Evolution in the News - March 2008
by Do-While Jones

Flogging the Flagellum

Evolutionists are still trying to explain the bacterial flagellum.

In case you tuned in late, here’s the simplified background. The flagellum is a little tail that bacteria spin to move from place to place. This little tail is driven by a very complex, incredibly tiny biologic motor. Intelligent Design proponents claim that there is no way such a complex motor could have evolved by chance. The basis of their argument is that all the parts have to be in place and functional for the parts to provide any survival advantage.

Proponents of ID [Intelligent Design] argue that the bacterial flagellum is exactly such a case: each of its interacting components is essential for the system to function, they claim, and if you remove any one of them the whole thing grinds to a halt. ID claims that because of this irreducible complexity, such systems cannot be explained by the stepwise process of natural selection and therefore must be the handiwork of an "intelligent designer". 1

It is a compelling argument that evolutionists are trying hard to refute.

In an oft-quoted passage from On the Origin of Species, Charles Darwin wrote: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." (In anti-evolution circles, the following line is often omitted: "But I can find no such case.") 2

Darwin could not find such a case because 19th century science was inadequate to discover DNA, metabolic pathways, and the flagellum. Perhaps Darwin wasn’t highly motivated enough to prove himself wrong. But Darwin was certainly correct to recognize that such a case would disprove his theory.

The more we learn about complex biological systems, the more examples of irreducibly complex systems will be discovered. Of course, it is difficult to give simple explanations of these complex systems because they are (duh) complex! But anyone, even someone without any scientific background, who cares to look at anything in nature (from the spinning of a spider web to the life cycle of the butterfly caught in that web) can see complex systems. The more you know about nature, the more reasons you discover not to believe that evolution could have caused it.

The Evolutionary Explanation

Dan Jones tried very hard to present an evolutionary explanation for the bacterial flagellum in New Scientist last month. This, presumably, is the best explanation the evolutionists have.

Biologists have been interested in the bacterial flagellum for decades, not least because it is a prime example of a complex molecular system - an intricate nanomachine beyond the craft of any human engineer. Explaining the origin of such systems is one of the most difficult and important challenges in evolutionary biology. 3

Right off the bat, evolutionary bias starts him down the wrong path. He thinks explaining the origin of such a system is an important challenge. No, figuring out how it works is the important challenge. As an engineer, I’m not ashamed to admit that engineers often look to nature for better design ideas. The flagellum can tell us a lot about how to design tiny mechanical devices. It is important to discover all that we can about how it works. But trying to guess how it could have evolved is a waste of valuable scientific resources.

The flagellum is certainly complex, but is it really too complex to have evolved through natural selection? Until recently it has been surprisingly hard for biologists to answer this question satisfactorily. … In the absence of this knowledge [about how the flagellum works], biologists all too often fell back on the assertion that "bacterial flagella evolved and that is that", according to Mark Pallen, a microbiologist at the University of Birmingham in the UK. 4

There is a lot we can agree with in this paragraph. Yes, it is complex, and yes, biologists have not previously come up with a satisfactory explanation for how it could have evolved. It is typical for evolutionists not to admit their explanation is unsatisfactory until they have another explanation that has not yet been shown to be unsatisfactory. As we will see, their new explanation is also unsatisfactory, but evolutionists haven’t admitted that yet.

The assertion that "bacterial flagella evolved and that is that" is still the foundational assumption, as we can see in the following explanation.

Variants of at least seven T3SS proteins are also found in the flagellum … Such similarities, or "homologies", are strong evidence that the two systems evolved from a common ancestor - analogous to the way that the arrangement of bones in the limbs of horses, bats and whales reveal their common ancestry despite their very different outward appearance and function. Similar homologies can be seen in the DNA sequences of genes, and in the amino acid sequences and 3D structures of proteins - all are clear evidence of shared descent. 5

Similarities are equally clear evidence of a common designer, but that possibility is never even considered by evolutionists because "bacterial flagella evolved and that is that."

