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The '''scientific method''' is how scientists investigate [[phenomenon|phenomena]] and acquire new [[knowledge]]. It is based on [[observable]], [[empirical]], measurable evidence, subject to the [[reasoning|principles of reasoning]]<ref>[[Isaac Newton]] (1687, 1713, 1726) "[4] Rules for the study of [[natural philosophy]]", ''[[Philosophiae Naturalis Principia Mathematica]]'', Third edition. The General Scholium containing the 4 rules follows Book '''3''', ''The System of the World'' on pp 794-796 of [[I. Bernard Cohen]] and Anne Whitman's 1999 translation, [[University of California Press]]  ISBN 0-520-08817-4</ref>. Scientists propose [[hypothesis|hypotheses]] to explain [[phenomena]], and test those hypotheses by examining the evidence from [[experiment]]al [[research|studies]]. Scientists also formulate [[Theory#Science|theories]] that encompass whole domains of inquiry, and which bind hypotheses together into logically coherent wholes.
 
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<!--Please see talk page for discussion on why the word "the" is not used here-->'''Scientific method''' is a body of techniques for investigating [[phenomenon|phenomena]] and acquiring new [[knowledge]], as well as for correcting and integrating previous knowledge. It is based on [[observable]], [[empirical]], measurable evidence, and subject to [[deductive reasoning|laws]] of [[inductive reasoning|reasoning]].
 
Although specialized procedures vary from one field of inquiry to another, there are identifiable features that distinguish scientific inquiry from other methods of developing knowledge. Scientific researchers propose specific [[hypothesis|hypotheses]] as explanations of natural [[phenomena]], and design [[experiment]]al [[research|studies]] that test these predictions for accuracy. These steps are repeated in order to make increasingly dependable predictions of future results.  [[Theory#Science|Theories]] that encompass whole domains of inquiry serve to bind more specific hypotheses together into logically coherent wholes. This in turn aids in the formation of new hypotheses, as well as in placing groups of specific hypotheses into a broader context of understanding.
 
Among other facets shared by the various fields of inquiry is the conviction that the process must be [[objectivity (philosophy)|objective]] so that the [[scientist]] does not [[bias]] the interpretation of the results or change the results outright.  Another basic expectation is that of making complete documentation of data and methodology available for careful scrutiny by other scientists and researchers, thereby allowing other researchers the opportunity to verify results by attempted [[Reproducibility|reproduction]] of them. Note that reproducibility can not be expected in all fields of science. This also allows statistical measures of the [[reliability (statistics)|reliability]] of the results to be established.  The scientific method also may involve attempts, if possible and appropriate, to achieve control over the factors involved in the area of inquiry, which may in turn be manipulated to test new hypotheses in order to gain further knowledge. 
 
==Elements of scientific method==
<blockquote>
"Science is a way of thinking much more than it is a body of knowledge."  ([[Carl Sagan]]<ref>Sagan C. The fine art of baloney detection. Parade Magazine, p 12­13, Feb 1, 1987.</ref>).
</blockquote>
<blockquote>  
<blockquote>  
". . .science consists in grouping facts so that general laws or conclusions may be drawn from them." ([[Charles Darwin]])
''"Science is a way of thinking much more than it is a body of knowledge." '' ([[Carl Sagan]])<ref>Sagan C (1987) The fine art of baloney detection ''Parade Magazine''Feb 1, p 12­13</ref>
</blockquote>
</blockquote>


There are multiple ways of outlining the basic method shared by all of the fields of scientific inquiry.  The following examples are typical classifications of the most important components of the method on which there is very wide agreement in the [[scientific community]] and among [[Philosophy of science|philosophers of science]], each of which are subject only to marginal disagreements about a few very specific aspects.
<blockquote>''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]])<ref>Medawar P (1982) ''Pluto's Republic'', Oxford University Press; see [http://www.the-rathouse.com/Medawar_PlutoRepublic.html]</ref></blockquote>
 
==Elements of scientific method==
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According to [[Charles Darwin]] ,
The scientific method involves the following basic facets:
:''". . .science consists in grouping facts so that general laws or conclusions may be drawn from them."'' <ref> From the autobiography of Charles Darwin [http://www.worldwideschool.org/library/books/hst/european/TheAutobiographyofCharlesDarwin/chap2.html]</ref>
* '''Observation'''.  A constant feature of scientific inquiry.
 
* '''Description'''.  Information must be reliable, i.e., replicable (repeatable) as well as valid (relevant to the inquiry).
 
* '''Prediction'''.  Information must be valid for observations past, present, and future of given phenomena, i.e., purported "one shot" phenomena do not give rise to the capability to predict, nor to the ability to repeat an experiment.
 
* '''Control'''.  Actively and fairly sampling the range of ''possible'' occurrences, whenever possible and proper, as opposed to the passive acceptance of opportunistic data, is the best way to control or counterbalance the risk of empirical bias.
 
* '''Falsifiability''', or the elimination of plausible alternatives.  This is a gradual process that requires repeated experiments by multiple researchers who must be able to replicate results in order to corroborate them.  This requirement, one of the most frequently contended, leads to the following:  ''All hypotheses and theories are in principle subject to disproof''.  Thus, there is a point at which there might be a consensus about a particular hypothesis or theory, yet it must in principle remain tentative. As a body of knowledge grows and a particular hypothesis or theory repeatedly brings predictable results, confidence in the hypothesis or theory increases.
 
* '''Causal explanation'''.  Many scientists and theorists on scientific method argue that concepts of causality are not obligatory to science, but are in fact well-defined only under particular, admittedly widespread conditions.  Under these conditions the following requirements are generally regarded as important to scientific understanding:
 
:* '''Identification of causes'''. Identification of the causes of a particular phenomenon to the best achievable extent.
:* '''Covariation of events'''.  The hypothesized causes must [[correlate]] with observed effects.
:* '''Time-order relationship'''.  The hypothesized causes must precede the observed effects in time.
</div>
 
The following is a more specific and technical description of the hypothesis/testing method, discussion of which follows below. This general set of elements and organization of procedures will in general tend to be more characteristic of natural sciences and experimental psychology than of disciplines such as sociology and a number of other fields commonly categorized as social sciences.  Among the latter, methods of verification and testing of hypotheses may involve less stringent mathematical and statistical interpretations of these elements within the respective disciplines. Nonetheless the cycle of hypothesis, verification and formulation of new hypotheses will tend to resemble the basic cycle described below.
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The essential elements of a scientific method are [[iteration]]s, [[recursion]]s, [[interleaving]]s, and [[Partially ordered set|orderings]] of the following:
*[[#Characterizations|Characterizations]] (Quantifications, observations, and measurements)
*[[#Hypothesis development|Hypotheses]] (theoretical, hypothetical [[explanation]]s of observations and measurements)
*[[#Predictions from the hypotheses|Predictions]] ([[reasoning]] including [[logic]]al [[deduction]] from [[hypotheses]] and [[theories]])
*[[#Experiments|Experiments]] ([[Experiment|test]]s of all of the above) </div>
 
<!-- Image with unknown copyright status removed: [[Image:Scietific_Method.jpg|right|thumb|Representation of the iterations of the scientific method.]] -->
 
The element of [[observation]] includes both unconditioned observations (prior to any theory) as well as the observation of the experiment and its results. The element of [[experimental design]] must consider the elements of hypothesis development, prediction, and the effects and limits of observation because all of these elements are typically necessary for a valid experiment. 
 
[[Imre Lakatos]] and [[Thomas Kuhn]] had done extensive work on the "theory laden" character of observation. Kuhn (1961) maintained that the scientist generally has a theory in mind before designing and undertaking experiments so as to make empirical observations, and that the "route from theory to measurement can almost never be travelled backward". This perspective implies that the way in which theory is tested is dictated by the nature of the theory itself which led Kuhn (1961, p. 166) to argue that "once it has been adopted by a profession ... no theory is recognized to be testable by any quantitative tests that it has not already passed".
 
Each element of scientific method is subject to [[peer review]] for possible mistakes. These activities do not describe all that scientists do ([[#Dimensions of practice|see below]]) but apply mostly to experimental sciences (e.g., physics, chemistry). The elements above are often taught in [[education|the educational system]].<ref>In the inquiry-based education paradigm, the stage of "characterization, observation, definition, …" is more briefly summed up under the rubric of a Question.</ref>
 
The scientific method is  not a recipe: it requires intelligence, imagination, and creativity.  Further, it is an ongoing cycle, constantly developing more useful, accurate and comprehensive models and methods.  For example, when Einstein developed the Special and General Theories of Relativity, he did not in any way refute or discount Newton's ''Principia''.  On the contrary, if one reduces out the astronomically large, the vanishingly small, and the extremely fast from Einstein's theories — all phenomena that Newton could not have observed — one is left with Newton's equations.  Einstein's theories are expansions and refinements of Newton's theories, and the observations that increase our confidence in them also increase our confidence in Newton's approximations to them.


