Editing Irreducible complexity (section)

=== Flagella ===
{{Main|Evolution of flagella}}

The [[flagella]] of certain bacteria constitute a [[molecular motor]] requiring the interaction of about 40 different protein parts. The flagellum (or cilium) developed from the pre-existing components of the eukaryotic cytoskeleton.<ref>{{Citation |last=Mitchell |first=David R. |title=The Evolution of Eukaryotic Cilia and Flagella as Motile and Sensory Organelles |date=2007 |url=https://doi.org/10.1007/978-0-387-74021-8_11 |work=Eukaryotic Membranes and Cytoskeleton: Origins and Evolution |pages=130–140 |access-date=2023-06-25 |series=Advances in Experimental Medicine and Biology |volume=607 |place=New York, NY |publisher=Springer |language=en |doi=10.1007/978-0-387-74021-8_11 |isbn=978-0-387-74021-8 |pmc=3322410 |pmid=17977465}}</ref><ref>{{Cite journal |last1=Wickstead |first1=Bill |last2=Gull |first2=Keith |date=2011-08-22 |title=The evolution of the cytoskeleton |url=https://doi.org/10.1083/jcb.201102065 |journal=Journal of Cell Biology |volume=194 |issue=4 |pages=513–525 |doi=10.1083/jcb.201102065 |issn=1540-8140 |pmc=3160578 |pmid=21859859}}</ref> In bacterial flagella, strong evidence points to an evolutionary pathway from a Type III secretory system, a simpler bacterial secretion system.<ref>{{Cite journal |last1=Milne-Davies |first1=Bailey |last2=Wimmi |first2=Stephan |last3=Diepold |first3=Andreas |date=March 2021 |title=Adaptivity and dynamics in type III secretion systems |journal=Molecular Microbiology |language=en |volume=115 |issue=3 |pages=395–411 |doi=10.1111/mmi.14658 |pmid=33251695 |issn=0950-382X|doi-access=free }}</ref> Despite this, 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" /> However, each of the three types of flagella—eukaryotic, bacterial, and archaeal—has been shown to have evolutionary pathways. For archaeal flagella, there is a molecular homology with bacterial Type IV pili, pointing to an evolutionary link.<ref>{{Cite journal |last1=Faguy |first1=David M. |last2=Jarrell |first2=Ken F. |last3=Kuzio |first3=John |last4=Kalmokoff |first4=Martin L. |date=1994-01-01 |title=Molecular analysis of archaeal flagellins: similarity to the type IV pilin – transport superfamily widespread in bacteria |url=http://www.nrcresearchpress.com/doi/10.1139/m94-011 |journal=Canadian Journal of Microbiology |language=en |volume=40 |issue=1 |pages=67–71 |doi=10.1139/m94-011 |pmid=7908603 |issn=0008-4166|url-access=subscription }}</ref> In all these cases, intermediary, simpler forms of the structures are possible and provide partial functionality.

'''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 |journal= Mol Syst Biol |volume= 3 |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 |journal= J Bacteriol |volume= 188 |issue= 21 |pages= 7700–6 |doi= 10.1128/JB.00820-06 |pmid= 16936039 |pmc=1636259}}</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 the [[Type three secretion system|type-III secretion system]] share several components which provides strong evidence of a shared evolutionary history (see below). In fact, this example shows how a complex system 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= 978-3-8055-8340-4 |pmid= 18753783}}</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|doi-access= free }}</ref> Multiple processes were involved in the evolution of the flagellum, including [[horizontal gene transfer]].<ref>{{cite journal|last1=Zuckerkandl|first1=Emile|title=Intelligent design and biological complexity|journal=Gene|date=December 2006|volume=385|pages=2–18|doi=10.1016/j.gene.2006.03.025|pmid=17011142}}</ref>

