Editing Irreducible complexity (section)

== Response of the scientific community ==
Like intelligent design, the concept it seeks to support, irreducible complexity has failed to gain any notable acceptance within the [[scientific community]].

=== Reducibility of "irreducible" systems ===
Researchers have proposed potentially viable evolutionary pathways for allegedly irreducibly complex systems such as blood clotting, the immune system<ref>Matt Inlay, 2002. "[http://www.talkdesign.org/faqs/Evolving_Immunity.html Evolving Immunity] {{webarchive|url=https://web.archive.org/web/20060111050740/http://www.talkdesign.org/faqs/Evolving_Immunity.html |date=2006-01-11 }}." In ''TalkDesign.org''.</ref> and the flagellum<ref>Nicholas J. Matzke, 2003. "[http://www.talkdesign.org/faqs/flagellum_background.html Evolution in (Brownian) space: a model for the origin of the bacterial flagellum] {{webarchive|url=https://web.archive.org/web/20051220185557/http://www.talkdesign.org/faqs/flagellum_background.html |date=2005-12-20 }}."</ref><ref>{{cite journal |vauthors= Pallen MJ, Matzke NJ |title= From The Origin of Species to the origin of bacterial flagella |journal= Nature Reviews Microbiology |volume= 4 |issue= 10 |pages= 784–90 |date= October 2006 |pmid= 16953248 |doi= 10.1038/nrmicro1493 |s2cid= 24057949 |url= http://www.pandasthumb.org/archives/2006/09/flagellum_evolu.html |url-status= dead |archive-url= https://web.archive.org/web/20060927162710/http://www.pandasthumb.org/archives/2006/09/flagellum_evolu.html |archive-date= 2006-09-27 |url-access= subscription }}</ref>—the three examples Behe proposed. John H. McDonald even showed his example of a mousetrap to be reducible.<ref name="trap" /> If irreducible complexity is an insurmountable obstacle to evolution, it should not be possible to conceive of such pathways.<ref>Pigliucci, Massimo {{cite web |url=http://www.infidels.org/library/modern/features/2000/pigliucci1.html |title=Secular Web Kiosk: Design Yes, Intelligent No: A Critique of Intelligent Design Theory and Neo-Creationism |access-date=2009-12-26 |url-status=live |archive-url=https://web.archive.org/web/20100105083259/http://www.infidels.org/library/modern/features/2000/pigliucci1.html |archive-date=2010-01-05 }} Collaboration Sept. 2001</ref>

Niall Shanks and Karl H. Joplin, both of [[East Tennessee State University]], have shown that systems satisfying Behe's characterization of irreducible biochemical complexity can arise naturally and spontaneously as the result of self-organizing chemical processes.<ref name="Redundant Complexity">{{cite journal |doi=10.1086/392687 |author1=Shanks, Niall |author2=Joplin, Karl H. |title=Redundant Complexity: A Critical Analysis of Intelligent Design in Biochemistry |journal=Philosophy of Science |year= 1999 |pages= 268–282 |volume= 66 |issue= 2, June |jstor=188646|s2cid=62198290 }}</ref><!--not working <ref>Niall Shanks and Karl H. Joplin. [http://www.asa3.org/ASA/topics/Apologetics/POS6-99ShenksJoplin.html Redundant Complexity:A Critical Analysis of Intelligent Design in Biochemistry.] East Tennessee State University.</ref>--> They also assert that what evolved biochemical and molecular systems actually exhibit is "redundant complexity"—a kind of complexity that is the product of an evolved biochemical process. They claim that Behe overestimated the significance of irreducible complexity because of his simple, linear view of biochemical reactions, resulting in his taking snapshots of selective features of biological systems, structures, and processes, while ignoring the redundant complexity of the context in which those features are naturally embedded. They also criticized his over-reliance on overly simplistic metaphors, such as his mousetrap.

A computer model of the co-evolution of proteins binding to DNA in the peer-reviewed journal ''[[Nucleic Acids Research]]'' consisted of several parts (DNA binders and DNA binding sites) which contribute to the basic function; removal of either one leads immediately to the death of the organism. This model fits the definition of irreducible complexity exactly, yet it evolves.<ref>{{cite journal |author=Schneider, TD |title=Evolution of Biological Information |journal= Nucleic Acids Research |year=2000 |pages=2794–2799 |volume=28 |issue=14 |pmid=10908337 |doi=10.1093/nar/28.14.2794 |pmc=102656|author-link=Thomas D. Schneider }}</ref> (The program can be run from [http://alum.mit.edu/www/toms/papers/ev/ Ev program].)