The Keystones of Science project, sponsored by the journal ''[[Science (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.  [http://www.sciencemag.org/feature/data/scope/keystone1/ Here] is an annotated example of the scientific method example titled ''Microbial Genes in the [[human genome|Human Genome]]: [[lateral gene transfer|Lateral Transfer]] or Gene Loss?''.
Darwin's simple account begs many questions. What do we mean by ‘facts’?  How much can we trust our senses to enable us to believe that what we see is true?  How do scientists ‘group’ facts? How do they choose which facts to pay attention to, and is it possible to do this in an objective way? And having done this, how do they draw any broader conclusions? How can we know ''more'' than we observe directly?


A linearized, pragmatical scheme of the four above points is sometimes offered as a guideline for proceeding:
We live in a world that is not directly understandable. We sometimes disagree about the ‘[[fact]]s’ we see around us, and some things in the world are at odds with our understanding. What we call the “scientific method” is an account of how scientists gather and report observations in ways that will be understood by others and accepted as valid evidence, and how they construct explanations that will be consistent with the world, withstand logical and experimental scrutiny, and provide the foundations for further increases in understanding.  
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# Define the question
# Gather information and resources
# Form hypothesis
# Perform experiment and collect data
# Analyze data
# Interpret data and draw conclusions that serve as a starting point for new hypotheses
# Publish results
</div>
The iterative cycle inherent in this step-by-step methodology goes from point 3 to 6 back to 3 again.


While this schema outlines a typical hypothesis/testing method,<ref>''See, e.g.'', Gauch, Hugh G., Jr., Scientific Method in Practice (2003), esp. chapters 5-8</ref> it should also be noted that a number of philosophers, historians and sociologists of science (perhaps most notably [[Paul Feyerabend]]) claim that such descriptions of scientific method have little relation to the ways science is actually practiced.
The English philosopher [[Francis Bacon (philosopher)|Francis Bacon]] is often credited as the pioneer of the modern scientific method. He proposed that scientists should "empty their minds" of self-evident truths and, by 'observation and experimentation' should generate hypotheses by a process known as [[induction]].<ref> [[Francis Bacon (philosopher)|Bacon, Francis]] (1620) ''Novum Organum (The New Organon)''</ref> Bacon described many of the commonly accepted principles of scientific method, in particular, he emphasised the importance of observation, experiments, and independent corroboration. He nevertheless recognised that to interpret nature, something more than observation and reason is needed:


====[[Image:DNA icon (25x25).png]]DNA example====
:''...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. And then the way is still to be made by the uncertain light of the sense, sometimes shining out, sometimes clouded over, through the woods of experience and particulars; while those who offer themselves for guides are (as was said) themselves also puzzled, and increase the number of errors and wanderers. In circumstances so difficult neither the natural force of man's judgement nor even any accidental felicity offers any chance of success. No excellence of wit, no repetition of chance experiments, can overcome such difficulties as these. Our steps must be guided by a clue...'' <ref>from ''Preface to The Great Instauration; 4.18'' quoted in Pesic P (2000)The Clue to the labyrinth: Francis Bacon and the decryption of nature [http://www.sirbacon.org/pesic.htm ''Cryptologia'']. Francis Bacon should not be confused with [[Roger Bacon]], a Franciscan friar who also has claims to be a pioneer of observation and experiment, and who was imprisoned when his work challenged the dogma of the Church.[http://www.newadvent.org/cathen/13111b.htm]</ref>
: Each element of scientific method is illustrated below by an example from the discovery of the structure of [[DNA]]:
:*''[[#DNA/characterizations|DNA/characterizations]]''
:*''[[#DNA/hypotheses|DNA/hypotheses]]''
:*''[[#DNA/predictions|DNA/predictions]]''
:*''[[#DNA/experiments|DNA/experiments]]''


: The examples are continued in [[#Evaluations and iterations|"Evaluations and iterations"]] with ''[[#DNA/iterations|DNA/iterations]]''.
The success of science, as measured by the technological achievements that have changed our world, have led many to conclude that this must reflect the success of some methodological rules that scientists follow. However, not all philosophers accept this conclusion; notably, the philosopher Paul [[Feyerabend]] 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 <ref> [[Paul Feyerabend|Feyerabend PK]] (1975) ''Against Method, Outline of an Anarchistic Theory of Knowledge'' Reprinted, Verso, London, UK, 1978</ref> . 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. <ref>[http://www.galilean-library.org/feyerabend.html Feyerabend's 'anything goes' argument explained] at the Galilean Library. Criticisms such as his led to the [[strong programme]], a radical approach to the sociology of science.
</ref> To Feyeraband, there is no fundamental 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." <ref>Huxley TH (1863) [http://www.fordham.edu/halsall/mod/1863huxley.html From a 1863 lecture series aimed at making science understandable to non-specialists]</ref>


===Characterizations===
Nevertheless, in the [[Daubert v. Merrell Dow Pharmaceuticals]] [509 U.S. 579 (1993)] 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."<ref> [http://straylight.law.cornell.edu/supct/html/92-102.ZS.html Text of the opinion, LII, Cornell University]; [http://www.defendingscience.org/upload/Daubert-The-Most-Influential-Supreme-Court-Decision-You-ve-Never-Heard-Of-2003.pdf Daubert-The Most Influential Supreme Court Decision You've Never Heard of]</ref>


The scientific method depends upon increasingly more sophisticated characterizations of subjects of the investigation. (The ''subjects'' can also be called ''[[list of unsolved problems|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.
==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. Most important of all, the man of science must exhibit foresight.''[[Henri Poincaré]]<ref>Henri Poincaré (1905)[http://spartan.ac.brocku.ca/~lward/Poincare/Poincare_1905_toc.html ''Science and Hypothesis'']</ref>


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.  
A ''[[hypothesis]]'' is a proposed explanation of a phenomenon. It is 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. Scientists use many different means to generate hypotheses, including their own creative imagination, ideas from other fields, and by [[induction (philosophy)|induction]].[[Charles Sanders Peirce]] described the incipient stages of [[inquiry]], instigated by the "irritation of doubt" to venture a plausible guess, as ''[[Inquiry#Abduction|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".<ref>cited in Bargar RR, Duncan JK (1982) Cultivating creative endeavor in doctoral research ''J Higher Educ 53:1-31 doi:10.2307/1981536</ref>


Measurements demand the use of ''[[operational definition]]s'' 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-iridium kept in a laboratory in France.  
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 plausible.


The scientific definition of a term sometimes differs substantially from their [[natural language]] usage. For example, [[mass]] and [[weight]] overlap in meaning 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 unit]]s when communicating the work.  
===Popper and Kuhn===
The philosopher  [[Karl Popper]], in ''[[The Logic of Scientific Discovery]]'', a book that Sir [[Peter Medawar]] called "one of the most important documents of the 20th century", argued that this 'hypothetico-deductive' method was the only sound way by which science makes progress. He argued that the alternative '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. 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.  


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.  
For Popper, theory is 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 therefore, 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.  


New theories sometimes arise upon realizing that certain terms had not previously been sufficiently clearly defined. For example, [[Albert Einstein|Albert Einstein's]] first paper on [[Special relativity|relativity]] begins by defining [[Relativity of simultaneity|simultaneity]] and the means for determining [[length]]. These ideas were skipped over by [[Isaac Newton]] with, "''I do not define [[time in physics#Galileo's water clock|time]], space, place and [[motion (physics)|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.<ref>Crick, Francis (1994), ''The Astonishing Hypothesis'' ISBN 0-684-19431-7 p.20</ref> 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.
Popper proposed that the content of a theory should be judged by the extent to which it inspired testable hypotheses; while theories always also contain many elements that are not falsifiable, Popper argued that these should be kept to a minimum. However, this was not the only criterion in choosing a theory; 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.


