[00:00:04] Speaker A: Id the Future, a podcast about evolution and intelligent design.
[00:00:12] Speaker B: Welcome to id the future. I'm your host, Andrew McDermott. Doctor Jonathan McClatchy joins me today to discuss the engineering elegance and irreducible complexity of the bacterial flagellar motor. Doctor McClatchy is a fellow and resident biologist at the Discovery Institute's center for Science and Culture. He was previously an assistant professor at Sattler College in Boston, where he lectured biology for four years. McClatchy holds a bachelors degree in forensic biology, a masters degree in evolutionary biology, a second masters degree in medical and molecular bioscience, and a PhD in evolutionary biology. His research interests include the scientific evidence of design and nature, arguments for the existence of God, and New Testament scholarship. Jonathan is also founder and director of talkaboutdoubts.com. Jonathan, welcome back to the program.
[00:01:04] Speaker A: Great to be here. Thanks for having me.
[00:01:06] Speaker B: You're welcome. The bacterial flagellum has been described as a nanotechnological marvel. Even non intelligent design scientists call it an awe inspiring object of divine beauty. It's a familiar icon of intelligent design and perhaps the flagship example of irreducible complexity.
If you've been following the work of the IED research community for a while, you'll likely have some familiarity with it. And if that's you, I'm betting you'll enhance your knowledge of it today. But I know there may be some out there who are pretty new to intelligent design, and you're not nearly as or not at all familiar with the bacterial flagellum as a prime example of irreducibly complex design.
So, Jonathan, I wonder if we could start there. I know you've studied and written on the flagellum for decades, but, but for those who are pretty new to it, what is the bacterial flagellum? And why do intelligent design proponents make such a fuss over it?
[00:02:00] Speaker A: Sure. So the bacterial flagellum is a rotary motor that propels bacterial cells through liquid, and it's an incredibly well engineered system that has essentially 100% energy conversion efficiency in organisms like salmonella or E. Coli. It can spin at speeds of up to 17,000 rotations per minute. In some organisms like Vibrio cholera, it can spin at speeds of up to 100,000 rpm, and it can change direction.
So its default setting is to spin counterclockwise. But it can change direction and spin clockwise almost instantaneously. So it's a remarkable feat of engineering. And unlike manmade motors, bacterial flagella are able to self assemble, so they actually have assembly instructions for building themselves from the inside out. So they're absolutely remarkable systems that I think cry out for explanation by design.
Wow.
[00:03:12] Speaker B: Yeah. Well, what are the various parts of the bacterial flagellar motor that are necessary for the motor to work?
[00:03:19] Speaker A: Sure. So the bacterial flagellar system has many of the components that you might recognize associated with a typical man made motor. So you have a universal joint, which is called the hook, and you have a drive shaft, which is called the rod, and you have bushings and bearings. You have the propeller, which is known as the filament, that spins within the stationary component, which is the stator you have.
And this has been visualized by electron microscopy.
And so it's a remarkable system that requires a number of different parts in order to work, and it basically functions by virtue of a proton gradient across the cell membrane.
So it's approximately 1200 protons are actually translocated per rotation, and protons flowing through the mot proteins exert electrostatic forces on helically arranged charges on the rotor proteins and alternating attractions between positive and negative charges on the rotor. As protons flow through the mot, proteins then cause the entire basal body to rotate. So it's a remarkable system.
[00:04:38] Speaker B: Yeah, well, and it's amazing that we even have the words to describe it. I mean, we have our motors that we've made, but they're recent inventions, you know, given, given how long we've been going, and, you know, and here's this, this motor, this machine, this molecular system that's been. Been around for a lot longer than we have, you know, and I actually think that's, that's a good argument against an evolutionary origin of this. You know, that if it were to come from a bottom up process like darwinian evolution, it really shouldn't look like the machines and motors and pieces that humans have been able to create. So it's pretty remarkable that we can even compare it with things that we've done because it's a lot older. Well, can you describe the process by which bacterial flagella self assemble? You mentioned that they can come together themselves.
