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'''Intelligent design''' (ID) is the designation for a claim that certain fundamental features of the universe and living things are best explained by purposeful causation—a "higher intelligence."  
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'''Intelligent design''' ('''ID''') is the claim that fundamental features of the [[universe]] and [[life|living things]] are best explained by purposeful causation—a "higher intelligence." Proponents of ID argue that conventional [[biology|biological]] theory of [[evolution]] through [[natural selection]] cannot explain the origin of many highly complex features of living [[organism]]s; they argue that some such features are better explained as the result of the intervention of a directed process that they describe as an intelligence. Critics of ID, including the overwhelming majority of academic biologists, consider that these arguments are [[logic]]ally unsound and reflect a flawed understanding of modern biology; they consider that conventional biological theories explain the evolution of complex features of organisms elegantly and efficiently. Critics have also accused its supporters, nearly all of whom believe in a personal [[God]], of using ID primarily as a way to get around U.S. legal restrictions on teaching about God in the classroom. However, ID proponents claim that ID does not require belief in a personal God to support its arguments.


Proponents of ID point to examples in the natural world, such as living organisms, whose origins, in their view, are the result of the intervention of a directed process that they describe as an intelligence, rather than by evolution through natural selection.  
The U.S. National Academy of Sciences has concluded that, in its present form, ID cannot be regarded as [[science|scientific]] because the claims made by its proponents are not testable.<ref>''The National Academies Press'': '[http://www.nap.edu/books/0309064066/html/25.html Science and Creationism: A View from the National Academy of Sciences, Second Edition (1999)].'</ref> See [[intelligent design movement]] for an account of political efforts to  promote education about ID in schools.


The U.S. National Academy of Sciences has concluded that in its present form, intelligent design cannot be classified as scientific hypothesis or theory because the claims made by proponents of intelligent design are not testable.<ref>''The National Academies Press'': '[http://www.nap.edu/books/0309064066/html/25.html Science and Creationism: A View from the National Academy of Sciences, Second Edition (1999)].'</ref>
==Arguments for intelligent design==
The classic [[Design argument for the existence of God|design argument]] for the existence of an intelligent creator may be traced from ancient philosophy, through the works of medieval scholastics such as the philosopher-theologian [[Thomas Aquinas|Saint Thomas Aquinas]] (1225-1274), who argued that the existence of God could be deduced by reason.  


See [[intelligent design movement]] for an account of the political efforts to employ ID to rebut evolution to better promote education about intelligent design within schools.
In the 18th century, the theologian [[William Paley (theologian)|William Paley]] (1743-1805) introduced the "watchmaker analogy", one of the best known metaphors in the philosophy of science, as an argument for the existence of God.<ref>*{{Gutenberg author|id=William_Paley|name=William Paley}}
 
==An Argument for Intelligent Design==
The classic [[Design argument for the existence of God|design argument]] for the existence of an intelligent creator may be traced from ancient philosophy, through the works of medieval scholastics such as the philosopher-theologian [[Saint Thomas Aquinas]] (1225-1274), who argued that the existence of God could be deduced by reason.
 
In the 18th century,  Deist theologian [[William Paley]] (1743-1805) introduced the "watchmaker analogy", one of the best known metaphors in the philosophy of science, as an argument for the existence of God.<ref>*{{gutenberg author|id=William_Paley|name=William Paley}}
*[http://www.ucmp.berkeley.edu/history/paley.html William Paley - the watchmaker analogy]
*[http://www.ucmp.berkeley.edu/history/paley.html William Paley - the watchmaker analogy]
*[http://www.anselm.edu/homepage/dbanach/dnr.htm text of David Hume, ''Dialogues concerning Natural Religion'']; see especially Parts II-VIII for Hume's classic refutation of the design argument
*[http://www.anselm.edu/homepage/dbanach/dnr.htm text of David Hume, ''Dialogues concerning Natural Religion'']; see especially Parts II-VIII for Hume's classic refutation of the design argument
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*[http://www.kids4truth.com/watchmaker/watch.html An Animated Presentation of the Watchmaker Analogy]
*[http://www.kids4truth.com/watchmaker/watch.html An Animated Presentation of the Watchmaker Analogy]
*{{cite book | first = Richard | last = Dawkins | authorlink = Richard Dawkins | title = The Blind Watchmaker | publisher = W. W. Norton & Company, Inc. | location = New York | origyear = 1986 | year = 1996 | id = ISBN 0-393-31570-3 }}</ref> The argument is, in essence, as follows:  
*{{cite book | first = Richard | last = Dawkins | authorlink = Richard Dawkins | title = The Blind Watchmaker | publisher = W. W. Norton & Company, Inc. | location = New York | origyear = 1986 | year = 1996 | id = ISBN 0-393-31570-3 }}</ref> The argument is, in essence, as follows:  
Imagine walking on a pebbled beach, where the pebbles may be wonderfully shaped, beautiful in different ways, interesting and varied one from another. However interesting and beautiful you find them, you will not doubt that they are the products of purely natural causes. However, if amongst the pebbles you find a watch, even if you have never seen a watch before, you will immediately recognise it as qualitatively different from the pebbles. Inspecting it, from the intricacy of its design, and the clear purpose of that design, you will inevitably and correctly conclude that the watch is not a 'natural' object but an artifact, something designed by a powerful and intelligent agent.  
Imagine walking on a pebbled beach, where the pebbles may be wonderfully shaped, beautiful in different ways, interesting and varied one from another. However interesting and beautiful you find them, you will not doubt that they are the products of purely natural causes. However, if amongst the pebbles you find a watch, even if you have never seen a watch before, you will immediately recognise it as qualitatively different from the pebbles. Inspecting it, from the intricacy of its design, and the clear purpose of that design, you will inevitably and correctly conclude that the watch is not a natural object but an artifact, something designed by a powerful and intelligent agent.  


Casual observation might similarly lead to the conclusion that, compared to a watch, even the simplest living form is incredibly complex, giving it the appearance of being designed for a purpose. There must be a ''designer'', said Paley, "and that designer is God."
Casual observation might similarly lead to the conclusion that, compared to a watch, even the simplest living form is incredibly complex, giving it the appearance of being designed for a purpose. There must be a ''designer'', said Paley, "and that designer is God."


To many who believe in a Creator of the universe, the idea that the nature of living things might contain some evidence that they have been built purposefully rather than having been evolved by natural selection is a natural one. Some modern proponents of intelligent design have accordingly broached this issue in a theoretical manner, by considering how, objectively, it might be possible to ascertain whether any particular object has been designed for a purpose as opposed to having evolved to fit an apparent purpose. These proponents have proposed two criteria for deciding whether something has been designed in this way. the second to the noption of "specified complexity".
To many who believe in a Creator of the universe, the idea that the nature of living things might contain some evidence that they have been built purposefully rather than having been evolved by natural selection is a natural one. Some modern proponents of ID have accordingly broached this issue in a theoretical manner, by considering how, objectively, it might be possible to ascertain whether any particular object has been designed for a purpose as opposed to having evolved to fit an apparent purpose<ref>[http://www.actionbioscience.org/evolution/nhmag.html Intelligent Design?] a special report reprinted from ''Natural History'' magazine</ref>. Thus, William Dembski has argued that ID can be formulated as a scientific theory of information that has empirical consequences and which is devoid of any religious commitments.[http://www.arn.org/docs/dembski/wd_idtheory.htm] By this view, intelligent design asks whether design can be detected in nature from purely scientific and mathematical considerations.
 
These proponents have proposed two criteria for deciding whether something has been designed in a way that cannot be accounted for by evolution through natural selection:


===Irreducible Complexity===
===Irreducible complexity===
The first criterion relates to the notion of "irreducible complexity". Proponents of intelligent design argue that irreducible complexity is a common feature of biological systems, but cannot plausibly be accounted for by evolution through 'undirected' natural selection. They argue instead that irreducibly complex systems must have arisen by some form of 'directed' evolution, i.e. towards a predetermined end.  They assume without argument or evidence that directedness presupposes an Intelligent Designer.
A complex system is a system with many component parts, and which depends on many interactions between those component parts to perform its particular defined function. A system is ''irreducibly complex'' if removing of any one of these parts causes it to cease functioning<ref>Michael Behe (1996), ''Darwin's Black Box: The Biochemical Challenge to Evolution'', Free Press</ref>. In ''No Free Lunch'',<ref>Dembski WA (2001) ''No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence'' Rowman & Littlefield, ISBN 0742512975 </ref> William Dembski extends this basic definition, and states that a system is irreducibly complex


A complex system is a system that performs a discrete function, where there are many interactions between its component parts. A system is ''irreducibly complex'' if removing of any one of the parts of a complex system causes it to effectively cease functioning. In ''No Free Lunch'',<ref>Dembski WA (2001) ''No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence'' Rowman & Littlefield, ISBN 0742512975 </ref> William Dembski extends this basic definition, and states that a system is irreducibly complex
if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function.


''"if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function."''
He and other proponents of ID argue that irreducible complexity is a common feature of biological systems, and claim that it cannot plausibly be accounted for by evolution through "undirected" natural selection. They argue that irreducibly complex systems must have arisen by some form of "directed" evolution, i.e. towards a predetermined end. 


Evolution by natural selection proceeds via successive minor alterations to the form of a structure, each of which results in an incremental improvement in fitness. It has long been recognised that one of the most difficult challenges for biologists is to explain how highly complex structures can have evolved in this way, as the requirement that every intermediate form must have a selection advantage beyond the previous form is a constraint that severely limits the possible paths by which evolution might have proceeded. This constraint becomes particularly hard to reconcile with evolutionary explanations when the final form absolutely requires the involvement of each of several different elements for the final form to have any effective functionality. Thus, a structure is said to be 'irreducibly complex' if any modification of any of several different elements leads to a wholly non-functional structure. To proponents of intelligent design, it is inconceivable that evolution by natural selection could have perfected multiple elements that only have any functionality when all are complete and assembled. To them, this is clear evidence of design in anticipation of a purpose, design according to a predetermined plan or "blueprint",
Evolution by natural selection can proceed via successive minor alterations to the form of a structure, each of which results in an incremental improvement in fitness. One of the challenges for biologists is to explain how complex structures can have evolved in this way, as the apparent requirement that every intermediate form must have a selection advantage beyond the previous form limits the possible paths by which evolution might have proceeded. For example, Richard Dawkins, in ''Climbing Mount Improbable'' (ISBN 0140179186) discusses evolution of the elephant's trunk. "In the evolution of the elephant from its short-nosed ancestors, there must have been a steady elongation of steadily longer noses...It must have been the case that, as each inch was added to the length of the average trunk, the trunk became better at its job. It must never be possible to say anything like 'That medium sized trunk is no good because it is neither one thing nor the other - falls between two stools, but don't worry, give it another few million years and it'll be fine. No animal ever made a living purely by being on the evolutionary path to something better."
 
However, modern evolutionary biologists point to many ways, by which complexity can emerge through natural selection. For example, it is not strictly required that every intermediate be fitter - some may harbour neutral mutations with incipient functionality. Natural selection acts primarily to eliminate harmful mutations and to actively sustain beneficial mutations; mutations that have little or no effect on fitness are called "neutral" and these will not be actively eliminated by selection pressures. Neutral mutations tend to accumulate in a population over time, contributing to inter-individual variability. This variability can provide the fuel for rapid evolution through natural selection when environmental conditions change, because some mutations that were originally neutral may have an effect on fitness in the changed conditions. Some intermediate forms in evolution may accordingly have neutral mutations that become beneficial when there is a subsequent mutation or when there is a change in selection pressure.


