Michael Behe Hasn't Been Refuted on the Flagellum - Evolution News & Views

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Michael Behe Hasn't Been Refuted on the Flagellum

cover-image-flagellum.jpg

Those of us who have been reading the literature surrounding the ID/evolution controversy for any length of time will be quite acquainted with the standard Darwinian retort with regards the "Behean" argument for irreducible complexity as far as the bacterial flagellum is concerned. There seems to be this unanimity of opinion among Darwinian theorists that the claims of irreducible complexity with respect to the bacterial flagellum have been refuted, and that we ID proponents are constantly shifting the goal posts, burying our heads in the sand, and generally clutching at straws. Indeed, one person on Facebook recently remarked,

My main gripe with the ID proponents is that they never seem to give up. How many times do you need to be told that something is wrong before you'll admit it? How many times does ID need to be refuted in the peer reviewed media before you'll give it up as a lost cause? The bacterial flagellum irreducible complexity story is completely and utterly dead. It's wrong. Get over it.

I recently brought up the flagellum, as a documented instance of irreducible complexity, at a lunch bar Q&A session on the science/faith intersect, and received responses to much the same effect.

But is this claim actually true? Has this argument been refuted by critics? About a year ago, I read Why Intelligent Design Fails - A Scientific Critique of the New Creationism (edited by Matt Young and Taner Edis). Chapter 5 of that book was contributed by Ian Musgrave and is titled "Evolution of the Bacterial Flagellum." Targeted as a response to Michael Behe and William Dembski, Musgrave attempts to dispel of the notion of irreducible complexity once and for all. Reading his chapter, I recall being deeply unimpressed. On page 82 of the book, Musgrave offers us the following argument:

Here is a possible scenario for the evolution of the eubacterial flagellum: a secretory system arose first, based around the SMC rod and pore-forming complex, which was the common ancestor of the type-III secretory system and the flagellar system. Association of an ion pump (which later became the motor protein) to this structure improved secretion. Even today, the motor proteins, part of a family of secretion-driving proteins, can freely dissociate and reassociate with the flagellar structure. The rod- and pore-forming complex may even have rotated at this stage, as it does in some gliding-motility systems. The protoflagellar filament arose next as part of the protein-secretion structure (compare the Pseudomonas pilus, the Salmonella filamentous appendages, and the E. coli filamentous structures). Gliding-twitching motility arose at this stage or later and was then refined into swimming motility. Regulation and switching can be added later, because there are modern eubacteria that lack these attributes but function well in their environment.(Shah and Sockett 1995). At every stage there is a benefit to the changes in the structure.

Indeed, Mark Pallen and Nick Matzke make a very similar argument in their 2006 Nature Reviews article (a paper which was raised by an audience member during the recent UK Behe tour). Ken Miller is also reputed for routinely making similar claims regarding the flagellum's evolution from the Type III Secretion System based largely on considerations of protein sequence homologies.

So, do these points succeed in laying to rest that pesky business of intelligent design once and for all? Well, actually no; they don't. In fact, I submit that the arguments of all of the aforementioned gentlemen fundamentally trivialize several important issues.

First and foremost, it trivializes the sheer complexity and sophistication of the flagellar system -- both its assembly apparatus, and its state-of-the-art design motif. Actually, the process by which the bacterial flagellum is self-assembled within the cell is so sophisticated that I have long struggled to convey it in an accessible way to lay-persons. Its core concepts are notoriously difficult to grasp for those not accustomed to thinking about the system or for those encountering it for the first time. But, at the same time, the mechanistic basis of flagellar assembly is so breath-takingly elegant and mesmerizing that the sheer engineering brilliance of the flagellar motor -- and, indeed, the magnitude of the challenge it brings to Darwinism -- cannot be properly appreciated without at minimum a cursory knowledge of its underpinning operations. Let's take a peek.

The Self-Assembly of the Flagellar Apparatus
flagellar assembly.jpg

The synthesis of the bacterial flagellum requires the orchestrated expression of more than 60 gene products. Its biosynthesis within the cell is orchestrated by genes which are organised into a tightly ordered cascade in which expression of one gene at a given level requires the prior expression of another gene at a higher level. The paradigm, or model, organism for flagellar assembly is Salmonella, a bacterium of the family Enterobacteriaceae. My discussion thus pertains principally to Salmonella, unless otherwise indicated.

The flagellar system in Salmonella has three classes of promoters (promoters are akin to a kind of molecular toggle switch which can initiate gene expression when recognised by RNA polymerase and an associated specialised protein called a "sigma factor"). These three classes of promoters are uninspirationally dubbed "Class I," "Class II," and "Class III." This sequential transcription is coupled to the process of flagellar assembly. Class I contains only two genes in one operon (called FlhD and FlhC). Class II consists of 35 genes across eight operons (including genes involved in the assembly of the hook-basal-body and other components of the flagellum, as well as the export apparatus and two regulatory genes called "FliA" and "FlgM"). Those genes which are involved in the synthesis of the filament are controlled by the Class III promoters.

The Class I promoter drives the expression of a master regulator (particular to the Enterobacteriaceae of which Salmonella is a member) called "FldH4C2" (don't worry about remembering it!). This enteric master regulator then turns on the Class II promoters in association with a sigma factor, σ70 (remember, I said that a sigma factor is a type of protein which enables specific binding of RNA polymerase to gene promoters). The Class II promoters are then responsible for the gene expression of the hook-basal-body subunits and its regulators, including another sigma factor called σ28 (which is encoded by a gene called FliA) and its anti-sigma factor, FlgM (anti-sigma factors, as their name suggests, binds to sigma factors to inhibit their transcriptional activity). The sigma factor σ28 is required to activate the Class III promoters. But here we potentially run into a problem. It makes absolutely no sense to start expressing the flagellin monomers before completion of the Hook-Basal-Body construction. Thus, in order to inhibit the σ28, the anti-sigma factor (FlgM) alluded to above inhibits its activity and prohibits it from interacting with the RNA polymerase holoenzyme complex. When construction of the Hook-Basal-Body is completed, the anti-sigma factor FlgM is secreted through the flagellar structures which are produced by the expression of the Class II hook-basal-body genes. The Class III promoters (which are responsible for the expression of flagellin monomers, the chemotaxis system and the motorforce generators) are then finally activated by the σ28 and the flagellum can be completed.

But it gets better. The flagellar export system (that is, the means by which FlgM is removed from the cell) has two substrate-specificity states: rod-/hook-type substrates and filament-type substrates. During the process of flagellar assembly, this substrate-specificity switch has to flick from the former of those states to the latter. Proteins which form part of the hook and rod need to be exported before those which form the filament. But how does this switch in substrate-specificity take place?

A membrane-bound protein called FlhB is the key player in this process. There is also a flagellar hook-length protein which is responsible for making sure that the hook length is of the right size (around 55nm) called FliK. This same protein is also responsible for initiating the switch export substrate specificity. As it turns out, without FliK, both the ability to switch and export filament and the hook length control are completely lost. FliK has two key domains, i.e. the N-terminal and C-terminal domains. During hook assembly, FliKN functions as a molecular sensor and transmitter of information on hook length. When the hook reaches the right length, the information is transmitted to FliKC and FliKCT, resulting in a conformational change, which in turn results in FliKCT binding to FlhBC. This, in turn, results in a conformational change in FlhBC. This causes the substrate specificity switch.

flagellum diagram.jpg

Flagellar assembly begins in the cytoplasmic membrane, progresses through the periplasmic space and finally extends outside the cell. The flagellum basically consists of two main parts: the secretion system and the axial structure. The principle components of the axial structure are FlgG for the rod, FlgE for the hook, and FliC for the filament. All of these assemble with the assistance of a cap protein (FlgJ, FlgD and FliD respectively). Of those, only FliD remains at the tip of the filament in the finished product. Other components of the axial structure (called FlgB, FlgC and FlgF) connect the rod and MS ring complex. The hook and filament are connected by FlgK and FlgL.

When the C ring and C rod attach to the M ring at its cytoplasmic surface, the MS ring complex -- which is the structural foundation of the apparatus -- can begin to secrete flagellar proteins.

The rod structure is built through the peptidoglycan layer. But its growth it isn't able to proceed past the physical barrier presented by the outer membrane without assistance. So, the outer ring complex cuts a hole in the membrane, so that the hook can grow beneath the FlgD scaffold until it reaches the critical length of 55nm. Then the substrates which are being secreted can switch from the rod-hook mode to flagellin mode, FlgD can be replaced by hook-associated-proteins, and the filament continues to grow. Without the presence of the cap protein FliD, these flagellin monomers become lost. This cap protein is thus essential for the process to take place.

