Stairways to Understanding (tentative books project)

This is nothing more than “I can’t come up with a story for how that evolved, therefore it didn’t, and God must have done it”. You can dress it up with pretty pictures, but that’s what you have. Most people don’t consider that a valid form of argument.

And I ask again: why do you pick fiat creation over divinely assisted evolution?

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How about this, and that, and the game of whack-a-mole, and moving goalposts? It’s the if-you-don’t-know-everything-you-don’t-know-anything fallacy. We can (and do)have entirely rational grounds for concluding that extant biodiversity and it’s genetic and physiological characteristics are the product of evolution without having to explain literally everything down to the last molecule.

No, it’s been comprehensively answered. Changes in the regulation of genes which affect the absorption and scattering of light hitting the cell is how cell transparency can evolve either up or down.

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Which naturally lend themselves to incremental mutational change, affecting how they function, encoded in a system of genetic molecular polymers which also naturally lend themselves to incremental mutational change. Heck, we even know of all the types of mutations that are possible, which are basically all the change, copy, insert, and rearrangement-tools one could imagine would be necessary for the function for an incrementally changing system of polymer sequences.

It’s almost like genetics is exactly the kind of thing that enables and facilitates the slow gradual process of evolution, whereby in splitting populations of organisms, the independent accumulation of genetic mutations with their changing effects on phenotype are subject to natural selection.

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Thank you for the references.

However, change in cell-type is repurposing a lot of pre-existing material as well.

I’ll look at your references. And again, thanks you for the papers that you provided on the Stairway to Life thread that had table 3 that showed non-biological means of creating ATP.

I think a lot of protein families are multi-purpose (not re-purposed). That is clear from the nested hierarchies that exist for major protein families.

Evolutionary biologists interpret this nested hierarchy as evidence of common descent, but I think that is mis-interpretation as illustrated by the problem of necessary paralogs needed for Microtubule polarity.

In humans, it has been experimentally confimred the Topoisomerase paralogs are also necessary as well as paralogs of collagen. If paralogs are simultaneously necessary for functioning organisms, it stands to reason the nested hierarchy is not necessarily the product of natural common descent.

Nevertheless, thank you for the papers.

To my knowledge all opsins ultimately derive from pre existing and even older GPC receptors involved in detecting and responding to chemicals detected in the environment. If that’s not olfactory reception, or a sense of smell and taste, what else would you call it?

I’m just reporting the what needs to change, the lentis retractor muscle (in some fish) to the ciliary muscles (in humans). This also involves changes in neurons and coordination. Obviously you and Dr. Harshman think this is a sufficiently easy transition, but I (and I expect some of the readers of the books project) to consider it absurd.

I KNOW from experience that when I start describing things like this in detail, people are inspired with wonder at the Creator and how insufficiently Darwinisim (and/or even neutral theory) are as explanations. I point out, fossils like the fishapod don’t explain the sort of fine transitions that are actually needed to convert a fish to a human. I point out the absurdity of suggesting that this fossil

tiktaalik

is good reason to believe the lentis retractor muscle in some fish can evolve into a ciliary muscle in humans.

Phylognetic reconstructions and nested hierarchies are not adequate to explain the issue of mechanistic feasibility of the numerous examples listed in this thread.

Many proteins like Zinc Fingers have specific binding targets on the genome at fine-tuned levels of binding affinity.

I demonstrated elsewhere the absurdity of nested hierarchical reasoning as some sort of mechanistic explanation for the evolution of Zinc Finger arrays:

The spelling of individual zinc fingers must be coordinated to bind with the right specificity and affinity to precise segments on the genome, otherwise the protein fails to funciton, and worse binds to the wrong places!

Appealing to hierarchical diagrams as some sort of explanation for how the zinc finger array matches the DNA is an absurd non sequitur.

Pointing out the non-sequitur of nested-hierarchy-type “explanations” in the above example is extensible to supposed zinc finger protein evolution between organisms, and really to nested-hierarchy explanations in general. The nested-hierarchies EXIST, but it is a non-sequitur to argue they are descriptions of the mechanical feasibility of evolving one thing to another – they are not because it takes more to make a protein functional in a functional context than just randomly evolving it. The KRAB Zinc Finger family proteins are an example.