====[[Image:DNA icon (25x25).png]]DNA/characterizations====
Popper's views on falsifiability were in marked contrast to those of his contemporary, the historian  [[Thomas Kuhn]]. Kuhn's own book "[[The Structure of Scientific Revolutions]]" was no less influential than Popper's, but its message was very different. Kuhn analysed times in the history of science when one dominant theory was replaced by another  - such as the replacement of [[Ptolemy]]'s heliocentric model of the Universe with the [[Copernicus| Copernican]] geocentric model, and the replacement of [[Newton]]ian laws of motion with [[Einstein]]'s theory of [[Relativity]]. In many respects Popper was asserting his rules for 'good science', Kuhn considered himself to be reporting what scientists actually did, although he believed that as what they did was successful, probably there was merit in what they did. Kuhn concluded that falsifiability had played almost no role in the 'scientific revolutions' where one [[paradigm]] was replaced by another. He argued that scientists working in a field resisted the alternative interpretations of 'outsiders', and tenaciously defended 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 field when one theory is dominant; progress occurs by the "puzzle solving" of scientists who are trying not to challenge it, but to extend its scope and explanatory power, bringing theory and fact ito closer agreement by a "strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education".<ref>
[[Thomas Kuhn|Kuhn TS]] (1961) The Function of Measurement in Modern Physical Science ''ISIS'' 52:161–193
* Kuhn TS (1962)''The Structure of Scientific Revolutions'' University of Chicago Press, Chicago, IL.  2nd edition 1970, 3rd edition 1996
* Kuhn TS (1977) ''The Essential Tension, Selected Studies in Scientific Tradition and Change'' University of Chicago Press, Chicago, IL
*A [http://www.des.emory.edu/mfp/kuhnsyn.html Synopsis] from the original by Professor Frank Pajares, From the Philosopher's Web Magazine
*Moloney DP (2000) ''First Things'' '''101'''[http://www.firstthings.com/ftissues/ft0003/articles/kuhn.html 53-5]</ref>


: [[DNA#The history of DNA research|The history of the discovery]] of the structure of [[DNA]] is a classic example of [[#Elements of scientific method|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 [[William Lawrence Bragg|Bragg's]] laboratory at [[University of Cambridge|Cambridge University]] made [[X-ray]] [[diffraction]] pictures of various [[molecule]]s, starting with [[crystal]]s 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.
==Experiments and observations==
[[Werner Heisenberg]] in a quote that he attributed to [[Albert Einstein]] , stated <ref>[[Werner Heisenberg|Heisenberg, Werner]] (1971) ''Physics and Beyond, Encounters and Conversations'', A.J. Pomerans (trans.), Harper and Row, New York, NY  pp.63–64</ref>


====Precession of Mercury====
: ''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.''
===Reductionism===
For much of the 20th century, the dominant approach to science has been [[reductionism]] – the attempt to explain all phenomena by basic laws of physics and chemistry. This  principle has ancient roots - [[Francis Bacon]] (1561-1626) quotes [[Aristotle]] as declaring "That the nature of everything is
best seen in his smallest portions." <ref>[[Francis Bacon]] 'The Advancement of Learning' [http://www.gutenberg.org/etext/5500]</ref>
In many fields, however, reductionist explanations are impractical, and all explanations involve 'high level' concepts. Nevertheless, the reductionist belief has been that the role of science is to progressively explain high level concepts by concepts closer and closer to the basic physics and chemistry. For example, to explain the behaviour of individuals we might refer to motivational states such as [[hunger]]. These reflect features of brain activity that are still poorly understood, but we can investigate, for example, the 'hunger centres' of the brain that house these drives. These centres involve many [[neural networks]] – interconnected nerve cells, and each network we can be probed in detail. These networks in turn are composed of specialised [[neuron]]s that can be analysed individually. These nerve cells have properties that are the product of a genetic program that is activated in development – and so are reducible to [[molecular biology]]. However, while behaviour is thus in principle reducible to basic elements, explaining the behaviour of an individual in terms of the most basic elements has little predictive value, because the uncertainties in our understanding are too great.
===Measurement===
The reductionist approach assigned particular importance to measurement of quantities. Measurements may be tabulated, graphed, or mapped, and statistical analysed; often these representations of the data use tools and conventions that are at a given time, accepted and understood by scientists within a given field. Measurements may need specialized instruments such as thermometers, microscopes, or voltmeters, whose properties and limitations are familiar within the field, and scientific progress is often intimately tied to their development. Measurements also provide ''[[operational definition]]s'': a scientific quantity is defined precisely by how it is measured, in terms that enable other scientists to reproduce the measurements. Scientific quantities are often characterized by [[units of measure]] which can be described in terms of conventional [[physical unit]]s. Ultimately, this may involve internationally agreed ‘standards’; for example, ''one second'' is defined as exactly 9,192,631,770 oscillations or cycles of the cesium atom's resonant frequency  [http://physics.nist.gov/GenInt/Time/atomic.html]. The scientific definition of a term sometimes differs substantially from their [[natural language]] use; [[mass]] and [[weight]] overlap in meaning in common use, but have different meanings in physics.  All measurements are accompanied by the possibility of error, so their [[uncertainty]] is often estimated by repeating measurements, and seeing by how much these differ. Counts of things, such as the number of people in a nation at a given time, may also have an uncertainty: counts may  represent only a sample, with an uncertainty that depends upon the sampling method and the size of the sample.


[[Image:Perihelion_precession.jpg|thumb|right|[[Precession]] of the [[perihelion]] (very exaggerated)]]
==The scientific method in practice==
The characterization element can require extended and extensive study, even centuries. It took thousands of years of measurements, from the  [[Chaldea]]n, [[India]]n, [[Persian Empire|Persia]]n, [[Greece|Greek]], [[Arab]]ic 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 (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]].
The UK Research Charity [[Cancer Research UK]] gives an outline of the scientific method, as practised by their scientists [http://info.cancerresearchuk.org/cancerandresearch/aboutcancerresearch/thescientificmethod/]. The quotes that follow are from this outline
 
<blockquote> ''[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. They then try to prove if their hypothesis is right or wrong.''
===Hypothesis development===
 
''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…'' </blockquote>
A [[hypothesis]] is a suggested explanation of a phenomenon, or alternately a reasoned proposal suggesting a possible correlation between or among a set of phenomena.
 
Normally hypotheses have the form of a [[mathematical model]]. Sometimes, but not always, they can also be formulated as [[existential quantification|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 quantification|universal statements]], stating that every instance of the phenomenon has a particular characteristic.
 
Scientists are free to use whatever resources they have — their own creativity, ideas from other fields, [[induction (philosophy)|induction]], [[Bayesian inference]], and so on — to imagine possible explanations for a phenomenon under study.  [[Charles Sanders Peirce]], borrowing a page from [[Aristotle]] (''[[Prior Analytics]]'', [[Inquiry#Abduction|2.25]]) described the incipient stages of [[inquiry]], instigated by the "irritation of doubt" to venture a plausible guess, as ''[[Inquiry#Abduction|abductive reasoning]]''.  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, notably [[Charles Peirce]], 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.
 
[[William Glen]] observes that
<blockquote>
the success of a hypothesis, or its service to science, lies not simply in its perceived "truth", or power to displace, subsume or reduce a predecessor idea, but perhaps more in its ability to stimulate the research that will illuminate … bald suppositions and areas of vagueness.<ref>Glen,William (ed.), The Mass-Extinction Debates: How Science Works in a Crisis, Stanford University Press, Stanford, CA, 1994. ISBN 0-8047-2285-4. pp. 37-38.</ref>
</blockquote>
 
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 from the hypothesis|prediction]]. Note that 'simplicity' may be perceived differently by different individuals and cultures.
 
====[[Image:DNA icon (25x25).png]]''DNA/hypotheses''====
 
: [[Linus Pauling]] proposed that DNA was a triple helix.  [[Francis Crick]] and [[James Watson]] learned of Pauling's hypothesis, understood from existing data 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!
 
===Predictions from the hypotheses===
Any useful hypothesis will enable [[prediction]]s, 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 [[#Hypothesis development|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.
 
====[[Image:DNA icon (25x25).png]]''DNA/predictions''====
 
: When [[James D. Watson|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".
 
====''General Relativity''====
[[Image:Gravitational lens-full.jpg|right|thumb|200px|[[gravitational lensing|Einstein's prediction (1907): Light bends in a gravitational field]]]]  
[[Image:Gravitational lens-full.jpg|right|thumb|200px|[[gravitational lensing|Einstein's prediction (1907): Light bends in a gravitational field]]]]  
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]].
From Einstein's theory of [[General Relativity]] several predictions can be derived. According to this theory, [[light]] will appear to 'bend' in a [[gravitational field]], by an amount that depends on the strength of the field. [[Arthur Eddington]]'s observations made during a [[solar eclipse]] in 1919 supported General Relativity rather than the Newtonian theories that it replaced.
 