'''Evolution from type three secretion systems'''. 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 [[eukaryote]] cells.<ref name="Flagellum Unspun">Miller, Kenneth R. [http://www.millerandlevine.com/km/evol/design2/article.html The Flagellum Unspun: The Collapse of "Irreducible Complexity"] {{webarchive|url=https://web.archive.org/web/20140214024810/http://www.millerandlevine.com/km/evol/design2/article.html |date=2014-02-14 }} with reply here {{cite web |url=http://www.designinference.com/documents/2003.02.Miller_Response.htm |title=The Bacterial Flagellum: Still Spinning Just Fine |access-date=2006-04-26 |url-status=dead |archive-url=https://web.archive.org/web/20060403013818/http://designinference.com/documents/2003.02.Miller_Response.htm |archive-date=2006-04-03 }}</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 |doi=10.1038/nrmicro1493 |pmid=16953248|s2cid=24057949 }}</ref> 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>[https://www.youtube.com/watch?v=RQQ7ubVIqo4 Kenneth Miller's The Collapse of Intelligent Design: Section 5 Bacterial Flagellum] {{webarchive|url=https://web.archive.org/web/20161017080729/https://www.youtube.com/watch?v=RQQ7ubVIqo4 |date=2016-10-17 }} (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>[https://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] {{webarchive|url=https://web.archive.org/web/20160919205453/http://www.talkdesign.org/faqs/flagellum.html |date=2016-09-19 }} (Talk Design, 2006 September)</ref> Studies have also shown that similar parts of the flagellum in different bacterial species can have different functions despite showing evidence of common descent, and that certain parts of the flagellum can be removed without eliminating its functionality.<ref>{{cite book |last1=Maloy |first1=Stanley |title=Brenner's Encyclopedia of Genetics (Second Edition)|date=1 January 2013 |pages=112–114   |publisher=Academic Press |doi=10.1016/B978-0-12-374984-0.00806-8|isbn=978-0-08-096156-9 }}</ref> Behe responded to Miller by asking "why doesn't he just take an appropriate bacterial species, knock out the genes for its flagellum, place the bacterium under selective pressure (for mobility, say), and experimentally produce a flagellum—or any equally complex system—in the laboratory?"<ref>{{Cite web |last=Michael |first=Behe |author-link=Michael Behe |date=2016-10-27 |title=Philosophical Objections to Intelligent Design: A Response to Critics |url=https://evolutionnews.org/2016/10/philosophical_o/ |access-date=2022-10-12 |website=Evolution News |language=en-US}}</ref> However 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">{{Cite journal |last1=Taylor |first1=Tiffany B. |last2=Mulley |first2=Geraldine |last3=Dills |first3=Alexander H. |last4=Alsohim |first4=Abdullah S. |last5=McGuffin |first5=Liam J. |last6=Studholme |first6=David J. |last7=Silby |first7=Mark W. |last8=Brockhurst |first8=Michael A. |last9=Johnson |first9=Louise J. |last10=Jackson |first10=Robert W. |date=2015-02-27 |title=Evolution. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system |url=https://pubmed.ncbi.nlm.nih.gov/25722415/ |journal=Science |volume=347 |issue=6225 |pages=1014–1017 |doi=10.1126/science.1259145 |issn=1095-9203 |pmid=25722415|s2cid=206561157 |hdl=10871/16523 |hdl-access=free }}</ref>

Dembski has argued that phylogenetically, the TTSS is found in a narrow range of bacteria which makes it seem to him to be a late innovation, whereas flagella are widespread throughout many bacterial groups, and he argues that it was an early innovation.<ref>{{cite web|url=http://www.evolutionnews.org/2010/01/spinning_tales_about_the_bacte031141.html|title=Spinning Tales About the Bacterial Flagellum – Evolution News|date=21 January 2010|website=evolutionnews.org|access-date=7 May 2018|url-status=live|archive-url=https://web.archive.org/web/20160304053315/http://www.evolutionnews.org/2010/01/spinning_tales_about_the_bacte031141.html|archive-date=4 March 2016}}</ref><ref>Dembski, [https://web.archive.org/web/20051026133901/http://www.designinference.com/documents/2005.09.Expert_Rebuttal_Dembski.pdf Rebuttal to Reports by Opposing Expert Witnesses, p. 52]</ref> Against Dembski's argument, different flagella use completely different mechanisms, and publications show a plausible path in which bacterial flagella could have evolved from a secretion system.<ref name="CB200.1:">{{cite web |last= Isaak |first= Mark |title= CB200.1: Bacterial flagella and Irreducibly Complexity |url= http://www.talkorigins.org/indexcc/CB/CB200_1.html |publisher= TalkOrigins Archive |year= 2006 |access-date= 25 June 2013 |url-status= live |archive-url= https://web.archive.org/web/20130704075446/http://www.talkorigins.org/indexcc/CB/CB200_1.html |archive-date= 4 July 2013 }}</ref>