One can compare a mousetrap with a cat in this context. Both normally function so as to control the mouse population. The cat has many parts that can be removed leaving it still functional; for example, its tail can be bobbed, or it can lose an ear in a fight. Comparing the cat and the mousetrap, then, one sees that the mousetrap (which is not alive) offers better evidence, in terms of irreducible complexity, for intelligent design than the cat. Even looking at the mousetrap analogy, several critics have described ways in which the parts of the mousetrap could have independent uses or could develop in stages, demonstrating that it is not irreducibly complex.<ref name="trap" /><ref name="Only" />

Moreover, even cases where removing a certain component in an organic system will cause the system to fail do not demonstrate that the system could not have been formed in a step-by-step, evolutionary process. By analogy, stone arches are irreducibly complex—if you remove any stone the arch will collapse—yet humans [[arch#Construction|build them]] easily enough, one stone at a time, by building over [[centring|centering]] that is removed afterward. Similarly, [[natural arch|naturally occurring arches]] of stone form by the weathering away of bits of stone from a large concretion that has formed previously.

Evolution can act to simplify as well as to complicate. This raises the possibility that seemingly irreducibly complex biological features may have been achieved with a period of increasing complexity, followed by a period of simplification.

A team led by [[Joseph Thornton (biologist)|Joseph Thornton]], assistant professor of biology at the [[University of Oregon]]'s Center for Ecology and Evolutionary Biology, using techniques for resurrecting ancient genes, reconstructed the evolution of an apparently irreducibly complex molecular system. The April 7, 2006 issue of ''Science'' published this research.<ref name="thornton2006">{{cite journal |vauthors=Bridgham JT, Carroll SM, Thornton JW |title=Evolution of hormone-receptor complexity by molecular exploitation |journal=Science |volume=312 |issue=5770 |pages=97–101 |date=April 2006 |pmid=16601189 |doi=10.1126/science.1123348 |bibcode= 2006Sci...312...97B|s2cid=9662677 }}</ref><ref>[http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=746 Press release] {{webarchive|url=https://web.archive.org/web/20070930033744/http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=746 |date=2007-09-30 }} University of Oregon, April 4, 2006.</ref>

Irreducible complexity may not actually exist in nature, and the examples given by Behe and others may not in fact represent irreducible complexity, but can be explained in terms of simpler precursors. The theory of [[facilitated variation]] challenges irreducible complexity. [[Marc W. Kirschner]], a professor and chair of Department of Systems Biology at [[Harvard Medical School]], and [[John C. Gerhart]], a professor in Molecular and Cell Biology, [[University of California, Berkeley]], presented this theory in 2005. They describe how certain mutation and changes can cause apparent irreducible complexity. Thus, seemingly irreducibly complex structures are merely "very complex", or they are simply misunderstood or misrepresented.

=== Gradual adaptation to new functions ===
{{Main|Exaptation}}
The precursors of complex systems, when they are not useful in themselves, may be useful to perform other, unrelated functions. Evolutionary biologists argue that evolution often works in this kind of blind, haphazard manner in which the function of an early form is not necessarily the same as the function of the later form. The term used for this process is [[exaptation]]. The [[evolution of mammalian auditory ossicles|mammalian middle ear]] (derived from a jawbone) and the [[giant panda|panda]]'s thumb (derived from a wrist bone spur) provide classic examples. A 2006 article in ''Nature'' demonstrates intermediate states leading toward the development of the ear in a [[Devonian]] fish (about 360 million years ago).<ref>{{cite journal |journal= Nature |volume= 439 |pages= 318–21 |date= January 19, 2006 |author1=M. Brazeau |author2=P. Ahlberg |doi= 10.1038/nature04196 |issue= 7074 |title= Tetrapod-like middle ear architecture in a Devonian fish |pmid= 16421569|bibcode= 2006Natur.439..318B|s2cid= 4301561 }}</ref> Furthermore, recent research shows that viruses play a heretofore unexpected role in evolution by mixing and matching genes from various hosts.<ref>{{Cite journal|last=Boto|first=Luis|date=October 28, 2009|title=Horizontal gene transfer in evolution: facts and challenges|journal=Proceedings of the Royal Society B|volume=277|issue=1683|pages=819–827|doi=10.1098/rspb.2009.1679|pmid=19864285|pmc=2842723}}</ref>

