Clockwise: A bacterium retracts its pili, reeling in a piece of DNA in the environment. This action facilitates “natural transformation,” a process by which bacterium acquire new genetic traits, including antibiotic resistance.
Image courtesy the Dalia Lab, Indiana University
Creationists have a problem of their own making. The same evolutionary processes they try to rebrand as evidence for a creator god are also the processes that produce parasites, pathogens and the molecular machinery by which they exploit their hosts. If Michael J. Behe wants to claim “irreducible complexity” as evidence of design, and William A. Dembski wants to claim “complex specified information” as the signature of an intelligent designer, then they cannot confine those arguments to the parts of biology they find theologically convenient. The same kinds of complexity and genetic information are also found in organisms that make us sick and increase the suffering in the world.
Although professional creationists, including fellows of the Discovery Institute such as Behe and Dembski, are careful to avoid naming their putative designer, their audience invariably identifies it with the supposedly omnibenevolent god of the Bible, Torah and Qur’an. But that creates an obvious problem: using their own criteria, this creator god must be credited not only with designing humans and other animals, but also with designing the bacteria, viruses, parasites and molecular mechanisms that infect, disable and kill them.
The significance of this is often lost on creationists because it requires a basic understanding of biology and a willingness to follow an argument to its logical conclusion. When they cite Behe’s favourite examples, such as the E. coli flagellum or anti-malarial drug resistance in Plasmodium falciparum, as evidence for their god, they are in effect crediting that god with designing mechanisms that help microbes move, invade, survive and evade our attempts to stop them. Point this out, however, and the same evidence that was allegedly scientific evidence for intelligent design is suddenly reinterpreted as evidence for “The Fall” and “Original Sin”. The pretence that creationism is science is abandoned in a hasty retreat into fundamentalist theology, where the same facts are repurposed to reach a more comfortable conclusion.
In addition to the two examples I recently discussed here and here, another example has now been reported — and this one involves a powerful molecular motor that should, by creationist standards, look very much like the sort of thing they would normally call “designed”. It is the type IV pilus retraction system, recently reported in Proceedings of the National Academy of Sciences of the USA (PNAS), which many bacteria use to retract tiny hair-like surface structures called pili. These pili act like microscopic grappling hooks, helping bacteria attach to surfaces and tissues, form antibiotic-resistant biofilms, and pull in fragments of DNA from their surroundings, including genes for drug resistance acquired from other bacteria.
The paper is by Abigail E. Teipen and colleagues from Indiana University Bloomington, Dartmouth College and the Georgia Institute of Technology. Their study examined how two motor ATPases, PilT and PilU, coordinate their activity during type IV pilus retraction in the cholera-causing bacterium Vibrio cholerae. Using AlphaFold 3 modelling, molecular dynamics simulations and laboratory experiments, the team showed that the interaction between PilT and the C-terminal “tail” of PilU is critical for the two motors to work together.
The motor system involves three key proteins: PilC, PilT and PilU. PilC is an inner-membrane platform protein that forms part of the pilus machinery and provides the interface through which the motor acts on the pilus. PilT and PilU are ATPase motor proteins that use the energy from ATP hydrolysis to retract the pilus. In the system studied here, PilT is essential both for retraction and for recruiting PilU into the working motor complex, where PilU’s distinctive tail wraps around PilT and helps the two motors coordinate their activity.
That matters because type IV pilus retraction is one of the most powerful mechanical actions known in biology. For the bacterium, it is not just an elegant molecular trick; it is a means of attachment, colonisation, biofilm formation and horizontal gene transfer — including the spread of antibiotic-resistance genes. In Vibrio cholerae, pili can reel in environmental DNA rather like a fishing line. In other pathogens, related systems help bacteria grip host tissues and persist in places where antibiotics and immune defences struggle to reach them.
A further significant finding is that this coordination mechanism is not unique to cholera bacteria. The same key molecular interaction was found in Acinetobacter baylyi, a distantly related species, and sequence analysis suggests that similar PilT-PilU coordination is broadly conserved across many bacteria, including disease-causing species such as Pseudomonas aeruginosa and Legionella pneumophila, the cause of Legionnaires’ disease. When distantly related species share such molecular machinery, biologists recognise the familiar pattern of evolutionary conservation. Creationists, however, typically dismiss common ancestry and call it “common design”. In this case, that would mean crediting their designer with a conserved bacterial motor that helps pathogens cling, spread, form biofilms and acquire antibiotic resistance.