Paralogs often evolve to specialise functions, yes. And? You’re conflating modern paralogs being necessary for modern organisms with modern paralogs being necessary for all organisms. Why do you find it the least bit surprising that paralogs evolve important functions? Make a change, then make it necessary. It’s not rocket science.

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That’s new to me. Is there a review or something you could point to?

Hi Sal,

I would be happy to provide some feedback from the perspective of a well-informed amateur. I’m not a degree-holder, but I’ve read a lot of discussions and not-a-few papers. Most importantly, over the past two decades I’ve gone from the school of:

“Wow! These changes are huge and amazing! No way they could be produced by evolution!”

To the school of:

“Wow! These changes are huge and amazing! And even more amazing is that biologists, created in God’s image, are thinking God’s thoughts after Him; they have identified mechanisms by which the huge, amazing changes happen!”

The Unsuitability of the Staircase Metaphor

In this thread biologists have identified a fundamental problem that you have never addressed: the suitability of the staircase metaphor.

The problem is that evolution does not really follow a staircase to complexity. Archaea first showed up 3bya, and they are still hanging around today. IIRC they are far more diverse and numerous than any other kingdom that emerged later. To paraphrase Etta James:

This is a man’s world, this is a man’s world
But it wouldn’t, it wouldn’t be nothing
Nothing without archaea or protozoa

We humans rely on symbiosis with thousands of species of prokaryotes. They are not in your field of vision because you have chosen an unfortunate metaphor–staircase–that is basically inaccurate.

The way you are tying the image of God to evolutionary outcomes is unsustainable. Yes, every human alive is created in God’s image! But the evidence for our divine imprint does not lie in natural history.

Appeal to Intuition

Secondly, you keep appealing to the large changes and implying that the size makes them so improbable as to be unreachable by evolution. Yet you are not presenting any statistical methodology; it’s an entirely an appeal to intuition.

Biologists have documented the power of neutral evolution and mutations in the regulatory gene network to produce huge, amazing changes. So when someone points out yet another huge, amazing change that occurred at some point, of course their prior is to think that it happened through neutral evolution and mutations in the regulatory gene network. That prior is what lies behind all the responses you have seen in this thread.

Moreover, biologists have strong evidence of negative selection to preserve delicate structures that have become essential for the survival of a living population.

Behind every post you have made in this thread is a negation of the biologists’ priors. Frankly, I don’t see that you have done the very hard work that would be necessary to disprove those priors. You are just saying “Huge! Amazing!” and choosing a different path.

You are allowed to choose a non-scientific path, of course. If you’re going to do that, though, you would do well to be candid about your method and acknowledge that it is the choice you are making.

The spiritual value of non-intuitive science

Ever since I learned about quantum mechanics, I stopped thinking that my intuition was of any help in evaluating the plausibility of a scientific theory. Evolution is another scientific discipline, like quantum mechanics, where stochastic, non-intuitive processes yield incredible results. The faithful in Christ who believe that all truth is God’s truth would do well to recognize the incompatibility of intuition and the stochastic branches of science.

In fact, there is a spiritual value to be gained from that incompatibility. If our intuition is unsuitable for understanding science, our intuition is probably not fully capable of understanding God, wouldn’t you think? The inadequacies of our intuition point to our need for God’s special revelation through the covenants, the incarnation, and the Scriptures.

I hope you–and maybe even your readers?–will find these thoughts helpful. :slight_smile:

Best,
Chris Falter

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I’ll try to dig something up. Meanwhile there’s this: Opsin evolution: orgins of opsins - genomewiki

  • Opsins are definitely not the ‘original’ GPCR because these were already widely deployed at much earlier divergence nodes – yeast, protozoa, choanflagellates, trichoplax have GPCR but lack opsins. Nor are opsins the prototype for the ‘rhodopsin class’ R of the GRAFS classification of GPCR which again was established far earlier. Indeed, even the Ralpha subgroup with of rhodopsin class GPCR was well-established prior to the first metazoan opsin.

  • Opsins are thus latecomers, not pioneers, to a rapidly expanding paralogous gene clade within already full-featured GPCR. Judging by their closest extant blastp relatives among tens of thousands of GPCR at GenBank, opsins specifically arose as a gene duplication within the peptide receptor subgroup PEP. Indeed, certain of these proteins list opsins among their top ten best back-blast matches (ie have better matches than to almost all non-opsin GPCR). Note here that blast scores can be misleading because the ‘floor’ of percent identity is about 25% just due to universal conserved residues plus accidental matches.