Why the Flagellum Evolution From the T3SS Doesn't Work
One might have thought that the description given above should be more than enough to render the hand-waving gestures of Kenneth Miller et al. trivializations in the extreme. But it gets even worse for the Darwinian story. Why exactly is flagellum biosynthesis so tightly regulated and orchestrated? Not only do the energy demands render the flagellum an extremely expensive system to run, but untimely expression of flagellum proteins may induce a strong immune response in the host system, something no bacterium wants to do.

What is the significance of this from the standpoint of evolutionary rationale? Well, flagellin monomers are somewhat potent cytokine inducers. If you are a Yersinia organism in possession of a Type-III Secretion System the last thing you want to do is display those flagellin peptides to the macrophages. Such would no doubt be detrimental to the Yersinia's anti-inflammatory mechanisms.

Conclusion
My description, given above, has really only scratched the surface of this spectacular item of nano-technology (for more detail, see here). I have not, for the sake of brevity, even discussed the remarkable processes of chemotaxis, two component signal transduction circuitry, rotational switching, and the proton motive force by which the flagellum is powered (for details on this, see my discussion here or, for more detail, see this review paper). But the bottom line is that modern Darwinian theory -- as classically understood -- has come no where close to explaining the origin of this remarkably complex and sophisticated motor engine. Just as Darwinian "explanations" of the eye may, at first, appear convincing to the uninitiated, largely unacquainted with the sheer engineering marvel of the biochemistry and molecular basis of vision, so too do the evolutionary "explanations" of the flagellum rapidly become void of any persuasiveness when one considers the molecular details of the system. When one couples the above details with demonstrations of the sheer impotence of neo-Darwinism to produce novel protein folds and novel protein-protein binding sites, do you really think that this system can be cobbled together by virtue of slight, successive modification, one small step at a time? Given that neo-Darwinism's key selling point lies in its purported efficacy in explaining away the overwhelming appearance of design, doesn't it stand to reason that its demonstrable impotence throws the design postulate back on the table as a viable and respectable scientific proposition?

Douglas Axe of the Biologic Institute showed in one recent paper in the journal Bio-complexity that the model of gene duplication and recruitment only works if very few changes are required to acquire novel selectable utility or neo-functionalization. If a duplicated gene is neutral (in terms of its cost to the organism), then the maximum number of mutations that a novel innovation in a bacterial population can require is up to six. If the duplicated gene has a slightly negative fitness cost, the maximum number drops to two or fewer (not inclusive of the duplication itself).

It seems that the bacterial flagellum is as much a -- and perhaps a greater -- challenge to Darwinism as it was when Behe first wrote Darwin's Black Box in 1996.


49 Comments

One last hat tossed into the ring.

So many of the comments here are much less than professional. Shouldn't the sophistication of the academy carry with it a sense of decorum? It's very disheartening to read rude comments among those who would fancy themselves academicians. Probing the depths of profound mysteries are one thing. To summarily dismiss the Golden Rule is quite another.

But then cowardice arises in many forms - especially in the anonymity of web communications.

I have a question that may have been answered already, but I've never seen it. If biological systems are irreducibly complex and need the intervention of a designer, has anybody done research on how the designer might have accomplished this?
For example: Did the designer use some sort of scaffold to place the atoms in a specific way until they were complex enough to be a self sufficient entity, then remove the scaffold? If so, what might that scaffold be? Did the designer make one life form which all others evolved from, or was each life form individually produced? Perhaps the designer built up life forms atom by atom without a scaffold, making small individual modules, and "clicked" them together to form the whole.
I was just curious if work has been done in this area and where I might go to read about it.

To drs

So my first point must be correct in that you had no problem with it. Thanks very much! Our side is right in saying that mutations do not create anything new, but only alter what is there.

I do believe you miss my point about not mattering. This is not a fear of mine, but a logical consequence of yours. (not you'res as you typed ;))

As you are a materialist, then please explain why you matter and why it would be wrong if a terrorist bomb wiped you out. No fair appealing to spreading your genes around, as then Darwinists ought to be screaming at all gays for not doing the same and abortionists for not allowing those babies to spread their genes around.

As I have shown, Darwinians are very inconsistent. You talk one way and live another as if Christianity were true.

Arthur Hunt wrote,

Um, one can indeed assert this, since we know enough about raw mutation rates to be sure that every conceivable point mutation can and will occur, even in relatively modest populations (such as are seen in mammals) over rather short time scales.

As Casey notes, this misses the point, for we are discussing specific and co-ordinated combinatorial mutations. If a novel function requires, say, 10 co-ordinated non-adaptive mutations, then I would envision that being well beyond the edge of evolution.

Casey wrote,

p.s. I want to genuinely compliment you: I think you are one of the most civil ID critics on the internet and it does not go unnoticed, nor is it unappreciated!

I will second this.

Thanks for your participation.

J

I used to be anxious that taking a lot of Biology and Biochemistry classes would challenge my faith. Then I took Metabolism, Cell Biology, and Immunology. What I discovered was such mind-blowing complexity that it's impossible to believe there wasn't some kind of Designer anymore. More education caused me to become more religious. Professors will try to offer naturalistic explanations for everything, and it's tempting to believe them because the have a PhD. However, once you start asking yourself if their explanations really make sense instead of taking their word for it, purely naturalistic evolution starts looking like the biggest hoax in the history of science.

Scott-
Physics today includes the notion of a multiverse- only one of the many universes are observable. So the idea that it must be observable to be physics doesn't jibe with current theorizing. (You might want to check out string theory as well).
Your choices (the laws of physics-whatever those are- or a wizard in the sky magic) seem to make for a false dilemma.

Hi Arthur,

Thanks for joining in. I'm not sure if you understood my argument, but I think my point is eminently reasonable. It’s beyond dispute that there are, at least in principle, some types of complex structures that are beyond the probabilistic resources available to Darwinian evolution. Let’s demonstrate this with an admittedly extreme example.

Let's say, hypothetically, that a structure required 10,000 mutations before any function was gained. If you only have 9,999 of those required mutations, then the organism dies. But once you get all 10,000 mutations in a single organism, you get a complex structure that confers a dramatic benefit. Surely you would not say that there are sufficient probabilistic resources for that structure to evolve. After all, even Jerry Coyne admits:

“It is indeed true that natural selection cannot build any feature in which intermediate steps do not confer a net benefit on the organism.” (Jerry Coyne, "The Great Mutator," The New Republic (June 14, 2007).)

Coyne asserts he knows of no example where this is the case. I assert that there are such examples. But the point is this: if Coyne is right then one better not just make the assertion that all structures can evolve. We'd better test this question and not just assume neo-Darwinism is true. In fact, your defense of Stuart's assertion is typifies exactly what is wrong with neo-Darwinian thinking: it just assumes there are sufficient probabilistic resources for all things to evolve, and does not show much interest in actually testing these questions.

In fact, take my hypothetical example above and change the requirements to only 2 slightly deleterious mutations and it seems likely that such structure are beyond the probabilistic resources available to neo-Darwinian evolution. At least that's what Axe's work shows.

Arthur, I know you're a smart guy, but I think my basic point—that there are some structures we which cannot evolve—seems pretty reasonable. Indeed, it seems likely that even some structures we observe cannot evolve by Darwinian evolution. Thanks.

Casey

p.s. I want to genuinely compliment you: I think you are one of the most civil ID critics on the internet and it does not go unnoticed, nor is it unappreciated!

Stuart, you're assuming that "Miscarriages, Down's syndrome, Fragile X etc. Not to mention our knees..." is not our own fault? And you base that assumption on what?

Things happen and go wrong, but there is cause-and-effect. On that much religionists and non-religionists should be able to agree. Actions have consequences, sometimes immediately, sometimes delayed, and sometimes hard to trace in a butterfly effect of expanding consequences where bad things happen to an individual even though that individual did not deserve it — whether you look at it scientifically, philosophically, or both.

There is no necessary basis to blame God for everything that is unpleasant. From an atheistic perspective there is especially no basis to blame God. But also from a religionist's perspective there is no basis to automatically assume that something bad is God's fault and not ours.

Hi CAsey,

You said: "You cannot simply assert that all mutations can and will occur, or that any structure we observe can and will evolve, even given large bacterial populations. "

Um, one can indeed assert this, since we know enough about raw mutation rates to be sure that every conceivable point mutation can and will occur, even in relatively modest populations (such as are seen in mammals) over rather short time scales.

If one is looking for some sort of limit to "probabilistic resources", one needs to look somewhere besides the rate with which mutations occur.

Dear Stuart,

Greetings and thanks for chiming in here. You cannot simply assert that all mutations can and will occur, or that any structure we observe can and will evolve, even given large bacterial populations. You have to determine whether there are sufficient probabilistic resources to generate the types of mutations necessary to evolve complex features.

Usually Darwinians simply ignore these problems and assume that whatever mutations are necessary can arise, even when multiple mutations are required to evolve a trait. ID proponents are interested in approaching these kinds of questions scientifically.