Glossary^ Type IV Pili and Bacterial Molecular Motors. ATP – Adenosine triphosphate, the small energy-carrying molecule used by cells to power many biochemical reactions. When ATP is broken down, energy is released for cellular work.The paper in PNAS was accompanied by a news item from the College of Arts and Sciences at Indiana University:
ATPase – An enzyme that breaks down ATP to release energy. In this bacterial system, PilT and PilU are ATPase motor proteins that use ATP to power pilus retraction.
Biofilm – A community of microorganisms attached to a surface and embedded in a protective matrix. Biofilms can make bacteria much harder for antibiotics and immune defences to remove.
Conserved – In evolutionary biology, a feature is said to be conserved when it is retained across different species because it has been inherited from a common ancestor and remains useful.
Horizontal gene transfer – The transfer of genetic material between organisms other than by parent-to-offspring inheritance. In bacteria, this can spread useful genes, including genes for antibiotic resistance.
Molecular motor – A protein or protein complex that converts chemical energy into mechanical movement. In this case, the motor retracts bacterial pili with remarkable force.
Pili – Tiny hair-like structures on the surface of many bacteria. A single one is called a pilus. Pili can help bacteria attach to surfaces, move, form biofilms and take up DNA from their surroundings.
PilC – A platform protein in the bacterial pilus machinery. It helps provide the structural interface through which the motor system acts on the pilus.
PilT – An ATPase motor protein essential for type IV pilus retraction. In the system studied here, PilT also acts as the key connector that recruits and positions PilU in the working motor complex.
PilU – A second ATPase motor protein that works with PilT. PilU cannot operate effectively on its own but, when coordinated with PilT, helps generate a stronger retraction force.
Retraction – The process by which a pilus is pulled back into the bacterium. This allows bacteria to drag themselves across surfaces, tighten their grip on host tissues, or pull in DNA from the environment.
Type IV pilus – A specialised bacterial pilus that can extend and retract. Type IV pili are involved in bacterial movement, attachment, biofilm formation, DNA uptake and, in some species, infection.
Natural transformation – A form of horizontal gene transfer in which bacteria take up DNA from their surroundings and incorporate it into their own genome. This can include DNA from dead bacteria.
Antibiotic resistance – The ability of bacteria to survive exposure to drugs that would normally kill them or stop them multiplying. Resistance genes can spread between bacteria by horizontal gene transfer.
AlphaFold 3 – A computational tool used to predict the three-dimensional structures of proteins and protein complexes. In this study, it helped model how PilT, PilU and PilC interact.
IU biologists uncover a molecular mechanism that helps bacteria spread antibiotic resistance genes
Every year bacteria kill more than a million people worldwide through infections that no longer respond to antibiotics. In many cases, why those bacteria are so hard to stop comes down to their uniquely powerful structure. Now, scientists in the College of Arts and Sciences at Indiana University Bloomington, with colleagues from Dartmouth College and the Georgia Institute of Technology, have solved a key mystery about how those bacteria work.
On the surfaces of many disease-causing bacteria, fibers thousands of times thinner than a human hair bristle, acting like biological grappling hooks. These fibers help bacteria latch onto body tissue, build biofilms, which are sticky bacterial communities that antibiotics struggle to penetrate, and reel in fragments of DNA from their environment, including genes that help them resist drugs.
Now, scientists in the College of Arts and Sciences at Indiana University Bloomington, with colleagues from Dartmouth College and the Georgia Institute of Technology, have solved a key mystery about how those hooks work. A new study, published in the Proceedings of the National Academy of Sciences, reveals the molecular mechanism behind one of the most powerful mechanical actions in all of biology, the reeling in of tiny surface fibers called type IV pili.
The findings shed light on how bacteria pull off this feat with such extraordinary force, and may point toward new ways to interfere with the resistance process in disease-causing species.
Type IV pili are whip-like fibers that extend from the outer surface of many bacteria, and are then reeled in at a force that ranks among the most powerful movements ever recorded in any living thing. The ability of these fibers to be reeled in is central to how bacteria make us sick.
For example, when Pseudomonas aeruginosa infects the lungs of a cystic fibrosis patient, it uses pili to grip the airway lining and hold on. When Neisseria gonorrhoeae colonizes the uro-genital tract, pili help it stick and multiply. And in Vibrio cholerae, the bacterium that causes cholera, the focus of this study, pili reel in fragments of DNA from the environment, including genes that give bacteria resistance to antibiotics, akin to a fishing rod pulling in a line.
That last function, which scientists call horizontal gene transfer, is one of the main engines driving the global antibiotic resistance crisis. Why? Because bacteria do not have to evolve resistance on their own. They can simply grab it from other bacteria, whether those bacteria are dead or alive, using their pili as fishing lines.
These tiny molecular motors are some of the strongest in nature, and understanding how they coordinate their activities to achieve such force is something the field has been working toward for a long time.
