Stairways to Understanding (tentative books project)

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My first mention of the Stairways to Understanding project is in a now archived thread.

Stairway to Understanding Hypothesis vs. Common Descent, my presentation to science students and church groups

Back then, after posting that thread, I was requested to not talk about the project. Thus I stopped participating in my own thread!

But now in light of some developments, such as the the book Stairway to Life finally coming out:

Stairway to Life by Change L. Tan and Rob Stadler - #6 by stcordova

and now that the Stairways to Understanding project/book has been tentatively commissioned, I’m now actively opening a dialogue to get editorial and critical feedback on the idea.

The fundamental thesis of the project is that the patterns of life only look superficially evolved by common descent, but can alternatively be interpreted as specially created systems and organisms that form a stairway to understanding life. Thus abiogenesis theory and evolutionary biology are like the geocentrism of old that finally collapsed in light of mechanistic anomalies.

The reason I’m putting this out is I want to identify areas where there is agreement and disagreement. I want readers to have access to some naturalistic viewpoints. The abridged editions of the books project will be aimed for highschoolers and college freshman, the advanced editions will be for specialist readers.

Unfortunately, creationists often deny the pattern of nested-hierarchies in biology, and they also deny that organisms can be approximately lined up in a progression like this one:

human_evolution
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However, many of the steps (and in this diagram abiogenesis is nicely included) are problematic from a mechanistic standpoint. Abiogenesis research is presently based on pure faith and has REGRESSED to the point that top evolutionary biologists like Koonin are invoking multiple universes as a solution to the improbability of abiogenesis.

Eukaryotic evolution is seriously problematic. But what is not show in the diagram are problems involving not just organisms, but systems, like Chromatin (which are hinted in Archaea and exist in Eukaryotes).

Meiotic evolution is problematic.

Nerve evolution is problematic.

Magnetic navigation is problematic.

etc. etc.

The stairway toward complexity is a bit like labyrinth of stairways, not a single stairway:

stairways_tokyo
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Here is one way of conceptualizing some of the steps, and they would require miracles or at least highly improbable events to originate and MAINTAIN each step:

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At the extreme specialist end of the project are patterns of diversity that are now being leveraged by structural bioloigsts but improperly attributed to random mutation. This paper (from which the diagram below is shown) shows this leveraging of patterns of diversity:

https://www.pnas.org/content/110/51/20533

dca_diagram

I doubt the “phylogenies” the structural biologists use are rooted, which pretty much makes evolutionary biology irrelevant to that aspect of structural biology!

Further, if the patterns were random, then why can’t we just use bacteria to make these patterns for proteins? Doesn’t make sense from evolution, but it does make sense from the perspective that God designed/specially created things to give some level of understanding for those open to seeing the designs.

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It is not archived, just moved off the front page. It is here: Stairway to Life by Change L. Tan and Rob Stadler.

Come again? Who said you should not talk about the project?

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Someone in the ID community as it was related to a potential peer-reviewed paper not yet published and it risked leaking some ideas at the time if I started talking about it. The parts I will talk about are pretty much public domain.

I don’t understand the whole peer-review thing, so I honored the request out of courtesy. I’ve gotten a release to talk about the material in this thread now.

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Things don’t become impossible or even unlikely just because you say so, even if you show colorful pictures.

Things don’t become untrue because you personally doubt them either. Why the quotes? What makes you think they’re unrooted? Why does that make evolutionary biology irrelevant?

I have no idea what that meant. What did it mean?

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@stcordova

It looks like your thinking and writing is geared towards convincing Atheist supporters of Evolution to reconsider.

But I should remind you that the GAE conversation is about Christian Creationists and Christian Evolutionists.

The LATTER party fully endorses God’s miraculous ways.

So how hard would evolution be with a miracle working GOD making the effort?

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No, it’s for creationists that are being fed bad creationist teaching material – materials that deny the existence of a (taxnomic) nested hierarchy and the obvious sequence of creatures from simple to more complex such as in my original post.

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If we assume random mutation created the patterns in the PNAS paper, bacteria should have all the necessary range of random mutation to make the 3D structure predictions. BUT, apparently Eukaryotes are needed to complete the puzzle – or did nature conspire to make the Eukaryotes necessary to complete the puzzle.

Bacteria are able to span large swaths of possible sequence space for a protein. It strains credulity to think Eukaryotes are needed to fill in the missing pieces of the puzzle. I might try to run Dr. Morcos algorithms myself. His and other algorithms are becoming widespread.

In any case, rooted phylogenies are out the window for these applications. They’d probably distort the structural predictions anyway.

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@stcordova

And so you wouldn’t even DREAM of God wanting to use Evolution to create species? With God, all things are possible, yes?

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No, still have no idea what you mean. As far as I can see, the paper makes no use of phylogenetic information at all. Nor do I see what bacteria vs. eukaryotes have to do with anything. Some protein families are found in bacteria, some are found in eukaryotes. So?

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I used to be an evolutonist once, and I thought it was a cool godly idea that primitive things evolve to more complex and beautiful things naturally and the universe would keep improving to utopia.

So I dreamed it once, on some level wish it could still be true.

