Biocomplexity article 2 and 3 for 2021

The follow-ups to Schulz’s Bio-complexity paper are now available.

The second one consists almost entirely of a description of the components and operation of a typical flagellum. As such there’s not much scope for fallacies and fantasies. There are a few noteworthy details though:

  1. The paper contains a “Future work” section. Normally this would describe the author’s proposals for follow-up research. Schulz’s “future work” section is unusual in that he describes future work for other people (evolutionary biologists, molecular biologists and molecular modellers), and can’t seem to think of anything that needs to be done from an ID point of view.

  2. Schulz quotes Cohen et al in support of the flagellum being irreducible:

The use of the knock-out experiments in hampering operation of the flagellum to identify protein functionality suggests the generally irreducible nature of the flagellum. Cohen et al. state:
The bacterial flagellum exemplifies a system where even small deviations from the highly regulated flagellar assembly process can abolish motility and cause negative physiological outcomes. Consequently, bacteria … [possess] robust regulatory mechanisms to ensure that flagellar morphogenesis follows a defined path, with each component self-assembling to predetermined dimensions.

Quoting the first sentence of the abstract immediately raises doubts about whether the citer read the whole paper, especially since the paper has got nothing to do with any irreducibility, but is about how the flagellum components become correctly sized. There’s also that suspicious use of [bracket]s. Cohen et al didn’t say that bacteria possess robust regulatory mechanisms, they say

…bacteria have evolved elegant and robust regulatory mechanisms…

Disagreeing with the cited authors’ views is ok; erasing them and substituting something different is quite another thing.

  1. Having suggested that evolutionary biologists provided a scenario for stepwise evolution of flagella and then claimed that “the evolutionary biological community has yet to hypothesize a likely, detailed, step-by-step scenario to explain how the flagellum and its control system could have been blindly engineered naturalistically” it’s (not in the least bit) surprising to find that Schulz has not cited a single one of the published papers that are tackling this question - not Pallen/Matzke, nor Liu/Ochman, nor anything else. Not even to say why those papers fall short. It’s as if he doesn’t want his readers to think there has been any such work. I’d reject Schulz’s paper immediately for that omission.
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Interesting–saying the quiet parts out loud. It may be useful to cite when pointing out ID unwillingness for (or fear of) testing hypotheses.

Exactly, for two instances of obviously unethical practices, as well as the falsehood in the first two words of the abstract–calling a review a study.

One would not even need to get into the problems with the author being wrong.

The conclusion is hilariously bad:

Can any partial implementation of a motility system be even slightly advantageous to a bacterium?

Yes, relative to its relatives.

Examples of a partial system might lack sensors, lack decision logic, lack control messages, …, or lack redirection means.

Advantages conferred by those 4 seem painfully obvious to me. I suspect that after I finish my morning coffee, I can almost as easily come up with advantages for the 3 that I elided with the ellipsis.

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Completely gives up the game. Not even making a pretense of participating in the scientific process. Just throwing stones.

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A quick scan through part 3 shows that it can effectively be reduced to this extract:

What seems incredible is that mindless, random mutations could ever innovate and instantiate any coherent, intricate functionality beyond trivial modifications to existing functionality.

There are a lot of questions with no attempted answers, such as this quote from Aizawa (2009) “What is Essential for Flagellar Assembly?” from “Pili and Flagella: Current Research and Future Trends”, Ken Jarrell, ed.:

“Since the flagellum is so well designed and beautifully constructed by an ordered assembly pathway, even I, who am not a creationist, get an awe-inspiring feeling from its ‘divine’ beauty…. However, if the flagellum has evolved from a primitive form, where are the remnants of its ancestor? Why don’t we see any intermediate or simpler forms of flagella than what they are today? How was it possible that the flagella have evolved without leaving traces in history?”

and a subsequent comment: “Indeed, Aizawa’s three questions above still stand unanswered.” Alas, I can’t find the full text of Aizawa, so can’t check whether Aizawa answered them anywhere in the pages following that extract.

Oh, and of course the now expected plea that “the challenge to the evolutionary biological community is to hypothesize some putative detailed, step-by-step scenario to explain how the flagellum and its control system was blindly engineered naturalistically” while not discussing any of the published papers that are attempting to do just that.

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Good catch.

It is bad enough to quote mine by taking out of context. This is worse. An ellipsis is usually placed and legitimate to join relevant parts of a paper which are separated by supporting detail and references to other parts of the paper, so one does not wind up lifting the whole work. Integrity demands that the quoted parts reflect the author’s overall intention. Here, the ellipsis is completely unwarranted as it does not at all shorten the quote. Nothing here is excised, but only substituted. Schulz just wanted to get rid of the word “evolved” while adducing support from scientific literature. This kind of tampering is dishonest.

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If/When biologists do provide a step-by-step scenario, there is still nothing to be learned about design, only that The Designer may have done it this way. Design cannot be falsified by testing hypothesis about evolution.

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Not really. Just playing the odds.

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Yeah I would agree the brackets thing is bad form. However, it could be simply that he is trying to interpret the word “evolved” for future readers since evolution will soon occupy the dustbin of history.

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Nice try, but one doesn’t interpret by omission.

“In the next five years, molecular Darwinism—the idea that Darwinian processes can produce complex molecular structures at the subcellular level—will be dead. When that happens, evolutionary biology will experience a crisis of confidence because evolutionary biology hinges on the evolution of the right molecules. I therefore foresee a Taliban-style collapse of Darwinism in the next ten years.”

Touchstone, volume 17, issue 6, pages 60-65

Dembski wrote that gem of a prediction in 2004. :rofl:

Of course, Dembski is showing his cluelessness about evolutionary biology, as neutral, non-Darwinian evolution had been a major part of it for a mere 36 years before he wrote that.

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I’m a bit amused by the expression “Taliban-style collapse” in that Dembski quote. That may have aged poorly. His people sure did a number on the Taliban, didn’t they? No Taliban any longer, no sirree.

Now, the comparison doesn’t work in all dimensions. Much as I strain to find similarities between evolutionary biologists and the Taliban apart from their shared immunity to Dembskiism, I can find no derived similarities – only the shared characters of humanity itself. But perhaps being a Talibangelical himself, Dembski thought that this would be a helpful verbal diversion.

Alas, at least for the Talibangelicals, their highest and best intellectuals, of whom Dembski surely is one, are simply not that bright, and not fit to wash the glassware of those who are. And so their prophecies, like their science, are bound to be of this character, seen through a glass dirtily.

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Since that could (and should) be done without deleting the word “evolved”, by quoting the passage as “Consequently, bacteria have evolved [i.e. they possess] elegant and robust regulatory mechanisms…”, Schulz would still be guilty of unethicalness.

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While I’m not particularly enamoured of Dembski, comparing him to violent murderous technophobic ecological pet-killers seems extreme.

Well, perhaps. But when I use the word “Talibangelical” I generally mean something more like a reference to a desire for enforcement, within our society, of a set of extreme orthodox views. And I think that was what Dembski was implying, too, in comparing the imminent fall of evolutionary biology to the fall of the Taliban: he thinks of evolutionary biologists as enforcers of a quasi-religious orthodoxy. And the amazing thing about Dembski is that that’s not the silliest thing he’s ever thought.

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This would be the same Dembski who was forced to recant at one of his last teaching jobs because he wrote something that just vaguely hinted that the story of Noah’s Ark just might be something other than an absolutely accurate historical account. But, right, it is the evolutionists who are doctrinaire enforcers of ideological purity.

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