Different kinds of gaps

Faith & Science Conversation
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Speaking of gaps, I do not agree that the bootstrapping challenge of abiogenesis applies to evolution of keratin and the eye and so forth. The family tree distribution of keratin conforms well to the emergence of dinosaurs from prior vertebrates, and birds from prior dinosaurs. Novelty is expected under evolution, and by definition will be absent in earlier forms. That is not something awkward or embarrassing in the history of life.

Certain biomolecule families, such as keratins, opsins, and chitins, are adaptable in that small changes yield significant differences in utility. Birds utilize keratins in beak, claw, and feather, for specializations of feeding, predation, flight, mating, and warmth.

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Dear Matthew, I am a microbiologist with scientific papers in the field of microbiology. The only thing, I ask for is evidence that meet common scientific standards. However in this discussion from the evolutionist side, until now, I have not seen any scientific argument.

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Yes you have. Scientists are rational, or rather science is; rationality, of course, transcends mere empiricism.

There is no rational, let alone scientific, argument for irrationality.

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Okay, that’s cool. What does that mean to our discussion in this context? I would guess there are maybe a few options here (feel free to add or subtract from this list):

  • Given that you are a microbiologist and I am not, we should defer to your expertise and evaluation of the relevant evidence
  • Given that you’ve published scientific papers, you know the rigor that goes into them and don’t see the same thing here with bacterial flagellum
  • You, like @Leyton, see yourself as a neutral arbiter of truth in these gaps of evolutionary theory and like consider your approach to be superior to that of anything in either that BioLogos article I shared or the scientific literature

And thus what you want is:

Okay fine. Here’s a nice paper closing some of the “evolutionary gap” for bacterial flagellum. It doesn’t explain everything, but it’s a piece of the puzzle.

How did the Campylobacter- type motor evolve from a simpler ancestral motor? During our previous work, we discovered that each accessory protein is essential, posing a conundrum: how could proteins have been added stepwise to form this (naively “irreducibly complex”) motor? To identify a possible incremental evolutionary pathway, we determined a phylogeny of ε-proteobacterial and related motors, used different accessory protein occurrences to identify and determine structures of the likely descendants of evolutionarily intermediate motors found in Wolinella succinogenes , Arcobacter butzleri , and Bdellovibrio bacteriovorus. W. succinogenes is a cattle rumen commensal12,13 while A. butzleri is a human gastrointestinal pathogen12,14, similar environments to C. jejuni . The more distantly related B. bacteriovorus can be found in a number of habitats including sewage and the human gut15. Subsequent to imaging the motor structures we related their structure to mechanical output using swimming speed assays. Our results enable us to propose a model for how the Campylobacter- type motor evolved by inferring a possible scenario for the order of protein recruitment events, and the selective benefits at each step.

Or another interesting review paper in microbiology from 2020:

Over the last decade, new single-molecule and in vivo biophysical methods have allowed investigation of the stability of this and other large protein complexes, working in their natural environment inside live cells. This has revealed that in the bacterial flagellar motor, protein molecules in both the rotor and stator exchange with freely circulating pools of spares on a timescale of minutes, even while motors are continuously rotating. This constant exchange has allowed the evolution of modified components allowing bacteria to keep swimming as the viscosity or the ion composition of the outside environment changes.

Or another highlighting some other features of motor evolution,

Complementing our imaging with bioinformatics analysis, we find a correlation between the motor’s stator system and its structural elaboration. Motors with a single H±driven stator have only the core periplasmic P- and L-rings; those with dual H±driven stators have an elaborated P-ring; and motors with Na+ or Na+/H±driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts.

Or another discussing other aspects of the evolution of these nanomachines:

Bacterial flagella have evolved as highly versatile nanomachines that enable bacteria to navigate and survive diverse environments such as the mucous of the mammalian gut. Over the last decade, cryo-ET has enabled direct visualization of conservation and adaptation of the bacterial flagellum to niche environments. Cryo-EM and X-ray crystallography have led to near-atomic views of purified flagellar proteins and subcomplexes, such as the MS ring, C ring, and stator complexes. By combining these techniques, it is becoming feasible to establish nearly complete models of the flagellar motor, such as the one shown in Figure 3. High-resolution views of the intact flagellar motor not only significantly enhance our understanding of flagellar structure and assembly but also provide the basis to address fundamental questions about bacterial flagella: How does proton motive force drive the flagellar assembly and rotation? How does the flagellum switch its rotational direction? And how has the flagellum evolved as a highly diverse nanomachine?

But nah yeah, evolutionists have no scientific arguments. Many people think their approach is superior, which is probably just an argument from incredulity a lot of the time. Such “contrarian” thinkers, superior to the deceived evolutionists, are the ones who are doing real science with real standards of evidence.

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Suggested reading:

I would call that a narrowed gap.

Will we ever know the mutation-by-mutation evolution of the bacterial flagellum? Absolutely not. There are just some things buried in history that are beyond our grasp. However, I see no reason to invoke a supernatural designer just because we can’t know something. Even more, I see no reason to invoke a supernatural designer just because we can’t think of a way that something can evolve.

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There are possibly two errors in your approach.

First, you are looking at the problem from the wrong direction. What we see in modern organisms is the solutions that were found. Those are only a subset of all possible solutions. What you should be asking is how many functions are possible, not the probability of finding one specific function.