===Experiments===
{{mainarticle|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 [[#Evaluations and iterations |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 [[aerodynamics|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 (astronomer)|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.
 
NOte that experioments are not a necessary part of scientific method. There are purelly observational sciences, or fields of science, like [[history]] and [[astronomy]].
 
====[[Image:DNA icon (25x25).png]]''DNA/experiments''====
 
: 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 [http://www.pbs.org/wgbh/nova/photo51/ X-shape] in X-ray images helped confirm the helical structure of DNA.
 
==Evaluation and iteration==
===Testing and improvement===
 
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.
 
====[[Image:DNA icon (25x25).png]]''DNA/iterations''====
 
: 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 [[model (abstract)|modelling]] [[DNA#Discovery of the structure of DNA|of the physical shapes]] of the [[nucleotide]]s 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]].
 
===Confirmation===
<!--Possibly unfree image removed--[[Image:Ball Lightning.jpg|thumb|right|200px|[[ball lightning|ball lightning?]]]]-->
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 [[lightning]] ([[1753]]) when attempting to replicate the [[1752]] [[kite flying|kite]] [[experiment]] of [[Benjamin Franklin]].<ref>See, e.g., Physics Today, Vol. 59, #1, p42. [http://www.physicstoday.org/vol-59/iss-1/p42.html]</ref>
 
==Models of scientific inquiry==
{{main|Models of scientific inquiry}}
 
===Classical model===
The classical model of scientific inquiry derives from [[Aristotle]], who distinguished the forms of approximate and exact reasoning, set out the threefold scheme of [[abductive reasoning|abductive]], [[deductive reasoning|deductive]], and [[inductive reasoning|inductive]] inference, and also treated the compound forms such as reasoning by [[analogy]].
 
===Pragmatic model===
{{main|Pragmatic theory of truth}}
[[Charles Peirce]] considered scientific inquiry to be a species of the genus ''inquiry'', which he defined as any means of fixing belief, that is, any means of arriving at a settled opinion on a matter in question.  He observed that inquiry in general begins with a state of uncertainty and moves toward a state of certainty, sufficient at least to terminate the inquiry for the time being.  He graded the prevalent forms of inquiry according to their evident success in achieving their common objective, scoring scientific inquiry at the high end of this scale.  At the low end he placed what he called the ''method of tenacity'', a die-hard attempt to deny uncertainty and fixate on a favored belief.  Next in line he placed the ''method of authority'', a determined attempt to conform to a chosen source of ready-made beliefs.  After that he placed what might be called the ''method of congruity'', also called the ''a priori'', the ''dilettante'', or the ''what is agreeable to reason'' method.  Peirce observed the fact of human nature that almost everybody uses almost all of these methods at one time or another, and that even scientists, being human, use the method of authority far more than they like to admit.  But what recommends the specifically scientific method of inquiry above all others is the fact that it is deliberately designed to arrive at the ultimately most secure beliefs, upon which the most successful actions can be based.
 
===Computational approaches===
{{section-stub}}
Many subspecialties of [[applied logic]] and [[computer science]], to name a few, [[artificial intelligence]], [[computational learning theory]], [[inferential statistics]], and [[knowledge representation]], are concerned with setting out computational, logical, and statistical frameworks for the various types of inference involved in scientific inquiry, in particular, [[abductive reasoning|hypothesis formation]], [[deductive reasoning|logical deduction]], and [[inductive reasoning|empirical testing]].  Some of these applications draw on [[measure (mathematics)|measures]] of [[complexity]] from [[algorithmic information theory]] to guide the making of predictions from prior [[probability distribution|distributions]] of experience, for example, see the complexity measure called the ''[[speed prior]]'' from which a computable strategy for optimal inductive reasoning can be derived.
 
==Philosophical issues==
{{main|Philosophy of science}}
 
Scientific researchers generally express a high level of confidence in scientific method.  It would hardly make sense for them to continue seeking knowledge that way if they did not.  What justifies their level of confidence that scientific method, under some conception, model, or recipe, is truly a good way to achieve the knowledge that it promises?  That is a question about the ''grounds of validity'' of scientific method, also referred to as the problem of ''justification'' or ''warrant''.
 
While the [[philosophy of science]] has limited direct impact on day-to-day scientific practice, it plays a vital role in justifying and defending the scientific approach.  There is disagreement over whether there exists a single 'scientific method' or a plurality of them. In philosophical circles scientific method has been the source of much debate. Despite this, there remains agreement on a set of core principles, discussed above and in the sections that follow, which apply across the gamut of scientific inquiry.
 
The [[philosophy of science]] has among its topics of interest the question of how far the actual practice of scientific researchers conforms to the ''[[method|espoused methods]]'' or the ''[[norm|ostensible norms]]'', to which the majority of them expressly or tacitly assent. In the process of subjecting the conventional assumptions to critically reflective examination, writers in these fields periodically generate controversies as to whether scientific knowledge is actually produced by a defined, describable, or determinate [[methodology]] (see, for instance, the writings of [[Paul Feyerabend|Feyerabend]] and [[Thomas Samuel Kuhn|Kuhn]]).
 
We find ourselves in a world that is not directly understandable. We find that we sometimes disagree with others as to the [[fact]]s 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 might work in such a way that [[rationality|rational]] application of the method would always result in agreement and understanding; a perfect method would arguably be [[algorithm|algorithmic]], and so not leave any room for rational agents to disagree. As with all [[Philosophy|philosophical]] topics, the search has been neither straightforward nor simple. [[Logical positivism|Logical Positivist]], [[empiricism|empiricist]], [[falsifiability|falsificationist]], and other theories have claimed to give a definitive account of the logic of science, but each has in turn been criticised.
 
[[Werner Heisenberg]] in a quote that he attributed to [[Albert Einstein]] many years after the fact, stated [Heisenberg 1971]:
: 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”.
 
Considerations such as these led [[Feyerabend]] to deny that science is genuinely a methodological 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 phenomenon. To the degree that sociological studies focus on cooperation and appreciation as well as conflict both within the scientific communities and beyond, however, the [[Science studies|sociology of science]] is also quite capable of accounting for sociological components of the ''success'' of the [[scientific enterprise]] which for much of the 20th century had fairly widely been taken as granted.  The [[strong programme]] has put forward a perspective of just this kind.
 
===Problem of demarcation===
 
The problem of evaluating a system of thought with regard to its status as science is often called the [[demarcation problem]].  The criteria for a system of assumptions, methods, and theories to qualify as science vary in their details from application to application, but they typically include (1) the formulation of hypotheses that meet the logical criterion of [[contingency]], defeasibility, or [[falsifiability]] and the closely related [[empirical]] and [[practical]] criterion of [[testability]], (2) a grounding in empirical evidence, and (3) the use of scientific method. The procedures of science typically include a number of [[heuristic]] guidelines, such as the principles of conceptual economy or theoretical [[parsimony]] that fall under the rubric of [[Ockham's razor]].  A conceptual system that fails to meet a significant number of these criteria is likely to be considered non-scientific. 
The following is a list of additional features that are highly desirable in a scientific theory.
 
:* Consistent.  Generates no obvious logical contradictions, and [[scientific formalism|'saves the phenomena']], being consistent with observation.
 
:* Parsimonious.  Economical in the number of assumptions and hypothetical entities.
 
:* Pertinent.  Describes and explains observed phenomena.


:* Falsifiable and testable.  See [[Falsifiability]] and [[Testability]].
In his 1958 book, ''Personal Knowledge,'' 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.  


:* Reproducible. Makes predictions that can be tested by any observer, with trials extending indefinitely into the future.
===Peer review===
<blockquote> ''…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…'' </blockquote>
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.  