ID proponents have done quite a bit of work on this, but as one example, pro-ID biologist Doug Axe recently published a peer-reviewed research paper which presented calculations modeling the evolution of bacteria evolving a structure which required multiple mutations to yield any benefit. Using assumptions which were generous towards Darwinian evolution, Axe found that molecular adaptations requiring more than six neutral mutations to function, or even two slightly maladaptive mutations to function, would not arise in the history of the earth given maximum probabilistic resources available to evolving bacteria. For details, please see:

“BIO-Complexity Paper Shows Many Multi-Mutation Features Unlikely to Evolve in History of the Earth.”

Regarding your other comments, about "god cares more about bacteria than humans" etc, these are not arguments against design. Suffering and the problem of evil are theological objections that have nothing to do with ID. For details, see Jay Richards article, “Can ID Explain the Origin of Evil?,” where he writes:

"Bad designs” and "evil designs” are still designs; neither of these arguments refutes ID. So why are these arguments so popular among ID critics? What's happening is that ID critics are smuggling in a theological objection under the guise of refuting ID. They're basically saying: God wouldn't do it that way—that is, an all-powerful God wouldn't design something poorly, and a good God wouldn't design something evil. Since there are bad and evil designs in nature, there is no God. QED.

To this, I respond: Nice try, guys. The problem of evil isn't an argument against ID. An argument for intelligent design is just that. Questions about evil and about the nature of the designer are separate questions.

To argue that such breakdowns or disease refute ID is no better than citing the age-old theological objection regarding the problem of evil. This argument has zero impact upon scientific arguments for ID (nor does it refute traditional theistic views of God unless you turn a blind eye to millennia of theological solutions to this problem).

And many of the supposed bad designs aren't so bad when you scrutinize them carefully. For example, you cited the laryngeal nerve. A lot of pop-arguments from evolutionists like Coyne and Dawkins on this point have been refuted. For details please see: "The Recurrent Laryngeal Nerve Does Not Refute Intelligent Design."

Your arguments are the sort of non-rigorous pop-evolution arguments that we hear all the time. I hope this helps clarify what does, and does not, count as evidence against ID. Thanks.

Sincerely,

Casey

To those that are surprised a lab experiment hasn't been done to show the flagellum could have evolved or think that one should have been done by now. A lot of nature can't be replicated in labs. Only 1% of bacteria can be cultured in the lab because many require extreme conditions. Also a lab can't replicate the sheer number of organisms. There are approximately 5000000000000000000000000000000 bacteria in the world all evolving at the same time. a mutation that would take 10 billion years in the lab happens every second in nature. Also lab work tends to rule out lateral gene transfer.
Another point I'd like to make is if intelligent design is correct and all bio systems are intelligently designed then you have proven god cares more about bacteria than humans since he didn't do a good job at childbirth. Miscarriages, Down's syndrome, Fragile X etc. Not to mention our knees or laryngeal nerve. And hey pancreas, why so vestigial?

My actual reply to Casey was removed from my post somehow, yet the portion to Barry was left. No matter.

I guess since it was a lengthy post, I'll just use bullet points:
*First he claims observing the relationships between similar structures irrelevant in a discussion about evolution, when the whole point of the original argument was to disprove the possibility that the similar structures had some relation, so it was directly related to the discussion.
*He's claiming it's irrelevant, despite not believing it to begin with, which makes me wonder what the stance is to begin with. Does the relationship exist, and if it doesn't, why is it you recognize that relationship when debating?
*Complexity cannot determine design. Nor can it disprove evolution.
*The arguments that something is too complex to be designed makes little sense. The current structures in their extensive complexity are STILL capable of evolving, and we DO observe complex biological structures will change gradually over generations. This is observation, not hypothesis on what happened. So one must wonder why it is if we can see the process happening today why the process was NOT capable of producing the complexity we see today, when it is certainly capable of manipulating equally complex life forms without total destruction.

To Chris:
I'm not sure what you're point is, but I'm guessing you are trying to make belief in evolution equate to a nihilistic existence because of the lack of a higher power. That's simply your own fear talking. It seems you're more afraid of not having meaning without a God than anything. It says more about you than it does about "Darwinists".

To NeilBJ:
I have read that there has been no step by step analysis of any evolutionary sequence, but these quotes are fairly old.

You would probably be correct. Evolution is a very lengthy process, and even when we observe the evolution of organisms, we can't always determine the exact generation that major changes took place, especially when observing microbes. Even though we can't directly observe each stage, we can see general progression. However it is NOT unreasonable to assume that the progression was entirely natural.

Its only something sad that science is now maybe, possibility, probably, somehow is now part of science.

a lay-man will think the earth is in the middle of the universe but its not.

evolution is just and hypothesis that has somehow become a theory. this is why a lot of things are wrong in our world today.

This is bad for science

I don't know how a bacterial flagellum came to be. The two most likely scenarios are that either the laws of physics are sufficient to organize matter into self-replicating systems, or that the invisible sky wizard did it magically.

Well, I can observe and measure the laws of physics. I know they exist. For that reason, the scientific method can be used to investigate them. Science, at its basic essence, is a three-step method- observe, hypothesize, experiment. Because the laws of physics are observable, science can investigate them. For this reason, science is materialistic. If it's not material, it's not observable, it's not science.

Intelligent Design postulates that materialism is insufficient to explain the universe, and that non-materialist, or supernatural, explanations should be included in science. My response: go for it. Find some supernatural phenomenon, observe it, formulate a hypothesis, and craft an experiment to test it.

However, finding gaps in current scientific knowledge is not the same as finding evidence for the supernatural.

You have asked essentially the same question I asked and that is if bacteria flagella evolved then this ought to be able to be demonstrated in a laboratory experiment. More to the point, I asked what feature would be indentified in the first generation such that those bacteria would be isolated to become the population for the test for the next feature?

I have read that there has been no step by step analysis of any evolutionary sequence, but these quotes are fairly old.

I have also read that certain long term tests with bacteria have shown that anything requiring more than two mutations is hard to come by.

Forget all the high level arguments. If scientists can't even postulate a plausible first step in the evolution of flagella, even if that first step is a step in an indirect route, then where does that leave the pausibility of the entire argument?

Two points : I remind the Darwinians that the analogy with computer code and DNA is very sound. True, not all computer programs crash, like not all mutations cause a cell to die. BUT point mutations do NOT create new information/structures and only change what is already there. Calling DNA a code and then saying that Nature (note deifying!) created a code is to do a disservice to the word. Darwinians need to STOP using our words to describe their world.

Second, Darwinians have to deal with the idea that they do NOT matter at all. The universe goes into universal heat death, or the BIG Crunch and either way nothing any of you do matters a whit - save the planet, global warming, whatever...who cares? You may say you have purpose, but that is an illusion or as Dawkins says, you are delusional. Nothing matters. How depressing!

Stuart Rayner said: "So no one remembers how in the dover trial Behe admitted under oath that intelligent design wasn't science..."

No one remembers because that's not what he said. You must be referring to the claim that for ID to be science astrology would be included as well so therefore ID isn't science. Actually, there's more to the picture. His definition of science really doesn't differ much from the NAS definition. Casey Luskin did a post several years ago (and you thought Dover would be the nail in the coffin of ID) pointing out that the NAS definition leads to the same conclusions as the one Behe presented:

http://www.evolutionnews.org/2005/10/500_years_ago_geocentrism_aamp_astrology001085.html

The problem with astrology isn't that it's not science, it's just plain wrong. Period. It's been tested and found wanting.

"...and that he had read none of the material that showed his hypothesis to be, at the very least, flawed?"

Once again you fail to recall an accurate account of what actually happen in that local district case. You must be referring to the claim that Behe was presented with literature that (supposedly) gave detailed evolutionary origins of the immune system. This has been covered on ENV before:

http://www.evolutionnews.org/2009/07/ken_millers_only_a_theory_atta_1023151.html

http://www.evolutionnews.org/2010/02/ken_miller_and_the_evolution_o031531.html

http://www.evolutionnews.org/2010/12/five_years_later_evolutionary_042001.html

Behe didn't read the material because (like many counter arguments made against him) it wasn't addressed at the anything he said.

"When building a house, you don't make it rely on hundreds of parts that need to be exactly right, so why would it be any different for a simple propulsion system?"

Correct me if I'm wrong but I believe a house does require certain constraints to be met in it's construction. The same goes for the flagellum. Below in a comment Luskin highlighted the fact that showing the origin of parts alone doesn't mean we know for sure an evolutionary origin to the bacterial flagellum is confirmed. Hurdles go from availability, synchronization, localization, interfering proteins, interfacing, assembly order, to general configuration.

It seems if one were to consider the claim ' the flagellum evolved by a Darwinian process' as an extraordinary claim, then one would have to say the evidence does not support it (no actual step-by-step method proposed or produced).
If one were to consider the claim not extraordinary, then one could easily accept a hand waving (less specific) explanation.
By considering the Darwinian explanation extraordinary we end up with the situation in which we would have to say how it (the flagellum) came about is an open question and demands further research and different hypothesis would be under consideration.
If we consider the explanation (Darwinian) complete, we can end the search for other hypothesis and feel secure in the knowledge that we know the answer to this and other important questions (eg.-How did man come about?).

