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The concept of Irreducible Complexity (IC) and, by extension Intelligent Design (ID) as a whole, is a defeatest and slothful concept. It’s proponents whine and wail that things are too complicated to have arisen through blind natural processes so don’t even bother to try to understand it. What kind of attitude is that? If everyone in history had this outlook we would still be throwing rocks to catch dinner. Science as we know it arose because there were those who did not accept that dogmatically-given answers are immune from being questioned. In other words, what we know as modern Science arose in spite of Religion and most definitely not because of it.

And – trust me on this – I did not need the opinon of Judge Jones III, as correct as it was, to know that ID is NOT Science. In Science, we deal in explanations that offer insight into the mechanisms of processes, not simply substituting another expression for “I don’t know”, like “a magic man done it”, and trying to pass it off as somehow being a satisfactory answer when it answers exactly nothing. How do we know when something is ‘too complex’ except when given as a ‘just so’ story? And ‘just so’ stories are as dogmatic as it gets. In Science we systematically work to divest ourselves of dogma, not embrace it!

In the Kitzmiller v. Dover case, Dr. Michael Behe was front and center for the defense trying to put forward the idea that this idiotic concept ‘explains’ the complexity of cellular structures that he feels (without ever presenting any data to corroborate his belief) could not come to be through the blind machinations of natural selection.

Poppycock. Behe tries to appeal to ignorance, which is not a logical argument at all. This is true in every single example supposedly supporting IC he has ever given. But his argument is never any more than throwing up his hands in self-fulfilling defeat at a real explanation. At the Kitzmiller trial, he was forced to admit that he was not even familliar with the relevant literature! This is the height of intellectual dishonesty, and because Behe espouses such nonsense his colleagues have completely (and rightly) disowned these nonsensical ideas (and let’s face it – him). This underscores a basic difference between ID (or should I say ‘cdesign proponentsists’?) and Evolution proponents in that the latter actually work to gather evidence in support of hypotheses while the former do nothing but sponge off the gullible by telling the faithful what they want to hear.

Today I’m going to discuss what proponents of ID consider the poster child for their position and why it is really far-and-away better represented by evolution.

What? You really thought I was going to cave in and endorse a vacuous concept like ID? Yeah. Right. I only endorse hypotheses that have positive evidence in support. Evidence against something does not strengthen another position in the least, and in the case of ID, it doesn’t even have negative evidence against Evolution beyond mere opinion. In other words, it has nada.

Enter his poster child for IC: the bacterial flagellum. The flagellum consists of six components: a basal body (including the MS ring, P ring and L ring – see figure below); a motor; a switch; a hook; a filament; and an export apparatus. To produce these parts requires about 50 genes, about half of which encode the structures themselves and the remainder are involved in regulatory processes which determine the length of the flagellar assembly or detecting and processing environmental signals to which the flagellum responds.

How does the flagellum work? It is powered by an ion gradient across the cell membrane (i.e., there is a higher concentration of ion, either proton or sodium, on one side of the membrane). The rotor transports ions across the membrane from the high concentration side to the low and the rotor is turned in the process. The rotor is capable of quite high speeds, on the order of 6,000-17,000 rpm, but with the flagellum attached speeds are typically 200-1,000 rpm. This allows the bacterium to move 50-60 body lengths per second.

There is no one bacterial flagellum and a great deal of diversity amongst bacterial species exists. In Spirochaetes, flagella are located in the periplasm between the outer membrane sheath and the cell cylinder. The C ring is thus larger than that in Salmonella and as a consequence has a different shape. Other bateria have more than one flagellar system (positioned at polar and lateral positions) with distinct genes and a completely different driving gradient (sodium versus proton).

Often, ‘cdesign proponentsists’ use the logical fallacy known as the Argument from Ignorance to make it appear that their position is much stronger than it actually is. They point to our poor understanding of how this complexity and diversification came about. This isn’t even an argument, and serves only to shore up their confirmation bias. Not only that, the knowledge gap ‘cdesign proponentsists’ are pointing to no longer exists. We now know the history of the genes involved and thus how the bacteria flagellum came to be in a very detailed and mechanistic way. Knowledge of the history of the genes involved in making the flagellum gives us a detailed look at how the structure evolved.

