Stairways to Understanding (tentative books project)

Sorry, no. How can you criticize a field when your misunderstanding is this basic?


Compare what you wrote here with my criticism of Intelligent Design:

A Design theorist might say that design of some feature (like the flagellum) can be disproved (falsified) by demonstrating an evolutionary pathway of “selectable steps”. My criticism is that a Designer capable of complex design must also be capable is simple design, and could design each step in the same manner as evolution might occur. Such broad claims about ID cannot be falsified (specific claims about the how/when/where/why of Design might falsified.).

I got interrupted and forgot what I wanted to add … oh well! :laughing:

I would not make this claim for abiogenesis because no one can fairly calculate such a probability yet (but I’ve seen a lot of bad math from people trying). We can do some calculations of probabilities for evolution (population genetics, phylogenic analysis).

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Agree, and in that case design (better said, improbability) can’t be detected if the transition is not sufficiently abrupt. Abrupt might be things like major new cell types that are transparent when other cell types were previously opaque. For example the eye has lenses made of transparent cells. This is an incredible innovation.

What science might establish is the improbability of a transition, I don’t think ID is science, even though I personally think it is true. However, I do believe estimating probability of certain changes falls well with in science.

In my book project, I will argue for the improbability or infeasibility of transitions (steps). I’m happy to point out no one can prove it happened by miracle, I can only convey reasons why one might think a transition is improbable.

Well, what about this diagram, do you have issues with it, is not evidence of evolution from simple to complex (at least as far as the human brain):

Or would you prefer nested hierarchy? How about nested hierarchy plus neutral evolution?

Seriously, give it your best and I’ll consider using your best in my works. Ok? I want to represent evolutionary theory as best as possible despite the conflicting definitions and the conflicting reasons it should be believed.

I can’t even read it. But I can imagine what it says. Yes, that’s one pathway through evolutionary history. But it’s only one lineage, and you make it a general rule.

Not really. I have no interest in your works, which seem limited to creationist apologetics. I merely advise you to learn something about the subject. It would help if you tried to learn rather than skim for things you can scoff at.


Would you be willing to include a bit about this things that would make the probability more likely?

If there weren’t such novel architectures in proteins, that would make some aspects of common descent without miracles more believable. That is, if we just take Dayhoff diagrams, of conserved proteins, common descent looks superficially plausible from random mutation and selection:


The problem arises in proteins that are unique and sudden in major groups. They are sometimes called Taxonomically Restricted Genes (Proteins). I’ve studied a few of the TRPs, and they pretty much come out of nowhere for major groups. But if we ignore those anomalies, then one can believe in common descent without miracles.

There are also morphological leaps in cell type. How did transparent cell types arise (like eye lenses)? Even with the same set of genes between cell types, that seems personally astonishing to me that the right cell type with the right properties is positioned to make tissues and organs at the right location.

BUT, if those abrupt changes weren’t there and we only looked at conserved protein phylogenies, I would find common descent without miracles more believable.

Behe accepts common descent with some sort of design. So I suppose there are some who can accept common descent with miracles or ID along the way. Behe doesn’t use the word miracle, and he had speculated in passing the idea of front-loaded designs.

I’m not sifting or anything, I’m merely stating considerations that have heretofore not been talked about.

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Clues can be found in more recently evolved genes: they can for example arise from junk DNA. Since it’s not conserved, that DNA will not be preserved in relatives given an ancient origin. No miracles needed. It isn’t that they come out of nowhere, it’s that the place they came from is no longer there.

Gradually, of course. How else? Your personal astonishment is misplaced.

So why isn’t that your preferred hypothesis?

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But what about the different helicases in one domain of life that goes 5’-3’ and in the other domain of life 3’-5’? This is NOT a gradual change – the helicase goes either one way or the other, not something in between.


This involves different genes/proteins to effect this. Invoking some random piece of non-coding DNA to effect this change is like invoking random changes. That won’t work.

And what about Archaea having one polarity of phospho lipids and ether bonds and eukaryotes AND bacteria having the opposite polarity and ester bonds?

Archaeal Phospholipids: Structural Properties and Biosynthesis - PubMed

They have different enzymes to effect this chirality differences and ether vs. ester bond differences.

Or how about the sort of multi-array KRAB zinc finger proteins that are coordinated to bind to certain sets of chromatin targets…the problem is so bad that evolutionists invoke co-evolution for KRAB zinc fingers and ERVs since if the zinc fingers change, the ERVs have to change with it, lest the regulatory machinery they are a part of goes berzerk.

Gradually, of course. How else? Your personal astonishment is misplaced.

Of course not for the following reasons. Why should a transparent lens cell type emerge? Here are some of its properties:

Mature lens fibers have no organelles or nuclei.