So no one remembers how in the dover trial Behe admitted under oath that intelligent design wasn't science and that he had read none of the material that showed his hypothesis to be, at the very least, flawed? Then you have the counter argument or why make it so complex? When building a house, you don't make it rely on hundreds of parts that need to be exactly right, so why would it be any different for a simple propulsion system?

If the evolutionary scientists have figured out a possible evolutionary scenario for the bacterial flagellum why don't they just go into the laboratory and do it? I'm willing to bet that with all their intelligence they can't.Yet we are supposed to believe that blind chance mutations with the help of natural selection did what these PhD scientists cannot do.They should be ashamed of themselves.

From Barry:
I look at it from this perspective; if you have a computer, the muck of amino acids created in the glass gar, the so called preshistoric soup that life supposedly sprang from, yet you have no operating system, the code in DNA that tells the amino acids "what to do" then the computer will just sit there and NEVER will code start to 'form' on this computer by reason of neo-darwian theory, life doesn't magically appear from non-living material into living material, coded and all by magic!

If we find a prehistoric computer on the moon, will the Evolutionary scientist call IT evolution?

Science doesn't say life magically sprang from non-living material. The Bible certainly does, because God is magical and he created life from dirt (and women from a rib). Science does believe that life could form under some very specific circumstances, and even if those circumstances are improbable, they are possible. But it took billions of years for life to get from it's origins to the diversity we see today.

I am pro ID.

The thing that always amazes me about neo-Darwinism is how much it relies on 'perhaps this', perhaps that, maybe, might, possibly etc. The idea seems to be that if you can imagine that this or that could just possibly, and no matter how surpassingly improbably, have happened by random chance then that is really more than enough to 'prove' that it is highly likely that it did so. Under this system mere speculation and fanciful conjecture quickly become 'fact'. I guess my car could have evolved randomly and self assembled under the necessity of various natural laws. All the evidence says not, but, who knows, maybe an axle was just floating around and then it attached to a wheel etc and became my car - and the fact that I can imagine this, no matter how improbable it may seem, proves that this must be how my car came to be.

Darwin saw that using intelligent (ie guiding) input human breeders were able to modify domesticated animals considerably (eg wolves to labradors, spaniels etc) and concluded that maybe this process could account for all creatures from amoeba to whale (if not for the origin of life itself). However, he ignored the well known fact that there are severe and unforgiving limits to such variations beyond which no breeder can take any species. No fruit fly was ever morphed into anything other than a damaged fruit fly and that was with the most intensive and intelligently guided evolution possible. So, at best, his idea of evolution by 'natural' 'selection' (nature obviously doesn't actually 'select' anything) could only provide a limited amount of variation.

Unintelligent evolutionary theory also ignores the fact that in undomesticated or wild nature species (eg wolves, cheetahs etc) tend to be confirmed in their type (ie stay the same) and not be deviated or 'evolved' (by RGM and NS) away from it. That some natural variation (micro evolution) within species does take place has been documented, eg peppered moths and finch beaks. And so it is that simply based on this minor evidence for limited (and also provenly reversible) micro evolution we are asked to believe that all of the living world can be explained as the product of an endless succession of random accidents. The fact that all biological life appears related and contains many homologies remains, as it was in Darwin's day, as much evidence in favour of and for Intelligent Evolution as it ever was for Darwin's theory of Unintelligent Evolution. Thus, even in the light of knowledge in Darwin's day (1859) let alone now, in the 21st Century the idea of Unintelligent Evolution and Unintelligent Design is so utterly and simplistically silly and so mind bogglingly absurd that it cannot be rationally explained.

However, sadly, most firm Darwinians simply cannot be guided by a reasonable and reasoned consideration of the overwhelming evidence for intelligent design staring them in the face but are forced, by their ideological commitments, to steer by a dogmatic, mystical and axiomatic materialism which propels them, no matter how irrationally or superstitiously, into finding pseudo 'natural' or materialistic explanations, no matter how impossibly improbable, ridiculous, contrived or far-fetched, because of their unquestioned and unquestionable conviction that Only Unintelligent Matter Exists and that there is no and could not possibly or conceivably be any Divine Creative Mind or Intelligence underlying, suffusing, guiding, upholding, all of reality at every level and dimension.

Evolution has been falsified many times, even endlessly, but here is a simple and elegant example, mentioned by Darwin's colleague and co-discoverer of Evolution by Natural Selection, Alfred Russell Wallace. Wallace believed in Intelligently Guided Evolution and was seen by Darwin as a traitor to his 'religion' of metaphysical materialism. As any one who is prepared to "Sit down before fact as a little child," (T. Huxley) can see there is not the remotest chance that Darwinian (or Neo-Darwinian) processes could bring about the astonishing existence of the caterpillar and the butterfly.

A caterpillar exists happily and functionally in its own right. It has no logical, or survival, need to dissolve into a bio-soup, as it does, before its utterly astonishing metamorphosis into a butterfly. No 'natural' selection, or occasional random genetic mutation can explain this astonishing mystery. Beyond this, the beautiful patterns, designs!, on many butterflies wings far surpass any protectional utility which 'natural' 'selection' might throw up and falsify, once more, the fallacious notion of unguided, purposeless, meaningless 'evolution'.

The whole bizarre idea of unguided evolution is, and was from the beginning, an ideological project, to promote metaphysical materialism dressed up as science. That many things, including life forms, and cars!, evolve is not in doubt. The idea that they do so by purely unguided processes is as absurd as saying a modern Ford Focus randomly descended from a model T because there was enough time for this to take place.

Dear Nick and all,

Thanks for joining in the dialogue here.

I see no evidence that Jonathan misread your paper since he didn't claim that all proteins in Salmonella flagellum are required in all flagella. Moreover, your point "that most of the required proteins have known alternative functions in nonflagellar systems" is almost completely irrelevant when compared to the overall argument Jonathan is making. The fact that you think it's important shows how weak Darwinian explanations are for the origin of these extremely complex systems.

Your 2006 paper with Mark Pallen claims that there are “sequence homologies linking flagellar components to the rest of the biological universe." Your paper is somewhat ambiguous, but it seems to cite 20 proteins that are "indispensible" to flagella. (That of course that makes the typological assumption that all flagella must be constructed in the same fashion. The fact that some flagella are missing a part doesn't imply that the part isn't necessary for those flagella that have it.)

In any case, of those 20, only 14 are claimed to have homology to non-flagellar proteins. Of those 14, a full 10 are to proteins found in the type 3 secretory system (T3SS).

But the type 3 secretory system is hardly "the rest of the biological universe"--it's a system that uses a highly similar basal body to the flagellum. This isn't news, and Everybody has known about this for years and in fact even the rudimentary ID video Unlocking the Mystery of Life points out why the T3SS cannot serve as a precursor to the flagellum.

T3SSs are found in a small subset of gram-negative bacteria that have a symbiotic or parasitic association with eukaryotes. Since eukaryotes evolved over a billion years after bacteria, this suggests that T3SSs arose after eukaryotes, and it's widely believed that flagella are far more ancient. Given the narrow range of T3SS-bearing bacteria, and the wide-range of bacteria with flagella, parsimony strongly suggests the flagellum predates the T3SS rather the reverse. So citing homology with the T3SS (or to some untestable hypothtetical, nondescript, invented-to-avoid-inconvenient-data common evolutionary ancestor of the T3SS and flagellum), isn't citing to the "rest of the biological universe" and does not explain how the flagellum evolved.

When Ken Miller cited flagellar homology with the T3SS to explain how the flagellum evolved, William Dembski explained:

"[F]inding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the [blender] motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the TTSS [T3SS] represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn't constitute a solution to the evolution of the bacterial flagellum. What's needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we've discovered the Hawaiian Islands. Evolutionary biology needs to do better than that."

(William A. Dembski, Rebuttal to Reports by Opposing Expert Witnesses)

Of course there are 4 additional flagellar proteins wherein you claim to have found homology. (So congratulations, you beat Ken Miller by 4 proteins.) But what about those 4 flagellar proteins that are both indispensible but had homology outside of the flagellum and T3SS? Those 4 are FliG, FliK, MotA, MotB.

For FliG and FliK, your paper didn't report sequence homology but instead reported: "These similarities fail to achieve unequivocal significance using BLAST/PSI–BLAST under any of the above conditions, but are supported by other structural or functional considerations."

Structural / functional similarity cannot explain how a structure evolved when there is no detected sequence homology.

As for MotA and MotB, you stated homology was found "performing multiple PSI-BLAST iterations at the NCBI site under default conditions."