===Specified complexity===
===Specified complexity===
The second criterion relates to the concept of "specified complexity". Complex structures can arise by natural processes, or by chance mechanisms and some may happen to have functionality that can be exploited; thus complexity ''per se'' is not evidence of intentional design, nor is the improbability of a structure or pattern arising by simple chance any evidence that it did not in fact arise by chance. However, proponents of intelligent design argue that when a structure clearly fulfils a function that is essential for the function of living things - in other words when an outcome of an evolutionary process is absolutely required by the organism, then they argue that it is legitimate to consider how likely it is that that outcome could have been achieved through the chance processes that are said to be involved.
Intelligent Design advocate William Dembski advances the concept of ''specified complexity'' as describing the procedure used to identify objects that have been apparently designed—objects that cannot be explained through natural mechanisms. Proponents of ID argue that when a structure fulfils a function that is ''essential'' for the function of living things, then it is legitimate to consider how likely it is that outcome could have been achieved through the chance processes that are said to be involved.


This is a complex argument, perhaps best explained by analogy. If an archer fires an arrow into the air at random, then it might land anywhere within a large area, and the probability of it landing at any particular place within this area is very low. In this case, we cannot draw any conclusions from the simple fact that the arrow lands at a place where it has a very low probability of landing - the arrow must, after all land somewhere. However, if it lands in the very centre of a predrawn target that lies on the grass, then we can draw some conclusions - we might reasonably conclude that the arrow was not fired at random, but was ''aimed''. This conclusion comes not solely from the fact that the outcome of firing the arrow was an unlikely complex event, but from this combined with the fact that it was a prespecified complex event - and the evidence of the specification is there in the form of the target on the grass.
This argument is perhaps best explained by analogy. If an archer fires an arrow into the air at random, then it might land anywhere within a large area, so the probability of it landing at any ''particular'' place within this area is very low. In this case, we cannot draw any conclusions from the simple fact that the arrow lands at a place where it has a very low probability of landing - the arrow must, after all, land somewhere. However, if it lands in the very centre of a predrawn target, then we might try to conclude that the arrow was not fired at random, but was ''aimed''. This conclusion comes not solely from the fact that the outcome of firing the arrow was an unlikely complex event, but from this combined with the fact that it was a prespecified complex event. However, this conclusion cannot be drawn without a statistical analysis of a population of fired arrows that shows the arrival at the target was not an accident. Of course, in the case of biology, all the organisms that had unsuccessful adaptions died out, providing a challenge to establish experimentally whether random adaptations existed in the past. Instead, one can argue on theoretical grounds the probability of Shakespeare being written during random typing by monkeys, without regard for any actual experimental findings.  
   
   
Proponents of intelligent design argue that there are features of living organisms that show such ''specified complexity''. In other words, evolutionary processes have achieved outcomes that are complex in specific ways that, to proponents of intelligent design, are suggestive of a predetermined purpose. These proponents argue that, for such outcomes, it is legitimate to calculate the probability of their occurrence according to the conditional probabilities of occurrence of the multiple chance elements that are involved. Dembski has argued that when such calculation produces an impossibly tiny figure for the conditional probability, then the hypothesis that it is the result of those chance processes must be discarded. He has proposed that conditional probabilities of the order of 10-120 are thus evidence of purpose, or intelligent design.
Proponents of ID argue that there are features of living organisms that show such specified complexity. These proponents argue that, for such features, it is legitimate to calculate the probability of their occurrence according to the conditional probabilities of occurrence of the multiple chance elements that are involved. Dembski has proposed that conditional probabilities of the order of 10<sup>-120</sup> are thus evidence of ''purpose'', and thus of some 'directing intelligence'.


The statistical reasoning behind these arguments is complex, and the notion of specified complexity is not one that has been widely endorsed by professional mathematicians and information theorists. Part of the problem with applying this approach is the problem of assigning probabilities to particular molecular events in a reliable way. Another part of the problem arises from the difficulty in deciding what exactly constitutes specified complexity in a biological context.
The notion of specified complexity has not been widely endorsed by professional mathematicians and information theorists<ref>Richard Wein, [http://www.talkorigins.org/design/faqs/nfl/ Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch]</ref><ref>John S. Wilkins and Wesley R. Elsberry, [http://www.talkdesign.org/faqs/theftovertoil/theftovertoil.html The advantages of theft over toil: the design inference and arguing from ignorance], ''Biology and Philosophy'', 2001.</ref>. One problem with applying this approach is the problem of assigning probabilities to particular molecular events in a reliable way. Another arises from the difficulty in deciding what exactly constitutes specified complexity in a biological context.


===Intelligent design and molecular biology===
===Intelligent design and molecular biology===
It is important to note that proponents of intelligent design do ''not'' deny evolution, nor do they dispute any of the findings of molecular biology. On the contrary, they regard evolution as part of the mechanisms by which living things are designed, and they consider that molecular biology, by displaying the vast complexity that underlies even the simplest living things, provides evidence that makes explanations based on natural selection less plausible rather than more plausible.
Proponents of ID do ''not'' deny evolution, nor do they dispute the findings of [[molecular biology]]. They regard evolution as part of the mechanisms by which living things are designed, and they consider that molecular biology, by displaying the vast complexity that underlies even the simplest living things, provides evidence that makes explanations based on natural selection less rather than more plausible.  


Interestingly, watches have been found in living organisms. These are molecular timing devices present in organisms, that produce 'circadian rhythms', biological cycles with a definite innately determined time period. For instance, such a timekeeper mechanism has been found in single celled blue-green algae and enables this microbe's genes to vary in their intensity of activity in rhythm with daily changes in sunlight. The biological watch inside the microbe is composed of widely distributed genetic components recruited from other signalling and information processing activities of the cell. In this case the watch is constructed from simple molecular components that function regularly and predictably according to well characterised principles of biochemistry - the timing mechanism arises as a result of feed back loops whereby gene products regulate gene expression; in this case there seems no need to postulate intelligent design in its construction. <ref>Robertson McClung C (2006) Two-component signaling provides the major output from the cyanobacterial circadian clock. Proc Natl Acad Sci USA 103: [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1832255 11819–20]</ref>
Interestingly, 'watches' have been found in living organisms. These are molecular timing devices that produce '[[circadian rhythms]]', biological cycles with an innately determined time period. One such timekeeping mechanism has been found in [[blue-green algae]], and it enables this microbe's genes to vary in their intensity of activity in rhythm with daily changes in sunlight. The biological watch inside the microbe is composed of widely distributed genetic components recruited from other signalling and information processing activities of the cell. In this case, the watch is constructed from simple molecular components that function regularly and predictably according to well characterised principles of biochemistry - the timing mechanism arises as a result of feedback loops whereby gene products regulate gene expression.<ref>Robertson McClung C (2006) Two-component signaling provides the major output from the cyanobacterial circadian clock. ''Proc Natl Acad Sci USA'' 103:[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1832255 11819–20]</ref>


==Modern Evolutionary Synthesis==
==Modern Evolutionary Synthesis==
The currently accepted account of the origin of living things is known as the "Modern Evolutionary Synthesis". Modern Evolutionary Synthesis is a theoretical and observational framework  which expresses the theory of evolution by natural selection in a form consistent with molecular biology and population genetics. By this theory, all extant living things are the products of descent with modification from common ancestors that lived 3-4 billion years ago. This theory (and an abundant array of evidence of evolutionary process that are seen in nature) explains all evolution as resulting from processes of natural selection among populations among which genetic novelty and novel combinations of genetic components are generated by numerous genetic mechanism. Natural selection is a creative process because, as favorable  genotypes accumulate over generations and combine in different ways, this produces a huge diversity of organisms - more than 10 million living species.  
ID proponents argue that the natural selection mechanisms that have been used to explain the "apparent design" of numerous components and interactions of living organisms cannot explain all features of organism complexity<ref>[http://www.intelligentdesignnetwork.org/ Intelligent Design] Intelligent Design network.</ref>, but their critics argue that they underestimate the sophistication of modern evolutionary theory, and in particular underestimate the creative capacity of natural selection.
The currently accepted account of the origin of living things is known as the "[[Modern Evolutionary Synthesis]]". This expresses the theory of evolution by natural selection in a form consistent with molecular biology and [[population genetics]]. By this theory, all extant living things are the products of descent with modification from [[common ancestor]]s that lived 3-4 billion years ago. This theory (and an abundant array of evidence of evolutionary process that are seen in nature) explains all evolution as resulting from processes of natural selection among populations among which genetic novelty and novel combinations of genetic components are generated by many different genetic mechanisms. Natural selection is not the single simplistic process that the common characterisation "survival of the fittest" suggests, but embraces a very wide array of processes and pressures that lead to differential reproductive success in populations. The creative elements of natural selection emerge because, as selected genotypes accumulate over many, many generations and combine in different ways to produce novel phenotypes, this produces a huge diversity of organisms (today there are more than 10 million living [[species]], a tiny percentage of all the species that ever existed).  


There are important features that distinguish the 'design' achieved by natural selection from the kind produced by an intelligent designer. Natural selection is undirected in that it has no preordained plan, but is simply a result of the differential survival and reproduction of living beings. Natural selection and genetic mechanism provide powerful ways of generating novel design features which are stored in the DNA code and passed on to the subsequent generations.. Natural selection has no foresight, and so environmental changes may threaten the survival of organisms that were thriving. As a result, species extinction is common: it is estimated that "more than 99% of all species that have ever lived on Earth are now extinct." <ref>Ayala FJ (2007) Colloquium Papers: Darwin's greatest discovery: Design without designer.
There are important features that distinguish the 'design' achieved by natural selection from the kind produced by an intelligent designer. Natural selection is undirected in that it has no preordained plan, but is simply a result of the differential survival and reproduction of living beings. Natural selection and genetic mechanism provide powerful ways of generating novel features which are stored in the DNA code and passed on to the subsequent generations, but natural selection has no foresight, and so environmental changes may threaten the survival of organisms that were thriving. As a result, species extinction is common: it is estimated that, of all the species that ever lived on Earth, more than 99% are now extinct. Critics of ID see the evidence of massive extinction of species as inconsistent with the notion of intelligent design of the world we live in.<ref>Ayala FJ (2007) Colloquium Papers: Darwin's greatest discovery: Design without designer.
Proc Natl Acad Sci U S A. 104 Suppl 1:8567-73. PMID 17494753</ref>
Proc Natl Acad Sci USA 104 Suppl 1:8567-73. PMID 17494753</ref>


Although most descriptions of evolution assume that all mutations are random with respect to their effects on fitness, some biologists argue that there are important mechanisms which make favourable mutations more likely to occur. For example, Lynne Caparole <ref>Caporale LH (2003) Natural selection and the emergence of a mutation phenotype: An update of the evolutionary synthesis considering mechanisms that affect genome variation. Ann Rev Microbiol 57:467–85
doi: 10.1146/annurev.micro.57.030502.090855 PMID 14527288</ref>
has argued that natural selection favours some mechanisms that increase the likelihood of mutations in particular genes. These mechanisms produce considerable diversity in gene function amongst progeny, and this diversity can facilitate rapid evolution.