What do ‘cdesign proponentsists’ have to say about how this complexity can arise? Here’s how Behe’s describes IC:

‘By irreducibly complex I mean 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.’

I’ve said many times in relation to this – his definition artificially and arbitrarily places limits on evolution (which evolution, caring not one whit for anything Behe says about it, ignores) by claiming that one of its most important mechanisms is not allowed: the coming together of structures to produce a new structure with a new function. The concept of IC, as Behe defines it, bizarrely ignores the fact that the parts of the bacteria flagellum each have been found to have their own function in related bacteria lacking the flagellum. This is a screaming clue as to how the flagellum came to be and what does Behe do? He puts on a blindfold, sticks his fingers in his ears and says ‘la la la la la la….’! Another problem with the ID camp is that they throw words around that sound good, like ‘function’ or ‘information’, but when looked at closely their terms are never well-defined. Just what does the word ‘function’ mean in this context? Many proteins can perform multiple tasks, including those making up the flagellum. Which one is its ‘function’? Whether Behe is being obtuse, ignorant or deceitful (deliberately or otherwise) I leave to the reader to decide. 

Another problem with irreducible complexity is that it implies evolution is a goal-oriented process. In this case, the goal is to generate a motor apparatus that can propel the bacterium. But evolution is not goal-oriented. It is blind. If duplication of an ancient gene with subsequent mutation (one way in which to increase the amount of information in the genome) produces a new protein which serves an advantageous function happens, great. The survival chance for the organism tends to increase and this gene will tend to be passed on to the next generation. But it does not matter what the products of the new gene do, only that it is advantageous for the organism in the environment it finds itself in. There is no goal in evolution. While it sounds like a very ad hoc process, it is a very powerful one, as computer scientists are discovering.

Fortunately, there are people in the world that aren’t satisfied with such contemptably defeatest and lazy thinking and go out to find real answers. I wrote earlier about clues to the evolutionary source of the bacteria flagellum. What are these clues of which I speak? Here are a few of them:

  • The homology (similarity of sequences) between the flagellum-specific ATPase FliI (part of the motor) and the β-subunit of ATP synthase is strongly suggestive of a conserved membrane-bound protein with units that rotate during ATP formation from ADP and inorganic phosphate.
  • The motor proteins MotA/B of the bacteria flagellum are homologous to simpler Tol-pal and Ton-B motor proteins, the more complex former could have evolved from proton-driven secretion system represented by the latter.
  • The piece-de-resistance is that both the sequence and structural homologies with the type III secretion system (TTSS) strongly suggest that the bacteria flagellum and the much older TTSS share common ancestry.

So we already have a significant body of evidence that suggests the flagellum developed through blind processes rather than design. This is already convincing evidence that ‘cdesign proponentsists’ simply choose to ignore which, incidentally, falsifies irreducible complexity (at least in this case).

Recently, complete genome sequences of a number of bacterial species has allowed for very sophisticated analyses (phylogenetic profiling methods) of the genetic history of the flagellum. Phylogenetic profiling is the process of building an evolutionary tree showing the relationships between various species. The vertices of the tree indicate a common ancestor for the species which branch off. Such trees can be generated by a number of comparisons, including anatomical or gene sequence comparison. Phylogenetic profiling does rely on a presumption of common ancestry, but its remarkable success is a total vindication of the method.

Most genes producing protein that constitute the parts of the flagellum are present across all bacterial phyla for which we have data for. This in itself suggests that the components of the flagellum existed prior to its evolution and prior to the diversification of bacteria. From a comparison of genomes across bacterial phyla, 21 genes specifying proteins in the:

  • filament (fliC)
  • hook-filament junction (flgK, flgL)
  • hook (flgE)
  • rod (flgB, flgC, flgG, flgF)
  • MS ring (flliF)
  • C ring (fliG, fliM, fliN)
  • motor (motA, motB)
  • export apparatus (flhA, flhB, fliI, fliP, fliR, fliQ)
  • hook-cap (flgD)

form an ancestral set of genes. Three other genes are included in the core gene set, but are not present in all phyla:

  • filament cap (fliD)
  • rod (fliE)
  • export apparatus (fliH)

Remarkably, the parts of the flagellum are capable of self-assembly and does not require enzymatic facilitation. The basal body of the flagellum has a hollow core through which the proteins comprising the flagellum move into position. During the assembly process, each component is added at the flagellar tip, not at the base.

