Taking on Behe’s Challenge: Evolve Me a Cilium

Evolution News & Views


In Darwin’s Black Box (1996) and again in The Edge of Evolution (2007), Michael Behe challenged the scientific community to explain irreducibly complex molecular machines, like the cilium and bacterial flagellum, in Darwinian terms. The eukaryotic cilium, especially, represented “irreducible complexity squared,” he said, with further research showing a complex transport system, Intraflagellar Transport (IFT), acting like a system of “freight cars” at a “construction site,” moving cargo up and down the cilium with forward and reverse motors. His first literature search in 1996 showed “only a few attempts” to Darwinize the cilium. By 2007, nothing had changed:

An updated search of the science journals, where experts in the field publish their work, again shows no serious progress on a Darwinian explanation for the ultracomplex cilium. Despite the amazing advance of molecular biology as a whole, despite the sequencing of hundreds of entire genomes and other leaps in knowledge, despite the provocation of Darwin’s Black Box itself, in the more than ten years since I pointed it out the situation concerning missing Darwinian explanations for the evolution of the cilium is utterly unchanged. (Behe, The Edge of Evolution, p. 95)

A footnote there observes, “But there is never a shortage of Darwinian conjecture.” Behe cited a “hypothesis” by Jekely and Arendt (2006), which suggested that intraflagellar transport evolved from pre-existing vesicle-coating systems. That paper, Behe complained, offered only speculation, suggestions and possibilities, leaving more questions than answers. 

Could Be a Contenda

Now, a team of scientists in the Netherlands has sent another contender into the ring. In an open-access paper in PNAS, “Evolution of modular intraflagellar transport from a coatomer-like progenitor,” Tuenis van Dam and six others make audacious claims in the introduction and again in the conclusion:

Here, we have reconstructed the evolution of the IFT complex in detail, and provide phylogenetic evidence that the IFT complex is indeed a sister structure to COPI [coat protein complex I]…. 

Our phylogenetic reconstruction provides compelling evidence for functional as well as structural modularity with in the IFT complex. Furthermore, the complex evolution of the IFT and its origin from a protocoatomer complex provides a keystone for understanding how the eukaryotic cell was able, by repurposingexisting pathways and complexes, to evolve such a complex and highly organized organelle as the cilium. (Emphasis added.)

The contest is on! Will they do better than Jekely and Arendt, whom they cite in the references? Will they indeed show how blind, undirected processes produced an irreducibly complex molecular machine? (We wouldn’t expect them to mention Behe or the term “irreducible complexity” — which they don’t — but their reference to “such a complex and highly organized organelle as the cilium” implies they understand the challenge.) 

Time Out

Several problems appear immediately in the passages cited above. First, they are only going to talk about a “phylogenetic reconstruction” — i.e., comparison of gene sequences, to try to build an “evolutionary scenario,” assuming common ancestry of the coating complex and IFT. They are not going to get into which mutations led to functional order. In fact, they just assume that the functional order somehow emerged. They used the word “emerge” six times. Here it is twice in one paragraph:

With respect to origins and acquisition of the IFT system, our results suggest that the BBSome and IFT-A emerged from an IFT-B-like complex by intracomplex duplications. Whether the IFT-A or the BBSome was the first additional subcomplexto emerge is unresolved at this time.

Similar question-begging words like “arose” or “the acquisition of” shield the authors from having to actually explain the cilium’s origin by natural selection. Why, it just appears! A caption in Figure 5 of the paper reads, “Invention of the cilium.” Imagine that! 

A second problem, shown by their reference to “structural modularity,” is that they speak of the cilium’s IFT system in gross terms. In this paper, it’s little more than a collection of “modules.” The main subcomplexes are designated IFT-A, IFT-B and the BBSome. These primary modules, though, are composed of multiple protein parts (in humans, 7, 17, and 10 respectively), each of which Behe describes as comparable in complexity to hemoglobin (Behe 2007, page 90). In their paper, van Dam et al. illustrate these proteins as cartoony colored balls. Elsewhere, they show amino acid sequences, or portions of protein folds within some of the subunits, but only briefly in the introduction do they explain what the cilium does and how it is composed of interrelated working parts. They say nothing about the “freight cart” operations Behe described.

