Death of the junk DNA myth?

On the one hand, naturalistic evolution predicted that large portions of DNA would happen to be useless, hence the term junk DNA. On the other hand, ID predicted the opposite, ie, that the vast majority of DNA would turn out to be useful. Clearly, the new study by Caltech scientists reported here supports ID prediction better than the naturalistic evolution one.
https://evolutionnews.org/2021/12/caltech-finds-amazing-role-for-noncoding-dna/III

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Here is a link to the referenced paper on a Caltech server:

RNA promotes the formation of spatial compartments in the nucleus

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Your title is wrong.

The myth that junk DNA is the same thing as non-coding DNA continues. And the EN post that you cite is promulgating that myth.

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Actually, “naturalistic evolution”, by which one assumes you mean evolutionary biologists, was surprised to discover that so much of the genome was junk, as it seemed at first thought that natural selection would eliminate such things. On the other hand, many ID folks disagree that ID predicts the absence of junk. So you’re wrong twice. The third time is citing Evolution News as if it were a credible source.

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Hundreds of long ncRNA found in close proximity to their transcriptional loci, therefore all DNA is functional? How big is the human genome again, and more importantly, why would even very similar species need such massive differences in DNA anyway?

That’s right, this one also fails the onion test.

Next!

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Curiously, none of the grandiose claims against junk-DNA made in the EN post are made in the paper itself. The paper contains no mention or discussion of the concept of junk DNA or the proportion of different eukaryotic species genomes that are functional and none of the papers on the cases or evidences for junk DNA are cited and discussed.

I must here simply reiterate what Larry Moran has said before: Sandwalk: Required reading for the junk DNA debate

Required reading for the junk DNA debate

This is a list of scientific papers on junk DNA that you need to read (and understand) in order to participate in the junk DNA debate. It’s not a comprehensive list because it’s mostly papers that defend junk DNA and refute arguments for massive amounts of function. The only exception is the paper by Mattick and Dinger (2013).1 It’s the only anti-junk paper that attempts to deal with the main evidence for junk DNA. If you know of any other papers that make a good case against junk DNA then I’d be happy to include them in the list.

If you come across a publication that argues against junk DNA, then you should immediately check the reference list. If you do not see some of these references in the list, then don’t bother reading the paper because you know the author is not knowledgeable about the subject.

Brenner, S. (1998) Refuge of spandrels. Current Biology, 8:R669-R669. [PDF]

Brunet, T.D., and Doolittle, W.F. (2014) Getting “function” right. Proceedings of the National Academy of Sciences, 111:E3365-E3365. [doi: 10.1073/pnas.1409762111]

Casane, D., Fumey, J., et Laurenti, P. (2015) L’apophénie d’ENCODE ou Pangloss examine le génome humain. Med. Sci. (Paris) 31: 680-686. [doi: 10.1051/medsci/20153106023] [The apophenia of ENCODE or Pangloss looks at the human genome]

Cavalier-Smith, T. (1978) Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA C-value paradox. Journal of Cell Science, 34(1), 247-278. [doi: PDF]

Doolittle, W.F. (2013) Is junk DNA bunk? A critique of ENCODE. Proc. Natl. Acad. Sci. (USA) published online March 11, 2013. [PubMed] [doi: 10.1073/pnas.1221376110]

Doolittle, W.F., Brunet, T.D., Linquist, S., and Gregory, T.R. (2014) Distinguishing between “function” and “effect” in genome biology. Genome biology and evolution 6, 1234-1237. [doi: 10.1093/gbe/evu098]

Doolittle, W.F., and Brunet, T.D. (2017) On causal roles and selected effects: our genome is mostly junk. BMC biology, 15:116. [doi: 10.1186/s12915-017-0460-9]

Eddy, S.R. (2012) The C-value paradox, junk DNA and ENCODE. Current Biology, 22:R898. [doi: 10.1016/j.cub.2012.10.002]

Eddy, S.R. (2013) The ENCODE project: missteps overshadowing a success. Current Biology, 23:R259-R261. [10.1016/j.cub.2013.03.023]

Graur, D. (2017) Rubbish DNA: The functionless fraction of the human genome Evolution of the Human Genome I (pp. 19-60): Springer. [doi: 10.1007/978-4-431-56603-8_2 (book)] [PDF]

Graur, D. (2017) An upper limit on the functional fraction of the human genome. Genome Biology and Evolution, 9:1880-1885. [doi: 10.1093/gbe/evx121]

Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., and Elhaik, E. (2013) On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution published online: February 20, 2013 [doi: 10.1093/gbe/evt028

Graur, D., Zheng, Y., and Azevedo, R.B. (2015) An evolutionary classification of genomic function. Genome Biology and Evolution, 7:642-645. [doi: 10.1093/gbe/evv021]

Gregory, T. R. (2005) Synergy between sequence and size in large-scale genomics. Nature Reviews Genetics, 6:699-708. [doi: 10.1038/nrg1674]

Haerty, W., and Ponting, C.P. (2014) No Gene in the Genome Makes Sense Except in the Light of Evolution. Annual review of genomics and human genetics, 15:71-92. [doi:10.1146/annurev-genom-090413-025621]

Hurst, L.D. (2013) Open questions: A logic (or lack thereof) of genome organization. BMC biology, 11:58. [doi:10.1186/1741-7007-11-58]

Kellis, M., Wold, B., Snyder, M.P., Bernstein, B.E., Kundaje, A., Marinov, G.K., Ward, L.D., Birney, E., Crawford, G. E., and Dekker, J. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) 111:6131-6138. [doi: 10.1073/pnas.1318948111]

Mattick, J. S., and Dinger, M. E. (2013) The extent of functionality in the human genome. The HUGO Journal, 7:2. [doi: 10.1186/1877-6566-7-2]

