In three previous articles (find the full series here), I offered a response to YouTuber Dave Farina’s criticisms of my defense of biochemist Michael Behe’s work. In this fourth installment, I will interact with Farina’s criticisms of my previous discussion of the bacterial flagellum. As I noted in my first article in this series, Farina had previously claimed that scientists had observed a flagellum evolve in real-time. I documented in a previous article (the one to which Farina is supposedly responding) that Farina had completely misinterpreted the paper. Rather than acknowledge correction, however, Farina chose to entirely drop this point in his most recent response.
In any case, let us review what Farina did in fact say in response to other aspects of my critique.
Is Machine Language Used in the Technical Literature?
Farina remarks,
Let’s move on to part two, which is about the bacterial flagellum, the honorary mascot of intelligent design. He starts by whining about how I identified the persistent tactic of using terminology related to man-made machines to describe biological systems, to manipulate the viewer into believing these systems were designed. Predictably, Jonny says that everyone talks like this!
This is not a “persistent tactic” intended “to manipulate the viewer into believing these systems were designed.” The use of machine language to describe biological systems is standard in the scientific literature. Farina alleges that,
People who aren’t pushing propaganda typically refer to these structures by saying “acts as a drive shaft,” or “molecular ‘clutch’” using quotation marks, to distinguish from a literal clutch. The functions are analogous. There have been numerous papers written to push back against this analogy of cells as machines…
To take but a single example, one paper is titled “Structural basis of the bacterial flagellar motor rotational switching.”1 Here, the term “motor” is used without qualification or quote marks. The same paper states that “The motor is a bidirectional rotary nanomachine” and “the hook functions as a joint that connects the motor to the filament, which acts as a propeller to propel bacteria for swimming in liquid medium and swarming on solid surface. The motor spans both the inner and outer membranes, and consists of the basal body and several stator units.” Moreover, “The LP ring acts as a bushing to stabilize the rotation of the rod, which serves as the drive shaft.” Examples of such language in the literature could be multiplied almost endlessly. That Farina is not aware of this indicates his lack of familiarity with the scientific literature.
In Defense of Behe and Snoke
Farina continues,
But here’s the big whiff for this one. I had taken Behe to school for a paper he wrote with David Snoke where he pretended that his simulation demonstrated the improbability of irreducibly complex traits arising. Here’s Jonny’s response: “Finally, Farina complains that ‘They also specified a pre-determined target sequence and only considered the simulation to have been successful if that specific target evolved.’ But this is incorrect. Rather, the paper provides estimates for how many organisms would be required, and over how long a time frame, for multiple co-dependent mutations (none of which by themselves confers an advantage) to become fixed in a population.” See what he does there? He states the critique, and then says something completely irrelevant. His response does not in any way address the critique.
But Behe and Snoke’s simulation does not assume a single magic sequence. Rather, it estimates the time required for the fixation of coordinated changes, where neither of the mutations by itself confers an adaptive advantage. Farina continues,
That does not refute what I said. It is objectively true that Behe and Snoke specified a target sequence, something that Jonny doesn’t even try to dispute, and that alone invalidates their conclusion, since evolution does not work that way. There are no predetermined goal sequences. Nature is not sentient.
The point of the paper, though, is to evaluate the time needed to evolve a new functional interaction that requires multiple specific mutations in multicellular organisms.
Farina goes on,
We have directly, experimentally demonstrated that there are usually many sequences that will do a specific job approximately equally well. For example, a 2018 study found that among random strings of 100 nucleotides, many will function as a promoter in E. coli, some equally as well, or even better than, the wild-type sequence. So setting a predetermined target to determine how fast or slow, or how likely or unlikely something is to evolve completely invalidates whatever conclusion you reach, period.
Farina’s Extremely Weak Argument
This is an extremely weak argument, and it’s not applicable to Behe and Snoke’s paper. First, they specifically looked at evolution in multicellular organisms, not bacteria. So any examples from E. coli bacteria don’t address the paper’s arguments. Second, promoters are relatively simple sequences that recruit RNA polymerase and basic transcription factors. They are short and many different sequences can do the job. A functional promoter is relatively easy to find in sequence space. On the other hand, protein-protein binding interfaces require highly specific and complementary shapes. A random DNA sequence is far more likely to weakly promote transcription than two proteins are to randomly evolve a new binding interface.
In the next installment in this series, I will offer a response to Farina’s criticisms of my previous defense of The Edge of Evolution.
Notes
- Tan J, Zhang L, Zhou X, Han S, Zhou Y, Zhu Y. Structural basis of the bacterial flagellar motor rotational switching. Cell Res. 2024 Nov;34(11):788-801. doi: 10.1038/s41422-024-01017-z. Epub 2024 Aug 23. PMID: 39179739; PMCID: PMC11528121.