Modern proponents of intelligent design argue that evolution by an 'undirected' process like natural selection cannot adequately account for the complexity of life. <ref>[http://www.actionbioscience.org/evolution/nhmag.html Intelligent Design?]
In particular, not all mutations rely on a random change to a single nucleotide base: some involve "mis-copying" the DNA, and these errors are very common for certain types of DNA sequence. For example, when a section of DNA contains a short repeated sequence of nucleotides, the number of repeats can be affected by a common "stuttering error" in DNA replication. The consequences will depend on exactly where in the genome the repeated sequence is located, but if, for example, it occurs in a region that affects how a bacterium responds to an antibiotic, then this diversity makes it more likely that some offspring will be antibiotic resistant. Thus, although accuracy is generally very important in reproducing a genome, some 'errors' are valuable, because the increased diversity of the offspring makes it more likely that some will be well fit to rapidly changing environmental conditions.
a special report reprinted from
Natural History magazine</ref>They argue that essential features of even the simplest extant living things are 'irreducibly complex', in that such features arise only in highly complex systems and do not appear in even a rudimentary form in simple systems. They argue that an irreducibly complex system is very unlikely to be produced by successive, slight modifications of a previously existing system, because any precursor that was missing a crucial part would be unable to function at all.
 
It has not been possible to reconstruct in reliable detail the events that gave rise to the [[Origin of life|simplest form of life]]; there is too much that remains unknown. Accordingly, intelligent design theory argues that it is just as appropriate to postulate an intelligent agent to explain the mysteries of life as it is to postulate an intelligent watchmaker to explain the watch found on a beach.
 
Some ID proponents believe that alternative explanations (including Darwinian evolution) are not feasible, as they argue that the well-documented natural selection mechanisms that have been used to explain the "apparent design" of numerous components and interactions of living organisms cannot explain all features of organism complexity. They see evolution as an "undirected, chance-based process"; ID does not emphasize that selection for reproductive success intrinsically directs evolutionary change towards functional design solutions, or that numerous genetic mechanisms exist to provide a vast array of genetic diversity from which well designed components can be selected. <ref>[http://www.intelligentdesignnetwork.org/ Intelligent Design] Intelligent Design network.</ref>  ID theorists have not considered whether ID is all direction by the designer or some combination of direction and chance.
 
 
==Contemporary and high profile proponents of intelligent design==
[[intelligent design movement| Prominent ID proponent]] William Dembski has a PhD in mathematics from the University of Chicago, and is research professor in philosophy at Southwestern Baptist Theological Seminary in Fort Worth, Texas. In 1998, Cambridge University Press published Dembski's first book, a philosophical monograph entitled ''The Design Inference: Eliminating Chance through Small Probabilities''. Dembski has published several books since, but has published no papers on intelligent design in the peer-reviewed scientific literature. Dembski is particularly associated with the concept of 'specified complexity'.
 
Another prominent proponent, and one particularly associated with arguments related to the concept of 'irreducible complexity', is Michael J. Behe. Behe is professor of biochemistry at Lehigh University in Pennsylvania. Behe holds that some biological structures are too biochemically complex to be plausibly explained as a result of evolution by natural selection. Unlike many in the intelligent design movement, Behe accepts the evidence for the common descent of species, including the conclusion that humans descended from other primates; however, he claims that common descent alone cannot fully explain the differences between species.
 
Both Dembski and Behe are senior fellows of the Discovery Institute's Center for Science and Culture in Seattle. The Discovery Institute is a Christian educational foundation established to promote creationist thought, founded by Stephen C. Meyer, Bruce Chapman and George Gilder. Meyer gained a Ph.D in [[history of science|history]] and [[philosophy of science]] from Cambridge University for a dissertation entitled "Of clues and causes : a methodological interpretation of origin of life studies."
 
The argument has been made that these proponents are not presenting scientific theory for the purpose of advancing science. Opponents have charged that the Discovery Institute and its fellows are using Intelligent Design as a wedge to drive their particular religious agenda into the public schools, where they hope to rebut the teachings and their perceptions about mainstream evolutionary science. Thus far the efforts of the [[Intelligent Design Movement]] have been unsuccessful due to their inability to craft an argument for intelligent design that mainstream science (and the courts) can recognize as scientific hypothesis or theory.


===ID publications===
===ID publications===
====Books====
Many books on ID have been written but few ID research papers or monographs have been published in conventional peer-reviewed scientific journals. However, ID advocates have created several journals devoted to publishing papers on ID (see Bibliography). The ''Kitzmiller vs Dover Area School'' case in 2005 was the first direct challenge brought in U.S. federal courts against a public school district that required ID to be presented to students as an alternative to evolution as an explanation of the origin of life. The plaintiffs successfully argued that ID is a form of creationism, and that the school board policy therefore violated the Establishment Clause of the First Amendment to the Constitution. In testimony, ID proponent Michael Behe admitted that “There are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred.” <ref>[http://en.wikisource.org/wiki/Kitzmiller_v._Dover_Area_School_District/4:Whether_ID_Is_Science#Page_88_of_139 In ''Kitzmiller vs Dover Area School_District 4:Whether ID Is Science]</ref>
Many books on ID have been written <ref>'''Books by Intelligent Design proponents'''
*Michael J. Behe (2006) ''Darwin's Black Box: The Biochemical Challenge to Evolution'' Free Press ISBN 0743290313
*Behe MJ, Dembski WA, Meyer SC (Eds) (2000)''Science and Evidence for Design in the Universe (Proceedings of the Wethersfield Institute)'' Ignatius Press  ISBN 0898708095
*William A. Dembski (2004) ''The Design Revolution: Answering the Toughest Questions About Intelligent Design'' InterVarsity Press, ISBN 0830823751
*William A. Dembski (1998) ''The Design Inference: Eliminating Chance through Small Probabilities'' (Cambridge Studies in Probability, Induction and Decision Theory) Cambridge University Press ISBN 0521623871
*William A. Dembski (2002) ''Intelligent Design: The Bridge Between Science & Theology'' InterVarsity Press ISBN 083082314X
*Percival Davis and Dean H. Kenyon (1989) ''Of Pandas and People: The Central Question of Biological Origins''  (2nd edition 1993) a school-level textbook published by the Foundation for Thought and Ethics ISBN 0-914513-40-0 See [http://www.ncseweb.org/resources/articles/9767_22_padian_1989_gross_misr_10_26_2004.asp a review] by paleontologist Kevin Padian of the [[National Center for Science Education]]
*Walter James Remine (1993). The Biotic Message: Evolution Versus Message Theory. Saint Paul Science ISBN 0-963799-90-8.
*Lee M. Spetner (1997). ''Not by Chance: Shattering the Modern Theory of Evolution''. Judaica Press. Spetner has a PhD in Physics from MIT.</ref>  


====Journals====
On 4 August 2004, a review article by Stephen Meyer, an ID proponent, appeared in the peer-reviewed ''Proceedings of the Biological Society of Washington'', questioning conventional evolutionary explanations for the [[Cambrian Explosion]] and proposing ID as an alternative<ref> Meyer S (2004) The origin of biological information and the higher taxonomic categories. Proc Biol Soc Washington
However, very few ID research papers or monographs have been published in connentional peer-reviewed scientific journals, but ID advocates have created several journals devoted to publishing ID materials.  
117:[http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2177 213-39}</ref> The review questions whether whether conventional biological theory can explain the information explosion evident during the Cambrian period. He says: "For neo-Darwinism, new functional genes either arise from non-coding sections in the genome or from preexisting genes. " He argues that the first leaves too much to luck and chance to be plausible, and the second has the problem that changes to existing genes are almost invariably deleterious. However this neglects many conventional accounts of how genes evolve, including probably the major known mechanism whereby novel genes arise, via gene duplication. Gene duplication is very common through evolution, and means that one copy of a gene can continue to sustain its normal function while the other is "surplus", and is free to accumulate mutations. Thus, by conventional explanations, a new gene doesn't have to be built from nothing - instead evolution is handed an already functional "toy" to play with.  


On 4 August 2004, an article by Stephen Meyer, an intelligent design proponent, appeared in the peer-reviewed ''Proceedings of the Biological Society of Washington'', questioning conventional evolutionary explanations for the Cambrian Explosion and proposing intelligent design as an alternative. Later, however, the Council of the Biological Society of Washington retracted the article. The managing editor for the journal at the time, the process structuralist Richard Sternberg, stated that the article had been properly peer reviewed by three well qualified referees. His decision to publish the paper nevertheless resulted in protests, and colleagues at the [[Smithsonian Institute]], where he was employed, sought to discredit him and created what the The U.S. [[Office of Special Council]] (which is authorized to investigate allegations of prohibited personnel practices and activities prohibited by civil service law) called "a hostile working environment".<ref>[http://www.rsternberg.net The homepage of Richard Sternberg]</ref><ref>[http://www.rsternberg.net/OSC_ltr.htm Decision of the Office of Special Council regarding Richard Sternberg's allegations]</ref>
Later, the Council of the Biological Society of Washington retracted the article. The managing editor for the journal at the time, the process structuralist Richard Sternberg, stated that the article had been properly peer reviewed by three well qualified referees. His decision to publish the paper nevertheless resulted in protests, and colleagues at the [[Smithsonian Institute]], where he was employed, sought to discredit him and created what the U.S. [[Office of Special Council]] (which is authorized to investigate allegations of prohibited personnel practices and activities prohibited by civil service law) called "a hostile working environment".<ref>[http://www.rsternberg.net The homepage of Richard Sternberg]</ref><ref>[http://www.rsternberg.net/OSC_ltr.htm Decision of the Office of Special Council regarding Richard Sternberg's allegations]</ref>


The lack of peer reviewed articles is cited by ID opponents as evidence that ID is unscientific. ID supporters point to the ''Proceedings'' incident as showing just the opposite: that the scientific climate is so prejudiced against ID that not even peer review is enough to overcome publication bias. ID proponent Dominque Tassot of the Center for Studies and Prospectives on Science, France, states the reasons as  
The lack of peer-reviewed articles is cited by some as evidence that ID is unscientific. ID supporters point to the ''Proceedings'' incident as showing the opposite: that the scientific climate is so prejudiced against ID that not even peer review is enough to overcome publication bias. ID proponent Dominque Tassot of the 'Center for Studies and Prospectives on Science', France, states the reasons as  
<blockquote>
<blockquote>[Evolutionary scientists] live and think inside the paradigm of evolution. As Thomas Kuhn explained [in ''The Structure of Scientific Revolutions''], theories are accepted or rejected in order to defend the dominant paradigm. Information which conflicts with that paradigm is set aside, it doesn’t get published.<ref name="InterviewTassot">{{cite journal | author=John L. Allen | title=Interview with Dominque Tassot| journal=National Catholic Reporter| year=22 Aug 2006| url=http://ncronline.org/mainpage/specialdocuments/tassot_interview.pdf}}</ref>
[Evolutionary scientists] live and think inside the paradigm of evolution. As Thomas
Kuhn explained [in the book The Structure of Scientific Revolutions], theories are accepted or
rejected in order to defend the dominant paradigm. Information which conflicts with that
paradigm is set aside, it doesn’t get published.<ref name="InterviewTassot">{{cite journal | author=John L. Allen | title=Interview with Dominque Tassot| journal=National Catholic Reporter| year=22 Aug 2006| url=http://ncronline.org/mainpage/specialdocuments/tassot_interview.pdf}}</ref>
</blockquote>
</blockquote>


==Distinct from creationism==
==Is intelligent design a form of creationism?==
Most proponents of the intelligent design hypothesis are also creationists, meaning they believe the universe was created by a deity or some other power beyond the full comprehension of mortal man. The hypothesis, however, is not the same as [[young earth creationism]], which is a belief that the account of the creation of the universe and of life as given by the Bible is literally true. Intelligent design does not try to identify the designer as supernatural, nor does it try to establish the veracity of a particular narrative, although some leading proponents of intelligent design have stated that they believe the designer to be the Christian God.  
Most proponents of ID are also creationists, meaning they believe the universe was created by a deity or some other power beyond the full comprehension of mortal man. The hypothesis, however, is not the same as [[young earth creationism]], which is a belief that the account of the creation of the universe and of life as given by the Bible is literally true. ID does not try to identify the designer as supernatural, nor does it try to establish the veracity of a particular narrative, although some leading proponents have stated that they believe the designer to be the Christian God. However, some proponents of ID see no conflict between it and evolution, and indeed see evolution as evidence of ID. Many proponents avoid any personification of the source of the ID, and so the focus of ID is different to that of arguments in [[natural theology]], such as the teleological argument.
 