[00:05:33] Speaker A: Absolutely. So, yeah. The bacterial flagellum, as I said, is capable of self assembly. So the Ms and LP rings of the flagellum form first. These are the rings that sit within the inner and outer membrane. In grim negative bacteria, which have two membranes, the bacterial flagella are capable of self directed assembly.
The base of the flagellum, which is the Ms and LP rings, which are rings that sit within the double membrane of gram negative bacteria, they assemble first, and then you have the construction of the rod and the hook and the flagellar filament.
In order to ensure the timely assembly of the flagellar parts, the genes that encode the proteins that form parts of the flagellum are arranged or organized into a transcriptional hierarchy such that you. I mean, it doesn't make any sense to start producing the propeller or the filament until you've already put in place the hook basal body apparatus. Right. And so you have to ensure that the genes encoding the flagellin proteins are only expressed after you've already put together the hooked basal body apparatus that anchors the flagellar system to the inner and outer membranes.
The genes are distributed across three different.
The genes are distributed across three different classes.
You've got class one genes. So I'm talking about the model system that you'll find in Salmonella and E. Coli. Obviously, this differs from among different bacterial taxa, but in salmonella, in the class one genes are made up of just two different genes, flu D and flu C, which code for proteins that form a transcriptional activation complex called the flu dc complex, or the enteric master regulator, which will then go and drive the expression of the class two genes.
And the class two genes is about 35 different genes distributed across eight operons are basically sequences of DNA and bacteria that are expressed together under control of a common promoter. And these genes, these 35 genes distributed across eight operons, are genes that encode proteins associated with the hooked basal body apparatus.
Among those genes are regulatory proteins called sigma 28, which is coded for by flea A and flac M.
Now, sigma 28 is what we call a sigma factor. And sigma factors in bacteria control the expression of genes by binding to the rna polymerase.
And so the sigma 28 is responsible for driving the expression of the class three genes. But flag M is what we call an anti sigma factor. Now, anti sigma factors, as their name suggests, inhibit sigma factors. And so flag M sequesters sigma 28 until such a time as the hook basal body has been completed. When there's an interaction that takes place within the hook region, it causes a substrate specificity switch, which results in flag M being exported through the type three secretion system. And this then liberates sigma 28 to drive the expression of the class three genes. And so this leads to the timely assembly of the various ethyl Geller proteins.
What's another interesting aspect of ethylagellar assembly is rod penetration. So the four rod proteins are flag b, flag c, flag f and flag d. And the rod cap protein, which is known as flag j, is bifunctional, so it has a c terminal domain that possesses hydrolyzing activity. So its role is to basically puncture a hole through the outer membrane to facilitate continual progression outside of the cell. And then the n terminal domain possesses binding affinity for rod proteins. And besides the four genes that encode rod subunit proteins, more than ten genes are necessary for rod assembly.
There's also the hook region. So the hook acts as a universal joint. It's constant at 55 nm in length. And there are two important proteins, namely fly k and flue b. And fly k is secreted intermittently and essentially acts as a molecular ruler that measures hook length. So it works like this.
The n terminal domain of fly k goes through a channel of the flagellar filament. It interacts with flag d, the cap protein of a growing hook, while the c terminal domain of fly k forms a globular structure and it stays in the cytoplasm. And when the internal domain of fly k reaches its maximum length, signal is transmitted to fly k, the c terminal domain of fly k, to interact with flue b, the secretion gate, at which point conformational change occurs to switch the substrip specificity. And that's the point at which flag m is exported out of the needle, out the type three secretion system, and thereby liberating sigma 28 to drive the expression of the class three genes. There's also, of course, the assembly of the filaments. So the flagellum monomers, which are known as fly c because of the narrowness of the channel through which they have to pass. It's only about 2 nm in diameter. They actually have to be unfolded for insertion into the channel and then subsequently refolded at the distal growing end. And so there's a filament capping protein called fly D, which basically acts as a chaperone that facilitates folding of the fly c monomers. The flagellum monomers at the distal growing end. It's a pentagonal disc shape with five leg like extensions which rotates and causes the flagellum subunits to fold.