Second, you may be overestimating the rarity of function. You are suggesting that functional protein sequences are extremely rare, but are they? How have you assessed this idea?

I just did a quick Google search for “searching functional space protein sequence” and ran across this interesting paper:

They were able to find function in quite a few proteins that had a mixture of defined modules and random sequences.

They were using just 8 different amino acids, 4 that were polar and 4 that were non-polar. They were able to find active sites in 1 out of every 10,000 random sequences, even with a very simple set of amino acids.

We also have the immune system as a great example of how random sequence can produce functional proteins. V(D)J recombination randomly shuffles short bits of sequence to form the binding domain of antibodies. This produces antibodies that have high specificity and affinity for different antigens.

So the real question here is how rare is function, really?

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What confuses me as a theistic evolutionist is at some point God does not just providentially act, but must directly act with an intentional design. And yet it seems as if this is inadmissible for you.

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Inadmissible seems a bit strong.

To use another example, I wouldn’t see a reason to invoke the supernatural if there was an unsolved murder. Perhaps God may have thrown a knife from the sky which embedded into the chest of the victim. Perhaps. However, I wouldn’t see a need or a compelling reason to invoke such an explanation.

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Oh yeah, I vaguely remember discussing this with you before.

I expressed a genuine question I have about theistic evolution, so maybe someone else can comment as I’m not interested in debating the possibility of non-theistic evolution right now.

Please, I don’t mean any offense. I’m really just curious about where and if the TE sees God directly or immediately acting.

Genetic mutations maybe? And even by exceptionally well timed coincidences in nature?

Coincidences could be termed as providential and not immediate, but when there are no separate actors God is working with, the distinction between providential and immediate begins to disappear. What difference does it make whether there are 1,000 or 100,000 separate events between God’s action and the observable event.

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Just for the record, I am an atheist, so I’m not a theistic evolutionist. However, I used to be a theistic evolutionist about 25 years ago, if that is worth anything. I do think science is an important social endeavor, and I find TE’s (and EC’s) to be an important ally in promoting science.

I leave that to the theist. What I do find encouraging is that a curious atheist like myself can find that same type of curiosity in Christians and other theists. For example, I really liked this article by Dennis Venema:

ID/creationism is ultimately telling us to quit looking for knowledge. God did it, so just close up your labs and go home. For those of us who are curious, that just doesn’t work.

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That is a good article. Thanks for bringing it to my attention.

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Thank you for your suggested reading. I agree that you don’t need to have all details, for regarding a gap closed. In reaction to the abstract, here, to my opinion with regards to the core genes they can only suggest that these derived one from another in certain order, but how that could work is not even suggested. I see an internal contradiction in that these genes were diversified for billions of years and therefore thousands of billions of generations and that after this eternity, you could trace phylogenetics based on common sequences. If these sequences had no function, they would have completely eroded, and if they have function, then how to distinguish between common origin and common function.

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I guess that “function” here is simple clumping together?

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You say it. And for yourself you show it. The papers that you mention are concerning the evolution of already existing flagellae and not the origin of flagellae. T. aquaticus does a better job. Maybe, you read his comments?

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In a way, we’re all methodical naturalists. When something was eating my hostas, I attributed that to deer, not God.

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Yes, ID is called a “science stopper” for good reason. The other problem with ID/God-of-the-gaps is that it turns God into a scared cockroach–always needing a new dark place to hide whenever a scientist makes a discovery that sheds light on something we didn’t understand.

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Let there be F-ATP synthase, and behold, a few years after it started raining, there was F-ATP synthase.

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Sorry for the delay responding further.

First, just for clarification

I know I certainly was never presented with evidence for evolution.

Did you mean this? if so please explain, or ‘evidence against evolution’ ?
If the latter, I’d be happy to present it.

But so far as the explanatory gap re new genes is concerned. If there is a gap, then it exists whatever my motivation – however good or bad - might be. And to raise the question of my motivation in answer to my raising the issue, looks like diversionary tactics – and is certainly unscientific.

The current standard models of cosmology, particle physics and quantum mechanics are remarkably successful (not that I understand them). But in both /all 3/ areas, there is contrary evidence and/or internal inconsistencies. When someone raises these questions they aren’t told to look at all that the theory does explain, and not to be a nuisance. On the contrary, it is recognised that they are applying scientific rationale, and their contribution is welcomed – even if they don’t have an answer or alternative to offer.

You suggested I might have a prior belief that evolution is wrong, but as I said previously, no I don’t. I’m not trying to prove evolution is false; but I am saying that there are serious explanatory gaps and contrary evidence that is usually swept under the rug – a rug called ‘but look at all evolution does explain’ and/or ‘scientific consensus’ and/or ‘you’re trying to close down scientific enquiry’ and/or ‘you’re just promoting a particular interpretation of the Bible’.

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What’s kind of peculiar, is no matter how far back in time or in space we look, there is always something there. It’s as if nature truly abhors nothingness.

I asked a person knowledgeable in cosmology once, what were to happen, if on the verge of the visible universe, they saw the faintest flicker of light in the void? They said they could not be sure whether they would be fascinated or terrified.

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There are no rational explanatory gaps whatsoever. Are there. Nothing that can possibly be filled by anything else other than evolution. Are there.