Is ID science? Redux

Who said once? Who said it disappeared? Are you sure you want to fight this fight?

In thread after thread, “mind” is offered as a ID mechanism, and despite multiple requests, it is never explained how “mind” is supposed to act upon nature.

There is a perfectly serviceable word in the English language to denote the mind of God intervening in nature and history - miracle. Whether or not one believes in the possibility of miracles, everybody understands the concept, and everybody knows that miracles are not the purview of science. So ID persists in this dance where any gap in scientific understanding is turned into a sophistry of information blather in an attempt to render a belief in the miraculous to something sounding like science. The preservation of this pretense compels “mind” messaging, and explicit references to God and miracles are studiously avoided.

Also avoided is a discussion of the teleology of “mind”, as that would display the theological underpinning of ID. But neither human nor supernatural minds, unless burdened by obsessive compulsion, organize or create complexity to no purpose. As has been pointed out before, many of the features of nature which manifest the highest orders of complexity are those which are inherent to the problem of evil and suffering. If mind is invoked as an explanation for the organization of irreducible complexity, implications as to the purpose of that mind are inseparable. Pretty much all of camouflage in nature revolves around predation. Our intricate immune systems are concerned with sickness and disease. While there may be legitimate theological approaches to the ramifications of death and pain in creation, it is not legitimate to appeal to mind to explain complexity while ignoring purpose.


You’re right here, there is a mistake in my formulation. I should have said the following : « V(D)J recombination doesn’t produce high FI for most of the genetic information necessary for implementing the function preexist in the stem cells that develop into B cell ». Thanks for the correction.

Please show your math.


You’re rising interesting and serious questions. Yes, the c-value paradox seems to be a difficulty for the idea that most DNA is functional in all organisms. But I stand by it for the moment, for postulating that most DNA is junk is the best way to deprive ourselves of the possibility of making major discoveries in this field.
As for me, I see the view expressed by
Forest M Mims III below as a promising line of research for elucidating the function of large amounts of « junk DNA »
« A do-nothing string of NOPs [no operations] might appear as “junk code” to the uninitiated, but, when inserted in a program loop, a string of NOPs can be used to achieve a precise time delay. Perhaps the “junk DNA” puzzle would be solved more rapidly if a few more computer scientists would make the switch to molecular biology ».

It is not necessary to do the math.
Take this first sequence of letters:
« V(D)J recombination doesn’t produce high FI for most of the genetic information necessary for implementing the function preexist in the stem cells that develop into B cell »

Now take this second sequence of letter:
« V(D)J reco/dejpecbfsjeetrxyd/mbination doesn’t pro/ctifhkeswbudhg/duce high FI/tufdhkerttpbcdgezkmds/for most of the genet/pmhezybcvfdjufpaaxd/ic information necess/apchfsjudftepmbdqa/ary for implementing the function/qgfuotyudgjdepnvxwhj/ preexist in the stem cells that/arvfhjdtupmdfzqo/ develop into B cell ».

Can you see that the functional information in the first sequence is already nearly there in the second so that the transition between the second and the first sequences doesn’t involve a large jump in FI?

If it did not disappear, then it would still be present and there would be no reason for there not to be “duplicable testable evidence” for its existence.

Wrong. I, for one, disagree with that claim. Take an example of something that most people would call a “miracle” if it happened: A person has been decapitated and is dead. A person who claims to be able to perform miracles haves his hand of the the person’s body, and the head rejoins the rest of the body and the person is now alive and well as if nothing happened.

Explain why we could not demonstrate that this has happened using empirical evidence?

So what is your answer to that problem.

I would say that pales by far in comparison to the damage that would be done if large amounts of scarce scientific resources were devoted to pursuing “Intelligent Design” and similar forms of junk pseudoscience.

There is no “junk DNA puzzle”. We know that most of many genomes is junk, and we know why this is the case. There remain parts of the genome that are non-coding but which are not known to be junk, and scientists are still investigating these. I fail to see how accepting the fact that junk DNA exists would be deleterious to science. Science does not thrive on denial and delusion.

No. Show your math.

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This talking point is based on a misapprehension about how research in genetics takes place. Scientists look at particular pieces of DNA usually because some type of GWAS has implicated a particular locus in some disease(at least that’s how it’s done in most medical research on heritable human diseases). Meaning that a particular cohort of people with particular symptoms have undergone genetic testing, and a correlation between people with those symptoms and particular stretches of their genome has been shown. This then provides a clue to motivate further research into trying to determine what it is about this implicated DNA locus, that could at least potentially contribute to the symptoms.