Experimental studies that have been conducted that knock out fly d, knock out that chaperone have shown that the consequences that the flagellum subunits are just lost into the medium. So it's absolutely critical for flagellular assembly.
Hopefully, your listeners are getting a sense of just the engineering marvel that is, uh, the flagellar system and its assembly.
[00:12:52] Speaker B: Yeah, yeah, it's fascinating and, you know, there, there's just so much to it, and I'm glad you can, you can articulate that. Um, obviously, we're not expected to remember, but you know, as b says, we've got to experience that complexity to appreciate it. And so you're helping us do that. Um, it really is fascinating. So the flagellar motor you mentioned switches gears on a dime. Uh, it's like a quarter turn and it can switch, uh, switch gears and reverse course and change direction. Why would it do that? And tell us a little bit about the process of how it does that signal transduction.
[00:13:27] Speaker A: Yeah. So this brings us to the topic of chemotaxis. Now, chemotaxis is the mechanism by which bacterial cells find reorient themselves, changing their bearings, changing their course, in order to move closer to chemical stimuli, attractants like glucose, for example, which is a food source, or move away from toxins, poisons. And how do bacteria accomplish this? Well, they spin their flagellar bundles in a counterclockwise direction, but in response to chemical stimuli. And we'll talk about how this functions at the molecular level. In, in a few moments, the flagellar motors can switch direction and start spinning clockwise. And because the flagellar, because flagella are typically in bundles, this actually causes the flagellar bundle to break apart and it results in the flagellar, it results in the bacterial cell tumbling in place.
And so it actually is able to change its direction, change its course.
In consequence of the flagellum changing its directional rotation, it's able to continually sample its environment in order to move in the direction of a chemical stimulus, a chemical attractant.
How does this work at the molecular level? How does the bacterial cell know when it is approaching or in close proximity to an attractant? And how does it cause the flagellum to change direction? Well, this is what we call a two component system. So two component systems are very common in microbiology. And basically, as the name suggests, a two component system has two components, and these two components are the histidine kinase and the response regulator. So the histidine kinase, in response to binding to a chemical signal, will, or receiving a chemical signal, will undergo artificial histidine residue, histidine, of course, being one of the amino acids. And there's a particular histidine that can undergo autophosphorylation by ATP in response to chemical signal. And then this, in turn, this phosphate that is now on the histein residue of the kinase can get transferred to an aspartate residue on a response regulator. And then the response regulator will go and drive the output or drive the response.
How does this work? In particular, when it comes to the flagellar system and chemotaxis. Well, there's a group of proteins on the surface of the cell known as methyl accepting chemotaxis proteins, and different methyl accepting chemotaxis proteins can detect different types of molecules and they're able to bind attractants or repellents. And then these receptors can communicate with and activate the so called key proteins. So proteins called key a and key w are bound to the receptor and key a is the histidine kinase for this system. And so upon activation of the receptor at the cell surface, the key a's conserved hisiting residue undergoes onto phosphorylation.
And there are two response regulators called key b and key Y. So there's a transfer of a phosphoryl group to their conserved aspartate residue from key a and key Y subsequently interacts with, with the flagellar switch protein called flee, called fly m. And this induces the switching in flagellar direction from counterclockwise to clockwise. Now, key b is the another response regulator and when it's activated by key a, it acts as a methyl esterase, removing methyl groups from glutamate residues on the cytosolic side of the receptor. And it works antagonistically with Cre, which is a methyl transferase which adds methyl groups to the same glutamate residues. And if the level of an attractant remains high, the level of phosphorylation of key A and therefore key Y and key B will remain low and the cell will swim smoothly and the level of methylation of the MCPs will increase because the phosphorylated QB is not present to demethylate and the methyl accepting chemotaxis proteins no longer respond to the attractant when they are fully methylated.
Even though the level of attractant might remain high, the level of the phosphorylated key a and phosphorylated key b increases and the cell begins to tumble. And the methyl accepting chemotaxis proteins can be demethylated by phosphorylated key b. And when this happens, the receptors can once again respond to attractants. So this basically ensures that the cell can, in response to chemical stimuli, it can increase its frequency of tumbles.