It appears I must eat my own words, as I can’t seem to find any specific references that suggest opsins derive specifically from GPC receptors classified as olfactory receptors(in fact I found a reference that explicitly stated the diametrically opposite)*. And I can’t remember where exactly I got this idea from, so I suppose it could just be a false memory and I’ve got something mixed up.

Rather the evidence appears to suggest they’re more closely related to hormone and peptide binding GPC receptors that could just as well have functioned in cell-cell signaling within a multicellular organism. This is also discussed further down in the link I gave.

*They write: The evolution of opsin genes is in sharp contrast to that of OR genes. Opsin genes also belong to the rhodopsin-like GPCR superfamily, and thus they are distant relatives of OR genes. Homologous opsin genes can be identified in vertebrates, insects and other invertebrates, however, indicating that the origin of the opsin gene family is much more ancient than that of the OR gene family[58].

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Could you explain what that colorful figure means?

It means just because we can pump sequences into computer and generate a nested hierarchy, it doesn’t mean the nested hierarchy was the product of random mutation and natural selection.

Having an almost correct Zinc Finger array (there are about 13 Zinc Finger in my colorful figure) is like having an almost correct computer password. There aren’t really good gradual evolutionary routes to a coherent zinc finger array that targets specific locations in the genome anymore than there are gradual routes to figuring out a computer password.

Each of the Zinc Fingers of about 30-32 residues correspond approximately to a target of 3 DNA bases, but it’s not as modular a design as synthetic chemists would like since a given Zinc Finger modifies the chemical behavior of the adjacent Zinc Fingers. This illustrates the password problem with a mere 3 Zinc Fingers:

Proteins like the KRAB Zinc Finger (KRAB KZNF in the diagram) attach to segments of DNA (often ERVs or other elements) to help recruit molecular machines:

The binding of KRAB-ZFP (KRAB Zinc Fingers) to ERVs or other elements means the Zinc Finger array must be matched to recognize a DNA target. The problem for evolutionary theory was that to have a nested hierarchy across species of KRAB-Zinc Fingers implied a corresponding nested hierarchy of targets!

I found that absurd, but nevertheless, evolutionary biologists declared this as some sort of evidence of co-evolution, which struck me as nothing more than an epicycle.

Anyway here is the related paper that talks about the co-evolution KRAB-ZFPs with evolution of a certain kind of transposon. It describes the problem I was mentioning, but I don’t agree with the “solution” of co-evolution. I’d sooner believe in miracles.

https://www.nature.com/articles/nature13760

Sorry for the delay in responding to your good question.

It isn’t my preferred hypothesis, but it would be my 2nd choice, that is if we’re talking Progressive/Old Earth Creationism which was (is?) Stephen Meyer’s view according to my interview with him in around 2010. Here is a link to my interview with him:

The 3rd choice would be Behe’s common descent with ID along the way, but how that is not different from miracles is not something Dr. Behe delves into.

But specifically to your question, the Faint Young Sun Paradox was the beginning of my doubts to the age of the fossil record. If the fossil record is young, then there was no time for progressive creationism anyway.

For the Faint Young Sun Paradox to be resolved it requires miracles of fine-tuned global warming. I suppose that’s a lesser miracle than special creation of all species, but still, it was my beginning of doubts for the age of the fossil record – doubts which obviously persist to this day, now also reinforced with the strong evidence the human genome is deteriorating and thus could not have evolved naturally. As Kondrashov said, “Why aren’t we dead 100 times over”?

2 posts were split to a new topic: Criticisms of Stairways to Understanding

No, please try again. Where is the figure from? What do the arrows represent? What sequences are shown at right? What data were used to build the tree? What algorithm?How robust is the tree? If you did that yourself, I’m suspecting that you aren’t quite clear on what you did and what it means. But at the moment it’s certainly unintelligible to other people.

That makes a sort of sense, but if the fossil record is young, there’s no reason for any correspondence between the record and phylogeny. You’re allowing one little anomaly to overrule all the rest of the data. Bad practice.