The phylogenetic analysis began by searching for homologs of each of the core genes within that living laboratory known as E. coli. E. coli has the highest proportion of functionally annotated genes of any bacterial species, so is a logical place to start. While E. coli contains only 10 of the 24 core genes, that was still enough to provide not only an overall view of the relationships between the core genes, but enough to also show that flagellar genes were derived from other flagellar genes with little input from genes apart from the core set. The full set of interrelationships between the core genes came after extending the analysis to include other genomes.

Phylogenetic analysis yielded the following results:

  1. Since they contain a significant sequence homologies, the core genes of the bacterium flagellum originated from one another through a series of duplications.
  2. The individual genes comprising the core set demonstrate phylogenetic histories congruent with one another (see second figure) with surprisingly few incongruents arising from horizontal gene transfer (interspecies gene exchange).

What congruence means is that the phylogenetic tree (an evolutionary tree generated for each of the 24 core genes) for each gene encoding protein for the flagellum is the same no matter which gene is looked at. Taken together, these data tell us that the whole of the core set of flagellum genes arose through gene duplication events starting from one are a few original gene(s).

Using the worked-out phylogeny of the core proteins, it is possible to determine the order in which they appeared. This then yields how the genetic progression then produced the flagellum, as the order of its assembly recapitulates its evolutionary history. The rod, hook and fliament proteins originated in an order which produced an ‘inside-out’ assembly process. The flagellum itself is thought to have originated as a primitive secretion system first involving ATPase and then adding the rod, hook and filament through gene duplication and diversification. Thus, the conclusions drawn from phylogenetic analysis are mirrored by what has long been suspected from the observed similarities between the flagellum and the TTSS.

Simplicity begetting complexity. That is how things evolve, even the bacterial flagellum. Contrary to Behe’s irrelevant viewpoint, something as complex as the flagellum can indeed arise through small steps via natural selection from gene duplication and modification from a single ancestral gene. Far from Behe’s remark that

‘The theory of undirected evolution is already dead, but the work of science continues…’,

descent with modification is alive, well, and far and away the most successful (not to mention only) theory explaining the diversity of life on this planet. The work presented in the paper by Liu and Ochman, itself built on the results of a great deal of fine detective work, is definitive confirmation that the bacterial flagellum came into being through, blind as it may be, the powerful naturalistic process we know by the name ‘Evolution’. Behe’s comment is purest fantasy.

Charles Darwin triumphs yet again.


  1. Blocker A, Komoriya K and Aizawa S, Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proc Natl Acad Sci 100:3027-2020 (2003)
  2. Cascales E, Lloubes R and Sturgis JN, The TolQ-TolR proteins energize TolA and share homologies with the flagellar motor proteins MotA-MotB. Mol Microbiol 42:795-807 (2001)
  3. Hueck CJ, Type III protein secretion systems in bacterial pathogens of animals and plants. Microbiol Mol Biol Rev 62:379-433 (1998)
  4. Liu R and Ochman H, Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci 104:7116-7121 (2008)
  5. Musgrave I, in Why Intelligent Design Fails: A Scientific Critique of the New Creationism. Young M and Edis T, eds.
  6. Pallen MJ and Matzke NJ, From The Origin of Species to the origin of bacterial flagella. Nat Rev Microbiol 4:784-790 (2006)
  7. Rizzotti M, Early Evolution: From the Appearance of the First Cell to the Modern Organisms (2000)


  1. I dont understand… I hate to say it but this is very confusing to me. Could it be better explained?

    • What parts are you having trouble with? Tell me and I’ll give it a shot.

  2. I am so with your sentiments, views and rationality. But please realise that so many people attracted to ID have to be dealt with as fellow intelligent beings with their own (possibly misguided) opinions. A harsh and arrogant manner does NOT help. My hero Richard Dawkins suffers a little from this problem as well. We must capture HEARTS as well as MINDS here!

    • “A harsh and arrogant manner does NOT help.” No, but neither does accomodationism, which must be avoided at all costs!

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