If it's running towards, if it's running in the direction of a repellent, you want to increase the number of tumbles and if it's running towards an attractant, you want to decrease the number of tumbles. And so the methyl accepting chemotaxis protein responds to repellents to generate tumbles. So when a repellent binds to the methyl exciting human taxis protein, that triggers the phosphorylation of the response regulator. But when it's bent by an attractant, it does not phosphorylate the response regulator. And so it's able to increase the frequency of tumbles in response to repellence and not when there's an attractant present, but when there's no attractant present, then of course you do want to increase the number of tumbles so that you can orient yourself in the direction of an attractant, potentially. So hopefully that was clear. It's more difficult to explain this without the aid of a visual, a visual diagram, but yeah, one can do one's best.
[00:20:20] Speaker B: Yeah, totally. Well, yeah, and it's amazing that this is all happening at the biochemical level, in a lowly bacteria, no less. So amazing levels of complexity. There's. And we don't just call it complex, we call it irreducibly complex. So let's move into that for a few minutes. What is just as a reminder to listeners, irreducible complexity? And why does it both challenge evolution and provide a positive argument for design?
[00:20:48] Speaker A: Right, so errors. Book complexity was a term that was coined by Michael Behe in his book Dharma's Black Box, published in 1996. He says, by Erds Book and Blacks, I mean a single system composed of several well matched interacting parts, parts that contribute to the basic function where the removal of any one of the parts causes the system to effectively cease functioning. And so irreducible complexity challenges evolution because it's very difficult to envision how, by an unguided process, you would arrive at a complex, higher level objective without knowing where the target is. Whereas on the other hand, that is not at all surprising, supposing a designer is involved, because explaining the origins of irritably complex features, I would maintain, requires a cause that possesses foresight. And only intelligent causes are able to visualize complex higher level objectives and then bring everything needed together to realize that end goal.
And so it points, I think, heavily towards intelligent design. So Michael Behe, in Darwin's black box, he talks about the flagellum specifically, and he's thinking about it kind of at a big picture level, rather than going to the molecular weeds that I just did. But he says, and I'm quoting, he says, the bacterial flagellum uses a paddling mechanism. Therefore it must meet the same requirements as other such swimming systems, because the bacterial flagellum is necessarily composed of at least three parts, a paddle, a rotor and a motor. It is irreversibly complex. Right. So the bacterial flagellum requires minimal level of, minimal number of parts in order to fulfill its job, and therefore, it's irreducible complex. And it seems implausible that it could have been brought about by an unguided, blind, natural process. Right.
[00:22:37] Speaker B: Yeah, we're talking optimal design, optimal efficiency, and optimal coordination, all coming together to suggest foresight and goal direction. Well, one of the most popular pushbacks to the idea that the flagellum is irreducibly complex is that parts may have been co opted from other systems, such as the type three secretion system. How would you respond to this?
[00:23:00] Speaker A: Yeah, so the, there's a lot of evidence that, well, I should mention what the type three secretion system is. The type three secretion system is also known as an injectosome. It basically injects poisons into multicellular organisms. And, for example, Yersinia pestis, which is the causative agent of bubonic plague, uses type three secretion systems to inject toxins into animals like ourselves. For example, in the Middle Ages, the bubonic plague wiped out about a third of Europe. And the triat three secretion system is the mechanism by which the bacteria causes its pathogenic effect.
And scientists have long recognized that the type three secretion system is also part of the bacterial flagellar system, because the type three secretion system, or type three export system, is used for secreting the flagellar proteins that make up the flagellar system.
And so various critics of intelligent design have made the case. This is most popularly associated with Ken Miller of Brown University. He's never tired, but has also been put forward by many other scientists and critics as well. And there's a number of problems with the hypothesis that the flagellum evolved from a type three secretion system.
For example, the type three secretion system is taxonomically restricted to a small set of gram negative bacteria, whereas flagella are much more widely distributed.
