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The Darwin Wall Still Stands; but for How Long?

Photo: Berlin Wall, by Noir, CC BY-SA 3.0 , via Wikimedia Commons.

Picture a city in which the city council has a super-majority in one political party. Those in the majority control the media outlets as well. Suppose they decide to flex their muscles and forbid any statements from the other party to be heard without having the right to filter them first. In this way, they keep the minority party in a virtual sound-proof room behind one-way glass. The majority leaders can hear the minority speaking, sometimes shouting to be heard, but nobody in the city can hear them because they are censored. Once in a while, the majority mentions something that the minority has complained about, but translates it for the media, and only responds with their own counterarguments. The minority can’t do anything about it because they lack the power, the communication channels, and the votes to change anything. Would this not be a case of totalitarian dictatorship?

Darwinians are like that. They control the narrative on origins in almost all the mainstream journals, the schools, the state universities, the national parks, and the natural history museums. The mainstream media join in and take their side. A few exceptions can be noted, but the influential, powerful forces in academia all toe the Darwinian line. Science reporters accept their pronouncements as gospel and regurgitate them to the public, masticating them first into easily digested tidbits with sugar and spice. Professors open to ID know to keep quiet unless they have tenure, and even that is not a guaranteed protection from harassment or censorship.

A Forbidden Phrase

In a paper in Nature Communications, the forbidden phrase “irreducible complexity” appeared in scare quotes. It was mentioned not for the purpose of considering it fairly, but for shooting it down immediately with a preemptive strike. It was mentioned in an essay about the Type III Secretion System (T3SS) and its alleged evolutionary relationship to the bacterial flagellum. Here’s the quote:

The bacterial type III secretion system (T3SS) is an impressive biological machine known not only for its importance in bacterial virulence (1,2) but also, due to its evolutionary relationship to the bacterial flagellum, for its role in the negation of the ‘irreducible complexity’ of flagella (3). In their recent publication (4), Kaval et al. present new data on the process of expression, production, and assembly of a T3SS (termed T3SS2) in the bacterium Vibrio parahaemolyticus…. [Emphasis added.]

Did authors Itzhak Fishov and Sharanya Namboodiri cite Michael Behe’s work? No; they didn’t even mention his name. Reference 3 points to another Darwinist paper that presumably negates Behe’s argument. With a quick flick of the wrist, they eliminated what could have been a lively discussion about the said “evolutionary relationship” between the T3SS and the flagellum. Like the dictatorial city council, it wouldn’t matter how loudly Dr. Behe might shout his objections to the statement from the sound-proof room behind the one-way glass, he could not be heard in this leading journal, because he is a well-known “enemy of the regime” in Darwin Party circles. This insult against a tenured professor was peer-reviewed and published by Nature. I didn’t find any popular science article about this paper, but one can assume a reporter would obediently take the dictation and regurgitate it like, “the T3SS is a molecular machine whose evolutionary relationship to the bacterial flagellum squashes the unscientific notion of ‘irreducible complexity’ promoted by some religious fanatics.”

Let’s Dig into This a Little

Does Reference 3 negate Behe’s argument for irreducible complexity? I read the paper in Molecular Microbiology by Bailey Milne-Davies, Stephan Wimmi, and Andreas Diepold from November 2020. If one screens out the arguments by assertion, the answer is clearly no. By assertion, I mean statements like this:

Bacteria do not live in isolation. They constantly interact with and often actively move through their environment. Interestingly, in many cases, a single evolutionary ancestor evolved to meet both requirements, protein export and locomotion….

The T3SS is at the core of both the bacterial flagellum, a rotary motor that is the most widely distributed means of bacterial locomotion (Miyata et al., 2020), and the injectisome, a molecular injection device used by many Gram-negative bacteria to manipulate the eukaryotic host cells. Both systems harness ion gradients across the membrane to export the subunits of their extracellular appendages. While the flagellum then rotates this appendage in order to propel the bacterium through the surrounding medium, the injectisome evolved to specialize in protein export, specifically the translocation of effector proteins into eukaryotic host cells.

Talk about begging the question. From there, the three authors list proteins common to the T3SS and flagellum (as if this demonstrates common ancestry), but they also point out many unique proteins in the flagellum. 

Although the proteins that form the cytosolic complex in the flagellum and injectisome display clear sequence homology, the function and quaternary structure of the cytosolic complex strongly differ between the two machineries. On the distal side, flagella assemble a hook and the long flagellar filament, while injectisomes form a hollow needle. Beyond this core of proteins, the flagellum has additional components that form a bushing for rotation in the periplasm (L-/P-ring), and stator proteins that serve as an anchor in the rigid peptidoglycan, against which the rotor can rotate, powered by the influx of ions (Figure 1 and Table 1).