Citing "multiple iterations" makes your results clear as mud because it's not clear what exactly you did or what exactly you found. So call me a skeptic. But let's assume that you did find real sequence homology between certain flagellar proteins and MotA and MotB. There are good reasons to understand why these are not relevant.

According to Cascales et al. (2001), the weak nature of the homologies indicates that “[t]he relevance of these sequence alignments [between MotA/B and the Exb-TonB and Tol-Pal systems] is difficult to quantify, depending on a large alignment of a relatively large number of proteins from a wide selection of organisms distributed in a rather non-random fashion across the phylogenetic space.”[1]

Indeed, these homologies appear largely trivial. The MotA/ MotB complex and their alleged homologues are each anchored in the cytoplasmic membrane. The homologies given by your paper are likely due to the fact that trans-membrane protein segments will likely have certain characteristics which allow them to locate there. Thus Cascales et al. (2001) found the homologies of the MotA / MotB complex are weak and restricted to the parts of the protein that cross the bacterial membrane.

These sections of the protein serve primarily as anchors to keep the proteins situated in the membrane; they have no relevance to the regions that control other functions (like transporting substrates or for generating motor rotational force for the flagellum).

Therefore, these homologies really shed little or no light on the origin of the rotation-relevant portions of the MotA/B complex, and provide few concrete conclusions about how MotA or MotB actually evolved.

My conclusion is this: Your paper doesn't find any relevant homologies for any protein that you claim is "indispensible" for the flagellum.

But what if you found homologies in "the rest of biological universe" for every single flagellar protein? Minnich and Meyer also explain how mere availability of parts is insufficient to explain the evolution of a system:

"[E]ven if all the protein parts were somehow available to make a flagellar motor during the evolution of life, the parts would need to be assembled in the correct temporal sequence similar to the way an automobile is assembled in factory. Yet, to choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions. Arguably, this system is itself irreducibly complex. In any case, the co-option argument tacitly presupposes the need for the very thing it seeks to explain--a functionally interdependent system of proteins." (Scott A. Minnich and Stephen C. Meyer, Genetic Analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria, pg. 8)

Similarly, philosopher Angus Menuge lays out a number of obstacles which must be overcome by "co-option" or "exaptation" explanations, none of which were addressed by Miller during the trial. Menuge writes:

"For a working flagellum to be built by exaptation, the five following conditions would all have to be met:

C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

C3: Localization. The selected parts must all be made available at the same 'construction site,' perhaps not simultaneously but certainly at the time they are needed.

C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

C5: Interface compatibility. The parts must be mutually compatible, that is, 'well-matched' and capable of properly 'interacting': even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly."

(Angus Menuge, Agents Under Fire: Materialism and the Rationality of Science, pp. 104-105 (Rowman & Littlefield, 2004).)

So what if you had found homology for every flagellar protein? That would only address C1. Clearly there's a lot more required to validate a co-option-based explanation of the evolution of the flagellum than mere homology.

You claim "Behe made some vague acknowledgements of indirect pathways in his book, but then just asserted, without any support or argument, that they were wildly improbable."

Actually, the people who assert something “without any support or argument” are those who claim that indirect pathways are probable. Here's what Behe actually said:

Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows

(Michael Behe, Darwin's Black Box, p. 40 (Free Press, 1996).))

In fact, Behe gave much support and argument to that claim when evaluating indirect explanations of the cilium:

"For example, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces couldn't form a functioning mousetrap without extensive modification, and while the modification was going on, they would be unable to work as a mousetrap. Their previous functions make them ill- suited for virtually any new role as part of a complex system. In the case of the cilium, there are analogous problems. The mutated protein that accidentally stuck to microtubules would block their function as "highways" of transport. A protein that indiscriminately bound microtubules together would disrupt the cell's shape--just as a building's shape would be disrupted by an erroneously placed cable that accidentally pulled together girders supporting the building. A linker that strengthened microtubule bundles for structural supports would tend to make them inflexible, unlike the flexible linker nexin. An unregulated motor protein, freshly binding to microtubules, would push apart micrutubules that should be close together. The incipient cilium would not be at the cell surface. If it were not at the cell surface, then internal beating could disrupt the cell; but even if it were at the cell surface, the number of motor proteins would probably not be enough to move the cilium. And even if the cilium moved, an awkward stroke would not necessarily move the cell. And if the cell did move, it would be an unregulated motion using energy and not corresponding to any need of the cell." (Michael Behe, Darwin's Black Box, pg. 66-67.)

So Behe’s claim was certainly not a mere assertion "without any support or argument."

Your paper with Mark Pallen contains no explanation for the evolution of the flagellum. It simply asserts, without any support or argument (other than vague appeals to C1, homology) that: "one can envisage the ur-flagellum arising from mergers between several modular subsystems: a secretion system built from proteins accreted around an ancient ATPase, a filament built from variants of two initial proteins, a motor built from an ion channel and a chemotaxis apparatus built from pre-existing regulatory domains."

Actually, I cannot envisage this because biological systems are NOT "modular" in this way such that parts can just be co-opted from different systems and naturally fit together like Lego pieces. That’s why any indirect explanation must address C2-C5. You have not addressed C2-C5, and your attempt to address C1 is far weaker than you have let on.

Thanks again.

Sincerely,

Casey

[1.] E. Cascales, R. Lloubès, and J. N. Sturgis, "The TolQ–TolR proteins energize TolA and share homologies with the flagellar motor proteins MotA–MotB," Molecular Microbiology, Vol. 42 (3):795-807 (November, 2001).

I look at it from this perspective; if you have a computer, the muck of amino acids created in the glass gar, the so called preshistoric soup that life supposedly sprang from, yet you have no operating system, the code in DNA that tells the amino acids "what to do" then the computer will just sit there and NEVER will code start to 'form' on this computer by reason of neo-darwian theory, life doesn't magically appear from non-living material into living material, coded and all by magic!

If we find a prehistoric computer on the moon, will the Evolutionary scientist call IT evolution?

to onthuhlist:

Ok, I'm back. Hopefully I can be more clear on my points, since I have more time to address them.

with a wave of their evolutionary wand and a gross oversimplification or two, all design problems are considered solved.

I wouldn't say that anybody could reasonably expect all design problems to be solved by natural explanation, but within limits certain design problems already exist in nature. For example, nearly perfect geometric structures already exist in nature without man's interaction, yet we know without doubt those structures can exist without intelligent intervention simply because they obey the laws of physics and chemistry.

Since they have no engineering experience, they don't realize how difficult it actually is to make ANY system of inter-related parts function without making one or more crippling oversights.

Interesting ad hominem, but I do have college level engineering education, with experience in aiding the design of propulsion systems. But that's besides the point: you know as a mechanical engineer(at least you should) that you can't simply apply those concepts to biology. The best way to explain it would probably be an example: ethylenediaminetetraacetate acid. By your standard, an EDTA molecule wouldn't formulate to create itself in the way it does without intervention. Yet, this acid is synthesized without direct intervention of any kind on a molecular level. Mechanical principles are get obliterated when applied to chemical processes, so it's odd you use your expertise in the area to put yourself on a pedestal.

In any low-level computer language, a single character that is mis-typed will break the computer program, causing it to catastrophically crash.

Don't lie to get your point across. Yes, the program will probably certainly not operate as intended, but that doesn't always equate to crashing. Yes, small errors can cause major problems, but most errors don't.

Operation of software systems often requires PERFECTION in a great portion of the code.

Yet you'll hardly ever see new software come out that doesn't have some form of critical error, but most programs still function normally without encountering them. You're over-emphasizing the perfection of software, but even with the strict rules software has to abide by, it is rarely perfect.

Do you get the point? Everything has to be planned and in place from the first day of the system's operation!

I think everybody understands that in order for the system to work, it needs all of its parts. The disagreement is whether it could have reached that point without the aid of a designer. In order for my body to work, it needs its most vital organs all at once. Yet, I still managed to live and grow to that point without at one point having most of them. Granted it was with support from my mothers body, but nobody stepped in an assembled me readily before enabling me.

Who in their right mind would see a car passing by and assume that "the present is the key to the past" and therefore since the car is heading down the road in one direction at some time in the past was located at the road's point of origin?

What? Nobody assumes that. But you're talking apples and oranges. The car is driving under the control of a being that can make choices. If at any point that person can just choose to change their direction, then nobody would assume that it came directly from the direction it was driving. But, what kind of person even tries to argue that light waves have the ability to just change their direction at their own whim. Light waves aren't intelligent, and they don't have control over what they do: they're bound by the laws of physics. This is an absurd claim, to say that what we observe now isn't actually what we're observing, but something that could have changed. This doesn't even have anything to do with evolution! You're arguing that we aren't actually seeing what we're seeing!

therefore the houses are evolutionary cousins and that neither were purposefully designed or built?