To quote Huxley:

The great tragedy of Science [is] the slaying of a beautiful hypothesis by an ugly fact

But in the case of abiogenesis and evolution, a deluge of ugly facts are destroying it.

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Destroying it would first require that we had some form of complete understanding. We have a working knowledge of evolution that is fruitful in leading us to new discoveries, which hardly “destroyed”.

For abiogenesis, to assert it is impossible first requires that we have a full understanding, which is not the claim. It appears to be a question that science can address. Not destroyed, just under construction.

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Great, I’m glad you’re initial impression is that phylogenetic “information” is totally irrelevant to this approach to structural biology. For a change we agree on something.

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Why do you wish it could still be true?

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WTF? Why did you bring up phylogeny at all? Why the quotes around “information”? Why the previous quotes around “phylogeny”? Do you have any control whatsoever over what you type?

So you’re saying that you have abandoned an idea that evolutionary biologists do not recognize as evolution. That’s good, I suppose.

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@stcordova

That seems like a contradiction of the discussion we were having.

In my scenario, God is behind the creation of life from chemicals … and behind the creation of species from other species.

If this scenario doesn’t interest you, that really should be the end of the discussion for you.

We are sifting through the audiences … looking for those that are inclined to think God can work in these ways!

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I appreciate Dr. Harshman’s interest in the cutting edge aspects of the Stairway to Understanding as it pertains to the utility of Common Design vs. Common Descent in the field of structural biology where 3D folds of proteins might be estimated without recourse to “visual” methods like X-ray crystallography. This is advanced Intellgent Design theory and not part of the abridged high school version of the book, but the subject of ID conferences…

The first generation use of Multiple Sequence Alignments might be described by looking for conserved residues in the alignment and inferring structural and chemical or other functional significance. For example, here is an alignment I made of “nylonase” beta-lactamases, and one can clearly see the conserved residues:

nylonase_alignments
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Some of the conserved motifs were definitely correlated to structurally and chemically significant residues as evidenced by X-ray crystallography, mutagenesis, and chemical experiments on nylonase activity of these beta-lactamases (x-ray graphs and mutagenesis and chemical experiments from Negoro 2005 associated with my alignment):

nylonase_aligmnent_catalytic_residues
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That was a first generation approach to combining sequence alignments with structural biology. It is perfectly compatible with evolutionary theory. But note, one doesn’t have to assume phylogeny, and I didn’t use any phylogeny assumptions to make the alignment nor correlation with the X-ray graph. Phylogeny wasn’t needed. One could just as well assume the bacteria were specially created to assist identifying important critical residues for a nylonase/beta-lactamase!

BUT, now with the second generation attempt to use multiple sequence alignments to elucidate protein structure, in fact potentially the complete suite 3-D folds (conformations), it becomes an interesting question whether common design is actually a better explanation for the success of second generation attempts.

The second generation attempts involve what is known as Direct Coupling Analysis and machine learning. This would then explain the utility of God making a squid, a fox, a chimp and a human and bacteria they way God made them. He made them in a way to help scientists understand life, and the pattern looks intelligently designed for human benefit.

For deeply conserved proteins, a testable hypothesis is that if we cut out the eukaryotic versions, the 3D prediction would fall a part. That would suggest the Eukaryotic architecture was made with 21st century science in mind and for people open to ID.

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I was trying to point out phylogeny was useless, even though the patterns of diversity and similarity across species for the same protein are pretty important to this aspect of structural biology.

I was trying to point out the assumption of common design will work just as well, if not better than the assumption of common descent as far as this aspect of structural biology is concerned. One asks, what’s the difference between common descent and common design, here is potentially one real world application where it makes a difference to the detriment of common descent.

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None of that has anything to do with the paper you cited. I can see that you really want there not to be such a thing as phylogeny. But that’s all.

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Not having a complete understanding shows that assertions of naturalistic evolution and naturalistic abiogenesis are largely faith based because, at least in the case of abiogenesis, experiment and chemical theory say abiogenesis is highly improbable.

How improbable does something have to be before we assert an event or series of events was a miracle?

IF life had been a miracle, and by definition miracles are not repeatable on demand, and hence outside of science, then no amount of continued experimentation can repeat the miracle, and on the other hand, neither will further research prove a natural origin for life and its complex features. So this results in a dilemma of establishing proof.

At best, it seems to me, each side argues why one viewpoint might be more believable than another, not for absolute proof or belief based on omniscient knowledge. Though it would be nice to know more, and have access to more facts, at some point, the arguments boil down to what viewpoint is more believable than another given what little facts we have. The 3rd option is to simple say we don’t know, we might not know.

Personally, the more I’ve studied the cell, the less I could believe it was highly probable event. Same for eukaryotes, meiosis, the human eye and many other system in biology. I could say, “I don’t know absolutely, but I find one view far more believable than the other.”

The main “evidence” for evolution is the progression or stairway toward complexity. I argue the stairway exists, but it is not proof of a natural progression any more than man-made stairways are products of mindless processes. The issue is the purpose of the stairway and why God made this stairway. I’m suggesting God made the stairway as a stairway to understanding and appreciating the constructs in biology.

The Stairway of Understanding has been mis-interpreted as evidence of common descent. That is the theme of the books project.