A third problem visible right off the bat is their reference to “repurposing existing pathways and complexes.” This is the old co-option argument. One has to assume that the cell already had complex, functioning organelles and pathways that were somehow “repurposed” or “co-opted” for IFT. Did you catch the contradiction in these speculations, as if a cell decided to do this? There is no purpose in Darwinism, yet they say “the cell was able…to evolve” a complex and highly organized organelle.

Co-option as an evolutionary strategy was dismantled in the Illustra film Unlocking the Mystery of Life. Scott Minnich explains that if Darwinian evolutionists want to account for the origin of every molecular machine as having borrowed parts from some other machine, eventually you are left borrowing from nothing. Even more significant, he continues, is accounting for the assembly instructions for the machine. Those are even more irreducibly complex than the machine itself. Jonathan Wells remarks, “It’s irreducible complexity all the way down.”

Ignore Those Proteins Behind the Curtain

What you find in the PNAS paper is basically this. They selected 21 of the 33 protein parts from the three IFT modules, “based on homology relationships,” and did a sequence search. Whoa, hold on there! That’s assuming what needs to be proved. (More on homology in a bit.)

This classification was based on sequence similarity of IFT subunits to the COPI-α and-β′ subunits, further supported by secondary structure predictions. However, a full phylogenetic reconstruction and structural analysis of the IFT complex has not been performed.

They weren’t about to perform one, either, in this paper at least. To make the problem more manageable (instead of having to explain a whole working cilium), they pared the data set down even more. When some of the domains “prevented unambiguous alignment” of sequences, they ignored all but two subunits for comparing. From those, they searched for a sequence common between COPI and IFT, finding one about 150 amino acid units long that “aligned consistently without the need to insert long gaps into the alignment.” How’s that for cherry picking? In other words, they only examined data that already fit their evolutionary hypothesis. What about the other 12 proteins that do not share sequence similarity with COPI? The flippancy with which they dismissed potential contrary evidence is breathtaking:

The remaining IFT subunits (Fig.1A, white) do not share any detectable sequence relationships with each other, or with any other proteins. Hence, as they do not contain any phylogenetic information on the origin of the IFT complex, they will not be further discussed.

Translation: since the other subunits do not fit our story line, we will ignore them. Arguably the most important question is, how did those other unique proteins, with no sequence relationships with any other proteins, “emerge” by a Darwinian process? 

In Signature in the Cell, Stephen Meyer cited Doug Axe’s work on the probability of getting one protein by chance. “The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebiotic soup,” he wrote, “is no better than 1 chance in 10164 ” (Meyer, p. 212). That staggering improbability is so inconceivably low, it would never happen in the entire universe. It doesn’t matter if you’re trying to get a protein to “emerge” in a prebiotic soup or a Darwinian cell: unguided processes are unguided processes. Evolutionists cannot invoke purpose, goal, or natural law, as Meyer explained. The unique proteins defy evolution from the starting gate. No wonder van Dam and team say, “they will not be further discussed.

Tricks of the Trade

The paper’s thesis boils down to the old homology argument. Jonathan Wells discussed this at length in Icons of Evolution (2000). It’s a fallacy of circular reasoning: “a vicious circle: Common ancestry demonstrates homology which demonstrates common ancestry” (Wells, p. 63). Evolutionists pick similarities that fit their evolutionary story and call them “homologous,” but reject similarities that don’t fit the story, calling them “analogous.” In their Supporting Information file, we find van Dam et al. using that old Darwinian trick, calling non-homologous parts “convergent”:

The origin of BBS4 and BBS8 from an ancestral e-IFT subunit argues against an independent origin of the BBSome and IFT as coatomer-like complexes, and argues instead for convergent evolution of the structures of the BBS1, -2, -7, and -9 subunits to resemble the coatomer β-propeller structure.

In other words, those proteins are analogous, not homologous. As if that helps. Now, they have to account for four independent origins converging on the same structures. Sorry; they used up their probabilistic resources long ago, trying to gloss over the origin of 12 unique IFT proteins. There aren’t any left for this tale. 

Another trick is to invoke language like “proto-IFT complex” and “protocoatomer” that embed evolutionary assumptions in their terminology. Where did IFT come from? From proto-IFT, of course. With tricks like that, Darwinism can’t lose.

