As I wrote here last week, biophysicist Matt Baker recently published an article at the Australian Broadcasting Corporation website, “The bacterial flagellar motor: brilliant evolution or intelligent design?,” arguing against Michael Behe and the intelligent design of the flagellum. Behe first offered his argument for ID based on irreducible complexity (IC) in his 1996 book Darwin’s Black Box. In the intervening couple of decades, Darwin defenders have offered the same assortment of ineffectual replies, again and again. Now there comes along Dr. Baker, who has very little that’s new to say. I’m taking the time to answer him because these objections, while unconvincing, are such hearty perennials.

He thinks he’s found one main flagellar component that can function outside the flagellar system and that this refutes irreducible complexity. It’s nothing new to ID proponents. It’s called the Type III Secretory System (T3SS) and it’s basically a pump that’s used to transport proteins across the cell membrane of bacteria. Baker frames his case this way:

Proof of the flagellar motor’s ‘reducibility’ — that its component parts can function elsewhere — comes in the form of the injectisome; another fabulous molecular machine found in bacteria. This needle-like complex is used by disease-causing bacteria to punch holes in the host’s target cells.

The protein machinery used to assemble the proteins that make up the punching needle is identical to that used to assemble the ‘propeller’ part of the flagellar motor — the filament and hook of the motor. In addition, nine core proteins of the flagellar motor share common ancestry with injectisome proteins — the genes that code for them are so similar they have clearly come from the same genetic ancestor.

This argument is so old that it was already dealt with and refuted in the 2003 ID documentary Unlocking the Mystery of Life.

So in the interest of accuracy, let’s reframe Baker’s argument for him. Part of the flagellum is a molecular pump, the T3SS, which is used to pump proteins from inside the cell to the outside of the cell where they self-assemble into the flagellum. The injectisome uses the T3SS for a similar function — it is involved in both assembling the injectisome and in the injectisome’s function.

The injectisome is used by certain predatory bacteria to inject toxic proteins into eukaryotic cells, which then kill the eukaryotic cells so they can be ingested by the bacterium. It’s just a molecular pump; that’s it.
Baker suggests that the injectisome’s proteins are “identical” to the “flagellar motor” but the T3SS isn’t actually part of the motor portion of the flagellum. It’s only part of the pump that is used during flagellar assembley, which then also serves as the basal body that anchors the flagellum in the cell membrane.

Nor is it the case that these proteins are “identical.” I’m quite willing to grant that some proteins between the T3SS and the flagellum appear homologous, but it’s certainly not correct to call them “identical.” One authoritative paper by Pallen and others in 2005 suggests that a flagellar protein (FliK) and a protein from the T3SS (YscP) are “homologous” because, across a stretch of about 58 amino acids within their 300 or so amino acids, 13 residues are identical in at least 50 percent of the proteins studied, and another 23 amino acids within that stretch have similar chemical properties. (See Pallen et al. (2005), Figure 4.) That means that less than 25 percent of the amino acids are identical across a stretch that represents less than 20 percent of the total protein. While the proteins are clearly similar — perhaps very similar — and probably homologous, it’s misleading to say they are “identical.”

But let’s say they are identical — it doesn’t really matter. In fact let’s grant that nine of the proteins in the T3SS of the injectisome are identical to the proteins of the T3SS used by the flagellum. Does this constitute an evolutionary explanation? No, for many reasons.

First, at most the sequence similarity can establish, as Baker puts it, that “they have clearly come from the same genetic ancestor.” But Michael Behe is quick to remind us why establishing common ancestry is different from establishing a Darwinian explanation:

• “Although useful for determining lines of descent … comparing sequences cannot show how a complex biochemical system achieved its function — the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter. … Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?” (Behe, Darwin’s Black Box, pp. 175-176.)
• “[M]odern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation.” (Behe, The Edge of Evolution, p. 95.)

Second, it’s doubtful that the T3SS is useful at all in explaining the origin of the flagellum. The injectisome is 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 the injectisome arose after eukaryotes. However, flagella are found across the range of bacteria, and the need for chemotaxis and motility (i.e., using the flagellum to find food) precede the need for parasitism. In other words, we’d expect that the flagellum long predates the injectisome. And indeed, given the narrow distribution of injectisome-bearing bacteria, and the very wide distribution of bacteria with flagella, parsimony suggests the flagellum long predates injectisome rather than the reverse. As one paper observes:

Based on patchy taxonomic distribution of the T3SS compared to that of the flagellum, widespread in bacterial phyla, previous phylogenetic analyses proposed that T3SS derived from a flagellar ancestor and spread through lateral gene transfers.”

(Sophie S. Abby and Eduardo P.C. Rocha, “An Evolutionary Analysis of the Type III Secretion System” (2012).)

Likewise, New Scientist reported:

One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. “The most parsimonious explanation is that the T3SS arose later,” says biochemist Howard Ochman at the University of Arizona in Tucson.

Now under normal evolutionary reasoning, one would take this kind of phylogenetic evidence to indicate that the flagellum long predates the T3SS, and that the T3SS is in no way a precursor (or closely related to a precursor) of the flagellum. But don’t expect evolutionists to use their normal reasoning when trying to oppose potent arguments for intelligent design. Here, they reject standard phylogenetic concepts like parsimony and assume that somehow the T3SS is (or is very similar to) some kind of a flagellar precursor. Normal evolutionary analysis would absolutely reject that hypothesis.

Additionally, it’s interesting that flagellar genes are always present (whether vestigial or suppressed) whenever injectisome genes are present. Thus, the injectisome is always found with the flagellum, but not vice versa. Again, this implies the injectisome has an origin that postdates the flagellum, and that it may even be derived from the flagellum.

So the evidence strongly suggests that the injectisome (or something like it) did not predate the flagellum, and thus can’t help explain how the flagellum evolved.

Finally, there’s the fact that the function of the T3SS (whether in the injectosome or in the flagellum) really has nothing to do with explaining the propulsion function of the flagellum. Again, the T3SS is just a pump that can move proteins across the cell membrane. It doesn’t in any way explain how the flagellum motor and its core propulsion function arose. I like how William Dembski captures the essence of the logical and empirical flaws in the T3SS argument:

[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 [Type III Secretory System] 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.)

Given that Baker nowhere tries to provide any kind of a stepwise explanation for the evolution of the flagellum, he certainly has not met his standard of proof nor has he met Dembski’s challenge.