So this suggests that the flagellum came first and the type three secretion system came later. Furthermore, it makes sense evolutionarily to have the flagellum first and three secretion system coming later, because selection for metal to precedes selection for virulence, because there's a selection pressure to be able to swim long before there's a selection pressure to inject poisons to multiple organisms in evolutionary history. Furthermore, bacteria that have type three secretion systems, such as Yersinia that I mentioned before, possess genes for making flagella, even if no flagella are assembled.
These evidences cumulatively suggest that the type three secretion system came later rather than before, that it's an evolutionary degradation product rather than the precursor or ancestor. Moreover, type three secretion system genes are commonly found in large virulence plasmids, whereas flagellar genes are split into 14 or so operons and are not found on plasmids.
And when the type three secretion system genes are found in the chromosomes of bacteria, their gc content is typically lower than the gc content of the surrounding genome, which suggests the foreign origin. So it's, I think, well supported that the type three secretion system came later than the flagellum. And so it's not very plausible, in my view, that the flagellum evolved from a type three secretion system. There's further problems, though, with acceptation scenarios, such as the idea that the flagellum evolved from other systems, like the type three secretion system. For example. Co opting those proteins to produce a flagellar system requires multiple coincident changes in order for the new system to be realized. For example, flagellar specific proteins would not confer a selective advantage until incorporated into the flagellar system. But the necessary proteins that serve rules in other systems will not become incorporated into the flagellar system before these flagellar specific proteins arise. There's also, of course, a need for complementary protein protein binding interfaces and, of course, a need for a choreographed assembly system to ensure that the proteins are assembled in the appropriate order, which is very dependent upon the precise order of the genes along the bacterial chromosome.
So, so these are some of the problems with the idea of co option to account for the origins of the flagellar system. Okay.
[00:27:13] Speaker B: All right. And that's one of the more common and popular pushbacks to the flagellum, and it's irreducibly complex nature. Now, very briefly, as we wrap up, I know, I understand there was a paper from 2006 in Nature Reviews and microbiology by Mark Palan and Nick Matsky titled from the origin of species to the origin of the bacterial flagella. And here the authors claimed a number of homologies to other systems, and they hold that there's a number of components of the flagellum that are dispensable. What's your response to this? Briefly?
[00:27:48] Speaker A: Sure. So of the 42 flagella proteins that Palamatsky surveyed in that paper in HRV's microbiology, they noted that at the time of their publication, 14 had no known homologs. And of the 28 flagella proteins that remain, they note eight to possess homology to other flagellar specific proteins. So these aren't very helpful for explaining the origins of the bacterial flagellum if their homology is to other proteins that are specific to the flagellum. Of the remaining 20 flagellar proteins, eleven are homologous to components that comprise the type three secretion system that we already talked about. And of the 42 flagellar proteins, the most interesting then, are the nine proteins with identifiable homologues outside of flagellar and type three secretion systems. But as we've already noted, there are other issues and problems to contend with when it comes to explaining the flagellar system by means of acceptation or co option scenarios. Now, in regards to the dispensability of flagellular components, of the 42 proteins that they surveyed, they conceded that 23 are in fact indispensable for flagellar function, and of the remaining 19, they concluded that they were dispensable for flagellar function either because it's absent from some flagellar systems or because mutants retain motility.
Now, as for proteins that are absent from other species, so they noted that the proteins that comprise l and p rings, flag a, flag h and flag I are not found in gram positive bacteria. But this is hardly surprising, of course, because gram positive bacteria characteristically do not possess an outer membrane. Gram positive bacteria have a single membrane, in contrast to gram negative bacteria that have a double membrane. So it shouldn't be very surprising that they don't have an Lp ring that would be anchored in the the additional membrane that gram positive bacteria don't have. So they also observe that the n terminal domain of flag j is absent from some systems. And again, this is true, although it has been demonstrated to be essential in Salmonella enterica.