:* Correctable and dynamic. Subject to modification as new observations are made.
Peer review has been widely adopted by the scientific community, but has weaknesses. In particular, it is easier to publish data consistent with a generally accepted theory than to publish data that contradict it. This helps to ensure the stability of the accepted theory, but 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]].<ref>Sagan L (1967) On the origin of mitosing cells" ''J. Theor Biol'' '''14''':255-74 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11541392&dopt=Citation Abstract]</ref> 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." <ref>John Brockman, [http://www.edge.org/documents/ThirdCulture/n-Ch.7.html ''The Third Culture''], New York: Touchstone 1995, 144</ref>


:* Integrative, robust, and corrigible.  Subsumes previous theories as approximations, and allows possible subsumption by future theories.  See [[Correspondence principle]]
==The scientific literature==
<blockquote> ''…If the study is found to be good enough, the findings are published and acknowledged by the wider scientific community…'' </blockquote>


:* Provisional or tentative.  Does not assert the absolute certainty of the theory.
Sir [[Peter Medawar]], Nobel laureate in Physiology and Medicine in his article [http://maagar.openu.ac.il/opus/static/binaries/editor/bank66/medawar_paper_fraud_1.pdf “Is the scientific paper a fraud?”] argued that "The scientific paper in its orthodox form does embody 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==
<blockquote> ''…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…'' </blockquote>
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 <ref> [[Georg Wilhelm Richmann]] was killed by [[lightning]] ([[1753]]) when attempting to replicate the [[1752]] [[kite flying|kite]] [[experiment]] of [[Benjamin Franklin]]. Krider P (2006) Benjamin Franklin and lightning rods ''Physics Today'' 59:42 [http://www.physicstoday.org/vol-59/iss-1/p42.html]</ref>. Accordingly, scientists keep detailed records of their experiments, to provide evidence of their effectiveness and integrity and assist in reproduction. 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. <ref>Carafoli E (2002) Calcium signalling: a tale for all seasons ''PNAS USA'' [http://www.pnas.org/cgi/content/abstract/99/3/1115 99:115-22]</ref>
===Scientific ethics===
It is rare for scientists to deliberately falsify their results, although there have been well publicised examples of this. Any scientist who does so takes an enormous risk, because if the claim is important it is likely to be subjected to close scrutiny, and if it is wrong then the reputation of the scientist will suffer regardless of whether his mistakes were honest or not. ''Honor in Science'', published by  [http://www.sigmaxi.org/about/overview/index.shtml Sigma Xi], quotes [[C.P. Snow]] (''The Search'' 1959): "The only ethical principle which has made science possible is that the truth shall be told all the time. If we do not penalise false statements made in error, we open up the way, don’t you see, for false statements by intention. And of course a false statement of fact, made deliberately, is the most serious crime a scientist can commit."<ref>Under Federal regulations (the Federal Register, [http://www.sc.doe.gov/misconduct/finalpolicy.pdf vol 65, no 235], December 6, 2000) A finding of 'research misconduct' requires that ''There be a significant departure from accepted practices of the relevant research community; and
The misconduct be committed intentionally, or knowingly, or recklessly; and
The allegation be proven by a preponderance of evidence.''</ref>


==Communication, community, culture==
==Statistics==
<blockquote>''…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…'' </blockquote>


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.  
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 following form
"If a given hypothesis is true, the chance of getting the results that we observed is (say) only 1 in 20 or less (P < 0.05), so it is very likely that the hypothesis is wrong, and accordingly we reject it.''


===Peer review evaluation===
This notion of a hypothesis is quite different to Popper's. For instance, we might predict that a certain chemical will produce a certain effect. However what we test is often not this, but the complementary ''[[null hypothesis]]'' - that the chemical will have '''no''' effect[http://chemistry.allinfoabout.com/features/scimethod.html]. The reason for thisis that if our original hypothesis tells us that there will be an effect but is vague about its expected magnitude, we can still logically disprove the null hypothesis (by showing an effect), even though we cannot disprove the hypothesis that the chemical is effective as we cannot exclude the possibility that the effect is  smaller than we can measure reliably. The best answer might be to choose hypotheses that give precise predictions, but in many areas of science 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, but might not know how big an effect to expect because of many uncertainties - how many people in a genetically variable population will be resistant to the drug? for example, and how quickly will tolerance to the drug develop in people who respond well?
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.


===Documentation and replication===
In fact, this is not hypothesis testing in Popper's sense, because this test does not put the original hypothesis 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 put measure the degree of support that such evidence gives to a hypothesis. <ref>In appendix ix to The Logic Popper states: "As to degree of corroboration, it is nothing but a measure of the degree to which hypothesis h has been tested...it must not be interpreted therefore as a degree of the rationality of our belief in the truth of h...rather it is a measure of the rationality of accepting, tentatively, a problematic guess."</ref>


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.  
An important school of Bayesian statistics seeks to provide a statistical basis for support by induction, and some areas of science use these approaches. However, often this approach is not tenable because of the difficulty of attaching ''a priori'' probabilities in any meaningful way to the alternative predicted outcomes of an experiment.


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.
==Progress in science==
<blockquote> ''…Over time, scientific opinion can change. This is because new technologies can allow us to re-examine old questions in greater detail.'' </blockquote>


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 questioned. 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'.
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 conntrol 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"<ref>McClintock B (1987) The discovery and characterization of transposable elements: the collected papers of Barbara McClintock ed John A. Moore. Garland Publishing, Inc. ISBN 0-8240-1391-3. (Introduction)</ref>


===Dimensions of practice===


The primary constraints on contemporary western science are:
==See Also==
* Publication, i.e. [[Peer review]]
*[[Models of scientific inquiry]]
* Resources (mostly funding)
*[[Pseudoscience]]
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.
 
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 [http://www.nature.com/nature/submit/get_published/index.html author guidelines] for ''[[Nature (journal)|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.
 
==History==
{{main|History of scientific method}}
:''See also [[Timeline of the history of scientific method]]''
 
The development of the scientific method is inseparable from the history of science itself. [[Ancient Egypt]]ian documents, such as early [[papyri]], describe methods of medical diagnosis. In [[Ancient Greece|ancient Greek]] culture, the first elements of the inductive scientific method clearly become well established. Significant progress in methodology was made in [[early Muslim philosophy]], in particular using experiments to distinguish between competing scientific theories set within a generally empirical orientation. The fundamental tenets of the basic scientific method crystallized no later than the rise of the modern [[physical science]]s, in the [[17th century|17th]] and [[18th century|18th]] centuries. In his work ''[[Novum Organum]]'' ([[1620]]) — a reference to [[Aristotle]]'s ''[[Organon]]'' — [[Francis Bacon]] outlined a new system of [[logic]] to improve upon the old [[philosophy|philosophical]] process of [[syllogism]]. Then, in [[1637]], [[René Descartes]] established the framework for a scientific method's guiding principles in his treatise, ''[[Discourse on Method]]''. These writings are considered critical in the historical development of the scientific method.
 
In the late 19th century, [[Charles Sanders Peirce]] proposed a schema that would turn out to have considerable influence in the development of current scientific method generally.  Peirce accelerated the progress on several fronts. Firstly, speaking in broader context in "How to Make Our Ideas Clear" (1878) [http://members.door.net/arisbe/menu/library/bycsp/ideas/id-frame.htm], Peirce outlined an objectively verifiable method to test the truth of putative knowledge on a way that goes beyond mere foundational alternatives, focusing upon both ''deduction'' and ''induction'' .  He thus placed induction and deduction in a complementary rather than competitive context (the latter of which had been the primary trend at least since [[David Hume]], who wrote in the mid-to-late 18th century).  Secondly, and of more direct importance to modern method, Peirce put forth the basic schema for hypotheis/testing that continues to prevail today.  Extracting the theory of inquiry from its raw materials in classical logic, he refined it in parallel with the early development of symbolic logic to address the then-current problems in scientific reasoning. Peirce examined and articulated the three fundamental modes of reasoning that, as discussed above in this article, play a role in inquiry today, the processes that are currently known as [[abductive reasoning|abductive]], [[deductive reasoning|deductive]], and [[inductive reasoning|inductive]] inference.  Thirdly, he played a major role in the progress of symbolic logic itself — indeed this was his primary specialty.
 
[[Karl Popper]] (1902-1994), beginning in the 1930s and with increased vigor after World War II, argued that a hypothesis must be [[falsifiable]] and, following Peirce and others, that science would best progress using deductive reasoning as its primary emphasis, known as [[critical rationalism]].  His astute formulations of logical procedure helped to rein in exessive use of inductive speculation upon inductive speculation, and also strengthened the conceptual foundation for today's peer review procedures.