As intelligent design avoids identifying the designer, its focus is different to that of arguments in [[natural theology]], such as the teleological argument. William Dembski argues that intelligent design can be formulated as a scientific theory of information that has empirical consequences and which is devoid of any religious commitments.[http://www.arn.org/docs/dembski/wd_idtheory.htm] By this view, intelligent design asks whether design can be detected in nature from purely scientific and mathematical considerations.
 
Other proponents of intelligent design see no conflict between intelligent design and evolution, and indeed see evolution as evidence of intelligent design.


==Criticisms of intelligent design==
==Criticisms of intelligent design==
One of the main weaknesses of the intelligent design is absence of factual peer-reviewed evidence to support the concept. It is a theoretical opinion which has not been tested by objective evidence demanded by professional science.
Proponents of ID argue that it is a scientific theory rather than a matter of religious belief, despite its base of support in the religious community.<ref> [http://www.ideacenter.org/contentmgr/showdetails.php/id/1136 Primer: Intelligent Design Theory in a Nutshell] Intelligent Design and Evolution Awareness (IDEA)</ref> Courts in the USA have rejected this argument, in part because, for a theory to be 'scientific', it must generate predictions by which it can be tested; in other words, it must be open to attempted disproof. <ref>Ruling, Kitzmiller vs Dover Area School District, [http://www.pamd.uscourts.gov/kitzmiller/kitzmiller_342.pdf Case No. 04cv2688. (PDF)] December 20 2005
*The philosopher of science [[Karl Popper]] argued that a theory that has no testable components "has no connection with the real world."  (see [[Scientific method]]).</ref>


Proponents of intelligent design argue that it is a scientific theory rather than a matter of religious belief, despite its base of support in the religious community.<ref> [http://www.ideacenter.org/contentmgr/showdetails.php/id/1136 Primer: Intelligent Design Theory in a Nutshell] Intelligent Design and Evolution Awareness (IDEA)</ref> Critics and US courts reject this assertion.  Scientists consider that for a theory to be 'scientific' it must generate predictions by which it can be tested; in other words it must be open to attempted disproof. For example, the philosopher of science [[Karl Popper]] argued that a theory that has no testable components "has no connection with the real world."  ID proponents have not yet proposed a test and so it is not a scientific theory in this sense (see [[Scientific method]]).
Critics also hold that the postulate of an intelligent designer is not an explanation for life at all, but a "deus ex machina"--that is, an evasion of attempted explanation. They consider that ID is not a serious alternative to modern biological theory, in particular they consider that the complexity of biological systems can be well explained by conventional biological theory. They also consider that the tenet of ID that perfection in design needs a directing intelligence is inconsistent with many examples in nature of imperfections in design of organisms.<ref>Sober E (2007) What is wrong with intelligent design? Q Rev Biol 82:3-8 PMID 17354991</ref>


Critics dismiss the "null hypothesis" claim that the intervention of a higher intelligence is the null hypothesis that must be accepted if science can not explain certain phenomenon. Critics do not regard such a lack of understanding as good evidence for any scientific or philosophical conclusions.  
There are also many critics of ID who are religious, and who believe that the role of science is to seek natural, physical explanations of the world; although they believe that there is a God who created the world and life in it, for them this is a matter of faith not of science. Some critics doubt the intellectual honesty of ID theory, in that they consider that the only reason for promoting it is for the religious message that it implies, not for the intrinsic merits of the arguments.


Critics hold that the postulate of an intelligent designer is not an explanation for life at all, but a "deus ex machina"--that is, an evasion of attempted explanation. By this view, intelligent design has no content: it concludes where there is ignorance, that is proof of ID.<ref>Sober E (2007) What is wrong with intelligent design? Q Rev Biol. 2007 Mar;82(1):3-8 PMID 17354991</ref>  
While some proponents of ID see evidence of design in how well complex structures fit their purpose, molecular biologists see something very different in the fine details of those structures. So far from seeing genetic information being perfectly and economically fashioned to suit a given purpose, they see wastefulness, duplication, errors, and the detritus of now redundant genes in gene sequences &mdash; in other words, things they would expect to see as the residue of evolution by natural selection. In short, despite the appearance of efficient design at a high level, at a molecular level the design shows few signs of purposeful intelligence but many signs of chance processes.
<ref>Zuckerkandl E (2006) Intelligent design and biological complexity. Gene 385:2-18 PMID 17011142 </ref> However, other proponents of ID note that ID does not imply perfection in design; after all, of the things that we know to be the result of intelligent design &mdash; things designed by people &mdash; few are perfect.


Opponents of intelligent design who are scientists consider that the evidence of complexity in biological systems can be explained by conventional biological theory. There are also many opponents of intelligent design who are religious, and who believe that the role of science is to seek natural, physical explanations of the world; although they believe that there is a God who created the world and life in it, for them this is a matter of faith not of science. Opponents of intelligent design doubt the intellectual honesty of intelligent design theory, in that they do not consider it to be a viable alternative to the theory of evolution by natural selection, and hence consider that the only reason for promoting it is for the religious message that it is said to contain, not for the intrinsic intellectual merits of the arguments.
===Conventional explanations for the origins of irreducible complexity===
By the original common and uncontroversial definition, many biological systems are irreducibly complex. However, conventional evolutionary theory has no intrinsic difficulty in explaining how a system can have arisen by natural selection and yet appear to be irreducibly complex.


The basic thesis of intelligent design that 'natural selection is undirected' is open to logical challenge. Natural selection of organism survival is indirectly specific on organism subcomponents, because many features of the subcomponents are determined by genes whose retention is determined by their importance for reproductive success of the organism. Organism survival selects for effective function of the organism sub-components as part of a coherently functioning whole. In any organism, survival places specific and subtle requirements and restrictions on particular components such as enzymes, sensors, organs and systems that interact to generate behavior of living things.
The key assumption which is problematic for ID is the assumption introduced by Dembski that ''the 'basic' function of a system is the same as its 'original' function''.  Biologists argue that, on the contrary, systems often evolved for one purpose and then were "exapted" to a different function. An example is the evolution of the wing: a small wing is useless for flying, so how could an aerodynamically effective wing ever have begun to evolve? However, even small wings can be used to increase running speed. <ref>Dial KP (2003) Wing-assisted incline running and the evolution of flight. ''Science'' 299:402-4 PMID 12532020 </ref> The aerodynamic properties of the wings would have been incidental to the original function, but once a species had evolved wings that were big enough for gliding, then this (originally incidental) benefit may have become the major focus of subsequent natural selection.  


While proponents of intelligent design see evidence of design in how well complex structures fit their purpose, molecular biologists see something very different in the fine details of those structures. So far from seeing genetic information being perfectly and economically fashioned to suit a given purpose, they see wastefulness, duplication, errors, the detritus of now redundant genes in gene sequences - in other words, things they would expect to see as the residue of evolution by natural selection. In short, despite the appearance of efficient design at a high level, at a molecular level the design shows little sign of purposeful intelligence but extensive signs of chance processes.
Another way by which a system might become irreducibly complex is via the eliminative actions of natural selection. For example, genes that were once important in precursor forms of an organism are likely to be eliminated by natural selection if they later become redundant. Many see this as analogous to the scaffolding and buttresses that are used to construct a building, which are then removed after the building is completed, thereby eliminating all evidence of exactly how the building was built. Thus, in a currently living organism we see only the final structure, with little remaining evidence of the "scaffolds" by which evolution built it.  
<ref>Zuckerkandl E (2006) Intelligent design and biological complexity. Gene 30;385:2-18.</ref>


===Problems with the logic and assumptions of irreducible complexity===
Michael Behe further adapted Dembski's definition to apply it to evolutionary pathways:
By the original common and uncontroversial definition many biological systems are irreducibly complex. However, conventional evolutionary theory has no intrinsic difficulty in explaining how a system can have arisen by natural selection and yet be irreducibly complex.


The key assumption which is problematic for Intelligent Design is the assumption introduced by Dembski that the basic function of a system is the same as its original function. This assumption is one that modern evolutionary biologists vigorously dispute. They claim that, on the contrary, systems often evolved for one purpose and then were "exapted" to a different function.
''"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations)."''


An example is the evolution of the wing. A small wing is useless for flying, so how could an aerodynamically effective wing ever have begun to evolve? The answer of evolutionary biologists is that small wings are indeed useless for flight but in insects, they are useful structures for thermoregulation - thus wings may have evolved for thermoregulation and increased in surface area to be more effective radiators of heat; while in mammals small wings can be used to increase running speed. <ref>Dial KP (2003)
This step makes an overt link between irreducible complexity and ID. As a definition, it can only be applied after assuming that evolution was directed (i.e. after assuming that there is any such thing as an unselected mutation)
Wing-assisted incline running and the evolution of flight.
Science 299:402-4 PMID 12532020 </ref> The aerodynamic consequences would have been incidental to the original basic function, but when species had evolved wings of a sufficient size for gliding, then this originally incidental benefit may have become the major focus of further natural selection.  


Another obvious way by which a system might become irreducibly complex is via the eliminative actions of natural selection. For example, genes that were once important in precursor forms of an organism are likely to be eliminated by natural selection if they later become redundant. Many see this as analogous to the scaffolding and buttresses that are used to construct a building and then removed after the building is completed, and therefore removing all evidence of the scaffolding. Thus in a currently living organism we see only the final structure - with little remaining evidence of the "scaffolds" by which evolution built it.  
===Conventional explanations for rapid evolution of complex traits===
ID proponents doubt that known genetic mechanisms can explain how organism evolve rapidly to achieve complex design outcomes, given that evolution requires rare mutations to arise through chance processes.  


Another explanation is that genes used in an irreducibly complex system were once used for another purpose, much like melanocyte stimulating hormone (MSH), which acts as an antioxidant in organisms that don't produce melanin.
According to conventional biological theory, spontaneous mutations are the ultimate source of genetic novelty. One of the first estimates of the rate of spontaneous mutation in humans was made in 1930 by [[J. B. S. Haldane|JBS Haldane]] <ref>Haldane JBS (1935)The rate of spontaneous mutation of a human gene ''J Genet'' 31:317-26)(Reprinted in 2004 in J Genet 83:235-44), with a commentary by
Nachman MW (2004) Haldane and the first estimates of human mutation rate. J Genet 83:231-3</ref>; his estimate, which was very close to the current best estimates, was that every new human baby that is born has 100-200 novel gene mutations. Thus, in every generation, vast numbers of new mutations arise within a population; most are neutral, but a few are beneficial. However, for any beneficial mutation to become fixed in a population takes many generations. In 1957, Haldane <ref>Haldane JBS (1957) The cost of natural selection ''J Genet'' 55:511-524
*Van Valen L (1963) Haldane's Dilemma, evolutionary rates, and heterosis ''Amer Nat'' 47:185-90</ref> estimated that, for a population of stable size, it takes about 300 generations for a new mutation to become fixed in a population. This conclusion was independent of the strength of selection pressure unless it is very intense, explaining the slowness of evolution by natural selection.


