Editing Irreducible complexity (section)

=== 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.