We know, from observation, that those houses were built, and not evolved. In the same regard, who in their right mind looks at cousins who share similar features and concludes they might be related? Everybody. Evolution just takes it a step further. You see, you do apply these principles, but for some reason when it goes beyond a certain scale suddenly you don't agree, even though it's perfectly fine within the constraints of each species. You started out so well, and started going downhill.

Let's assume these houses were of unknown origin. Admittedly the houses are not sophisticated enough to build copies of themselves (as all living things can do)

Which defeats the whole point. If they can't reproduce, but the structure is there, then I would admit that no process exists to create it, therefor it must be designed. If I saw any structure that did not have a process of self-replication, and it had an obvious structure, the only conclusion I could possibly make is that it was designed, and I would readily admit that.

yet we're too proud and in denial to admit that our bodies are designed machines.

If we are machines that are the product of design, we have many unnecessary flaws with simple fixes. Pride wouldn't recognize these flaws. It's astounding that you think people would be more proud to have evolved from apes than be designed by a god.

Hello Nick,

You wrote:

...but parts and subsystems with other functions in the wild proves that the system did not have to originate "in one fell swoop". Thus the IC argument fails.

Not so. Again, this trivialises the sheer difficulty of specifying even a single novel protein fold or acquiring novel protein-protein binding sites. You are correct to point out that many of the components used in the flagellar system can be used in other systems as well (we also see this pattern in man-made designed systems, by the way).

The co-option model of evolution, where novel systems emerge by virtue of indirect pathways, has always been rather unimpressive to me. The components of the said systems would need to break free of the systems in which they were formerly integrated (without harming those systems) and be made available at the right place with respect to the ‘construction site’ of the evolving system. With regard to the flagellum, it also requires a tightly regulated assembly sequence to be put in place. To posit all of those specific and co-ordinated changes occurring by chance is a sheer fantasy.

There is also the problem of interfering cross-reactions. Meyer and Minnich (Link: http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=389) have pointed out that if flagellum biosynthesis were to be expressed simultaneously with the Yop T3SS, flagellin monomers would likely be exported out the needle-like structure as well as the flagellar basal body, potentially limiting the efficiency of both systems.

As for an alternative causal hypothesis, I would draw a distinction between a theory of design implementation and a theory of design detection. One can have a testable theory with respect to the latter without having a well-articulated account of the modus operandi of the intelligent causal agent.

Thanks again for your comments.

Respectfully in discourse,

Jonathan

Even though our explanation of design is unquantifiable, the observations regarding the flagellum prove evolution to be false, which is actually less then unquantifiable. So we can safely say that the real answer is that we don't know, however, the runner up would be ID, although we cannot show a designer, and last would be evolution, since it fails to explain the flagellum. Even if ID is metaphysical it is better than being wrong, which evolution is. You can show the explanations in this order: evolution(failed)- ID (metaphysical)- unknown.

Well, parts with other functions is clearly relevant to the IC argument, because the core of Behe's argument was:

========
An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition non-functional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.
========

...but parts and subsystems with other functions in the wild proves that the system did not have to originate "in one fell swoop". Thus the IC argument fails.

Behe made some vague acknowledgements of indirect pathways in his book, but then just asserted, without any support or argument, that they were wildly improbable. Never mind that change-of-function and indirect pathways have always been a preferred explanation for the origin of complex systems, ever since Darwin's Origin of Species, especially because of the vast number of systems in which homologous systems have different functions (e.g. fins --> legs --> wings --> flippers). His whole book should have been about the implausibility of indirect pathways, if he actually wanted to make a serious argument that complex systems could not originate gradually. Instead, the whole IC argument is apparently a big bait-and-switch.

As for being "vague" -- our hypothesis is detailed enough to be testable, and has passed several tests. Please give us your more detailed, more testable hypothesis for the origin of the bacterial flagellum.

drs said: "Perhaps my understanding of "Irreducibly Complex" is incorrect..."

While it's not a total misunderstanding, I think it misses the point.

"...but I thought the concept meant that certain systems are too complex to have evolved."

Here's a good starting point on this subject:

Primer: Irreducible Complexity in a Nutshell

And in case you have some beef with the mousetrap example because an intelligent agent can modify the parts to get a one-piece system (in which the analogy would no longer apply to features in question), see the following:

A Mousetrap Defended: Response to Critics

Yes, you are right. This is way more complicated than what the evolutionists argue for. I don't see how many of them believe that simple proteins could just be lying around and suddenly poof!, a highly refined mechanism appears. At least that what their argument seems to stand for. Anyways, good job on the explanation. I'm tired of seeing Ken Miller's argument be seen as the viable explanation of the bacteria flagellum.

A great article. Thanks.

As always the Darwinists pretend not to see any link to IC in this article. This is for exactly the same reasons why Dawkins, wearing intellectual blinders, cannot see any evidence for God and so pretends none exists.

The truth is that Darwinists feel threatened by the reality of the situation. They so fear that their empty and nefarious, materialist world-view will crumble to pieces under scrutiny (indeed it does), that they subconsciously close their minds from against the salient facts and obvious implications shown them. They become incapable of objectivity through such acute cognitive dissonance. In Hoyle's words they become "mentally ill".

In reality, the macro evolution problem, by any Darwinian mechanism, is a matter of statistical mechanics. Not argument from ignorance or incredulity.

The probabilities of chance and necessity + selection creating a flagellum are so astronomically small it is sheer obstinacy to continue denying the necessity of teleology and design in all living organisms.

Engineers can understand this in terms of combinatorial dependencies that absolutely require design. Biologists generally, know nothing of statistical mechanics, engineering or information theory. Thus they go astray at every mention of such, spewing forth speculations with narrative gloss as though they actually believed their own conjecture were fact.

Musgrave, cited above, is such a one. It is incredible how childishly over-simplistic his just-so story is. Miller et al. are just as bad.

Moreover , the burgeoning domain of biosemiotics is killing Darwinism all by itself.

Still, the Darwian fundamentalists are so blissfully ignorant of this it is egregious.

Nor do they show any notion of comprehension of the basic engineering principles of building inter-dependent structural components that they continue to chase their tails all while disingenuously misleading the public.

They have been woefully mis-educated - by the ruling materialist elite that rules academia with a fist intimidation - and remain profoundly ignorant.

Sad but true.

Kuartis, you're the only commentator here who hasn't shown any intellectual ability.

Everything you've said can be placed into two categories:
*Telling people to go look up the information (because to you it's so obvious, yet despite how simple it is you have difficulty taking the effort to actually present anything).
*Belittling people who don't agree with you.

Neither of those takes any kind of intellectual effort. I would ask, with all due respect, that if you want be taken seriously and respected, that you act seriously and respectfully.

Jonathan, A suggestion.
The ignorance being displayed by pro darwinist commenters on your post is apalling! I suspect no good can come from a conversation with these people.If I were you I would disable comments.

The amazing thing to me is that biological systems have tools, processes and other mechanisms that they know how to use with a very high degree of acuracy. I would like to hear more from the evolutionary side where does information come from? Random assignment does not seem to explain these highly efficient mechanisms. Please forgive my terminology I am an artist. I'm simply blown away by the artistry of these molecular sculptures. It just seems to me that information needs to be present prior to the literal piece that is formed. MotA requires MotB not a derivative or something close. Finally once the motor is built the organism still needs to know how to use it. It seems that the flaggelum would actually be a liability connected to the first organisms that were unlucky enough to have them. What was the mode of motility prior to the flagellum that did not work? How do neighboring bacteria stay alive when they are constantly being whacked by a propeller spinning at 1500 rpms?

Truly amazing!!

The flat earth evolutionists certainly amuse me. They try to explain away the obvious and sound like fools in the process. Using the evolutionist way of explaining things lets make a textual evolutionary tree for a computer. First you have a pile of silicone dust then that becomes an integrated circuit chip (after some heat and them some cold and maybe a whole bunch of time LOL). Once that chip is formed it joins together with other chips to form a printed circuit board covered with chips. As those chips formed, complex programs developed themselves inside the memory chips. Finally a protective covering formed with a power source and bang a sophisticated computer has evolved. Of coarse this is a bad example because the Darwin worshipers have written this fairy tail about far more complex systems than a computer. It amazes me how far removed from reality the evolutionist cult really is. It seems obvious that the creative love affair they have with time will only turn against them when our grandchildren look back and laugh hysterically at the parrots of Darwin. Giggling at this strange cult called evolution where its followers were required to remove intelligence from themselves (how ironic) and embrace a tail that only a blind fool would accept.

Drs,you are completely clueless. Its really just sad to see the rantings of pro darwinists. They think their illogic makes sense. God help them.