Abigail E. Teipen, lead author.
Department of Biology
Indiana University
Bloomington, IN, USA.
Scientists already knew that snapping a pilus back requires two motor proteins, called PilT and PilU, working in tandem inside the bacterial cell. What still needed to be determined was why both were needed, and how they coordinated at the molecular level.
To solve the puzzle, the study co-authors used a leading-edge computer modeling tool, AlphaFold 3, which predicts how proteins fit together. The team modeled the interaction between PilT, PilU, and a third protein called PilC, which anchors the whole motor system to the pilus machine.
The models revealed a clear division of labor. PilT is the essential connector, anchoring the whole motor system to the pilus machine and which simultaneously holds PilU in place. But PilU cannot get there on its own. Once both proteins lock in, they stack on top of each other, and a unique tail on PilU wraps around PilT like a hand gripping a handle, which may allow the two motors to move as one. The team also ran molecular dynamics simulations, high-powered computer animations of atoms in motion, to watch the two motors interact in real time over hundreds of nanoseconds. Those simulations helped confirm exactly which molecular contacts hold PilT and PilU together.
The researchers then validated those predictions through rigorous lab experiments, deliberately altering specific molecular contact points and watching what happened to bacterial behavior. Breaking the PilT-PilU connection did not kill the bacteria outright, but it did stop them from pulling in DNA the way they otherwise would.
The results show that it is not just having two motors that matters, it’s how they physically interact and coordinate. If we can find ways to disrupt that coordination, we may have a new avenue for stopping bacteria from spreading antibiotic-resistant genes and establishing infections.
Professor Ankur Dalia, senior author.
Department of Biology
Indiana University
Bloomington, IN, USA.
The researchers calculated that one motor protein working alone should top out at roughly 50 piconewtons of force, an almost incomprehensibly small unit of measurement, yet for a structure millions of times smaller than anything visible to the naked eye, this is a remarkable amount of power. Still, pili in living bacteria have been measured pulling at more than twice that force. This suggests that the PilU tail wrapping around PilT allows the two motors to synchronize their energy cycles to pull pili at a force that neither motor could achieve alone.
One of the study’s significant findings is that this coordination mechanism is not unique to cholera bacteria. The same key molecular contact was found in Acinetobacter baylyi, a distantly related species, and sequence analysis suggests it is broadly conserved across many disease-causing bacteria, including Pseudomonas aeruginosa and Legionella pneumophila, which causes Legionnaires’ disease. That conservation suggests the coordination strategy evolved early and has been preserved because it is essential to bacterial survival.
Publication:
So here again we have a system that, had it been found in some harmless or superficially appealing organism, would almost certainly have been paraded by intelligent design advocates as evidence of engineering brilliance. It is a tiny, coordinated molecular motor, powered by ATP, involving interacting protein components and producing a mechanical force out of all proportion to its size. In creationist rhetoric, that is exactly the sort of thing that is supposed to leave us gasping in admiration at the handiwork of a designer.
But this particular example is not a decorative flourish in a flower or a convenient adaptation in some useful domestic animal. It is part of the machinery by which bacteria cling to surfaces, form biofilms, colonise hosts and acquire DNA from their surroundings, including genes that can help them resist antibiotics. If the design argument is to be taken seriously, then the designer must be credited with designing not only the host but also the mechanisms by which pathogens exploit that host.
And that is where creationism collapses into special pleading. The same complexity is “evidence of design” when it appears useful, beautiful or emotionally comforting, but becomes “evidence of The Fall” when it appears in a pathogen. The evidence has not changed; only the theology has been shuffled to protect the conclusion. That is not science. It is a device for ensuring that no observation, however awkward, is ever allowed to count against the belief.
For biologists, however, there is no mystery and no need for theological rescue clauses. Type IV pili, ATPase motors, conserved protein interactions, horizontal gene transfer and bacterial pathogenicity are all understandable within the framework of evolution. Related bacteria inherit, modify and repurpose molecular systems because descent with modification is how biology works. Natural selection has no moral purpose and no concern for human welfare; it preserves what works for the organism carrying it, whether that organism is a human, a harmless soil bacterium, or a pathogen spreading antibiotic resistance.
The creationist can call this “common design” if they wish, but then they must explain why their supposedly omnibenevolent designer repeatedly uses the same clever engineering to equip bacteria with tools for adhesion, infection, biofilm formation and genetic piracy. The scientific explanation is simpler, more honest and supported by the evidence: these are evolved systems, shaped by selection, inherited through common ancestry and modified by the relentless opportunism of natural processes. No magic is needed, and no benevolent designer is helped by pretending otherwise.
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