Where did those come from? They evolved. Enough said. They share components, don’t they? What more proof do you need? 

Here’s where they mention irreducible complexity without attribution.

The T3SS is one of the most complex bacterial molecular machines, incorporating one to over a hundred copies of more than 15 different proteins into a multi-MDa transmembrane complex (Table 1). The system, especially the flagellum, has, therefore often been quoted as an example for “irreducible complexity,” based on the argument that the evolution of such a complex system with no beneficial intermediates would be exceedingly unlikely. However, it is now clear that, far from having evolved as independent entities, many secretion systems share components between each other and with other cellular machineries (Egelman, 2010; Pallen and Gophna, 2007).

So if a Porsche and a Chevy both have door handles and steering wheels, the former clearly evolved from the latter. Is that the depth of reasoning here?

Most of the paper involves similarities between protein machines. These protagonists on the one-sided debate stage smother the reader with similarities. They knock down their straw-man interlocutor by misconstruing his argument. As usual, they mis-define IC and ID with the boilerplate definitions that these machines are so complex, their evolution is “unlikely.” The true ID definition is that irreducibly complex systems are “best explained by an intelligent cause, not an undirected process such as natural selection.” IC systems are composed of a number of independent parts, each necessary for the function of the system.

Even with their media advantage, the authors in Reference 3 admit, “the exact evolutionary relation between injectisomes and flagella is debated.” Species with supposed intermediate forms are proposed, but they look to me like broken T3SS or flagella, not machines evolving into each other. They wave the co-option argument and engage in possibility thinking, with 14 instances of the word “possible” to suggest what might be evolving.

Evolutionary Magic

Finally, they land on their trusty magic wand, convergent evolution: “Besides the general diversification of both systems, a case of convergent evolution of flagella and injectisomes was recently discovered.”  Their final summary turns evolution into a magician, and personifies bacteria and molecular machines as if they take conscious charge of their own evolution:

Evolution allows adaptation of a functional concept to many different needs. In this review, we highlighted the amazing capability of the T3SS to vary its components, structure, and function to the specific requirements of bacteria in different ecological niches and under changing external conditions. Flagella not only ensure motility in a variety of environments, but also play an essential role in pathogenicity. By modifying their flagella, bacteria can find suitable colonization sites and enhance attachment to surfaces, which can increase infection success. In the same light, the injectisome permits the bacterium to exploit host cells for promoting infection, whether by controlling immune responses or establishing suitable sites for dissemination. Together these systems work to promote bacterial survival in constantly changing environments. Beyond these adaptations, it has become clear that the T3SS is a dynamic structure, with subunits exchanging in working complexes. Given the limited number of studies on protein exchange in the T3SS, it is possible that more cases of dynamic components will be discovered and that the benefits for the bacteria will become clearer. Research on how bacteria can adapt and evolve virulence mechanisms such as the T3SS will not only allow to better understand how bacteria and their environment interact, but also uncover potential ways to combat pathogenic bacteria by targeting their T3SS.

This is known as cheating. The whole point of Darwinian evolution was to rid biology of teleology. Irreducible complexity is ignored other than the one swipe at the straw man. Only once do they demonstrate loss of function from an essential part: “Although most flagellins are partially functionally redundant, deletions of additional flagellins negatively affects flagellar formation and function.” Nowhere do they point to random mutations able to innovate essential proteins to build a flagellum or T3SS in the first place.

Behind the one-way soundproof glass, Casey Luskin is waving his article (also here) on why these machines could not have evolved from one another, and Michael Behe is giving his debate rebuttal unheard by the audience. 

Censorship Is a Doomed Strategy

In my experience as a science writer, I have never in 22 years seen a Darwin-orthodox journal or science news site take ID arguments seriously. If mentioned at all, they are mis-defined and immediately dismissed. The science establishment, consisting of academic deans, lobbyists, and journal editors, pretty much treats the thriving ID community like it doesn’t exist. 

On the bright side, one can always tell who is on the wrong side of history. It’s the totalitarians — the ones who try to stifle debate and censor those not friendly to the regime. We can take heart that experience shows that Berlin walls are erected to fall. They have finite lifetimes. Not everyone in East Germany agreed with the regime, but they were powerless, and many were scared. If we stay the course, and continue to influence individuals, we will undoubtedly find many behind the Darwin Wall welcoming a path to freedom of thought.