How do you think the world got here?

onthuhlist:

What one could call an "oversimplification" is simply claiming that something is too complex to understand how it would have gotten here naturally, so it must have been designed. Making that jump is a gross simplification, and an answer that doesn't actually have any supporting evidence other than a non-quantifiable observation. You can't simply wave a magic wand and say, "Poof! Too complex!" because you haven't even defined what "too complex" is. I think you miss a few fundamental points, and I wish I had time to address them all, but I'll stick with just your first example of programming, and hopefully I'll get back later:

"So where does the unrealistic evolutionary expectation come from that it's easy for natural selection to build these systems from random changes?"

Because when a single change is made to an biological life-form, it doesn't automatically kill the life form. This has been observed countless times. You claim that a computer program will utterly break if it's not written correctly, when in reality it will only utterly break if it breaks the rules by which it is allowed to operate, otherwise the program will merely function incorrectly. The "rules" that will kill a program can be compared to basic physical law, because to a program the computers rules are it's physical law. You're saying a program breaking is equivalent to a component in a living being not functioning correctly, when in reality a program breaking is more like a living being breaking the laws of physics or chemistry. It's not.

Ok, well I'm currently out of time. I'll return.

Hi everyone,

Thank you for your interest in my essay. Having read your comments, I just wanted to make a few additional points.

Nick Matzke alleged that I had not read his Nature Reviews paper, in which he documented that "many of the proteins that [I mentioned] from the Salmonella flagellum are not universally required in all flagella. And that most of the required proteins have known alternative functions in nonflagellar systems."

First, let me re-assure Matzke that I have read his paper -- more than once. I had only referred to it in passing in my previous post because he offers a similarly vague evolutionary "explanation" of the flagellar apparatus as do the other authors I mentioned. My purpose in describing the complexities undergirding the processes of flagellar assembly were simply to highlight the inadequacies and trivialisations of the proposed "refutations" of Behe's argument.

That being said, maybe some are wondering how one might respond to the claim made by Matzke regarding the dispensability or redundancy of certain flagellar components in various species of bacteria. So let's do that.

Firstly, a few clarifications are in order. Let's go back to what Michael Behe had to say in Darwin's Black Box:

To feel the full force of the conclusion that a system is irreducible complex and therefore has no functional precursors, we need to distinguish between a physical precursor and a conceptual precursor. The trap described above is not the only system that can immobilize a mouse. On other occasions my family has used a glue trap. In theory, at least, one can use a box propped open with a stick that could be tripped. Or one can simply shoot the mouse with a BB gun. These are not physical precursors to the standard mousetrap, however, since they cannot be transformed, step by Darwinian step, into a trap with a base, hammer, spring, catch and holding bar. [page 43; emphasis added]

In a similar way, the Salmonella flagellar model is not the only way in which one can construct a flagellum. Moreover, many of the alluded-to parts may indeed be dispensable -- even in Salmonella. An irreducibly complex core does not require that every component be indispensable. Moreover, the argument proposed by Matzke is strikingly similar to John McDonald's attempt to show that the mouse-trap could have evolved (see Michael Behe's response here). One might be able to reduce a mouse trap -- or, indeed, a flagellum -- by virtue of surreptitious intelligent tinkering, making multiple adjustments at every stage. As Michael Behe explains with regards to McDonald's second stage of his mouse-trap sequence,

The second mousetrap (above) has a spring and a platform. One of the extended arms stands under tension at the very edge of the platform. The idea is that if a mouse in the vicinity jiggles the trap, the end of the arm slips over the edge and comes rushing down, and may pin the mouse’s paw or tail against the platform. Now, the first thing to notice is that the arms of the spring are in a different relationship to each other than in the first trap. To get to the configuration of the spring in the second trap from the configuration in the first, it seems to me one would have to proceed through the following steps[4]: (1) twist the arm that has one bend through about 90° so that the end segment is perpendicular to the axis of the spring and points toward the platform; (2) twist the other arm through about 180° so the first segment is pointing opposite to where it originally pointed (the exact value of the rotations depend on the lengths of the arms); (3) shorten one arm so that its length is less than the distance from the top of the platform to the floor (so that the end doesn’t first hit the floor before pinning the mouse). While the arms were being rotated and adjusted, the original one-piece trap would have lost function, and the second trap would not yet be working.

It seems to me that Matzke's idea of flagellar evolution is quite akin to this. It is also quite correct that there are components of the flagellar system which can be used for other purposes. But so what? Michael Behe subscribes to the tenets of universal common ancestry, and would expect to see nothing less. A mere demonstration of homology is not, in and of itself, a causal explanation!

Nonetheless, I want to revisit this subject on this blog at some point when time permits.

Someone else asked,

“Is there a level of complexity that we know evolution is incapable of achieving or explaining? And if there is, what it is the general level of complexity and how do we know said complexity is beyond explanations of evolution?”

Yes, I think there is. Michael Behe addresses this point in his second book, The Edge of Evolution. Moreover, Gauger et al. (2010) demonstrated that the process of reductive evolution was sufficient to prevent lines of E. coli from taking a simple two-step pathway to a new fitness function. In this study, a trpA gene was "broken" in such a way that it could recover the ability to synthesize the amino acid, Tryptophan, by reverting only two single point mutations. The authors here also concluded that the cost of transcribing a broken gene incurs significant fitness cost, and thus its removal is facilitated by positive selection. My original essay also cited two studies pertinent to this topic (Axe, 2010 and Behe & Snoke, 2004) regarding the impotence of the Darwinian mechanism to produce novel protein folds and binding sites. I also cited an even more recent study by Axe on the limitations of the gene duplication/recruitment model of neo-functionalisation (check the original article above for the links to those articles).

I could continue in a similar vein for some time. As for my article’s relevance, by honing in on the molecular detail, I hoped to show readers why Darwinists are going to need to do a lot better than they have thus far done if they seek to posit a plausible causal explanation for such a system. I also want to re-focus the discussion somewhat. It may no longer be regarded as sufficient to posit the sequential evolution of each structure (such as the rod or protoflagellar filament) without attention to the details of the molecular basis for their assembly within the cell. The point of contention between Darwinists and ourselves hangs around the sufficiency of undirected natural processes to produce those incredibly sophisticated items of nano-technology within the cell. And it remains as true today as it did when Behe first penned Darwin's Black Box, back in 1996, that no neo-Darwinian account of this system has been forthcoming.

Pretty much everyone is agreed that such marvels of engineering give the overwhelming appearance of having been designed. Indeed, computational cell biologist Kathryn Appelgate (an ardent Darwinist, many essays of whom feature on the Biologos website) wrote an essay last year entitled "Bacterial Flagellum: Appearances Can Be Deceiving", noting:

The resemblance is so striking, we find it difficult to resist extending the analogy to how the flagellum originated. We know that all outboard motors are designed by intelligent engineers; the parts are carefully crafted to work together for an intended purpose. The bacterial flagellum also has many well-matched components. Together they perform the same job as the outboard motor—swimming. Since the flagellum wasn’t designed by human engineers, it seems only reasonable to infer that it was designed by Someone Else.

Meanwhile, the legitimate question has been raised as to how such a system arose: Is this system actually designed? Or is the design merely apparent? Well, since we all -- at least most of us -- are in agreement that the flagellum looks like a designed system, it would be unwise to rule out that proposition a priori. By closing off one possible answer, we potentially limit ourselves to a set of false choices. Since all of the purported naturalistic "explanations" of this system fail, and since we have positive reason (i.e. our uniform and repeated experience of cause-and-effect) to suspect that this system might really be the product of intelligent causality, it seems to stand to reason that the design inference be regarded as a scientifically respectable point of view to take.

I hope this serves to clarify one or two things here.

Thanks again for your contributions!

Sincerely,

Jonathan

Its interesting how the commenters here are unable to see the fallacies of the common objections raised by evolution proponents in response to irreducible complexity.
Let me save to some time buddies.
The common responses raised against irreducible complexity do nothing to refute the concept.
Go educate yourselves with material not proceeding from darwinist trolls like Miller.

That is the coolest 'rant' I have ever read!

Completely agree. I'm going to rant here, but as a mechanical engineer, my patience quickly wears thin hearing the evolutionary story-tellers wax eloquent with their "once upon a time" oversimplifications; with a wave of their evolutionary wand and a gross oversimplification or two, all design problems are considered solved. Since they have no engineering experience, they don't realize how difficult it actually is to make ANY system of inter-related parts function without making one or more crippling oversights. So many aspects must be simultaneously considered, balanced, matched together, properly scaled, and custom-fitted. Power demand must not exceed power production (and the cell only has about a 3 minute supply of ATP before it runs out, according to my copy of MBOTC). Power produced must be scaled to a level and produced in a form that can be utilized by the machines it powers (oh yeah, we overlooked that without design intervention it almost certainly would have been different and therefore almost certainly would have been nonfunctional.) I could go on with a list of at least 50 considerations off the top of my head for any such system to work - design problems that engineers regularly solve, often without realizing the multi-faceted sophistication of what they are doing.