Arguments for irreducibility often assume that things started out the same way they ended up—as we see them now. However, that may not necessarily be the case. In the ''Dover'' trial an expert witness for the plaintiffs, Ken Miller, demonstrated this possibility using Behe's mousetrap analogy. By removing several parts, Miller made the object unusable as a mousetrap, but he pointed out that it was now a perfectly functional, if unstylish, [[tie clip]].<ref name="Only" /><ref name=NOVAChapter8>{{cite web |url= https://www.pbs.org/wgbh/nova/transcripts/3416_id_08.html |title= NOVA: Transcripts: Judgment Day: Intelligent Design on Trial Chapter 8 |date= November 13, 2007 |publisher= [[Public Broadcasting Service|PBS]] |access-date= 2008-12-17 |url-status= live |archive-url= https://web.archive.org/web/20081123085214/http://www.pbs.org/wgbh/nova/transcripts/3416_id_08.html |archive-date= November 23, 2008 }}</ref>

=== Methods by which irreducible complexity may evolve ===
{{further|Evolvability}}

Irreducible complexity can be seen as equivalent to an "uncrossable valley" in a [[fitness landscape]].<ref name="trotter2014">{{cite journal|last1=Trotter|first1=Meredith V.|last2=Weissman |first2=Daniel B. |last3=Peterson |first3=Grant I. |last4=Peck|first4=Kayla M.|last5=Masel|first5=Joanna |author5-link=Joanna Masel|title=Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations|journal=Evolution|date=December 2014|volume=68 |issue=12 |pages=3357–3367 |doi=10.1111/evo.12517 |pmid=25178652|pmc=4258170}}</ref> A number of mathematical models of evolution have explored the circumstances under which such valleys can, nevertheless, be crossed.<ref>{{cite journal|last1=Weissman|first1=Daniel B.|last2=Desai|first2=Michael M.|last3=Fisher|first3=Daniel S. |last4=Feldman |first4=Marcus W.|title=The rate at which asexual populations cross fitness valleys|journal=Theoretical Population Biology|date=June 2009 |volume=75 |issue=4|pages=286–300|doi=10.1016/j.tpb.2009.02.006|pmid=19285994|pmc=2992471}}</ref><ref>{{cite journal|last1=Weissman|first1=D. B.|last2=Feldman|first2=M. W. |last3=Fisher|first3=D. S. |title=The Rate of Fitness-Valley Crossing in Sexual Populations|journal=Genetics|date=5 October 2010|volume=186 |issue=4 |pages=1389–1410 |doi=10.1534/genetics.110.123240 |pmid=20923976|pmc=2998319}}</ref><ref name="trotter2014" /><ref>{{cite journal |last1=Covert|first1=Arthur|last2=Lenski |first2=Richard |last3=Wilke |first3=Claus |last4=Ofria |first4=Charles |title=Experiments on the role of deleterious mutations as stepping stones in adaptive evolution |journal=Proceedings of the National Academy of Sciences |date=2013|volume=110|issue=34|pages=E3171–E3178|doi=10.1073/pnas.1313424110|pmid=23918358|pmc=3752215|bibcode=2013PNAS..110E3171C|doi-access=free}}</ref>

