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The most commonly used examples of irreducibly complex biological systems are the human compound eye, the [[blood clotting cascade]], and the bacterial [[flagellum]].
The most commonly used examples of irreducibly complex biological systems are the human compound eye, the [[blood clotting cascade]], and the bacterial [[flagellum]].
In addition William Dembski wrote the following in a essay:
<blockquote style="background: #F9F9F9; border: 1px solid #AAAAAA; padding: .3em;">
In a 1996 review of Michael Behe’s book Darwin's Black Box, James Shapiro, a molecular biologist at the University of Chicago, wrote: "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation for such a vast subject -- evolution -- with so little rigorous examination of how well its basic theses work in illuminating specific instances of biological adaptation or diversity" (National Review, 16 September 1996). Five years later cell biologist Franklin Harold wrote a book for Oxford University Press titled The Way of the Cell. In virtually identical language, he notes: "There are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations."
</blockquote>
It has been argued that such examples are flawed. Many biologists have pointed to possible pathways to the evolution of the human compound eye from the primitive [[eyespot]]. Kenneth R. Miller, for example, describes precursors to the flagellum's being used as ionic channels within [[bacteria]], known as the ''Type III Secretory System''.<ref>[http://www.millerandlevine.com/km/evol/design2/article.html The Flagellum Unspun]</ref> However, Professor Behe counters that Miller's criticism of his work is flawed. <ref>http://www.arn.org/docs/behe/mb_trueacidtest.htm</ref> Nick Matzke suggests that this is true for most of the structure of the flagellum in general; suggesting that of the 42 proteins found in the flagellum, 40 have already been found in use in different biological pathways.<ref>[http://www.pandasthumb.org/archives/2006/12/ode_to_the_flag.html Ode to the Flagellum</ref> However, William Dembski has argued that Matke has offered poor analysis of Behe's work. <ref>http://www.arn.org/docs/dembski/wd_biologusubjunctive.htm</ref> Critics, including biology professor John McDonald, have countered Even Behe's toy model, the mouse trap, used to illustrate the concept. McDonald produced examples of how he considered the mousetrap to be "easy to reduce", eventually to a single part.<ref name=trap>[http://udel.edu/~mcdonald/mousetrap.html A reducibly complex mousetrap] (graphics-intensive, requires [[JavaScript]])</ref> <!--Critics consider that most, or all, of the examples were based on misunderstandings of the workings of the biological systems in question, and consider the low quality of these examples excellent evidence for the argument from ignorance.-->However, Professor Behe disputes the criticism of John McDonald. <ref>http://www.arn.org/docs/behe/mb_mousetrapdefended.htm</ref>
It has been argued that such examples are flawed. Many biologists have pointed to possible pathways to the evolution of the human compound eye from the primitive [[eyespot]]. Kenneth R. Miller, for example, describes precursors to the flagellum's being used as ionic channels within [[bacteria]], known as the ''Type III Secretory System''.<ref>[http://www.millerandlevine.com/km/evol/design2/article.html The Flagellum Unspun]</ref> However, Professor Behe counters that Miller's criticism of his work is flawed. <ref>http://www.arn.org/docs/behe/mb_trueacidtest.htm</ref> Nick Matzke suggests that this is true for most of the structure of the flagellum in general; suggesting that of the 42 proteins found in the flagellum, 40 have already been found in use in different biological pathways.<ref>[http://www.pandasthumb.org/archives/2006/12/ode_to_the_flag.html Ode to the Flagellum</ref> However, William Dembski has argued that Matke has offered poor analysis of Behe's work. <ref>http://www.arn.org/docs/dembski/wd_biologusubjunctive.htm</ref> Critics, including biology professor John McDonald, have countered Even Behe's toy model, the mouse trap, used to illustrate the concept. McDonald produced examples of how he considered the mousetrap to be "easy to reduce", eventually to a single part.<ref name=trap>[http://udel.edu/~mcdonald/mousetrap.html A reducibly complex mousetrap] (graphics-intensive, requires [[JavaScript]])</ref> <!--Critics consider that most, or all, of the examples were based on misunderstandings of the workings of the biological systems in question, and consider the low quality of these examples excellent evidence for the argument from ignorance.-->However, Professor Behe disputes the criticism of John McDonald. <ref>http://www.arn.org/docs/behe/mb_mousetrapdefended.htm</ref>