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The [[flagella]] of certain bacteria constitute a [[molecular motor]] requiring the interaction of about 40 different protein parts. Behe presents this as a prime example of an irreducibly complex structure defined as "a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning", and argues that since "an irreducibly complex system that is missing a part is by definition nonfunctional", it could not have evolved gradually through [[natural selection]].<ref name="Flagellum Unspun"/>
'''Reducible complexity'''. In contrast to Behe's claims, many proteins can be deleted or mutated and the flagellum still works, even though sometimes at reduced efficiency.<ref>{{cite journal |vauthors=Rajagopala SV, Titz B, Goll J, Parrish JR, Wohlbold K, McKevitt MT, Palzkill T, Mori H, ((Finley RL Jr)), Uetz P |year= 2007 |title= The protein network of bacterial motility |url= |journal= Mol Syst Biol. |volume= 3 |issue= |page= 128 |doi= 10.1038/msb4100166 |pmid= 17667950 |pmc=1943423}}</ref> In fact, the composition of flagella is surprisingly diverse across bacteria with many proteins only found in some species but not others.<ref>{{cite journal |vauthors=Titz B, Rajagopala SV, Ester C, Häuser R, Uetz P |date= Nov 2006 |title= Novel conserved assembly factor of the bacterial flagellum |url= |journal= J Bacteriol |volume= 188 |issue= 21 |pages= 7700–6 |doi= 10.1128/JB.00820-06 |pmid= 16936039}}</ref> Hence the flagellar apparatus is clearly very flexible in evolutionary terms and perfectly able to lose or gain protein components. Further studies have shown that, contrary to claims of "irreducible complexity", flagella and related [[protein targeting|protein transport mechanisms]] show evidence of evolution through Darwinian processes, providing case studies in how complex systems can evolve from simpler components.<ref>{{cite journal |last1= Pallen |first1= M. J. |last2= Gophna |first2= U. |doi= 10.1159/000107602 |title= Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity |journal= Gene and Protein Evolution |series= Genome Dynamics |volume= 3 |pages= 30–47 |year= 2007 |isbn= 3-8055-8340-0 |pmid= |pmc=}}</ref><ref>{{cite journal |last1= Clements |first1= A. |last2= Bursac |first2= D. |last3= Gatsos |first3= X. |last4= Perry |first4= A. |last5= Civciristov |first5= S. |last6= Celik |first6= N. |last7= Likic |first7= V. |last8= Poggio |first8= S. |last9= Jacobs-Wagner |first9= C. |last10= Strugnell |first10= R. A. |last11= Lithgow |first11= T. |title= The reducible complexity of a mitochondrial molecular machine |journal= Proceedings of the National Academy of Sciences of the United States of America |volume= 106 |issue= 37 |pages= 15791–15795 |year= 2009 |pmid= 19717453 |pmc= 2747197 |doi= 10.1073/pnas.0908264106|bibcode= 2009PNAS..10615791C}}</ref>
'''Evolution from Type Three Secretion Systems'''. Scientists regard this argument as having been disproved in the light of research dating back to 1996 as well as more recent findings.<ref name="Flagellum Unspun">Miller, Kenneth R. [http://www.millerandlevine.com/km/evol/design2/article.html The Flagellum Unspun: The Collapse of "Irreducible Complexity"] with reply here [http://www.designinference.com/documents/2003.02.Miller_Response.htm]</ref><ref>{{cite journal |last1=Pallen |first1=M.J. |last2=Matzke |first2=N.J. |year=2006 |title=From ''The Origin of Species'' to the origin of bacterial flagella |journal=Nature Reviews Microbiology |volume=4 |issue= 10|pages=784–790 |publisher= |doi=10.1038/nrmicro1493 |url= |accessdate= |pmid=16953248}}</ref> They point out that the basal body of the flagella has been found to be similar to the [[Type three secretion system|Type III secretion system]] (TTSS), a needle-like structure that pathogenic germs such as ''[[Salmonella]]'' and ''[[Yersinia pestis]]'' use to inject [[toxin]]s into living [[eucaryote]] cells. The needle's base has ten elements in common with the flagellum, but it is missing forty of the proteins that make a flagellum work.<ref>[http://www.youtube.com/watch?v=RQQ7ubVIqo4 Kenneth Miller's The Collapse of Intelligent Design: Section 5 Bacterial Flagellum] (Case Western Reserve University, 2006 January 3)</ref> The TTSS system negates Behe's claim that taking away any one of the flagellum's parts would prevent the system from functioning. On this basis, [[Kenneth R. Miller|Kenneth Miller]] notes that, "The parts of this supposedly irreducibly complex system actually have functions of their own."<ref>[http://web.archive.org/web/20071010035647/http://debatebothsides.com/showthread.php?t=38338 Unlocking cell secrets bolsters evolutionists] (Chicago Tribune, 2006 February 13)</ref><ref>[http://www.talkdesign.org/faqs/flagellum.html Evolution in (Brownian) space: a model for the origin of the bacterial flagellum] (Talk Design, 2006 September)</ref>
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