An example of a structure that is claimed in Dembski's book ''No Free Lunch'' to be irreducibly complex, but evidently has evolved, is the protein T-urf13,<ref name="Wein 2002">{{cite web | last=Wein | first=Richard | title=Not a Free Lunch But a Box of Chocolates. A critique of William Dembski's book No Free Lunch| website=TalkOrigins Archive | date=23 April 2002 | url=http://www.talkorigins.org/design/faqs/nfl/#evid | access-date=25 August 2022|quote=Dembski considers the case of a gene, T-urf13, which occurs in a particular strain of maize ... Specified complexity (CSI) is not a marker of intelligent design. If specified complexity is determined according to the uniform-probability interpretation, then natural processes are perfectly capable of generating it. If it is determined by the chance-elimination method, then specified complexity is just a disguise for the god-of-the-gaps argument.}}</ref> which is responsible for the [[cytoplasmic male sterility]] of [[waxy corn]] and is due to a completely new gene.<ref>Levings 3rd, C.S. (1990) The Texas cytoplasm of maize: cytoplasmic male sterility and disease susceptibility. Science 250, 942–947.</ref> It arose from the fusion of several non-protein-coding fragments of mitochondrial DNA and the occurrence of several mutations, all of which were necessary. Behe's book ''Darwin Devolves'' claims that things like this would take billions of years and could not arise from random tinkering, but the corn was bred during the 20th century. When presented with T-urf13 as an example for the evolvability of irreducibly complex systems, the Discovery Institute resorted to its flawed probability argument based on false premises, akin to the [[Texas sharpshooter fallacy]].<ref>Andreas Beyer, Hansjörg Hemminger & Martin Neukamm: [https://www.ag-evolutionsbiologie.net/pdf/2022/evolution-of-t-urf13-irreducible-complexity.pdf The Evolution of T-URF13: Does Irreducible Complexity count or not?], and as [https://pandasthumb.org/archives/2022/06/evolution-of-t-urf13.html HTML document on the website of "Panda's Thumb".]</ref>

=== Falsifiability and experimental evidence ===
Some critics, such as [[Jerry Coyne]] (professor of [[evolutionary biology]] at the [[University of Chicago]]) and [[Eugenie Scott]] (a [[physical anthropology|physical anthropologist]] and former executive director of the [[National Center for Science Education]]) have argued that the concept of irreducible complexity and, more generally, [[intelligent design]] is not [[falsifiability|falsifiable]] and, therefore, not [[scientific]].{{citation needed|date=September 2020}}

Behe argues that the theory that irreducibly complex systems could not have evolved can be falsified by an experiment where such systems are evolved. For example, he posits taking bacteria with no [[flagella|flagellum]] and imposing a selective pressure for mobility. If, after a few thousand generations, the bacteria evolved the bacterial flagellum, then Behe believes that this would refute his theory.<ref>{{Cite web|url=https://evolutionnews.org/2016/10/philosophical_o/|title=Philosophical Objections to Intelligent Design: A Response to Critics|last=Behe|first=Michael|date=October 27, 2016|website=Evolution News & Science Today|access-date=August 17, 2018}}</ref>{{primary source inline|date=August 2018}} This has been done: a laboratory experiment has been performed where "immotile strains of the bacterium ''Pseudomonas fluorescens'' that lack flagella [...] regained flagella within 96 hours via a two-step evolutionary pathway", concluding that "natural selection can rapidly rewire regulatory networks in very few, repeatable mutational steps".<ref name=":0" />{{Update inline|date=December 2023|reason=For reactions, probably}}

Other critics take a different approach, pointing to experimental evidence that they consider falsification of the argument for intelligent design from irreducible complexity. For example, [[Kenneth R. Miller|Kenneth Miller]] describes the lab work of Barry G. Hall on [[Escherichia coli|''E. coli'']] as showing that "Behe is wrong".<ref>{{cite book |author= Miller, K |title= Finding Darwin's God: a scientist's search for common ground between God and evolution |publisher= Cliff Street Books |location= New York |year= 1999 |isbn= 978-0-06-093049-3}}</ref>

Other evidence that irreducible complexity is not a problem for evolution comes from the field of [[computer science]], which routinely uses computer analogues of the processes of evolution in order to automatically design complex solutions to problems. The results of such [[genetic algorithm]]s are frequently irreducibly complex since the process, like evolution, both removes non-essential components over time as well as adding new components. The removal of unused components with no essential function, like the natural process where rock underneath a [[natural arch]] is removed, can produce irreducibly complex structures without requiring the intervention of a designer. Researchers applying these algorithms automatically produce human-competitive designs—but no human designer is required.<ref>{{cite web|url=http://www.genetic-programming.com/humancompetitive.html|title=Human Competitive|website=www.genetic-programming.com|access-date=7 May 2018|url-status=live|archive-url=https://web.archive.org/web/20160708052427/http://www.genetic-programming.com/humancompetitive.html|archive-date=8 July 2016}}</ref>

