Kitzmiller, the Universe, and Everything

I apologize for the misuse of splicing codes. I was thinking and referring to the proteins that were involved in controlling AS. Here was my claim.

Evidence of splicing codes is offered in newer papers and attributed to specific transcription factor proteins. Splicing is active in embryo development and its accuracy seems important as changes have implications in human disease. Random changes may incur purifying selection.

Here is the paper mentioning these proteins in the abstract.

. Integrative modeling suggests that these switches are under direct and combinatorial regulation by distinct sets of neuronal RNA-binding proteins including Nova, Rbfox, Mbnl, and Ptbp. Surprisingly, various neuronal subtypes in the sensory systems lack Nova and/or Rbfox expression. These neurons retain the “immature” splicing program in early-switch exons, affecting numerous synaptic genes. These results provide new insights into the organization and regulation of the neurodevelopmental transcriptome.

Did you read the paper where they were using AI models to understand AS. Maybe @swamidass may want to weigh in.

Deep Splicing Code: Classifying Alternative Splicing Events Using Deep LearningGenes (Basel). 2019 Aug; 10(8): 587.

Published online 2019 Aug 1. doi: 10.3390/genes10080587

PMCID: PMC6722613

Review Article

Free Access

I wasn’t following this, mainly because the proteins that regulate alternative splicing (some of which are mentioned) are not transcription factor proteins. Rather, they are

As I discussed, these proteins do not represent a new splicing code. Rather, they help to determine when and where specific aspects of the common “code” are manifest during growth and development.

And their actions are guided by well-established rules of biochemistry. No need to invoke unknown mechanisms.


First thanks for the clarification and you are right. . Did you read the paper doing the AI alternative splicing modeling?

Since I had just explained that, I do not know what you’re confused about. As I hope you understand, an argument from analogy is never compelling even when it is strong. Arguments from analogy gain strength from the similarity of the two sides of the analogy. Using a person as an analogue for a supernatural force is very weak because no similarity can be demonstrated at all. Using a person as an analogue for another person is stronger. Using an identical twin as an analogue for his twin is stronger still. But even then, argument by analogy isn’t a particularly great way to reach conclusions. If one twin is enrolled in a certain Spanish class at his college, it does not follow that the other twin is also enrolled in that Spanish class at that college.

So, since the strength of an analogy depends upon the similarity of the things analogized, I pointed out that you have absolutely none of these similarities in your favor:

Well, not just one thing, for certain. We have confirmation of the mechanisms and confirmation of the results. We see the mechanisms – variation being generated and reproduced, and features being fixed in populations. We see the way that the morphology of creatures sits in a vast nested hierarchy, consistent with descent rather than with each creature being sui generis. We had the chance to massively falsify that, however, when genomes became readable; if spider monkeys had turned out to be more closely related to spiders than to monkeys, THAT would have required some explaining. Instead, what’d we get? Confirmation that all living things sit within a nested hierarchy consistent with descent.

And then, of course, there are the fossils. All of that evidence in creatures now living is quite compelling, but the faunal succession shows us that there really is an intelligible procession through history. Chordates, but no fish. Then jawless fish, but no jawed fish. Then jawed fish. Then bony fish. Then lobe-finned fish. Then tetrapodomorphs who couldn’t have walked on the land. Then tetrapods who could. Then amniotes. Then pelycosaurs. Then therapsids. Then mammals. Then rodents, and then the pinnacle of all creation, the Eastern Gray Squirrel. And while that is the best and highest of all lineages, there are many more.

Now, at every stage in that faunal succession, we see something weird, which is that the earliest of the one sort look a lot more like their contemporaries of the preceding sort. The dermal skull roof of Eusthenopteron somehow winds up being the pattern of the dermal skull roof of the early tetrapodomorphs, with little tweaks here and there. The same observation applies again, and again, and again through the faunal succession.

And then, now and again, despite the fact that many interesting creatures must have existed that are not known from fossils, we get a real showstopper. There’s no way, one might suppose, to get from the basal amniote jaw to the mammalian jaw; one of them is compound, while the other is a single bone, and they don’t even hinge from the same location on the skull! And then a range of interesting creatures, including the aptly-named Diarthrognathus, pop up and the picture snaps into clarity. Just a few weeks ago, Science had a marvelous piece on some new creatures that shed further light on that transition.

This is not all, of course. Embryology is another hugely important source of insights, for one.

And each of these classes of observations is backed by a body of research literature so vast that no human being could read it all in a lifetime. Bio-Complexity, meanwhile, strains to manage to produce the occasional literature review, or some gob-stopping imbecility like the paper they printed on the important question: who should be called the “parents” of a synthetic organism?

I am astonished. The “must have” clause is essential to your argument. It is precisely what you repeatedly have argued here. It does you no good to argue that because a human intelligence CAN design things, therefore another kind of intelligence, if it existed, could also have designed things. The design inference you seek to make is that supernatural beings MUST have designed living things. If you were not interested in showing that this MUST be the case, why would you bother trying to attack evolutionary theory? Whether evolutionary theory is generally right or generally wrong would have no impact whatsoever upon a god’s ABILITY to design living things.

