Criticisms of Stairways to Understanding

I have to say that your posts are becoming increasingly incoherent.

No, you’re not just reporting on what needs to change, you’re spamming the thread in a prototypical example of the Gish-gallop.

Yes I’m quite certain that your creationist audiences who deign to seek out Salvador Cordova to tell them reassuring but science-sounding fables with lots of colored arrows, abbreviations, and symbol-filled tables, are all deeply impressed with your characterizations.

Well first of all one has to wonder why such a thing like a “fishapod” with clearly derived and morphologically intermediate characteristics should even exist in the first place.

When you do this pointing out, do you also explain that nobody actually think such cases are ever based on single fossils, but rather inferred from highly statistically significant patterns in much larger collections of data based on dusins if not hundreds of both living and fossil species? Let’s not kid ourselves here, of course you don’t.

No, they don’t so much “explain” the “mechanistic feasiblities” of such transitions. But the feasiblity is nevertheless implied by a consistent nested hierarchy. Additional and more detailed reasons to think such transitions are feasible is found in our understanding of the molecular and population-dynamical mechanisms of evolutionary change. The physical and chemical causes of, and known types of mutation, subject to natural selection and genetic drift.

Surely that must be impossible to evolve. Gee I just can’t figure out how, and you used the “fine-tuning” term. Therefore God!

A sentence that doesn’t parse meaningfully into english. “Nested hierarchical reasoning” (whatever that means) isn’t postulated as explanations for the evolution of Zinc Finger arrays. The evolutionary history, as in the genealogical lines of descent from common ancestors, is mapped out and displayed in a phylogenetic tree. This tree in turn implies the sorts of changes that would occur on individual branches of the tree to give rise to the differences that distinguish one molecule from another.

The explanation then becomes the types of mutations that cause these differences. Substitutions, insertions, deletions, duplications, or what have you.

I’m sure they’re impressed both by your crayon skills and your ability to mindlessly declare with great conviction what you think can or can’t possibly function, in the church basement.

This statement is even less sensible than the previous. What in the world does it mean to say that “the zing finger array matches the DNA”? And who has ever posited that “hierarchical diagrams” are explanations for that incoherent gibberish?

What do you respond when your church audience asks you this?

Non-sequitur specifically are you referring to? Who is it that actually makes this incoherent straw-man of an argument you’re trying to knock down. Can you quote them?

It is not a non-sequitur to argue something. An argument may commit a non-sequitur fallacy, but we’d have to see this supposed argument first before we can make such a judgement call.

And to be sure, it isn’t actually a non-sequitur to argue that a nested hierarchy implies the feasibility of such evolutionary divergences, because manifest nesting hierarchical structure in the data(which you just agreed there really is) is exactly what you would expect to have if such evolutionary divergences actually occurred. And if they actually occurred, they are of course strongly implied to be feasible.

He said, quite sure of himself. He never explained why.

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You’re confusing common descent with the origin of innovations again. That makes your comment highly word-salady.

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These posts have been moved to Side Conversation. These comments are not conducive to achieving any mutual understanding. If you want to show @stcordova what he is getting wrong, please do so patiently in the main thread.


Who are these people? Do we have any reason to actually believe they understand something like neutral theory?

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The structure of this web site is becoming increasingly chaotic. This is all directly related to the main topic. Sal put up a colorful figure, as is his habit. He didn’t explain it at all, and its meaning is otherwise opaque. I invited him to explain, which he did not. I invited him a second time. And that’s where we are now.

What, if anything, is your complaint?


I don’t have a complaint, or I wouldn’t have allowed the response.

I just don’t see how this contributes to the conversation. You can certainly make substantive comments on the main thread, if you choose. I think it would be fantastic if you were able to explain what he is missing in a way he can understand.

EDIT: Your latest post at the main conversation does a much better job of actually explaining what @stcordova is missing and invites him to reflect and formulate a response.


I’m reminding Sal of past conversations in which that point was made at length.

So do I. All past attempts have proven useless. I would invite anyone else to try.


The figure in question has been presented elsewhere and here in venues Dr. Harshman visited. I presumed he actually understood what the figure was since I’ve been talking about the information for around a year.

I’ve posted it many times at Peaceful Science, and I presumed Dr. Harshman understood it.

The figure is of a KRAB Zinc Finger Protein ZN136 for humans (it was right there in the figure) in the comment on the FASTA file. Do you understand protein FASTA files Dr. Harshman? Can you recognize Zinc Finger Domains? Do you know what a zinc finger domain is? Do you know it’s purpose?

If you do, then why are you having problems understanding the diagram?

The protein in the diagram is described here.

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, whatever…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 is there 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. I gave an example where it would be absurd to think this actually evolved because it would be functionally broken along the way.

I presumed, since I’ve been discussing this particular protein with Dr. Harshman since 2018 or so, that he understood the diagram.

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.

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

At this point, I was expecting thoughtful readers to understand what would happen with random changes to zinc fingers. It 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 random zinc fingers would be selected for at all at any stage of evolution of the zinc finger protein?


If the change positively affects reproductive success. Change the protein and you might change how it binds, or how well it binds, or where it binds. Which in turn can affect the expression of associated genes either up or down.

It’s not like figuring this out is hard, your empty rhetorical questions notwithstanding. You appear to be just assuming, or rather declaring without evidence, that any conceivable change to such a protein would unavoidably be deleterious. But there’s just no reason to think that is true.

Beneficial evolution of changing regulation patterns by mutating DNA binding proteins is an observed fact.

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Now you’re just making stuff up.

You have done no work to show that any would-be reconstructed intermediate or ancestral state would be broken. You’re making up your own, deliberately silly strawman scenarios to knock down, all of which have nothing at all to do with how molecular biologists actually think these proteins evolve to acquire novel bindings sites, or more or fewer zinc finger domains.

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So the tree is just a neighbor-joining tree of the zinc finger domains. One would certainly expect analysis, especially a neighbor-joining analysis, of such short sequences to produce a questionable tree. But I see 13 sequences and 14 arrows. What is “1 degnerate”?

All this shows is that you don’t understand how phylogenetics works. Nothing more.

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1 degenerate = ZF number 1 is degenerate, it is missing a Cysteine “C” residue

Your statement assumes that phylogenetics across species unrelated by common descent actually works to begin with. Circular reasoning again.

There aren’t any species unrelated by common descent. The only question for any two species is how far back their particular common ancestor lived.

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What is that arrow pointing to?

What species unrelated by common descent? Phylogenetics shows species to be related. You have been unable to come up with a plausible alternative explanation.

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First it points FROM:


and it points TO the corresponding location on the unrooted NJ tree for that sequence.

How do you know that’s a degenerate zinc finger domain? For that matter, what does that mean to a YEC? Why not the line above it too? Why would you even propose a tree of adjacent domains? What would you expect to see?

True, I’m pointing out what needs to change, especially stuff that isn’t mechanisticlally explained by phylogenetic “reconstructions” from protein/gene trees. One can’t just say look at the similarity of the genes and say that explains why a lentis retractor eye muscle in some fish will evolve into ciliary musles in the eye muscle of humans – but that is pretty much the template a lot of evolutionary biologists fall back on when in reality they don’t have an explanation of mechanistic feasibility.

Doesn’t matter if it’s a Gish-gallop or not, the problem for evolution remains, and there are many more things like that. The scientifically responsible thing then would be to say this is no better than a speculation, much less a confirmed fact. Perhaps the more accurate thing to say is that the claim of common descent is faith belief.