There is no such evidence, but if there were, shouldn’t it apply to all species, and shouldn’t the faster-reproducing ones be all extinct by now?

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The protein in the one of the diagrams is described here.

https://www.uniprot.org/uniprot/P52737

Note the identifier “P52737” is also in my diagram. It gives the same name as in the diagram. The website provides the same FASTA sequence as in the diagram.

The coordinates of the zinc fingers are also there at that website:

|Zinc fingeri|140 – 162|C2H2-type 1; degeneratePROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|168 – 190|C2H2-type 2PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|196 – 218|C2H2-type 3PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|224 – 246|C2H2-type 4PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|252 – 274|C2H2-type 5PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|280 – 302|C2H2-type 6PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|308 – 330|C2H2-type 7PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|336 – 358|C2H2-type 8PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|364 – 386|C2H2-type 9PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|392 – 414|C2H2-type 10PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|420 – 442|C2H2-type 11PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|448 – 470|C2H2-type 12PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|476 – 498|C2H2-type 13PROSITE-ProRule annotationAdd BLAST||23|
|Zinc fingeri|504 – 526|C2H2-type 14PROSITE-ProRule annotationAdd BLAST||23|

One could add the amino acids between zinc fingers to make the rows in my diagram. The colored columns indicated conserved residues or conserved classes of residues (like aromatic residues).

The arrows point to a hierarchy generated by MEGA by taking the individual zinc finger rows. Note, I even put the FASTA coordinates in the tree, identifying the protein by name and the coordinates of the particular zinc finger and the ZF number as designated by UNIPROT.

Whether one uses rooted or unrooted neighbor joining, maximum likelihood, bootstrapped or not, …the point was all of these would be pretty much fictions because of the problem of creating a functional binding as the zinc finger array evolved.

Whatever hierarchical structure derived by supposed phylogenetic methods is only an imagination in the mind of the phylogeneticist unless he can justify the functional of the protein in each of the evolutionary phases it goes through.

The point is, making hierarchies isn’t proof of evolution, it’s proof things can be arranged hierarchically! The ZN136 protein is an example where it would be absurd to think this actually evolved because the protein would be functionally broken in almost every step of evolution.

The problem of hierarchy of domains in a single protein can be extended to paralogs in a single organism and then to orthologs across organisms. Just because one can make a hierarchical tree doesn’t mean that it can reasonably be evolved. Zinc finger proteins such as in the KRAB family are counter examples to that belief.

This is a model of zinc finger domains binding to 3 DNA bases per zinc finger:

In light of this diagram it is hopefully apparent that random changes to zinc fingers wouldn’t be good.

One only needs to scour medical literature to see the consequences of mutations to the zinc finger array.

If that’s the case, why should it be expected randomly emerged zinc finger arrays would be selected for at all at any stage of evolution of the zinc finger protein?

To clarify for the reader’s benefit, here is a diagram that includes the FASTA file of the Human ZN136 protein. It shows the rows in the FASTA file that implement a valid classical C2H2 Zinc Finger motif. I show the conceptual fold of the Zinc Finger domain, as well as a more realistic 3D fold of the domain:

Turning the FASTA file on it side, I show conceptually how the fold of the multliple zinc fingers correspond to the sequences:

conceptually this is how a multizinc finger protein might bind to DNA:

The TFIIIA protein, btw, binds to 55 bases. It is a little different than other zinc finger proteins, and doesn’t exactly conform to the 3-bases-per-zinc finger rule.

But hierarchical clustering is a great way of understanding relatedness. For example, this technique of tracking mutations to show relationships is common in immunology: showing the relatedness of clones of B cells or T cells that have mutated and selected as they develop higher affinities for their target antigen. (In a sense, these immune cells are “evolving” under selective pressures in their environment, and developing higher affinity for their target antigens as immune cells with detrimental or unproductive mutations die off)

See figure 5 in this paper, as an example:
Salmonella Infection Drives Promiscuous B Cell Activation Followed by Extrafollicular Affinity Maturation

I presume the hierarchical clustering technique is also how scientists are currently tracking the transmission of the covid-19 virus, allowing them to determine if the virus came to NYC from Europe or directly from China, for example.

So I do believe that comparing mutations across phylogenic trees is a powerful evidence for common descent.

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