Michael Behe further adapted Dembski's definition to apply it to evolutionary pathways:
Accordingly, ID proponents have questioned, for example, whether there is enough time since the last common ancestor of humans and chimpanzees to explain the genetic differences between them<ref>ReMine WJ (1993) ''The Biotic Message'', St. Paul Science, Saint Paul, MN</ref>.


''"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations)."''
This is not an argument that can be easily dismissed. Evolution does not proceed serially, by fixing first one genetic change and then the next, but in parallel: selection pressures apply simultaneously to all mutations that arise. It is not at all clear how quickly evolution by natural selection can occur when several traits are being selected for simultaneously, but Haldane warned that it could be very slow. However, he noted that evolution can occur much more rapidly when environmental pressures are changing. The last 10 million years has seen dramatic global changes in climate, and any species, over such a timescale, will encounter many other changes in selection pressure through the ever-changing ecological balance.


This step makes an overt link between irreducible complexity and intelligent design. As a definition, it can only be applied after assuming that evolution was directed (i.e. after assuming that there is any such thing as an unselected mutation)
Modern genetics has identified many mechanisms that enable some organisms to evolve rapidly in a quasi-directed fashion<ref> Koonin EV, Dolja VV (2006) Evolution of complexity in the viral world: the dawn of a new vision ''Virus Res'' 117:1-4 PMID 16497406. The introduction to a special issue of ''Virus Research'' that focuses on mechanisms of rapid evolutionary change in viruses.
* Caporale, LH (2003) Natural selection and emergence of mutation phenotype: An update of the evolutionary synthesis considering mechanisms that affect genome variation ''Ann Rev Microbiol'' 57:467–85 doi: 10.1146/annurev.micro.57.030502.090855</ref>  In multicellular organisms, [[sexual selection]] is one of these, and [[Mobile DNA]]s are another (See [[DNA#DNA and molecular evolution|DNA and molecular evolution]].)
The human immune system is a good illustration of such mechanisms. The creation of highly adapted antibodies that neutralise poisons and pathogens to which the body has never been exposed before, occurs by such natural selection events in rapidly evolving cells of the [[immune system]] (see [[Clonal Selection Theory of Acquired Immunity]]). Conversely,[[pathogen]]s use equally powerful genetic strategies (such as sets of alternative genes for related structures) to evolve rapidly and to deftly switch their antigenic features so as to evade the immune system.


===Problems with assuming genetic mechanisms cannot produce intelligent design===
===Could the flagellum have evolved by natural selection?===
An assumption in intelligent design is that genetic mechanisms cannot accomplish complex design outcomes, and that they are intrinsically random. Detailed modern genetics has, to the contrary, discovered that organisms have evolved mechanisms to evolve rapidly in a quasi-directed fashion. Sexual reproduction is one of these, and [[Mobile DNA]]s are another. ( See [[DNA#DNA and molecular evolution|DNA and molecular evolution]].)
Many ID arguments are based on the notion that every piece of a biological machine must be assembled in its final form before anything useful can emerge.  


The human immune system is a good illustration of the design capabilities of such genetic mechanisms. The creation of highly adapted antibodies that neutralise poisons and pathogens to which the body has never been previously exposed occurs by such natural selection events occurring in rapidly evolving cells of the immune system ( see [[Clonal Selection Theory of Acquired Immunity]]. Conversely pathogens use equally powerful genetic strategies ( such as sets of alternative genes for related structures) to evolve rapidly and to deftly switch their antigenic features so as to evade the immune system.
For example, the [[flagellum]] is a complex structure that allows [[bacteria]] to move; up to 40 different [[protein]]s must be arranged in a very particular way for the flagellum to work. Proponents of ID argue that a flagellum is useless if it won't move, that it needs all of its parts to function, and that it is hard to conceive that it could have arisen by classical natural selection. Natural selection involves gradual cumulative mutations, each of which produces a gain in fitness; the ID argument is that the flagellum has adaptive value only when fully assembled - the intermediates are useless.


The power of such quasi-intelligent systems is recognised by artificial intelligence engineers when they create software that exploits a [[genetic algorithm]].
To biologists generally, this idea is a misconception. Evolution by natural selection produces complex biochemical machines by copying, modifying, and combining proteins that were previously used for other functions. Evolutionary theorists argue that many features of organisms evolved to fit one function and were then adapted through natural selection to fulfill a different function. By this view, natural selection is not a single path, but a multiply branching path with many dead ends, with many branching points where genes were duplicated, and with many changes of direction where the 'destination' changed.  


===Could the flagellum have evolved by natural selection?===
====Flagella are modular devices and the modules serve other functions====
Critics of intelligent design argue that the idea that every piece of any biological machine must be assembled in its final form before anything useful can emerge is wrong. Evolution produces complex biochemical machines by copying, modifying, and combining proteins that were previously used for other functions. For example, Michael Behe argues that if you remove almost any of its parts, the bacterial flagellum does not work. However, it is argued by evolutionary theorists that many features of organisms evolved to fit one function and were then adapted through natural selection to fulfill a different function. By this view, natural selection is not a single path, but a multiply branching path with many dead ends, with many branching points where genes were duplicated, and with many changes of direction where the 'destination' changed. In other words, critics argue that the proponents of intelligent design misrepresent or misunderstand the processes involved in natural selection.
Flagella are modular devices, that exist in thousands, if not millions of versions in nature. Many radically different variations of flagella design occur: some rotate in two directions, others only in one. However, there is evidence that the flagellum structure arose from structurally simpler structures by gene duplication and further evolution. It appears that the flagellum proteins evolved from just two precursors (a proto-flagellin and a proto-rod/hook protein) by several rounds of gene duplication and diversification.  


In particular, the flagellum is a structure that allows bacteria to move: 30 to 40 different proteins may be required in a particular arrangement for the flagellum to work, and it is argued by proponents of Intelligent design that a flagellum is useless if it won't move, needs all its parts to function, and that it is difficult to conceive that it arose by successive gradual mutations.
Many of the versions of flagella lack many of the particular components that, in other versions, seem to be irreplaceable. For example, in Gram positive bacteria the P- and L-rings present in the flagella of Gram negative bacteria are missing.


====Flagella are modular devices and the modules serve other functions====
Relatives of some flagellum proteins are used in other bacterial structures. A protein similar to flagellum component FlgA is used in assembly of Type IV [[pilus|pili]] surface appendages; these are superficially like flagella, but have no major role in movement. Flagellum protein FlgJ contains a region that digests the rigid bacterial cell wall during flagellum insertion through the wall, and many similar bacterial proteins do other tasks.<ref>Pallen MJ, Matzke NJ (2006) From The Origin of Species to the origin of bacterial flagella. ''Nat Rev Microbiol'' 4:784-90 PMID 16953248  
Flagella are modular devices, that exist in thousands, if not millions  of different versions in nature. Many of these versions lack many of the components deemed by Intelligent design to be irreplaceable (for example in [[Gram positive bacteria]] the P- and L-rings present in the flagella of [[Gram negative bacteria]] are missing.  Many different radical variations of flagella design occur, some rotate in two directions, others only in one. All flagella include modular, fully functional subcomponents called T3SS that are devices widely used by bacteria for secretion of proteins. This T3SS submodule is used to assemble the flagella, but it also is used to secrete other molecules from the cell. There are also versions of flagella that are defective in providing motility, but which have a distinct functional role in infection (eg in the pathogen ''Brucella melitensis'')- evidence that flagellum related components have useful biological functions apart from movement.
*Soscia C ''et al.''' (2007) Cross talk between type III secretion and flagellar assembly systems in Pseudomonas aeruginosa ''J Bacteriol'' 189:3124-32</ref>
   
Additionally, there is evidence that the flagellum structure arose from structurally simpler parental structures by gene duplication and further evolution, a common mechanism of gene evolution. Thus when the similarities among the different flagellum protein components are examined it appears that the flagellum proteins evolved from just two precursors (a proto-flagellin and a proto-rod/hook protein) by multiple rounds of gene duplication and diversification.


Relatives of some flagellum proteins are used in other bacterial structures. A protein similar to flagellum component FlgA is used in assembly of Type IV [[pilus|pili]] surface appendages superficially like flagella but having no necessary role in movement. Flagellum protein FlgJ contains a region that digests the rigid bacterial cell wall during flagellum insertion through the wall, and many similar bacterial proteins do other tasks.<ref>Pallen MJ, Matzke NJ. (2006)
All flagella include modular subcomponents called T3SS that are widely used by bacteria for secretion of proteins. This T3SS submodule is used to assemble the flagella, but is also used to secrete other molecules from the cell. There are also versions of flagella that are defective in providing motility, but which have a functional role in [[infection]] (e.g., in the pathogen ''Brucella melitensis''), evidence that components of flagella have useful biological functions ''apart'' from movement.
From The Origin of Species to the origin of bacterial flagella.
Nat Rev Microbiol. 4:784-90 PMID 16953248 
*Soscia C ''et al.''' (2007) Cross talk between type III secretion and flagellar assembly systems in Pseudomonas aeruginosa. J Bacteriol 189:3124-32</ref>


In summary, many of the components of the flagellum are used by bacteria for other functions, such as for injecting poisons into other cells and enabling infections of animals, and they are not irreducibly complex. Accordingly, biologists believe it is likely that different elements of the flagellum evolved separately to fulfill other functions such as secretion or adherence to surfaces in ancestral organisms, and that motility arose relatively late in evolution, once many of the elements used in the flagellum were already in place for other reasons. The modularity of flagella is not surprising. There are diverse complex surface structures in bacteria (such as [[Pilus|pili]], secretion systems, and conjugation machinery ). Modular adaption and mixing and matching of system sub-components to serve several roles such as secretion, uptake, protein of DNA injection or twitching motility is a richly documented general rule. This general rule provides evolutionary explanations of biodiversity.
The modularity of flagella is not unusual in complex biological structures. Bacteria possess a wide variety of complex structures such as [[Pilus|pili]], secretion systems, and conjugation machinery. As a (richly documented) general rule, any particular module may have several different roles (in for example, secretion, uptake, protein of DNA injection or twitching motility) and complex structures are built by "mixing and matching" different sub-components. This general rule provides evolutionary explanations of biodiversity.


==Unconstitutionality of teaching Intelligent design in US state schools==
In summary, many components of the flagellum are used by bacteria for other functions, such as for injecting poisons into other cells, and these components are ''not'' irreducibly complex in these other functions. Accordingly, biologists think that different elements of the flagellum evolved separately to fulfill other functions in ancestral organisms. They thus think that motility arose relatively late in bacterial evolution, after many of the elements used in the flagellum had already evolved.
Similar reasoning about flagella to that just given was presented in the 2006 Kitzmiller versus Dover trial in Pennsylvania. The findings of the trial Judge John E. Jones III were that it is "... abundantly clear the board's intelligent design' (ID) policy violates the establishment clause. In making this determination, we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents". This court ruling demonstrated that teaching of Intelligent design in American state schools is unconstitutional, as it violates the 'establishment clause' of the First Amendment of the US Constitution stating that 'Congress shall make no law respecting an establishment of religion'.