==Notes and references==
==Notes and references==
<references/>
<references/>
* [[Aristotle]], "[[Prior Analytics]]", [[Hugh Tredennick]] (trans.), pp. 181-531 in ''Aristotle, Volume&nbsp;1'', [[Loeb Classical Library]], William Heinemann, London, UK, 1938.
* [[Noam Chomsky|Chomsky, Noam]], ''Reflections on Language'', Pantheon Books, New York, NY, 1975.
* [[Charles Sanders Peirce|Peirce, C.S.]], ''Essays in the Philosophy of Science'', Vincent Tomas (ed.), Bobbs–Merrill, New York, NY, 1957.
* [[Charles Sanders Peirce|Peirce, C.S.]], "Lectures on Pragmatism", Cambridge, MA, March 26 – May 17, 1903.  Reprinted in part, ''Collected Papers'', CP 5.14–212.  Reprinted with Introduction and Commentary, Patricia Ann Turisi (ed.), ''Pragmatism as a Principle and a Method of Right Thinking:  The 1903 Harvard "Lectures on Pragmatism"'', State University of New York Press, Albany, NY, 1997.  Reprinted, pp. 133–241, Peirce Edition Project (eds.), ''The Essential Peirce, Selected Philosophical Writings, Volume 2 (1893–1913)'', Indiana University Press, Bloomington, IN, 1998.
* [[Charles Peirce|Peirce, C.S.]], ''Collected Papers of Charles Sanders Peirce'', vols. 1-6, [[Charles Hartshorne]] and [[Paul Weiss (philosopher)|Paul Weiss]] (eds.), vols. 7-8, [[Arthur W. Burks]] (ed.), Harvard University Press, Cambridge, MA, 1931-1935, 1958.  Cited as CP vol.para.
* [[Wesley C. Salmon|Salmon, Wesley C.]], ''Four Decades of Scientific Explanation'', University of Minnesota Press, Minneapolis, MN, 1990.
==Further reading==
* [[Francis Bacon (philosopher)|Bacon, Francis]] ''Novum Organum (The New Organon)'', 1620.  Bacon's work described many of the accepted principles, underscoring the importance of [[Theory]], empirical results, data gathering, experiment, and independent corroboration.
* [[Henry H. Bauer|Bauer, Henry H.]], ''Scientific Literacy and the Myth of the Scientific Method'', University of Illinois Press, Champaign, IL, 1992
* [[William I. B. Beveridge|Beveridge, William I. B.]], ''The Art of Scientific Investigation'', Vintage/Alfred A. Knopf, 1957.
* [[Richard J. Bernstein|Bernstein, Richard J.]], ''Beyond Objectivism and Relativism:  Science, Hermeneutics, and Praxis'', University of Pennsylvania Press, Philadelphia, PA, 1983.
* [[Stevo Bozinovski|Bozinovski, Stevo]], ''Consequence Driven Systems:  Teaching, Learning, and Self-Learning Agents'', GOCMAR Publishers, Bitola, Macedonia, 1995.
* [[Baruch A. Brody|Brody, Baruch A.]], and [[Richard E. Grandy|Grandy, Richard E.]], ''Readings in the Philosophy of Science'', 2nd edition, Prentice Hall, Englewood Cliffs, NJ, 1989.
* [[Arthur W. Burks|Burks, Arthur W.]], ''Chance, Cause, Reason — An Inquiry into the Nature of Scientific Evidence'', University of Chicago Press, Chicago, IL, 1977.
* [[John Dewey|Dewey, John]], ''How We Think'', D.C. Heath, Lexington, MA, 1910.  Reprinted, [[Prometheus Books]], Buffalo, NY, 1991.
* [[John Earman|Earman, John]] (ed.), ''Inference, Explanation, and Other Frustrations:  Essays in the Philosophy of Science'', University of California Press, Berkeley & Los Angeles, CA, 1992.
* [[Bas C. van Fraassen|Fraassen, Bas C. van]], ''The Scientific Image'', Oxford University Press, Oxford, UK, 1980.
* [[Paul Feyerabend|Feyerabend, Paul K.]], ''Against Method, Outline of an Anarchistic Theory of Knowledge'', 1st published, 1975.  Reprinted, Verso, London, UK, 1978.
* [[Hans-Georg Gadamer|Gadamer, Hans-Georg]], ''Reason in the Age of Science'', Frederick G. Lawrence (trans.), MIT Press, Cambridge, MA, 1981.
* [[Ronald N. Giere|Giere, Ronald N.]] (ed.), ''Cognitive Models of Science'', vol. 15 in 'Minnesota Studies in the Philosophy of Science', University of Minnesota Press, Minneapolis, MN, 1992.
* [[Ian Hacking|Hacking, Ian]], ''Representing and Intervening, Introductory Topics in the Philosophy of Natural Science'', Cambridge University Press, Cambridge, UK, 1983.
* [[Werner Heisenberg|Heisenberg, Werner]], ''Physics and Beyond, Encounters and Conversations'', A.J. Pomerans (trans.), Harper and Row, New York, NY 1971, pp. 63–64.
* [[Gerald Holton|Holton, Gerald]], ''Thematic Origins of Scientific Thought, Kepler to Einstein'', 1st edition 1973, revised edition, Harvard University Press, Cambridge, MA, 1988.
* [[William Stanley Jevons|Jevons, William Stanley]], ''The Principles of Science: A Treatise on Logic and Scientific Method'', 1874, 1877, 1879.  Reprinted with a foreword by [[Ernst Nagel]], Dover Publications, New York, NY, 1958.
* [[Thomas Kuhn|Kuhn, Thomas S.]], "The Function of Measurement in Modern Physical Science", ''ISIS'' 52(2),  161–193, 1961.
* Kuhn, Thomas S., ''The Structure of Scientific Revolutions'', University of Chicago Press, Chicago, IL, 1962.  2nd edition 1970.  3rd edition 1996.
* Kuhn, Thomas S., ''The Essential Tension, Selected Studies in Scientific Tradition and Change'', University of Chicago Press, Chicago, IL, 1977.
* [[Bruno Latour|Latour, Bruno]], ''Science in Action, How to Follow Scientists and Engineers through Society'', Harvard University Press, Cambridge, MA, 1987.
* [[John Losee|Losee, John]], ''A Historical Introduction to the Philosophy of Science'', Oxford University Press, Oxford, UK, 1972.  2nd edition, 1980.
* [[William McComas|McComas, William F.]], ed. [http://www.usc.edu/dept/education/science-edu/Myths%20of%20Science.pdf The Principle Elements of the Nature of Science: Dispelling the Myths], from ''The Nature of Science in Science Education'', pp53-70, Kluwer Academic Publishers, Netherlands 1998.
* [[Cheryl J. Misak|Misak, Cheryl J.]], ''Truth and the End of Inquiry, A Peircean Account of Truth'', Oxford University Press, Oxford, UK, 1991.
* [[Allen Newell|Newell, Allen]], ''Unified Theories of Cognition'', Harvard University Press, Cambridge, MA, 1990.
* [[Massimo Piattelli-Palmarini|Piattelli-Palmarini, Massimo]] (ed.), ''Language and Learning, The Debate between Jean Piaget and Noam Chomsky'', Harvard University Press, Cambridge, MA, 1980.
* [[Henri Poincaré|Poincaré, Henri]], ''Science and Hypothesis'', 1905, [http://spartan.ac.brocku.ca/~lward/Poincare/Poincare_1905_toc.html Eprint]
* [[Karl Popper|Popper, Karl R.]], ''Unended Quest, An Intellectual Autobiography'', Open Court, La Salle, IL, 1982.
* [[Hilary Putnam|Putnam, Hilary]], ''Renewing Philosophy'', Harvard University Press, Cambridge, MA, 1992.
* [[Richard Rorty|Rorty, Richard]], ''Philosophy and the Mirror of Nature'', Princeton University Press, Princeton, NJ, 1979.
* [[Abner Shimony|Shimony, Abner]], ''Search for a Naturalistic World View:  Vol. 1, Scientific Method and Epistemology, Vol. 2, Natural Science and Metaphysics'', Cambridge University Press, Cambridge, UK, 1993.
* [[Paul Thagard|Thagard, Paul]], ''Conceptual Revolutions'', Princeton University Press, Princeton, NJ, 1992.
==See also==
===Synopsis of related topics===
{{col-begin}}
{{col-break}}
* [[Confirmability]]
* [[Contingency]]
* [[Falsifiability]]
* [[Hypothesis]]
{{col-break}}
* [[Statistical hypothesis testing|Hypothesis testing]]
* [[Inquiry]]
* [[Reproducibility]]
* [[Research]]
{{col-break}}
* [[Statistics]]
* [[Tautology]]
* [[Testability]]
* [[Theory]]
{{col-end}}
===Logic, mathematics, methodology===
{{col-begin}}
{{col-break}}
* [[Inference]]
** [[Abductive reasoning]]
** [[Deductive reasoning]]
** [[Inductive reasoning]]
{{col-break}}
* [[Information theory]]
* [[Logic]]
* [[Mathematics]]
* [[Methodology]]
{{col-end}}
===Problems and issues===
{{col-begin}}
{{col-break}}
* [[Ockham's razor]]
* [[Poverty of the stimulus]]
* [[Reference class problem]]
{{col-break}}
* [[Underdetermination]]
* [[Holistic science]]
{{col-end}}
===History, philosophy, sociology===
{{col-begin}}
{{col-break}}
* [[Epistemology]]
* [[Epistemic theories of truth|Epistemic truth]]
* [[History of science]]
{{col-break}}
* [[History of scientific method]]
* [[Philosophy of science]]
* [[Science studies]]
{{col-break}}
* [[Social research]]
* [[Sociology of scientific knowledge]]
* [[Timeline of the history of scientific method|Timeline of scientific method]]
{{col-end}}