So how exactly is the flagellum's protein export system related to the T3SS? One possibility is that the T3SS evolved first and was later co-opted as part of the flagellum. A second is that the flagellum evolved first and its protein-export system gave rise to the T3SS. It is also possible that both evolved in parallel from a common ancestor. 6

Possibilities? He is talking about possibilities? This is supposed to be a scientific explanation, not speculation! Notice that all three possibilities presuppose that evolution is even possible.

There is no evidence to support the first possibility, that T3SS evolved from something else and somehow magically found a use in the flagellum.

The second possibility, that the flagellum evolved first, is just begging the question. He is supposed to be explaining how the flagellum could have evolved, and his answer is that the flagellum evolved and then created T3SS proteins.

The third possibility, that it somehow evolved in some unknown ancestor in some unknown way, is simply desperation.

The evolutionary events linking flagella and T3SSs are not clear, but the homology between them is a devastating blow to the claim of irreducible complexity. 7

The evolutionary events aren’t clear. No kidding! They have no idea what the supposed evolutionary events were. They simply believe by faith that there must have been some evolutionary events because bacterial flagella evolved and that is that.


They believe that homology is a “devastating blow to the claim of irreducible complexity” because they believe similarity must be the result of a common ancestor.

Taken together, this abundance of homology provides incontrovertible evidence that bacterial flagella are cobbled together from recycled components of other systems - and vice versa - through gene duplication and diversification. In other words, they evolved. 8

They won’t even consider the possibility that similarity is the result of a common designer. All these parts that work so well together were “cobbled together from recycled components of other systems” by accidental gene copying errors. It makes the “Luck of the Irish” pale by comparison! (Sorry, this newsletter was published the day after St. Patrick’s Day.)

Creationists, on the other hand, consider homology to be a devastating blow to the claim of evolution. They look at the arrangement of bones in the limbs of horses, bats and whales, and it reveals their common designer despite their very different outward appearance and function. The fact that the same solution can be used to solve so many different problems testifies to brilliant conscious effort.

Since homology can be viewed as proof for evolution, and also as proof for creation, it can’t really be proof for either.

The Million-dollar Question

Although New Scientist would like you to believe that the questions surrounding the origin of the flagellum have been solved, they do make this admission:

The million-dollar question now is this: to what extent is it possible to reconstruct the entire sequence of evolutionary events that led to the flagellum? Last year Ochman and his colleague Renyi Liu made the most ambitious push yet in this direction. … Liu and Ochman even inferred the order in which these genes evolved. Duplication and divergence, they argue, initially created the rod proteins, which in turn gave rise to the hook proteins and, finally, the filament.

Yet biologists have been quick to point out potential problems with these conclusions. One is that Ochman assigned homology based on gene sequence even when the proteins the genes code for were completely different shapes. "This is strong evidence against homology," says Pallen. "The prevailing wisdom is that [protein] structure is a better guide than sequence." Another criticism is the emphasis Liu and Ochman gave to gene duplication as the principle source of genetic novelty. While the majority of new bacterial genes arise in this way, bacteria also pick up genes by lateral gene transfer from unrelated species. Previous studies suggest that lateral gene transfer has played an important role in flagellum evolution, says Uri Gophna, a geneticist at Tel Aviv University in Israel. Furthermore, geneticists W. Ford Doolittle and Olga Zhaxybayeva of Dalhousie University in Halifax, Canada, argued that Liu and Ochman probably overlooked some documented events of lateral gene transfer (Current Biology, vol 17, p R510). 9

Ultimately, it all comes down to this:

Ultimately, though, it is unrealistic to hope to unravel every twist and turn of the bacterial flagellum's 3-billion-year-plus evolutionary journey. "That is impossible," says Doolittle. But he argues that the scientific imperative is not to reconstruct the entire process but simply to prove that the evolution of the flagellum is plausible using well-established natural processes. 10

They are never going to be able to figure out how the flagellum evolved because it did not, in fact, evolve. But for some reason (which you can surmise for yourself) it is imperative to prove that the evolution of the flagellum is plausible using well-established natural processes.

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1 Dan Jones, New Scientist, 16 February 2008, “Engines of evolution”, pages 40-43 2 ibid.
3 ibid.
4 ibid.
5 ibid.
6 ibid.
7 ibid.
8 ibid.
9 ibid.
10 ibid.