==Bibliography==
==Does science stand in opposition to intelligent design?==
* Simon Coleman and Leslie Carlin, eds. ''The Cultures of Creationism: Anti-Evolution in English-Speaking Countries'' (2004) [http://www.arsdisputandi.org/publish/articles/000185/article.pdf online review]
The modern scientific ethos involves two principles between which there is continual tension. One principle is that of skepticism &mdash; in the sense of doubt about all that we believe, not in the sense of denial of alternative views. The second principle is conservative: scientists build theories on conventionally accepted foundations, without which there is no common language in science and no progress. Thus scientists resist attacks on the foundations from which they proceed, and a theory that has led to significant increases in knowledge and understanding and which continues to direct science in productive ways will be retained unless an alternative theory promises a significant enhancement of understanding.
* Lienesch, Michael ''In the Beginning: Fundamentalism, the Scopes Trial, and the Making of the Antievolution Movement'' (2007)
* Numbers, Ronald L. ''The Creationists: From Scientific Creationism to Intelligent Design'' (2nd ed 2006)


==Footnotes==
No scientist should consider it illegitimate to question current evolutionary theory: the right to challenge ‘’anything’’ is an essential element in science, and science that denies the right to challenge becomes mere dogma. The core question addressed by some ID proponents - ''is there a way in which we can test, by analytical processes, whether or not a feature has evolved by the known mechanisms of natural selection?'', when phrased in this way, is consistent with scientific approaches, and indeed, is a question often asked by biologists. So why is there such antagonism between scientists and the proponents of ID?
<references/>


==See also==
First, for scientists who seek to test a theory, any test should be designed without preconception about what the “right” answer is. The [[Intelligent Design Movement]] is accused by some as having an "agenda" – it presupposes that there is an intelligent creator, and seeks to provide an apparently scientific buttress for this preconception. This approach  is anti-scientific.
*[[Creationism]]
*[[Intelligent design movement]]
*[[Design argument for the existence of God]]
*[[Evolution]]


==External links==
Second, the ID movement seeks to draw conclusions beyond the bounds of testable knowledge. Thus, it is reasonable to question whether a proposed explanation for, say, the evolution of flagella, is logically tenable given present evolutionary theory. However, if the explanation is incomplete, scientists consider it unreasonable to conclude that the whole edifice of evolutionary theory is therefore wrong and must be replaced by a theory that invokes an extravagant and untestable presumption. In their own challenges to accepted theory, scientists respond to anomalies by considering how they might be reconciled by minor adjustments to existing theory. Thus they first adopt a conservative approach, and do so because of the wider context – their awareness of how much modern theory has contributed to knowledge, and of what is at stake, for the progress of science, in rejecting it. The process of falsification of hypotheses is important in science, but a major theory is not something to be rejected lightly.
*''[http://www.actionbioscience.org/evolution/nhmag.html Intelligent Design?]'' A special report reprinted from ''Natural History'' magazine. Three proponents of intelligent design present their views. Each view is followed by a response from a proponent of evolution.
* Coyne, Jerry, [http://www.edge.org/3rd_culture/coyne07/coyne07_index.html  ''Don't know much biology''] ''Edge''  (2007)


All scientists are creatures of the times in which they live, subject to the same pressures of society, politics and economics as others, and individually they have prejudices and preconceptions which can never be wholly shed. However, some scientists throughout history have resisted attempts by religious authorities, society or governments to impose interpretations that are not warranted objectively. This resistance has not been universal, nor has it been consistently effective; nevertheless, such resistance is celebrated by scientists as a mark of integrity. Today, an ethical scientist might accept funding from a pharmaceutical company to study the actions of a drug, but will reject funding that is conditional on a given outcome: a study should be designed in such a way as not to favour a particular preconceived conclusion. By this view, the ID movement, insofar as it seeks to provide evidence to support a particular thesis, is anti-scientific, and scientists who accept funding that it is conditional on a given conclusion are in breach of scientific ethics.


[[Category: CZ Live]]
Finally, science is about things that can be tested, whereas religious faith is a matter of inner conviction, and is not externally testable. The existence of a God is not something that is, even in principle, capable of disproof, so any explanations that invoke this are unscientific. Some proponents of ID have tried to separate what are legitimate challenges to current theory from their religious conclusions. Thus far, few scientists are convinced that this separation is a sincere attempt at objectivity, few believe that ID poses a significant challenge to current understanding, and many believe that its proponents are so compromised by their preconceptions, by the nature of their funding, and by the manner in which they publish their work, as to place them outside the bounds of normal science.


[[Category:Philosophy Workgroup]]
==Footnotes==
[[Category:Religion Workgroup]]
{{reflist|2}}[[Category:Suggestion Bot Tag]]
[[Category:Politics Workgroup]]

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Intelligent design (ID) is the claim that fundamental features of the universe and living things are best explained by purposeful causation—a "higher intelligence." Proponents of ID argue that conventional biological theory of evolution through natural selection cannot explain the origin of many highly complex features of living organisms; they argue that some such features are better explained as the result of the intervention of a directed process that they describe as an intelligence. Critics of ID, including the overwhelming majority of academic biologists, consider that these arguments are logically unsound and reflect a flawed understanding of modern biology; they consider that conventional biological theories explain the evolution of complex features of organisms elegantly and efficiently. Critics have also accused its supporters, nearly all of whom believe in a personal God, of using ID primarily as a way to get around U.S. legal restrictions on teaching about God in the classroom. However, ID proponents claim that ID does not require belief in a personal God to support its arguments.

The U.S. National Academy of Sciences has concluded that, in its present form, ID cannot be regarded as scientific because the claims made by its proponents are not testable.[1] See intelligent design movement for an account of political efforts to promote education about ID in schools.

Arguments for intelligent design

The classic design argument for the existence of an intelligent creator may be traced from ancient philosophy, through the works of medieval scholastics such as the philosopher-theologian Saint Thomas Aquinas (1225-1274), who argued that the existence of God could be deduced by reason.

In the 18th century, the theologian William Paley (1743-1805) introduced the "watchmaker analogy", one of the best known metaphors in the philosophy of science, as an argument for the existence of God.[2] The argument is, in essence, as follows: Imagine walking on a pebbled beach, where the pebbles may be wonderfully shaped, beautiful in different ways, interesting and varied one from another. However interesting and beautiful you find them, you will not doubt that they are the products of purely natural causes. However, if amongst the pebbles you find a watch, even if you have never seen a watch before, you will immediately recognise it as qualitatively different from the pebbles. Inspecting it, from the intricacy of its design, and the clear purpose of that design, you will inevitably and correctly conclude that the watch is not a natural object but an artifact, something designed by a powerful and intelligent agent.

Casual observation might similarly lead to the conclusion that, compared to a watch, even the simplest living form is incredibly complex, giving it the appearance of being designed for a purpose. There must be a designer, said Paley, "and that designer is God."

To many who believe in a Creator of the universe, the idea that the nature of living things might contain some evidence that they have been built purposefully rather than having been evolved by natural selection is a natural one. Some modern proponents of ID have accordingly broached this issue in a theoretical manner, by considering how, objectively, it might be possible to ascertain whether any particular object has been designed for a purpose as opposed to having evolved to fit an apparent purpose[3]. Thus, William Dembski has argued that ID can be formulated as a scientific theory of information that has empirical consequences and which is devoid of any religious commitments.[1] By this view, intelligent design asks whether design can be detected in nature from purely scientific and mathematical considerations.

These proponents have proposed two criteria for deciding whether something has been designed in a way that cannot be accounted for by evolution through natural selection:

Irreducible complexity

A complex system is a system with many component parts, and which depends on many interactions between those component parts to perform its particular defined function. A system is irreducibly complex if removing of any one of these parts causes it to cease functioning[4]. In No Free Lunch,[5] William Dembski extends this basic definition, and states that a system is irreducibly complex

if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function.

He and other proponents of ID argue that irreducible complexity is a common feature of biological systems, and claim that it cannot plausibly be accounted for by evolution through "undirected" natural selection. They argue that irreducibly complex systems must have arisen by some form of "directed" evolution, i.e. towards a predetermined end.

Evolution by natural selection can proceed via successive minor alterations to the form of a structure, each of which results in an incremental improvement in fitness. One of the challenges for biologists is to explain how complex structures can have evolved in this way, as the apparent requirement that every intermediate form must have a selection advantage beyond the previous form limits the possible paths by which evolution might have proceeded. For example, Richard Dawkins, in Climbing Mount Improbable (ISBN 0140179186) discusses evolution of the elephant's trunk. "In the evolution of the elephant from its short-nosed ancestors, there must have been a steady elongation of steadily longer noses...It must have been the case that, as each inch was added to the length of the average trunk, the trunk became better at its job. It must never be possible to say anything like 'That medium sized trunk is no good because it is neither one thing nor the other - falls between two stools, but don't worry, give it another few million years and it'll be fine. No animal ever made a living purely by being on the evolutionary path to something better."

However, modern evolutionary biologists point to many ways, by which complexity can emerge through natural selection. For example, it is not strictly required that every intermediate be fitter - some may harbour neutral mutations with incipient functionality. Natural selection acts primarily to eliminate harmful mutations and to actively sustain beneficial mutations; mutations that have little or no effect on fitness are called "neutral" and these will not be actively eliminated by selection pressures. Neutral mutations tend to accumulate in a population over time, contributing to inter-individual variability. This variability can provide the fuel for rapid evolution through natural selection when environmental conditions change, because some mutations that were originally neutral may have an effect on fitness in the changed conditions. Some intermediate forms in evolution may accordingly have neutral mutations that become beneficial when there is a subsequent mutation or when there is a change in selection pressure.

Specified complexity

Intelligent Design advocate William Dembski advances the concept of specified complexity as describing the procedure used to identify objects that have been apparently designed—objects that cannot be explained through natural mechanisms. Proponents of ID argue that when a structure fulfils a function that is essential for the function of living things, then it is legitimate to consider how likely it is that outcome could have been achieved through the chance processes that are said to be involved.

This argument is perhaps best explained by analogy. If an archer fires an arrow into the air at random, then it might land anywhere within a large area, so the probability of it landing at any particular place within this area is very low. In this case, we cannot draw any conclusions from the simple fact that the arrow lands at a place where it has a very low probability of landing - the arrow must, after all, land somewhere. However, if it lands in the very centre of a predrawn target, then we might try to conclude that the arrow was not fired at random, but was aimed. This conclusion comes not solely from the fact that the outcome of firing the arrow was an unlikely complex event, but from this combined with the fact that it was a prespecified complex event. However, this conclusion cannot be drawn without a statistical analysis of a population of fired arrows that shows the arrival at the target was not an accident. Of course, in the case of biology, all the organisms that had unsuccessful adaptions died out, providing a challenge to establish experimentally whether random adaptations existed in the past. Instead, one can argue on theoretical grounds the probability of Shakespeare being written during random typing by monkeys, without regard for any actual experimental findings.

Proponents of ID argue that there are features of living organisms that show such specified complexity. These proponents argue that, for such features, it is legitimate to calculate the probability of their occurrence according to the conditional probabilities of occurrence of the multiple chance elements that are involved. Dembski has proposed that conditional probabilities of the order of 10-120 are thus evidence of purpose, and thus of some 'directing intelligence'.