On that: everyone has got to concede that IF a supernatural entity with vast knowledge and whatever physical tools are required were shown to exist and have the capability to design living things, living things COULD have been designed by such a thing. This much is just obvious. Your difficulty is that you need to show that the entity exists and can do this – which you cannot – and then you need to show that this actually is the cause of living things – something else you cannot do.


What you are missing is a mechanistic explanation for new innovative features. This is where the design agreement comes in.

It’s not what I have argued. I have argued that a mind is a viable explanation for what we are observing as it can over come problems that perturb evolutionary mechanisms such as long sequences, functionally arranged parts, long waiting time for fixation in populations and the good old chicken and egg paradoxes.

No, that’s not “missing.” That’s something you didn’t ask about. Goalposts have attachments to the ground for a reason, you know. I note that you apparently have no quarrel with the point that these lines of evidence provide substantial empirical confirmation of common descent, which is the thing you DID ask about.

But if you’d like a mechanistic explanation for a new feature, take a look at the mammalian jaw situation which I described. Nothing in that poses any intractable problem for straightforward evolutionary mechanisms.

But everyone agrees that if you grant the existence of an infinitely powerful mind coupled to some mighty capability to make living things, this would be a viable explanation for anything you can possibly imagine. One can hardly dispute that! How does that help you show that living things were designed?


Well phooey! I’m still 150 comments behind … I’ll just throw this in, feel free to ignore.

Eric didn’t seem bothered when I pointed out where Dembski CSI (Dembski 2005) requires that probabilities can be greater than 1.0, and are even used in an example where CSI is negative. If violating the very definition of probability isn’t a refutation, then what is?

The WEASEL program finds the target by evaluating the function “number of matched letters to [TARGET]”. In that example the input target was hard-coded. BUT it could easily be otherwise, The algorithm can be applied to any input function (which might be input from a source external to the program. In term of evolution, the input comes from the environment, which is not coded in the DNA.

I recall we have a discussion of this last year. Among the many objections to Eric’s argument was a lack of definition of what was being computed, what constitutes a Halting State, and why this should apply to evolution? (A point I never got to make in that discussion was that the only relevant halting state seems to be “extinction of all life on Earth.”)

An excellent example of a Genetic Algorithm conquering a fitness landscape. :slight_smile:
I also recommend, Genetic Cars, inspired by BoxCar2D. It has fewer options, but runs multiple car in parallel, meaning you don’t have to watch it for nearly so long to see the progress.

The fitness landscapes for BoxCar2D are separate from the Genetic Algorithm, NOT hard coded as they were in the WEASEL example. BoxCar2D has a literal “landscape” that the cars must traverse, and the only input “fitness” is the distance traversed.

OK, now someone can tell me my late comments are now irrelevant. :slight_smile:


We have a very good mechanistic explanation Bill. We’ve had it for the better part of a century. It’s called evolution and you had it explained to you countless times already.

Why do you keep pretending this same tired question of yours hasn’t been answered?


The motto of the ID movement is “If we can keep talking, we haven’t lost the argument!”


It’s a metaphorical code. Codes require abstractions, and there are none involved in that mechanism–unless we are talking about it.

And in general, alternative splicing is sloppy, so not a good place to stuff the diminished ID idea of God into.

This seems to be the source of a lot of the confusion. In DNA sequences, McLuhan’s law applies: the medium is the message. Instead of arbitrary symbols referring to abstractions, we have chemical substances which react with other chemical substances and produce results which are purely the result of chemistry. We can view these abstractly and talk about them as “codes” and whatnot as a shortcut aid to understanding, but these abstractions belong to us alone; DNA knows nothing of them and does its own thing.

It ought to be obvious, but apparently isn’t always: the explanation of a thing, as expressed by a human mind, is not the thing itself.

Once one points it out and clearly explains it, confusion is no longer a viable explanation.

Indeed not. I find that the explanation sometimes has traction with those who have not yet had the full gallon of Kool-Aid, but after that, the explanation just results in further proof that the motto of ID is “If I’m still talking, I haven’t lost the argument!”


The challenge for evolution is to find a functional sequence without a target.

Fair point.

Short of granting the existence how about evidence of the existence?

Which evolution has been doing successfully for 3.5 billion years. :slightly_smiling_face:

I’d love to see it. I hope, however, that it will neither take the form of scriptures nor of subjective experience, as such things are not likely to be convincing.

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Yes, but ID has only been working without a target since “creation science” died in Edwards v. Aguillard, 34 years ago. It’s true that the arguments today are indistinguishable from those made then, but perhaps the accumulation of slight modifications over millions of years will eventually lead to a hypothesis, then perhaps to something even greater.

Yeah, I don’t see that happening, either.


On that: one of the really funny things about the ID discussion is precisely the fact that it never changes. Practically every word that has been spoken in this thread could have been said in 1990. ID never has new evidence, and never has new arguments, except that the same terrible arguments that didn’t make a lick of sense thirty years ago do hop, like fleas, from old research findings that don’t support ID to new research findings that don’t support ID, always accompanied by some sort of horrid force-fit that argues that these new findings do indeed somehow lead to conclusions that nobody would ever actually draw from them.

As Gould noted, stasis is not the absence of data. Stasis can mean something.