=== Argument from ignorance ===
Intelligent design proponents attribute to an intelligent designer those biological structures they believe are irreducibly complex and therefore they say a natural explanation is insufficient to account for them.<ref>Michael Behe. [http://www.discovery.org/scripts/viewDB/index.php?command=view&id=51 Evidence for Intelligent Design from Biochemistry.] {{webarchive|url=https://web.archive.org/web/20060903185728/http://www.discovery.org/scripts/viewDB/index.php?command=view&id=51 |date=2006-09-03 }} 1996.</ref> However, critics view irreducible complexity as a special case of the "complexity indicates design" claim, and thus see it as an [[argument from ignorance]] and as a [[God of the gaps|God-of-the-gaps]] argument.<ref name="isaak_ci101">Index to Creationist Claims. Mark Isaak. The Talk.Origins Archive. "Irreducible complexity and complex specified information are special cases of the "complexity indicates design" claim; they are also arguments from incredulity." {{cite web |url=http://www.talkorigins.org/indexcc/CI/CI101.html |title=CI101: Complexity and design |access-date=2014-03-24 |url-status=live |archive-url=https://web.archive.org/web/20131004031017/http://www.talkorigins.org/indexcc//CI/CI101.html |archive-date=2013-10-04 }} "The argument from incredulity creates a god of the gaps." {{cite web |url=http://www.talkorigins.org/indexcc/CA/CA100.html |title=CA100: Argument from incredulity |access-date=2014-03-24 |url-status=live |archive-url=https://web.archive.org/web/20131020072309/http://www.talkorigins.org/indexcc/CA/CA100.html |archive-date=2013-10-20 }}</ref>

[[Eugenie Scott]] and [[Glenn Branch]] of the [[National Center for Science Education]] note that intelligent design arguments from irreducible complexity rest on the false assumption that a lack of knowledge of a natural explanation allows intelligent design proponents to assume an intelligent cause, when the proper response of scientists would be to say that we do not know, and further investigation is needed.<ref>[[Eugenie C. Scott]] and Glenn Branch, [http://ncseweb.org/creationism/general/intelligent-design-not-accepted-by-most-scientists "Intelligent Design" Not Accepted by Most Scientists] {{webarchive|url=https://web.archive.org/web/20090330203658/http://ncseweb.org/creationism/general/intelligent-design-not-accepted-by-most-scientists |date=2009-03-30 }}, National Center for Science Education website, September 10, 2002.</ref> Other critics describe Behe as saying that evolutionary explanations are not detailed enough to meet his standards, while at the same time presenting intelligent design as exempt from having to provide any positive evidence at all.<ref>{{cite web |url=http://www.patheos.com/blogs/daylightatheism/essays/darwins-black-box/ |title=Darwin's Black Box by Michael Behe |access-date=2015-07-15 |url-status=live |archive-url=https://web.archive.org/web/20150715212827/http://www.patheos.com/blogs/daylightatheism/essays/darwins-black-box/ |archive-date=2015-07-15 }}</ref><ref>Amerikanbeat.net: A Critique of Behe, Dembski on "Irreducible Complexity"[https://web.archive.org/web/20100910063051/http://amerikanbeat.net/contact-amerikanbeat/a-critique-of-behe-dembski-on-%E2%80%9Cirreducible-complexity%E2%80%9D/]</ref>

=== False dilemma ===
Irreducible complexity is at its core an argument against evolution. If truly irreducible systems are found, the argument goes, then [[intelligent design]] must be the correct explanation for their existence. However, this conclusion is based on the assumption that current [[evolution]]ary theory and intelligent design are the only two valid models to explain life, a [[false dilemma]].<ref>[http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html IC and Evolution] {{webarchive|url=https://web.archive.org/web/20040813171254/http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html |date=2004-08-13 }} makes the point that: if "irreducible complexity" is tautologically redefined to allow a valid argument that [[intelligent design]] is the correct explanation for life then there is no such thing as "irreducible complexity" in the mechanisms of life; while, if we use the unmodified original definition then "irreducible complexity" has nothing whatever to do with evolution.</ref><ref>The Court in ''[[Kitzmiller v. Dover Area School District|Dover]]'' noted that this implicit assumption of the defendant school board created a "flawed and illogical contrived dualism" (Opinion p. 64).</ref>