But although the monofunctional flag j is possessed by rotobacter sporoides and colobacter chrysanthemum lack the intermodal domain, and thus lytic activity has been shown that this is compensated for by production of putative lytic transcorcosylases. So the lytic transcosylases are bacterial enzymes that catalyze the non hydrolytic cleavage of the peptoglycan structure of the bacterial cell wall, so they're not catalysts of glycan synthesis, as might be surmised from their name.
Pal and Matsky also note that the sigma factor sigma 28, which is encoded by fly a, and its corresponding anti sigma factor flag m, are absent from collobacter. But collobacter species utilize a different regulatory mechanism, which I won't get into in the interest of time, but it has a different regulatory mechanism. And so.
So I prefer to think about, irrespective of complexity, not in terms of the number of, or the identity of the parts that are necessary for the flagellum to work, but rather in terms of the number of functions that have to be performed. And if there's an alternative way of performing essentially the same function, well, sure, a protein might be dispensable, but the function itself is not dispensable. And as I said, colobacter just use a different regulatory mechanism.
They also note that the fly z regulator and the fludisi enteric master regulator are absent from many systems.
But again, colobacter has a phosphorylay system that replaces flu Dc and fleezy.
Again, in the interest of time, I won't get into the details there.
Paolomatsky also note that fly D is missing from colobacter, but fly D is. That's the cabbing protein on the filament. But fly D is demonstrably critical in salmonella. In fact, as I mentioned earlier, experimental studies knocking out flea D result in losing flagellum monomers into the medium. There are some components that I would concede are dispensable. So the chaperone proteins, fly n, fly s and fly t, appear to be dispensable for flagellar assembly. The fly b methylase is not essential for flagellar assembly. Fly J is dispensable for flagellar export. Fly O, which is a component of the type three secretion system, which maintains the stability of fly P through the transmembrane domain interactions, is also non essential. And so we're in agreement that six proteins out of 42 that they surveyed are dispensable for flagellular assembly and function. So I think that there are arguments against iridescent complexity of the flagellum are not particularly compelling.
[00:32:57] Speaker B: Okay. All right. Well, I guess it's safe to say that to date, no scenario in substantive detail exists for how this system could have come about through an evolutionary step wise fashion. Well, some listening to this conversation, Jonathan, may want to dig deeper into the design and irreducible complexity of this fascinating motor. Where can they turn to do that?
[00:33:21] Speaker A: Sure. So there's some of my essays evolutionnews.org dot.
There's also a wealth of academic papers that they can find at the NCBI literature database. There's also a great technical monograph called Pilla and Current research and future trends. It is very expensive, though I think it's like $300. So it's an expensive book. There's a really great essay in there by japanese scientist called Shin Iki Izawa, and he has one of my favorite quotes, he says, concerning the flagellar system, since the flagellum is so well designed and beautifully constructed by an ordered assembly pathway, even I, who am not a creationist, get an awe inspiring feeling from its divine beauty. However, if the flagellum has evolved from a primitive form, where are the remnants of its ancestor? Why dont we see any intermediate or simpler forms of flagella than what they are today? How is it possible that the flagella have evolved without leaving traces in history?
[00:34:16] Speaker B: Yeah, yeah, that's, that's really nice. And to be honest, listeners, you know, a good place to start is, as Jonathan says, evolutionnews.org dot. I mean, when I was prepping for this episode, I hopped on there and it just, there's a wealth of articles arranged chronologically so you can see what, what's been said about the bacterial flagellum to date. But it goes back years and years, and you can pull out all sorts of really fascinating material that will give you more to understand about it. So we'll put a few links in the show notes for those who want to learn more. And of course, if you want to go back to the beginning of all this, go to Michael Behe's book, Darwin's Black Box. Well, jonathan, it's been a pleasure as always, and folks can learn more about your
[email protected]. As well as evolutionnews.org. So many resources and so little time. Jonathan, thanks for joining me. Thank you for id the future. I'm andrew mcdermott. Thanks for listening.
[00:35:15] Speaker A: Visit
[email protected] and intelligentdesign.org dot this program is Copyright Discovery Institute and recorded by its center for Science and Culture.