Five Things You Should Know if You Want to Participate in the Junk DNA Debate

Morange, M. (2014) Genome as a Multipurpose Structure Built by Evolution. Perspectives in biology and medicine, 57:162-171. [doi: 10.1353/pbm.2014.000]

Niu, D. K., and Jiang, L. (2012) Can ENCODE tell us how much junk DNA we carry in our genome?. Biochemical and biophysical research communications 430:1340-1343. [doi: 10.1016/j.bbrc.2012.12.074]

Ohno, S. (1972) An argument for the genetic simplicity of man and other mammals. Journal of Human Evolution, 1:651-662. [doi: 10.1016/0047-2484(72)90011-5]

Ohno, S. (1972) So much “junk” in our genome. In H. H. Smith (Ed.), Evolution of genetic systems (Vol. 23, pp. 366-370): Brookhaven symposia in biology.

Palazzo, A.F., and Gregory, T.R. (2014) The Case for Junk DNA. PLoS Genetics, 10:e1004351. [doi: 10.1371/journal.pgen.1004351]

Rands, C. M., Meader, S., Ponting, C. P., and Lunter, G. (2014) 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage. PLOS Genetics, 10:e1004525. [doi: 10.1371/journal.pgen.1004525]

Thomas Jr, C.A. (1971) The genetic organization of chromosomes. Annual review of genetics, 5:237-256. [doi: annurev.ge.05.120171.001321]

  1. The paper by Kellis et al. (2014) is ambiguous. It’s clear that most of the ENCODE authors are still opposed to junk DNA even though the paper is mostly a retraction of their original claim that 80% of the genome is functional.
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No. Junk DNA is very real. Do we need to do this thread like every month or so?

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You forgot to say that Gil was wrong about the paper supporting the idea that “the vast majority of DNA would turn out to be useful”.

So wrong at least four times.

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That’s just a consequence of #3, Gil using Evolution News as a source. You can’t imagine he actually looked at the paper, can you?

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You are misrepresenting me. I said that ID predicts that the vast majority of DNA will turn out to be functional, not the all DNA will turn out to be functional.

The paper supports the idea that many ncRNAs thought to be useless transcriptional noise (for example ncRNAs transcribed from satellite DNA regions within centromeric and pericentromeric regions) are in fact essential players in shaping nuclear structures.

It has been known for a long time that a lot of non-coding DNA is functional. This is another example. It is not at all surprising that this should happen as the result of evolution. And the original paper does nothing to justify the claim that “the vast majority” of DNA is turning out to be useful.

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With my emphasis:

Over the past decade it has become clear that mammalian genomes encode thousands of nuclear-enriched ncRNAs, several of which play critical roles in the regulation of essential nuclear functions.

They then identified 642 loci. What is the average length of these loci? I didn’t see it in the paper, but most lncRNAs are under 2kbp, so we’ve got about 1.2Mbp of function at most, and by all indications much less than this. So does this support the idea that “the vast majority of DNA would turn out to be useful”? Not even a little bit.

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What proportion of DNA is currently known to have function?

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ID predicts no such thing, in fact, ID predicts nothing at all. The existence of junk DNA is perfectly compatible with ID in the same way a broken microwave is. Things that are designed can break down.

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Okay, but the “vast majority” of DNA hasn’t been shown to be functional in the EN post (nor the paper from which EN’s grandiose conclusions are grossly extrapolated), either.

[Citation needed]

Who thought which of these ncRNA transcripts were useless transcriptional noise?

That a transcript has some physical effect does actually not mean that effect is beneficial or essential.

This is the same basic fallacy that permeated the ENCODE fiasco, who took the mere fact that transcription happened to automatically entail the produced transcripts were functional. This just adds another layer on top. Here the physical influence of some transcript on the 3dimensional arrangement of itself and surrounding molecules are also taken as basically proof of these arrangements being adaptively functional or essential.

Something has some physical effect =/= that effect is it’s functional purpose.

Puddles of water on the ground reflect sunlight into my eyes at certain angles, but I don’t think that’s their function.

Oh and hey, I also have to once again note the inconsistency between different things ID proponents argue. Shouldn’t different functions also be incredibly rare and isolated in sequence space? And yet here we see ID proponents suggest that things like simple repetitive elements, and even pre-mRNA transcripts can simultaneously function as message-carriers for translation, transcriptional blockers or initiators, and spatial and 3-dimensional guides and compartments for gene regulation and splicing. There seems to be literally no end to the number of possible simultaneous functions you can rationalize some fragment of DNA or RNA can have, and yet also that such functions should be so unbelievably and impossibly rare and isolated from each other that none worthy of note could ever be expected to evolve by any known process of blind sampling of sequence space.

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Really? Why wouldn’t it be a really smart design to put lots of spare DNA in a genome?

When I pack for a long trip, I pack a good many things that I probably won’t need just in case. Why wouldn’t an intelligent designer think the same way about the genome?

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Someone predicts that the vast majority of swans will turn out to be black.

He finds 3 black swans.

Does this finding support his finding better than it does the prediction that most swans are white?

I guess it does so better than if he had not found any black swans.

But, still, it does not demonstrate that the prediction is true.

And if we already have conclusive evidence that over 90% of swans are white, his finding would be of no significance to the question, since we would already know his prediction was wrong.

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  1. ID proponents claim that Junk DNA does not exist.

  2. ID proponents also claim that functional sequences are so rare that, for all practical purposes, it is impossible for random mutations to result in functional sequences.

It is an empirical observation that the average person is born with somewhere between 50 and 200 mutations that were possessed by neither parent.

This would be impossible if 1 and 2 were correct.

It is possible, however, for both 1 and 2 to be false. And they are.

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