The notion of specified complexity has not been widely endorsed by professional mathematicians and information theorists[6][7]. One problem with applying this approach is the problem of assigning probabilities to particular molecular events in a reliable way. Another arises from the difficulty in deciding what exactly constitutes specified complexity in a biological context.

Intelligent design and molecular biology

Proponents of ID do not deny evolution, nor do they dispute the findings of molecular biology. They regard evolution as part of the mechanisms by which living things are designed, and they consider that molecular biology, by displaying the vast complexity that underlies even the simplest living things, provides evidence that makes explanations based on natural selection less rather than more plausible.

Interestingly, 'watches' have been found in living organisms. These are molecular timing devices that produce 'circadian rhythms', biological cycles with an innately determined time period. One such timekeeping mechanism has been found in blue-green algae, and it enables this microbe's genes to vary in their intensity of activity in rhythm with daily changes in sunlight. The biological watch inside the microbe is composed of widely distributed genetic components recruited from other signalling and information processing activities of the cell. In this case, the watch is constructed from simple molecular components that function regularly and predictably according to well characterised principles of biochemistry - the timing mechanism arises as a result of feedback loops whereby gene products regulate gene expression.[8]

Modern Evolutionary Synthesis

ID proponents argue that the natural selection mechanisms that have been used to explain the "apparent design" of numerous components and interactions of living organisms cannot explain all features of organism complexity[9], but their critics argue that they underestimate the sophistication of modern evolutionary theory, and in particular underestimate the creative capacity of natural selection.

The currently accepted account of the origin of living things is known as the "Modern Evolutionary Synthesis". This expresses the theory of evolution by natural selection in a form consistent with molecular biology and population genetics. By this theory, all extant living things are the products of descent with modification from common ancestors that lived 3-4 billion years ago. This theory (and an abundant array of evidence of evolutionary process that are seen in nature) explains all evolution as resulting from processes of natural selection among populations among which genetic novelty and novel combinations of genetic components are generated by many different genetic mechanisms. Natural selection is not the single simplistic process that the common characterisation "survival of the fittest" suggests, but embraces a very wide array of processes and pressures that lead to differential reproductive success in populations. The creative elements of natural selection emerge because, as selected genotypes accumulate over many, many generations and combine in different ways to produce novel phenotypes, this produces a huge diversity of organisms (today there are more than 10 million living species, a tiny percentage of all the species that ever existed).

There are important features that distinguish the 'design' achieved by natural selection from the kind produced by an intelligent designer. Natural selection is undirected in that it has no preordained plan, but is simply a result of the differential survival and reproduction of living beings. Natural selection and genetic mechanism provide powerful ways of generating novel features which are stored in the DNA code and passed on to the subsequent generations, but natural selection has no foresight, and so environmental changes may threaten the survival of organisms that were thriving. As a result, species extinction is common: it is estimated that, of all the species that ever lived on Earth, more than 99% are now extinct. Critics of ID see the evidence of massive extinction of species as inconsistent with the notion of intelligent design of the world we live in.[10]

Although most descriptions of evolution assume that all mutations are random with respect to their effects on fitness, some biologists argue that there are important mechanisms which make favourable mutations more likely to occur. For example, Lynne Caparole [11] has argued that natural selection favours some mechanisms that increase the likelihood of mutations in particular genes. These mechanisms produce considerable diversity in gene function amongst progeny, and this diversity can facilitate rapid evolution.

In particular, not all mutations rely on a random change to a single nucleotide base: some involve "mis-copying" the DNA, and these errors are very common for certain types of DNA sequence. For example, when a section of DNA contains a short repeated sequence of nucleotides, the number of repeats can be affected by a common "stuttering error" in DNA replication. The consequences will depend on exactly where in the genome the repeated sequence is located, but if, for example, it occurs in a region that affects how a bacterium responds to an antibiotic, then this diversity makes it more likely that some offspring will be antibiotic resistant. Thus, although accuracy is generally very important in reproducing a genome, some 'errors' are valuable, because the increased diversity of the offspring makes it more likely that some will be well fit to rapidly changing environmental conditions.

ID publications

Many books on ID have been written but few ID research papers or monographs have been published in conventional peer-reviewed scientific journals. However, ID advocates have created several journals devoted to publishing papers on ID (see Bibliography). The Kitzmiller vs Dover Area School case in 2005 was the first direct challenge brought in U.S. federal courts against a public school district that required ID to be presented to students as an alternative to evolution as an explanation of the origin of life. The plaintiffs successfully argued that ID is a form of creationism, and that the school board policy therefore violated the Establishment Clause of the First Amendment to the Constitution. In testimony, ID proponent Michael Behe admitted that “There are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred.” [12]

On 4 August 2004, a review article by Stephen Meyer, an ID proponent, appeared in the peer-reviewed Proceedings of the Biological Society of Washington, questioning conventional evolutionary explanations for the Cambrian Explosion and proposing ID as an alternative[13] The review questions whether whether conventional biological theory can explain the information explosion evident during the Cambrian period. He says: "For neo-Darwinism, new functional genes either arise from non-coding sections in the genome or from preexisting genes. " He argues that the first leaves too much to luck and chance to be plausible, and the second has the problem that changes to existing genes are almost invariably deleterious. However this neglects many conventional accounts of how genes evolve, including probably the major known mechanism whereby novel genes arise, via gene duplication. Gene duplication is very common through evolution, and means that one copy of a gene can continue to sustain its normal function while the other is "surplus", and is free to accumulate mutations. Thus, by conventional explanations, a new gene doesn't have to be built from nothing - instead evolution is handed an already functional "toy" to play with.

Later, the Council of the Biological Society of Washington retracted the article. The managing editor for the journal at the time, the process structuralist Richard Sternberg, stated that the article had been properly peer reviewed by three well qualified referees. His decision to publish the paper nevertheless resulted in protests, and colleagues at the Smithsonian Institute, where he was employed, sought to discredit him and created what the U.S. Office of Special Council (which is authorized to investigate allegations of prohibited personnel practices and activities prohibited by civil service law) called "a hostile working environment".[14][15]

The lack of peer-reviewed articles is cited by some as evidence that ID is unscientific. ID supporters point to the Proceedings incident as showing the opposite: that the scientific climate is so prejudiced against ID that not even peer review is enough to overcome publication bias. ID proponent Dominque Tassot of the 'Center for Studies and Prospectives on Science', France, states the reasons as

[Evolutionary scientists] live and think inside the paradigm of evolution. As Thomas Kuhn explained [in The Structure of Scientific Revolutions], theories are accepted or rejected in order to defend the dominant paradigm. Information which conflicts with that paradigm is set aside, it doesn’t get published.[16]

Is intelligent design a form of creationism?

Most proponents of ID are also creationists, meaning they believe the universe was created by a deity or some other power beyond the full comprehension of mortal man. The hypothesis, however, is not the same as young earth creationism, which is a belief that the account of the creation of the universe and of life as given by the Bible is literally true. ID does not try to identify the designer as supernatural, nor does it try to establish the veracity of a particular narrative, although some leading proponents have stated that they believe the designer to be the Christian God. However, some proponents of ID see no conflict between it and evolution, and indeed see evolution as evidence of ID. Many proponents avoid any personification of the source of the ID, and so the focus of ID is different to that of arguments in natural theology, such as the teleological argument.

Criticisms of intelligent design

Proponents of ID argue that it is a scientific theory rather than a matter of religious belief, despite its base of support in the religious community.[17] Courts in the USA have rejected this argument, in part because, for a theory to be 'scientific', it must generate predictions by which it can be tested; in other words, it must be open to attempted disproof. [18]

Critics also hold that the postulate of an intelligent designer is not an explanation for life at all, but a "deus ex machina"--that is, an evasion of attempted explanation. They consider that ID is not a serious alternative to modern biological theory, in particular they consider that the complexity of biological systems can be well explained by conventional biological theory. They also consider that the tenet of ID that perfection in design needs a directing intelligence is inconsistent with many examples in nature of imperfections in design of organisms.[19]

There are also many critics of ID who are religious, and who believe that the role of science is to seek natural, physical explanations of the world; although they believe that there is a God who created the world and life in it, for them this is a matter of faith not of science. Some critics doubt the intellectual honesty of ID theory, in that they consider that the only reason for promoting it is for the religious message that it implies, not for the intrinsic merits of the arguments.

While some proponents of ID see evidence of design in how well complex structures fit their purpose, molecular biologists see something very different in the fine details of those structures. So far from seeing genetic information being perfectly and economically fashioned to suit a given purpose, they see wastefulness, duplication, errors, and the detritus of now redundant genes in gene sequences — in other words, things they would expect to see as the residue of evolution by natural selection. In short, despite the appearance of efficient design at a high level, at a molecular level the design shows few signs of purposeful intelligence but many signs of chance processes. [20] However, other proponents of ID note that ID does not imply perfection in design; after all, of the things that we know to be the result of intelligent design — things designed by people — few are perfect.

Conventional explanations for the origins of irreducible complexity

By the original common and uncontroversial definition, many biological systems are irreducibly complex. However, conventional evolutionary theory has no intrinsic difficulty in explaining how a system can have arisen by natural selection and yet appear to be irreducibly complex.

The key assumption which is problematic for ID is the assumption introduced by Dembski that the 'basic' function of a system is the same as its 'original' function. Biologists argue that, on the contrary, systems often evolved for one purpose and then were "exapted" to a different function. An example is the evolution of the wing: a small wing is useless for flying, so how could an aerodynamically effective wing ever have begun to evolve? However, even small wings can be used to increase running speed. [21] The aerodynamic properties of the wings would have been incidental to the original function, but once a species had evolved wings that were big enough for gliding, then this (originally incidental) benefit may have become the major focus of subsequent natural selection.

Another way by which a system might become irreducibly complex is via the eliminative actions of natural selection. For example, genes that were once important in precursor forms of an organism are likely to be eliminated by natural selection if they later become redundant. Many see this as analogous to the scaffolding and buttresses that are used to construct a building, which are then removed after the building is completed, thereby eliminating all evidence of exactly how the building was built. Thus, in a currently living organism we see only the final structure, with little remaining evidence of the "scaffolds" by which evolution built it.

Michael Behe further adapted Dembski's definition to apply it to evolutionary pathways:

"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations)."

This step makes an overt link between irreducible complexity and ID. As a definition, it can only be applied after assuming that evolution was directed (i.e. after assuming that there is any such thing as an unselected mutation)

Conventional explanations for rapid evolution of complex traits

ID proponents doubt that known genetic mechanisms can explain how organism evolve rapidly to achieve complex design outcomes, given that evolution requires rare mutations to arise through chance processes.

According to conventional biological theory, spontaneous mutations are the ultimate source of genetic novelty. One of the first estimates of the rate of spontaneous mutation in humans was made in 1930 by JBS Haldane [22]; his estimate, which was very close to the current best estimates, was that every new human baby that is born has 100-200 novel gene mutations. Thus, in every generation, vast numbers of new mutations arise within a population; most are neutral, but a few are beneficial. However, for any beneficial mutation to become fixed in a population takes many generations. In 1957, Haldane [23] estimated that, for a population of stable size, it takes about 300 generations for a new mutation to become fixed in a population. This conclusion was independent of the strength of selection pressure unless it is very intense, explaining the slowness of evolution by natural selection.

Accordingly, ID proponents have questioned, for example, whether there is enough time since the last common ancestor of humans and chimpanzees to explain the genetic differences between them[24].

