baltimore. ISBN

0-8018-7944-2