==External links==
==External links==
===Science treatments===
*The Keystones of Science project, sponsored by the journal ''[[Science (journal)|Science]]'' has selected a number of scientific articles from that journal and annotated them, illustrating how different parts embody the scientific method.  [http://www.sciencemag.org/feature/data/scope/keystone1/ Here] is an annotated example of the scientific method example
* [http://www.freeinquiry.com/intro-to-sci.html An Introduction to Science: Scientific Thinking and a scientific method] by Steven D. Schafersman.
* [http://www.freeinquiry.com/intro-to-sci.html An Introduction to Science: Scientific Thinking and a scientific method] by Steven D. Schafersman.
* [http://teacher.nsrl.rochester.edu/phy_labs/AppendixE/AppendixE.html Introduction to a scientific method]
* [http://teacher.nsrl.rochester.edu/phy_labs/AppendixE/AppendixE.html Introduction to a scientific method]
Line 408: Line 119:
* [http://www.swemorph.com/pdf/anaeng-r.pdf Analysis and Synthesis: On Scientific Method based on a study by Bernhard Riemann] From the [http://www.swemorph.com  Swedish Morphological Society]
* [http://www.swemorph.com/pdf/anaeng-r.pdf Analysis and Synthesis: On Scientific Method based on a study by Bernhard Riemann] From the [http://www.swemorph.com  Swedish Morphological Society]
* [http://www.sciencemadesimple.com/scientific_method.html Using the scientific method for designing science fair projects] from [http://www.sciencemadesimple.com Science Made Simple]
* [http://www.sciencemadesimple.com/scientific_method.html Using the scientific method for designing science fair projects] from [http://www.sciencemadesimple.com Science Made Simple]
* [http://www.fordham.edu/halsall/mod/modsbook09.html Scientific Revolution] from the ''Internet History Sourcebooks Project''


===Alternative scientific treatments===
[[Category:Philosophy Workgroup]]
* [http://dharma-haven.org/science/myth-of-scientific-method.htm 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.)
[[Category:CZ Live]]
* [http://www.stickyminds.com/sitewide.asp?ObjectId=8965&Function=DETAILBROWSE&ObjectType=ART The Test Case As A Scientific Experiment] (An article that compares the scientific method and [[software testing]])
* [http://www.aeriagloris.com/HowToLearn/TheScientificPrinciple.htm The Scientific Principle] - a simplistic overview
 
===Humor===
* [http://www.audienceoftwo.com/mag.php?art_id=526 Updated Scientific Method]
 
[[Category:Scientific method| ]]
 
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Revision as of 01:01, 20 January 2007

The scientific method is how scientists investigate phenomena and acquire new knowledge. It is based on observable, empirical, measurable evidence, subject to the principles of reasoning[1]. Scientists propose hypotheses to explain phenomena, and test those hypotheses by examining the evidence from experimental studies. Scientists also formulate theories that encompass whole domains of inquiry, and which bind hypotheses together into logically coherent wholes.

"Science is a way of thinking much more than it is a body of knowledge." (Carl Sagan)[2]

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)[3]

Elements of scientific method

According to Charles Darwin ,

". . .science consists in grouping facts so that general laws or conclusions may be drawn from them." [4]

Darwin's simple account begs many questions. What do we mean by ‘facts’? How much can we trust our senses to enable us to believe that what we see is true? How do scientists ‘group’ facts? How do they choose which facts to pay attention to, and is it possible to do this in an objective way? And having done this, how do they draw any broader conclusions? How can we know more than we observe directly?

We live in a world that is not directly understandable. We sometimes disagree about the ‘facts’ we see around us, and some things in the world are at odds with our understanding. What we call the “scientific method” is an account of how scientists gather and report observations in ways that will be understood by others and accepted as valid evidence, and how they construct explanations that will be consistent with the world, withstand logical and experimental scrutiny, and provide the foundations for further increases in understanding.

The English philosopher Francis Bacon is often credited as the pioneer of the modern scientific method. He proposed that scientists should "empty their minds" of self-evident truths and, by 'observation and experimentation' should generate hypotheses by a process known as induction.[5] Bacon described many of the commonly accepted principles of scientific method, in particular, he emphasised the importance of observation, experiments, and independent corroboration. He nevertheless 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. And then the way is still to be made by the uncertain light of the sense, sometimes shining out, sometimes clouded over, through the woods of experience and particulars; while those who offer themselves for guides are (as was said) themselves also puzzled, and increase the number of errors and wanderers. In circumstances so difficult neither the natural force of man's judgement nor even any accidental felicity offers any chance of success. No excellence of wit, no repetition of chance experiments, can overcome such difficulties as these. Our steps must be guided by a clue... [6]

The success of science, as measured by the technological achievements that have changed our world, have led many to conclude that this must reflect the success of some methodological rules that scientists follow. However, not all philosophers accept this conclusion; notably, the philosopher Paul Feyerabend 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 [7] . 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. [8] To Feyeraband, there is no fundamental 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." [9]

Nevertheless, in the Daubert v. Merrell Dow Pharmaceuticals [509 U.S. 579 (1993)] 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."[10]

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. Most important of all, the man of science must exhibit foresight.Henri Poincaré[11]

A hypothesis is a proposed explanation of a phenomenon. It is 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. Scientists use many different means to generate hypotheses, including their own creative imagination, ideas from other fields, and by induction.Charles Sanders Peirce 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".[12]

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 plausible.

Popper and Kuhn

The philosopher Karl Popper, in The Logic of Scientific Discovery, a book that Sir Peter Medawar called "one of the most important documents of the 20th century", argued that this 'hypothetico-deductive' method was the only sound way by which science makes progress. He argued that the alternative '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. 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.

For Popper, theory is 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 therefore, 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 the content of a theory should be judged by the extent to which it inspired testable hypotheses; while theories always also contain many elements that are not falsifiable, Popper argued that these should be kept to a minimum. However, this was not the only criterion in choosing a theory; 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.

Popper's views on falsifiability were in marked contrast to those of his contemporary, the historian Thomas Kuhn. Kuhn's own book "The Structure of Scientific Revolutions" was no less influential than Popper's, but its message was very different. Kuhn analysed times in the history of science when one dominant theory was replaced by another - such as the replacement of Ptolemy's heliocentric model of the Universe with the Copernican geocentric model, and the replacement of Newtonian laws of motion with Einstein's theory of Relativity. In many respects Popper was asserting his rules for 'good science', Kuhn considered himself to be reporting what scientists actually did, although he believed that as what they did was successful, probably there was merit in what they did. Kuhn concluded that falsifiability had played almost no role in the 'scientific revolutions' where one paradigm was replaced by another. He argued that scientists working in a field resisted the alternative interpretations of 'outsiders', and tenaciously defended 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 field when one theory is dominant; progress occurs by the "puzzle solving" of scientists who are trying not to challenge it, but to extend its scope and explanatory power, bringing theory and fact ito closer agreement by a "strenuous and devoted attempt to force nature into the conceptual boxes supplied by professional education".[13]

Experiments and observations

Werner Heisenberg in a quote that he attributed to Albert Einstein , stated [14]

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.

Reductionism

For much of the 20th century, the dominant approach to science has been reductionism – the attempt to explain all phenomena by basic laws of physics and chemistry. This principle has ancient roots - Francis Bacon (1561-1626) quotes Aristotle as declaring "That the nature of everything is best seen in his smallest portions." [15] In many fields, however, reductionist explanations are impractical, and all explanations involve 'high level' concepts. Nevertheless, the reductionist belief has been that the role of science is to progressively explain high level concepts by concepts closer and closer to the basic physics and chemistry. For example, to explain the behaviour of individuals we might refer to motivational states such as hunger. These reflect features of brain activity that are still poorly understood, but we can investigate, for example, the 'hunger centres' of the brain that house these drives. These centres involve many neural networks – interconnected nerve cells, and each network we can be probed in detail. These networks in turn are composed of specialised neurons that can be analysed individually. These nerve cells have properties that are the product of a genetic program that is activated in development – and so are reducible to molecular biology. However, while behaviour is thus in principle reducible to basic elements, explaining the behaviour of an individual in terms of the most basic elements has little predictive value, because the uncertainties in our understanding are too great.