There’s nobody around, and there never were, EVER, anyone who said “we shouldn’t bother studying this DNA here because evolution says it’s junk”.

That a particular pieces of DNA might be junk-DNA, which can be inferred by how well it is conserved, would still not tell you anything about whether that DNA is likely to contribute a genetic component to a disease of some sort. There are so many was that even nonfunctional DNA, which normally does not contribute to any selected organismal function (whatever that might be, metabolism, development, or what have you), can still end up interfering with “normal” cellular functions under the right conditions.

That’s nice but the problem here is that junk-DNA isn’t a “do-nothing string of no operations”. Junk-DNA is known to still be biochemically active in the sense that the transcriptional machinery will still reliably recruit and express even completely randomized DNA, though most of the time at a low level. That’s actually one of the reasons why junk-DNA is still worth studying, because it can still end up having some effect that can contribute to disease.

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So you’re assuming the truth of something objectively false in order to free up your scientific research? That seems counterproductive. Junk DNA isn’t an assumption, as you seem to think. It’s not DNA whose function we don’t know, as many people unacquainted with the science seem to think. There is positive evidence for lack of function, which you are choosing to look past. That isn’t how science ought to work.

Small amounts, perhaps. Essentially, it might explain the sizes of a few introns. For most introns, the c-value paradox in miniature — intron lengths varying dramatically between closely related species — kills off the general case. And of course it’s completely irrelevant for non-genic sequences.

There is no puzzle unless you make the unwarranted assumption that all DNA is functional. The computer code analogy is a blind alley.

Objectively false! Your view isn’t share anymore by many biologists that used to believe the junk DNA thesis, as you can see below. (The quotes below are taken from a piece by John Berea. Here is the link to the entire piece: Predictions of Junk versus Functional DNA | Berean Archive)

Perspectives change

As new research revealed higher-than-expected levels of function, some former junk DNA proponents changed their minds:

Francis Collins, 2010
Francis Collins was the former head of the human genome project and currently heads the National Institutes of Health. He wrote:

The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more ‘junk DNA’, think again.34

Also in 2015:

I would say, in terms of junk DNA, we don’t use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn’t functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu’s, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that’s where the epigenome gets involved, and is teaching us a lot.42
Richard Dawkins, 2012

I have noticed that there are some creationists who are jumping on [the 2012 ENCODE results] because they think that’s awkward for Darwinism. Quite the contrary it’s exactly what a Darwinist would hope for, is to find usefulness in the living world […] we thought only a minority of the genome was doing something, mainly that minority which only codes for protein, and now we find that actually the majority of it is doing something. What it’s doing is calling into action the protein coding genes. […] The program that’s calling them into action is the rest that had previously been written off as junk.35
Thomas Gingeras, 2012
A lead ENCODE researcher (paraphrased in the New York Times)

The thought before the start of the [ENCODE] project, was that only 5 to 10 percent of the DNA in a human being was actually being used. The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches.62

Richard Dawkins’ own selfish gene theory led to the expectation that most of the human genome was junk,5 6 25 27 while neutral theory and the problem of genetic load require it outright. So it doesn’t make sense for Dawkins to say “it’s exactly what a Darwinist would hope for.”

Even shortly before the landmark ENCODE phase 2 announcement of 80% function in 2012, biochemist and junk DNA proponent Larry Moran blogged that most evolutionary biologists he meets no longer share his view:

Other functional genome researchers expect even more functions to be found in the future:

#### Ewan Birney, 2012

Birney led the analysis group for the ENCODE project.

It’s likely that 80 percent [estimate of functional human DNA] will go to 100 percent. We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.61
#### John Mattick, 2013

John Mattick is a non-coding DNA researcher who is the CEO of Genomics England, which runs the 100,000 genomes project.

Where tested, these [differentially expressed] noncoding RNAs usually show evidence of biological function in different developmental and disease contexts, with, by our estimate, hundreds of validated cases already published and many more en route, which is a big enough subset to draw broader conclusions about the likely functionality of the rest.60

In 2018, Mattick noted that more biologists were coming around to the idea that most DNA is not junk:

While not everyone yet agrees with me, the evidence is very strong and my thesis is more widely accepted than it once was.66

Gil I’m still waiting for an explanation of how you know what God would or wouldn’t do.

“It’s existence” is not what is in question here. It is potential meddling by the “it” that is in question.

Same thing here. There is a way to empirically test whether the body was dead and then alive, but the vehicle that would have caused such an event is supernatural and outside of science (even observation.) You could only test the death to life aspect. The cause would be outside of science because it is supernatural. Literally outside of nature.