This is not an argument that can be easily dismissed. Evolution does not proceed serially, by fixing first one genetic change and then the next, but in parallel: selection pressures apply simultaneously to all mutations that arise. It is not at all clear how quickly evolution by natural selection can occur when several traits are being selected for simultaneously, but Haldane warned that it could be very slow. However, he noted that evolution can occur much more rapidly when environmental pressures are changing. The last 10 million years has seen dramatic global changes in climate, and any species, over such a timescale, will encounter many other changes in selection pressure through the ever-changing ecological balance.

Modern genetics has identified many mechanisms that enable some organisms to evolve rapidly in a quasi-directed fashion[25] In multicellular organisms, sexual selection is one of these, and Mobile DNAs are another (See DNA and molecular evolution.) The human immune system is a good illustration of such mechanisms. The creation of highly adapted antibodies that neutralise poisons and pathogens to which the body has never been exposed before, occurs by such natural selection events in rapidly evolving cells of the immune system (see Clonal Selection Theory of Acquired Immunity). Conversely,pathogens use equally powerful genetic strategies (such as sets of alternative genes for related structures) to evolve rapidly and to deftly switch their antigenic features so as to evade the immune system.

Could the flagellum have evolved by natural selection?

Many ID arguments are based on the notion that every piece of a biological machine must be assembled in its final form before anything useful can emerge.

For example, the flagellum is a complex structure that allows bacteria to move; up to 40 different proteins must be arranged in a very particular way for the flagellum to work. Proponents of ID argue that a flagellum is useless if it won't move, that it needs all of its parts to function, and that it is hard to conceive that it could have arisen by classical natural selection. Natural selection involves gradual cumulative mutations, each of which produces a gain in fitness; the ID argument is that the flagellum has adaptive value only when fully assembled - the intermediates are useless.

To biologists generally, this idea is a misconception. Evolution by natural selection produces complex biochemical machines by copying, modifying, and combining proteins that were previously used for other functions. Evolutionary theorists argue that many features of organisms evolved to fit one function and were then adapted through natural selection to fulfill a different function. By this view, natural selection is not a single path, but a multiply branching path with many dead ends, with many branching points where genes were duplicated, and with many changes of direction where the 'destination' changed.

Flagella are modular devices and the modules serve other functions

Flagella are modular devices, that exist in thousands, if not millions of versions in nature. Many radically different variations of flagella design occur: some rotate in two directions, others only in one. However, there is evidence that the flagellum structure arose from structurally simpler structures by gene duplication and further evolution. It appears that the flagellum proteins evolved from just two precursors (a proto-flagellin and a proto-rod/hook protein) by several rounds of gene duplication and diversification.

Many of the versions of flagella lack many of the particular components that, in other versions, seem to be irreplaceable. For example, in Gram positive bacteria the P- and L-rings present in the flagella of Gram negative bacteria are missing.

Relatives of some flagellum proteins are used in other bacterial structures. A protein similar to flagellum component FlgA is used in assembly of Type IV pili surface appendages; these are superficially like flagella, but have no major role in movement. Flagellum protein FlgJ contains a region that digests the rigid bacterial cell wall during flagellum insertion through the wall, and many similar bacterial proteins do other tasks.[26]

All flagella include modular subcomponents called T3SS that are widely used by bacteria for secretion of proteins. This T3SS submodule is used to assemble the flagella, but is also used to secrete other molecules from the cell. There are also versions of flagella that are defective in providing motility, but which have a functional role in infection (e.g., in the pathogen Brucella melitensis), evidence that components of flagella have useful biological functions apart from movement.

The modularity of flagella is not unusual in complex biological structures. Bacteria possess a wide variety of complex structures such as pili, secretion systems, and conjugation machinery. As a (richly documented) general rule, any particular module may have several different roles (in for example, secretion, uptake, protein of DNA injection or twitching motility) and complex structures are built by "mixing and matching" different sub-components. This general rule provides evolutionary explanations of biodiversity.

In summary, many components of the flagellum are used by bacteria for other functions, such as for injecting poisons into other cells, and these components are not irreducibly complex in these other functions. Accordingly, biologists think that different elements of the flagellum evolved separately to fulfill other functions in ancestral organisms. They thus think that motility arose relatively late in bacterial evolution, after many of the elements used in the flagellum had already evolved.

Does science stand in opposition to intelligent design?

The modern scientific ethos involves two principles between which there is continual tension. One principle is that of skepticism — in the sense of doubt about all that we believe, not in the sense of denial of alternative views. The second principle is conservative: scientists build theories on conventionally accepted foundations, without which there is no common language in science and no progress. Thus scientists resist attacks on the foundations from which they proceed, and a theory that has led to significant increases in knowledge and understanding and which continues to direct science in productive ways will be retained unless an alternative theory promises a significant enhancement of understanding.

No scientist should consider it illegitimate to question current evolutionary theory: the right to challenge ‘’anything’’ is an essential element in science, and science that denies the right to challenge becomes mere dogma. The core question addressed by some ID proponents - is there a way in which we can test, by analytical processes, whether or not a feature has evolved by the known mechanisms of natural selection?, when phrased in this way, is consistent with scientific approaches, and indeed, is a question often asked by biologists. So why is there such antagonism between scientists and the proponents of ID?

First, for scientists who seek to test a theory, any test should be designed without preconception about what the “right” answer is. The Intelligent Design Movement is accused by some as having an "agenda" – it presupposes that there is an intelligent creator, and seeks to provide an apparently scientific buttress for this preconception. This approach is anti-scientific.

Second, the ID movement seeks to draw conclusions beyond the bounds of testable knowledge. Thus, it is reasonable to question whether a proposed explanation for, say, the evolution of flagella, is logically tenable given present evolutionary theory. However, if the explanation is incomplete, scientists consider it unreasonable to conclude that the whole edifice of evolutionary theory is therefore wrong and must be replaced by a theory that invokes an extravagant and untestable presumption. In their own challenges to accepted theory, scientists respond to anomalies by considering how they might be reconciled by minor adjustments to existing theory. Thus they first adopt a conservative approach, and do so because of the wider context – their awareness of how much modern theory has contributed to knowledge, and of what is at stake, for the progress of science, in rejecting it. The process of falsification of hypotheses is important in science, but a major theory is not something to be rejected lightly.

All scientists are creatures of the times in which they live, subject to the same pressures of society, politics and economics as others, and individually they have prejudices and preconceptions which can never be wholly shed. However, some scientists throughout history have resisted attempts by religious authorities, society or governments to impose interpretations that are not warranted objectively. This resistance has not been universal, nor has it been consistently effective; nevertheless, such resistance is celebrated by scientists as a mark of integrity. Today, an ethical scientist might accept funding from a pharmaceutical company to study the actions of a drug, but will reject funding that is conditional on a given outcome: a study should be designed in such a way as not to favour a particular preconceived conclusion. By this view, the ID movement, insofar as it seeks to provide evidence to support a particular thesis, is anti-scientific, and scientists who accept funding that it is conditional on a given conclusion are in breach of scientific ethics.

Finally, science is about things that can be tested, whereas religious faith is a matter of inner conviction, and is not externally testable. The existence of a God is not something that is, even in principle, capable of disproof, so any explanations that invoke this are unscientific. Some proponents of ID have tried to separate what are legitimate challenges to current theory from their religious conclusions. Thus far, few scientists are convinced that this separation is a sincere attempt at objectivity, few believe that ID poses a significant challenge to current understanding, and many believe that its proponents are so compromised by their preconceptions, by the nature of their funding, and by the manner in which they publish their work, as to place them outside the bounds of normal science.

Footnotes

  1. The National Academies Press: 'Science and Creationism: A View from the National Academy of Sciences, Second Edition (1999).'
  2. *Works by William Paley at Project Gutenberg
  3. Intelligent Design? a special report reprinted from Natural History magazine
  4. Michael Behe (1996), Darwin's Black Box: The Biochemical Challenge to Evolution, Free Press
  5. Dembski WA (2001) No Free Lunch: Why Specified Complexity Cannot Be Purchased Without Intelligence Rowman & Littlefield, ISBN 0742512975
  6. Richard Wein, Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch
  7. John S. Wilkins and Wesley R. Elsberry, The advantages of theft over toil: the design inference and arguing from ignorance, Biology and Philosophy, 2001.
  8. Robertson McClung C (2006) Two-component signaling provides the major output from the cyanobacterial circadian clock. Proc Natl Acad Sci USA 103:11819–20
  9. Intelligent Design Intelligent Design network.
  10. Ayala FJ (2007) Colloquium Papers: Darwin's greatest discovery: Design without designer. Proc Natl Acad Sci USA 104 Suppl 1:8567-73. PMID 17494753
  11. Caporale LH (2003) Natural selection and the emergence of a mutation phenotype: An update of the evolutionary synthesis considering mechanisms that affect genome variation. Ann Rev Microbiol 57:467–85 doi: 10.1146/annurev.micro.57.030502.090855 PMID 14527288
  12. In Kitzmiller vs Dover Area School_District 4:Whether ID Is Science
  13. Meyer S (2004) The origin of biological information and the higher taxonomic categories. Proc Biol Soc Washington 117:[http://www.discovery.org/scripts/viewDB/index.php?command=view&id=2177 213-39}
  14. The homepage of Richard Sternberg
  15. Decision of the Office of Special Council regarding Richard Sternberg's allegations
  16. John L. Allen (22 Aug 2006). "Interview with Dominque Tassot". National Catholic Reporter.
  17. Primer: Intelligent Design Theory in a Nutshell Intelligent Design and Evolution Awareness (IDEA)
  18. Ruling, Kitzmiller vs Dover Area School District, Case No. 04cv2688. (PDF) December 20 2005
    • The philosopher of science Karl Popper argued that a theory that has no testable components "has no connection with the real world." (see Scientific method).
  19. Sober E (2007) What is wrong with intelligent design? Q Rev Biol 82:3-8 PMID 17354991
  20. Zuckerkandl E (2006) Intelligent design and biological complexity. Gene 385:2-18 PMID 17011142
  21. Dial KP (2003) Wing-assisted incline running and the evolution of flight. Science 299:402-4 PMID 12532020
  22. Haldane JBS (1935)The rate of spontaneous mutation of a human gene J Genet 31:317-26)(Reprinted in 2004 in J Genet 83:235-44), with a commentary by Nachman MW (2004) Haldane and the first estimates of human mutation rate. J Genet 83:231-3
  23. Haldane JBS (1957) The cost of natural selection J Genet 55:511-524
    • Van Valen L (1963) Haldane's Dilemma, evolutionary rates, and heterosis Amer Nat 47:185-90
  24. ReMine WJ (1993) The Biotic Message, St. Paul Science, Saint Paul, MN
  25. Koonin EV, Dolja VV (2006) Evolution of complexity in the viral world: the dawn of a new vision Virus Res 117:1-4 PMID 16497406. The introduction to a special issue of Virus Research that focuses on mechanisms of rapid evolutionary change in viruses.
    • Caporale, LH (2003) Natural selection and emergence of mutation phenotype: An update of the evolutionary synthesis considering mechanisms that affect genome variation Ann Rev Microbiol 57:467–85 doi: 10.1146/annurev.micro.57.030502.090855
  26. Pallen MJ, Matzke NJ (2006) From The Origin of Species to the origin of bacterial flagella. Nat Rev Microbiol 4:784-90 PMID 16953248
    • Soscia C et al.' (2007) Cross talk between type III secretion and flagellar assembly systems in Pseudomonas aeruginosa J Bacteriol 189:3124-32