In any low-level computer language, a single character that is mis-typed will break the computer program, causing it to catastrophically crash. Anyone with computer programming experience can agree with me. And all of us programmers love those compilers like the Ada compilers that ferret out as many procedural errors up front (like type conversion errors). Those compilers are preferrable to those that require the debugging to be done by actually running the code and watching it fail, then fixing that portion that failed. (READ: Trial and error that must occur PRIOR to the system being operational, which poses one of evolution's greatest challenges - how does an evolutionary system survive its own evolutionary creation, when it must remain operational 24/7 during its own formation?) Operation of software systems often requires PERFECTION in a great portion of the code. Even a single imperfection, and you get the blue screen of death. So where does the unrealistic evolutionary expectation come from that it's easy for natural selection to build these systems from random changes? I'll tell you where it comes from. It comes from their religious belief in the ultimate cause of methodological naturalism. Since they are committed to this cause, they are unwilling to question it. End of story. And the most laughable idea they promulgate is that the teaching of intelligent design to students will cause them to abandon a healthy scientific skepticism. Such statements are utterly hypocritical, when they are unwilling to skeptically question their own religious god of naturalism and evolutionary theory.

Let's take an automobile whose Engine Control Module communicates with the Body Control Module over a J1939 interface. Which came first? The J1939 protocol, or the computer chips in the ECM/BCM that implement the protocol, or the specially shielded cable that connects the modules, without which the protocol could not operate, or the vehicle power feed wires that power the modules, or the grounding wires that provide a current return, or the vehicle battery and alternator and voltage regulator that generate the power, or the vehicle engine that turns the alternator, or the vehicle starter that starts the engine, or the fuel that powers the engine, or the gas station that fueled the car, or the fuel tanker that delivered the fuel to the gas station, or the refinery that refined the gas from oil, or the oil rig that extracted the oil from the ground, or the existence of oil in the ground, etc. etc. etc. etc???? And yes, I'm GREATLY oversimplifying here. Do you get the point? Everything has to be planned and in place from the first day of the system's operation!

The multiple hardware/software/protocol levels that exist in such a system are not only physical, but conceptual as well. In other words, you can only explain what's going on by appealing to an interpretive domain that does not exist in the physical world. The J1939 protocols, though implemented in physical hardware, carry layers of meaning that are defined only on a conceptual level defined by a previously spec'd protocol which was then imposed upon the design of the components which communicate using this protocol. From the viewpoint of a consumer seeing that car for the first time, the car's design conforms to an unseen guide! The guide (the J1939 protocol's multiple conceptual/physical layers and defined interfaces) can be deduced from a close examination of the system's function. The existence of such unseen guides can also be deduced from a study of the systems within living systems. Nervous systems, circulatory systems, brains, lymph systems, and yes, bacterial flagellum design, construction, operation, and sensory feedback mechanisms. The imposition of such high-level conceptual constructs upon matter is a sure indicator of not only intelligent, but INGENIOUS design. And yes, MBOTC uses the word "ingenious" to describe these designs. And that word is a very interesting choice of words because it carries a supposition of mental acuity, something which methodological naturalism does not admittedly possess (though in reality it must possess, since it is invoked as an ultimate cause).

Who in their right mind would see a car passing by and assume that "the present is the key to the past" and therefore since the car is heading down the road in one direction at some time in the past was located at the road's point of origin? Yet since the universe is now expanding, it supposedly must have originated from a point where all matter in the universe was compressed into an infinitesmal dot, right? Get real, people. Does anyone else out there see through the silliness of this assumption? Maybe the car got on the road at some point besides its origin. Maybe it's time to look at some other options, because methodological naturalism is turning our minds to mush, causing us to accept laughable tenets as "scientific fact." Maybe we should just go back to believing that the world is sitting on the back of a turtle. This would be better than wasting our time answering a question whose presuppositions are ludicrous, such as trying to figure out how the entire physical content of the universe came into existence as a small dot, when a physical observable law exists that says that matter and energy cannot be created. Why is the big bang believed? Because it artificially minimizes the problem by compressing the universe's matter to a small spec. I say artificially, because this really does nothing to solve the problem, as the entire universe's mass is supposedly present in this small dot. But as is true with all propaganda, it is easier to overlook glaring issues when they are trivialized, either literally or figuratively.

Who in their right mind would see two houses that utilize 2x4 beams in their construction and conclude that since the houses contain similar/identical parts, therefore the houses are evolutionary cousins and that neither were purposefully designed or built? Who in their right mind would impose methodological naturalism on all attempts to explain the houses' origins? But let's take a step back and assume that we didn't know how houses were made. Let's assume these houses were of unknown origin. Admittedly the houses are not sophisticated enough to build copies of themselves (as all living things can do), but still any 10-yr-old would call you a lunatic if you told him the house got there by natural processes including wind, erosion, tsunamis, earthquakes, fires, tornadoes, and volcanoes. Yet so many PhDs today, while experts in their respective niches, have lost sight of the big picture that the 10-yr-old can readily see. The trailer for the upcoming Transformers movie makes an intuitive point: If you're hopping around on the moon in your space suit and come across a sophisticated system of interacting parts whose function is clearly deduced from its design as being a crashed spaceship, then the conclusion naturally follows: "We are not alone." Yet in molecular biology we observe the universe's most sophisticated machinery, and as a result we should be thinking, "We are not alone," yet we're too proud and in denial to admit that our bodies are designed machines. Intead, we wave around the magic wand of evolutionary theory as if it were a viable alternative. It isn't even close. Evolutionary theory isn't in the same ballpark to be a viable alternative. It isn't on the same planet. It isn't even in the same universe. It's in the realm of Disneyland Imagineering.

I'm trying to understand your argument.

You go into great detail about the complexities of bacterial flagellum, but I didn't see the connection to being irreducibly complex.

Perhaps my understanding of "Irreducibly Complex" is incorrect, but I thought the concept meant that certain systems are too complex to have evolved.

Even if you point out the sheer awesomeness and extreme complexity of bacterial flagellum, I still have a couple of questions that I've been trying to clarify and I haven't found answers for yet:
Is there a level of complexity that we know evolution is incapable of achieving or explaining?
And if there is, what it is the general level of complexity and how do we know said complexity is beyond explanations of evolution?

I think some of the points you made seem to be implying that the system would be non-functional with broken or missing components, but that doesn't automatically indicate how a system got to its current state. It also doesn't indicate that the system as a whole has always functioned in a manner that necessitates each component.

Regardless of what the refutations to Behe's ideas actually were, I don't see the support of irreducible complexity in the article.

I absolutely agree that it's extraordinarily complex; and that it certainly appears as though there is some design behind it, but as much as I'd like to be able to just jump to that conclusion, information that would be directly relevant to supporting said conclusion is still missing.

This simply describes the genetic instruction and development. The same as describing the development of an embryo. Trying to wow the layman with a description of a process does not infer design nor refute the evolution of the bacteria.

Nonsense and devious to the point.

I'm glad to see a post like this. Surprised at how the straw man Ken Miller first formulated is still
alive and well though.


If anything, the only criticism that doesn't receive enough attention from either side of the
debate is Matzke's Evolution in Brownian Space. I think me and Casey would agree on this,
namely that while Miller and many others tend to flatly misrepresent what Behe actually tries to
argue, Matzke at least tries to make responses that keep Behe in original context.


Bookmarking this as one of the better posts on Irreducibility. In a moment though, there's a few
things that need to be said about Miller's argument because it's so prevalent. I'll get to that in a
moment...

Hmm, looks like you didn't actually read our paper. If you had, you would have realized that many of the proteins that you mention from the Salmonella flagellum are not universally required in all flagella. And that most of the required proteins have known alternative functions in nonflagellar systems. Oh well.

I recall that sometime ago Dr. Behe issued a challenge that someone should conduct an experiment to see if a bacterium could evolve a flagellum.

As a non-biologist I don't see how this could be done. I assume that if such an experiment could be conducted, it would be similar to dog breeding.

When offspring are observed that have the chosen characteristics, those offspring are isolated and they become the parents of the next generation, and so on.

What characteristic in a first generation bacterium would suggest that bacteria with that characteristic should be isolated to become the population that is the next step in the evolution of a flagellum?

Thanks Jonathan,

notes;

Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video
http://www.metacafe.com/watch/3994630/

Bacterial Flagellum: Visualizing the Complete Machine In Situ
Excerpt: Electron tomography of frozen-hydrated bacteria, combined with single particle averaging, has produced stunning images of the intact bacterial flagellum, revealing features of the rotor, stator and export apparatus.
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4M8WTCF-K&_user=10&_coverDate=11%2F07%2F2006&_rdoc=1&_fmt=full&_orig=search&_cdi=6243&_sort=d&_docanchor&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=8d7e0ad266148c9d917cf0c2a9d12e82&artImgPref=F

Bacterial Flagella: A Paradigm for Design – Dr. Scott Minnich – video
http://www.vimeo.com/9032112

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