Take this discussion and apply it to the ID world. They are saying that some intelligence has intervened so as to cause things to be how they are. No one is looking for the existence of the intelligence itself to determine whether or not this has happened. Instead, they are looking to the living object purportedly affected by the intelligence. You have changed subjects here.

The point that I was making (and @ronsewell also) was that there are separate domains for these kinds of events. Science is not capable of handling both kinds.

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9 posts were split to a new topic: The Fossil Record and Evolution

Might it not kill of the general case for common descent instead?

How do you know that these NOPs strings are completely irrelevant for non-genic sequences? As for me, I can see for example that they could be essential for proper timing of gene expression during development.

With all due respect, I am wandering whether you are not falling into « the pretense of knowledge » pitfall.

Or you have no idea what you’re talking about and are trying to bluff your way through using Behe’s lame excuses.

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How do you know that? Have you actually encountered such a situation and tried to determine the cause? Has anyone?

Yes, that’s unfortunate. So many people into genomics are ignorant of the relevant science. How interesting that you believe all these people about junk DNA based purely on credentialism, but discredit their views on evolution. You need to stop getting all your information from creationist cherrypicking. I advise checking out Larry Moran’s blog for a corrective.

I don’t think that’s what Larry actually said. Molecular biologists, perhaps.

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There are certainly many people who have been misled by the ENCODE hype fiasco, but even the ENCODE leaders have been out there walking back their claims.

It didn’t. Some researchers(ENCODE) mistakenly confused biochemical activity, aka low-level transcription, with function. But as explained in my previous post, the mere fact that most DNA is transcribed doesn’t show it its functional. As revealed by experiments that show that the cellular transcription machinery will actively transcribe even random DNA designed to have no function.

Which knowledgeable biochemists had known about for almost half a century already at that point.

And they were misled. They, too, had the misconception that junk-DNA was supposed to mean completely chemically inert DNA. But it never did. They were uninformed about the concept, has got the history of it completely wrong because they’ve been reading people like John Mattick who also never understood it, combined with the fact that a lot of bad science press has been mistakenly hyping every new finding in genetics as the Next Big Thing that “overturns everything we used to think”. And the concept of junk-DNA never fails to catch people’s attention and generate clicks. Sadly a lot of otherwise well-meaning researchers have been misled by these click-bait articles too.

All you have succeeded in doing is find a list of people who didn’t understand the case for junk-DNA, don’t know it’s history, and don’t understand how the inference were made in the first place, or what evidence for and against it is.

LOL. No it didn’t. Your understanding of this subject is truly abysmal if you think so.

Dawkins “selfish gene theory” is really just another description for the gene-centric view of evolution. It made ZERO predictions about the proportion of the genome that should constitute junk DNA.

If you disagree, then find the prediction. Give a reference to the theory of selfish genes being employed to derive a prediction about how much junk DNA there should be in the human genome.

Let me save you some time: No such reference exists.

What actually happened, in real history instead of the extremely misleading pseudohistorical nonsense you’re actively participating in propagating here, is that the “selfish gene theory” about the gene-centric view of evolution made sense of the discovery that a large proportion of the human genome constitutes accumulated remnants of selfish genetic elements such as retrotransposons.
Helped make sense of, it was not “predicted” by “selfish gene theory”.

None of the references you give actually support the claim. Dawkins sefish gene concept is just a theory of adaptive evolution that says selection is best understood to occur at the level of genes, not at the level of species or populations. It’s called the gene-centric view of evolution.

Yes it does, you’ve got it completely wrong. The idea is that if the DNA is truly nonfunctional and does nothing for the organism, then it has an energy cost in terms of replicating it during cell division, and a cost associated with expressing it, in turn leading to the naive prediction that to get rid of it would be beneficial because it would save energy for the cell. So a priori, without looking at the strength of the selective pressures actually involved, a Darwinist would predict no junk-DNA because selection would work against it’s existence.

Now once other factors are included, the naive prediction changes.

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Is ID science?

I’ve said, **“NO” for years.

I’ve not been quite forgiven by my colleagues for saying so.

Saying however, “origin of life is so improbable and violates normative expectation of accepted laws of chemistry and physics that it is a statistical miracle” is science.

No. That makes no sense, and it suggests you don’t understand the data at all. The mechanism by which large indels occur is well understood.

What would they do? What do you think is the point of timing?

How would they do that?

Yes, you are wandering quite a bit.

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