Measurement

The reductionist approach assigned particular importance to measurement of quantities. Measurements may be tabulated, graphed, or mapped, and statistical analysed; often these representations of the data use tools and conventions that are at a given time, accepted and understood by scientists within a given field. Measurements may need specialized instruments such as thermometers, microscopes, or voltmeters, whose properties and limitations are familiar within the field, and scientific progress is often intimately tied to their development. Measurements also provide operational definitions: a scientific quantity is defined precisely by how it is measured, in terms that enable other scientists to reproduce the measurements. Scientific quantities are often characterized by units of measure which can be described in terms of conventional physical units. Ultimately, this may involve internationally agreed ‘standards’; for example, one second is defined as exactly 9,192,631,770 oscillations or cycles of the cesium atom's resonant frequency [6]. The scientific definition of a term sometimes differs substantially from their natural language use; mass and weight overlap in meaning in common use, but have different meanings in physics. All measurements are accompanied by the possibility of error, so their uncertainty is often estimated by repeating measurements, and seeing by how much these differ. Counts of things, such as the number of people in a nation at a given time, may also have an uncertainty: counts may represent only a sample, with an uncertainty that depends upon the sampling method and the size of the sample.

The scientific method in practice

The UK Research Charity Cancer Research UK gives an outline of the scientific method, as practised by their scientists [7]. The quotes that follow are from this outline

[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. They then try to prove if their hypothesis is right or wrong. 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…

Einstein's prediction (1907): Light bends in a gravitational field

From Einstein's theory of General Relativity several predictions can be derived. According to this theory, light will appear to 'bend' in a gravitational field, by an amount that depends on the strength of the field. Arthur Eddington's observations made during a solar eclipse in 1919 supported General Relativity rather than the Newtonian theories that it replaced.

In his 1958 book, Personal Knowledge, 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.

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…

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 consistent with a generally accepted theory than to publish data that contradict it. This helps to ensure the stability of the accepted theory, but 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.[16] 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." [17]

The scientific literature

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

Sir Peter Medawar, Nobel laureate in Physiology and Medicine in his article “Is the scientific paper a fraud?” argued that "The scientific paper in its orthodox form does embody 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 [18]. Accordingly, scientists keep detailed records of their experiments, to provide evidence of their effectiveness and integrity and assist in reproduction. 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. [19]

Scientific ethics

It is rare for scientists to deliberately falsify their results, although there have been well publicised examples of this. Any scientist who does so takes an enormous risk, because if the claim is important it is likely to be subjected to close scrutiny, and if it is wrong then the reputation of the scientist will suffer regardless of whether his mistakes were honest or not. Honor in Science, published by Sigma Xi, quotes C.P. Snow (The Search 1959): "The only ethical principle which has made science possible is that the truth shall be told all the time. If we do not penalise false statements made in error, we open up the way, don’t you see, for false statements by intention. And of course a false statement of fact, made deliberately, is the most serious crime a scientist can commit."[20]

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 following form "If a given hypothesis is true, the chance of getting the results that we observed is (say) only 1 in 20 or less (P < 0.05), so it is very likely that the hypothesis is wrong, and accordingly we reject it.

This notion of a hypothesis is quite different to Popper's. For instance, we might predict that a certain chemical will produce a certain effect. However what we test is often not this, but the complementary null hypothesis - that the chemical will have no effect[8]. The reason for thisis that if our original hypothesis tells us that there will be an effect but is vague about its expected magnitude, we can still logically disprove the null hypothesis (by showing an effect), even though we cannot disprove the hypothesis that the chemical is effective as we cannot exclude the possibility that the effect is smaller than we can measure reliably. The best answer might be to choose hypotheses that give precise predictions, but in many areas of science 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, but might not know how big an effect to expect because of many uncertainties - how many people in a genetically variable population will be resistant to the drug? for example, and how quickly will tolerance to the drug develop in people who respond well?

In fact, this is not hypothesis testing in Popper's sense, because this test does not put the original hypothesis 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 put measure the degree of support that such evidence gives to a hypothesis. [21]

An important school of Bayesian statistics seeks to provide a statistical basis for support by induction, and some areas of science use these approaches. However, often this approach is not tenable because of the difficulty of attaching a priori probabilities in any meaningful way to the alternative predicted outcomes of an experiment.

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 conntrol 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"[22]


See Also

Notes and references

  1. ↑ Isaac Newton (1687, 1713, 1726) "[4] Rules for the study of natural philosophy", Philosophiae Naturalis Principia Mathematica, Third edition. The General Scholium containing the 4 rules follows Book 3, The System of the World on pp 794-796 of I. Bernard Cohen and Anne Whitman's 1999 translation, University of California Press ISBN 0-520-08817-4
  2. ↑ Sagan C (1987) The fine art of baloney detection Parade MagazineFeb 1, p 12­13
  3. ↑ Medawar P (1982) Pluto's Republic, Oxford University Press; see [1]
  4. ↑ From the autobiography of Charles Darwin [2]
  5. ↑ Bacon, Francis (1620) Novum Organum (The New Organon)
  6. ↑ from Preface to The Great Instauration; 4.18 quoted in Pesic P (2000)The Clue to the labyrinth: Francis Bacon and the decryption of nature Cryptologia. Francis Bacon should not be confused with Roger Bacon, a Franciscan friar who also has claims to be a pioneer of observation and experiment, and who was imprisoned when his work challenged the dogma of the Church.[3]
  7. ↑ Feyerabend PK (1975) Against Method, Outline of an Anarchistic Theory of Knowledge Reprinted, Verso, London, UK, 1978
  8. ↑ Feyerabend's 'anything goes' argument explained at the Galilean Library. Criticisms such as his led to the strong programme, a radical approach to the sociology of science.
  9. ↑ Huxley TH (1863) From a 1863 lecture series aimed at making science understandable to non-specialists
  10. ↑ Text of the opinion, LII, Cornell University; Daubert-The Most Influential Supreme Court Decision You've Never Heard of
  11. ↑ Henri Poincaré (1905)Science and Hypothesis
  12. ↑ cited in Bargar RR, Duncan JK (1982) Cultivating creative endeavor in doctoral research J Higher Educ 53:1-31 doi:10.2307/1981536
  13. ↑ Kuhn TS (1961) The Function of Measurement in Modern Physical Science ISIS 52:161–193
    • Kuhn TS (1962)The Structure of Scientific Revolutions University of Chicago Press, Chicago, IL. 2nd edition 1970, 3rd edition 1996
    • Kuhn TS (1977) The Essential Tension, Selected Studies in Scientific Tradition and Change University of Chicago Press, Chicago, IL
    • A Synopsis from the original by Professor Frank Pajares, From the Philosopher's Web Magazine
    • Moloney DP (2000) First Things 10153-5
  14. ↑ Heisenberg, Werner (1971) Physics and Beyond, Encounters and Conversations, A.J. Pomerans (trans.), Harper and Row, New York, NY pp.63–64
  15. ↑ Francis Bacon 'The Advancement of Learning' [4]
  16. ↑ Sagan L (1967) On the origin of mitosing cells" J. Theor Biol 14:255-74 Abstract
  17. ↑ John Brockman, The Third Culture, New York: Touchstone 1995, 144
  18. ↑ Georg Wilhelm Richmann was killed by lightning (1753) when attempting to replicate the 1752 kite experiment of Benjamin Franklin. Krider P (2006) Benjamin Franklin and lightning rods Physics Today 59:42 [5]
  19. ↑ Carafoli E (2002) Calcium signalling: a tale for all seasons PNAS USA 99:115-22
  20. ↑ Under Federal regulations (the Federal Register, vol 65, no 235, December 6, 2000) A finding of 'research misconduct' requires that There be a significant departure from accepted practices of the relevant research community; and The misconduct be committed intentionally, or knowingly, or recklessly; and The allegation be proven by a preponderance of evidence.
  21. ↑ In appendix ix to The Logic Popper states: "As to degree of corroboration, it is nothing but a measure of the degree to which hypothesis h has been tested...it must not be interpreted therefore as a degree of the rationality of our belief in the truth of h...rather it is a measure of the rationality of accepting, tentatively, a problematic guess."
  22. ↑ McClintock B (1987) The discovery and characterization of transposable elements: the collected papers of Barbara McClintock ed John A. Moore. Garland Publishing, Inc. ISBN 0-8240-1391-3. (Introduction)

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