Progress Through Loss

The most illuminating section of their paper concerns IFT loss, not gain. They discuss how seed plants and most fungi lack cilia entirely, but some fungi and protists get by with only part of the IFT set. It appears, for instance, that the BBSome, which packages proteins for the freight cars, is not essential. A fungus, a moss, a lycophyte and some parasitic protists have cilia without it. (Note: “flagellum” is often used as a synonym for “eukaryotic cilium” but is unrelated to the bacterial flagellum.)

This pattern of BBSome loss thus appears to precede the loss of the cilium, and may indicate a reduced role for cilia in BBSome-negative lineages before the cilium is lost entirely. The existence of multiple species with functional flagella, but lacking the BBSome, suggests that the BBSome is a nonessential component of IFT…. 

Disrupting the expression of BBSome subunits has profound effects on the other IFT complexes. BBSome dysfunction results in instability and incorrect assembly of the IFT complex, resulting in dissociated IFT-A and IFT-B complexes. This suggests that there is functional interaction between the BBSome and IFT-A and B. However, from our analysis, it appears that the removal of the BBSome can be tolerated in some species, indicating that this functional interaction must be nonessential. It will be interesting to understand how species compensate for lossof the BBSome, and what evolutionary steps are required to facilitate that loss.

They point out that Bardet-Biedl Syndrome, a severe genetic disease in humans that leads to many problems as diverse as obesity, night blindness, kidney failure, and dental crowding, is the result of BBSome malfunction. Sufferers of this “ciliopathy” can live and produce viable offspring. That doesn’t mean they are making evolutionary progress. 

For the other organisms that “tolerate” BBSome loss, the researchers ask a fair question: how do they compensate? Would they be better off with the BBSome? That might be a good project for ID research. Trypanosomes even get by without IFT-A, leading them to postulate that “IFT-B could be viewed as the most critical subcomplex, as it is the last to be retained, and hence its presence essentially dictates if a cilium is present.” Such observations might provoke another ID project: what is the extent of a cilium’s irreducible complexity? The Darwinian team errs, though, by assuming “evolutionary steps are required to facilitate that loss” of the BBSome or IFT-A. That’s nonsense; requirements are written by intelligent designers.

Concession Stand

The authors make admissions that argue against their hypothesis. For instance, they concede that conservation (not evolution) is so pervasive, it’s “remarkable”:

The orthologous IFT and BBSome subunit sequences are well conserved, despite the large evolutionary distances between them, and despite the variable presence of the subunits per species…. The high similarity between the predicted secondary structure elements suggests that the orthologous proteins in the IFT complex arestructurally conserved to a remarkable level.

They did find sequence variations. They did outline possible patterns of loss in various lineages. But those are not the big issue. Mutations or substitutions that do not affect the structural operation of IFT might be tolerated. But clearly, an intact cilium with all the components working is optimal. Some boaters can get by with oars or hand paddling when the outboard motor is broken or sputtering. How the motor got there is the big question. For that, van Dam et al. make a huge concession that undermines their whole Darwinian tale:

All the subunits reported for the human IFT complexes are conserved throughout the eukaryotic lineage. Therefore, IFT-A, IFT-B, and BBSome werelikely present in the last eukaryotic common ancestor (LECA) and comprised all currently known IFT subunits from human and Chlamydomonas reinhardtii, in agreement with earlier observations.

Let’s get this story straight. Once upon a time, a complete, working cilium with all the correct components, and with all the right genetic assembly instructions, just “emerged” in some mythical common ancestor. Maybe evolution “repurposed” some protein-coating genes after a mistake duplicated them. However it happened, all those parts were “conserved” the rest of the way, from simple one-celled Chlammy to complex trillion-celled Sammy. During evolution, some branches of the eukaryotic tree lost some parts, but the ones that didn’t die are getting along OK. 

This proves Darwinism can explain “such a complex and highly organized organelle as the cilium.” Take that, Dr. Behe!

Final Score

We can predict Behe’s yawning response to the new “Darwinian conjecture” in this paper: “in the more than [now 17] years since I pointed it out the situation concerning missing Darwinian explanations for the evolution of the cilium is utterly unchanged.”




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