What sort of celltype like that will get selected for – one that dumps its organelles and nuclei??? It dumps these organelles and nuclei to help it become transparent.

Suppose we have a proto lens without this kind of transparent celltype – something like a typical opaque skin cell? Light won’t do a good job passing to the retina if the cell is opaque like skin? I suppose it could see a bit, but then well, why have a covering at all in the first place, why not a primitive type eye with no lens? The intermediate proto-lens should be selected against unless of course a cell type with no organelles and nucleii are already available, BUT why create such a cell type if not for a lens?

Further the human eye’s lens works by changing its curvature and is controlled by ciliary muscles but it is not moved around.

Contrast with the fish lens that is fixed in shape but is moved around by the Retractor Lentis muscle:


The muscle arrangements are totally different in the eyes of fish and man.

Citing Tiktaalik as proof of evolution of tetrapods doesn’t solve problems like transitioning an eye like the one in some fish to an eye like that in a human. The retractor lentis muscle doesn’t at all look like the ciliary muscles in the human eye, not to mention, there is no point in having ciliary muscles in the human eye if the lens isn’t flexible! The lens in a fish is not flexible relative to the lens in the human eye.

But all the focus is on Tiktaalik and its gross morphology, not the problems of fine transitions such as I just described.

That’s why I say, common descent looks superficially plausible until one examines the transitions in finer detail. It’s under such examination, changes are seen as discrete, like steps, rather than a smooth ramp.

I don’t think evolutionary biologist think through the mechanical challenges of invoking natural selection. Ironically the computer scientists understand the problem better with fitness peaks and the barriers that prevent selection from finding a higher peak because it is stuck in a local peak. That is the problem of forming a flexible lens like that found in the human eye.

Thank you for the long and detailed response, but that did not address my question.

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That’s not an anomaly in any sense of the word. That’s what you’d get when novel genes evolve from non-coding DNA, of if they evolve(diverge) too quickly, or if they’re the product of fusions of smaller fragments of other genes, etc. etc.

If you’d ever peered into a microscope you’d know that all cells are actually transparent to some degree. Heck, you can even see through your hand with a strong enough lightsource*(and I’m sure you’re aware if you think about it, that even your eyelids are transparent enough that you can tell the difference between night and day even with your eyes closed). So to make a cell more or less transparent is simply a matter of regulating the expression and localization of those proteins (and other molecules) that contribute most to absorption and scattering of light. Gene regulation changes evolve extremely easily, as even single substitutions can have very large effects on expression levels.

Skin is far from opaque. You can see your blood vessels through it even millimeters thick layers of skin. Have you ever tried looking at a single-cell-layer thick sheet of cells?

Zoom in on the red circle in this picture. That colony is up to 3 cells thick in the densest places.


Not just a few cells in a culture dish either. Here’s an image I took this morning of some 2-day old zebrafish larvae. You can see that the entire larvae is pretty much transparent (the light source is beneath the embryos, my camera is above), to the extent where you can see both pigmented eyes, even when the entire head is in front of one of them! (look at the bottom embryo - the top of the 2 dark blobs - this eye is on the other side of the head, facing away from my camera).
Just for scale here, the larvae are about 3mm long, and are dozens to hundreds of cells thick.


Yes and it’s important to understand that eyes are thought to have first evolved when animals were no bigger than that. In essentially completely transparent, microscopic organisms.

Eyes did not suddenly pop up in socketed holes in the furry hides of giant mammals. They evolved from already existing olfactory receptors on the surfaces of tiny, effectively transparent, worm-like organisms.


I’m afraid I didn’t understand then what you were asking. Sorry.

Thank you all for the feedback on transparent cells. I will revise my wording in light of what you all said. The papers that describe the lens cell type were more specific in pointing out the importance of the optical properties of the removal of the nucleus and organelles to in connection with the lens. I’ll have to think of a way to phrase the issue.

Thank you all again for the feedback.


You can get these glass catfish for your aquarium.

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You may want to fix that word.

It would be better to revise your ideas once they have been shown to be incorrect. Instead of looking for different support for your pre-ordained conclusion, try letting the data drive the conclusion.


One of the early set of steps in the Stairways to Understanding is the steps to the origin of life. That is mostly already covered in the Stairway to Life book by Tan and Stadler.

I had the chance to get an interview with Dr. Tan which I provide here:

She briefly explained that her motivation for visiting the origin of life was her astonishment with Eukaryotic evolution. This is the diagram (or close to it) of the problem of Eukaryotic evolution which she mentioned in her interview. This is of course a fraction of the problem.

The problem of Eukaryotic evolution will be some of the steps in the Stairways to Understanding book project.