"So-called junk DNA plays critical role in mammalian development"

Do you know anything about what a retrotransposon looks like? If not, then we may have to start at the very beginning.


Every so often,someone expresses surprise at anew example of non-coding DNA being useful or endogenous retroviral DNA having been coopted to a function, even though we have known about these things for decades. So we often have good science being oversold by underinformed commentators. physorg is rather bad at this, I’m afraid


Here are some quotes from the article that support the widespread functional role of genomic repeats:

- We propose that genomic repeats shape transcription regulatory networks to achieve orchestrated activation or silencing of genes with distinct functions at specific stages
- These results demonstrate a role of L1 DNA and RNA in gene silencing and suggest a general theme of genomic repeats in orchestrating the function, regulation, and expression of their host genes.
- Here, we conducted a comprehensive and quantitative analysis of diverse repeat subclasses in mouse and human genomes and revealed a striking association of genic repeats with the function, regulation, and expression of their host genes. Importantly, we demonstrate a key role of L1 RNA in transacting L1 DNA information and in sequestering a large set of genes that are specialized in functions associated with terminally differentiated cells, in the heterochromatic nucleolar and nuclear peripheries for transcriptional silencing in ESCs. These results reveal a general theme of repeat sequences in shaping gene regulatory networks within their host genome.

And here are the Highlights:

SINE, L1, and low-complexity repeats barcode genes with distinct functions

Genomic repeats dictate the time and level of gene expression during development

L1-enriched genes are sequestered in the inactive NAD/LAD domains for silencing

L1 RNA promotes the nuclear localization and repression of L1-enriched genes

And none of that suggests that most repeats are involved in anything.

Your position was ‘most X does Y’.

Your quote says ‘some Y has X’.

I hope you understand why that doesn’t support your position.


Francis Colins used to be sure of that also. But before the accumulation of new data, he has changed his mind. Here is what he said at a J. P. Morgan Healthcare Conference in San Francisco: “In terms of junk DNA, we don’t use that term anymore because 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. . . . Most of the genome that we used to think was there for spacer turns out to be doing stuff.”

Also relevant to this discussion, this quote taken from the paper below :

«As we increasingly apply computational metaphors to cellular function, we expect that a deeper understanding of retroele- ments and other repeats, the integrative fraction of cellular DNA, will lead to increased understanding of the logical archi- tecture inherent to genome organization. In the era of biocom- puting and systems biology, the study of cellular information processing promises to revolutionize not only the life sciences but also the information sciences. We anticipate learning pow- erful new computational paradigms as we come to understand how cells use myriad molecular components to regulate mil- lions of biochemical events that occur every minute of every cell cycle. Our expectation is that, one day, we will think of what used to be called “junk DNA” as a critical component of truly “expert” cellular control regimes »

Collins would seem to be unaware of the onion test. Are you?


I’m pretty sure Collins is aware of the onion test. But maybe the piece below has convinced him that it was irrelevant

Unsurprisingly, the ellipses in that ‘quote’ are in the same place as they are in various articles written by DI charlatans - which suggests you don’t know what they omitted, don’t know whether it affects Collins’ meaning, and don’t even know whether that is what Collins actually said.

And since you’ve cited Collins directly, rather than via a secondary source, any distortion of his words or meaning lies with you and you alone.

Will you take full responsibility for any omissions or distortions of Collins’ words, or will you retract that ‘quote’ as being unreliable?

The odds of a ‘quote’ cited by a creationist being genuine, accurate and in context are worse than the odds in Russian roulette. Do you feel lucky, punk?


No need for Harry Callahan, I think.

@Giltil It would really help to present the full context of a quote before expecting anyone else to consider it credible. This saves everyone a lot of time fussing over what someone else said or thinks.

That said, I haven’t been following the discussion, but I trust you guys to sort this out in a reasonable manner.


Sadly your Collins quote contains no actual evidence, nor any putative rebuttal to the case for junk DNA. It’s nothing but pure speculation.

Were you there, Gil?

May we infer from your Gish Gallop that you are conceding that the paper you cited did not say what you claimed it did?


Suffice it to say that if Collins was persuaded by that article, his reasoning powers leave much to be desired. I also think Collins would find the terminology of the writer weird and call his competence into question. For example, a “transcriptase” doesn’t zip along DNA making protein:

As the transcriptase zipped along the DNA, the cell made proteins successively, and the ordering and timing of the proteins were such as to drive the embryogenesis and development.

Uhm, RNA polymerase is transcribing DNA into RNA. The RNA is translated into proteins.

Charitably putting that aside as possibly just sloppy writing, the case being advanced there is straightforwardly nonsensical. The author suggests that if cells had lots of junk DNA, their genome sizes should be expected to be smaller because then it would have “lower fractal dimensionality”???

Back to the lowly onion. The DNA is software. The proteins are the video feed. The nucleus is the CPU. Humans have highly complex coding/decoding machinery in the nucleus. When mathematical analysis is performed on human DNA, it is found to have a fractal information dimension greater than 3 — indicating that at least three different codes are simultaneously present. This is a number bigger than with chimpanzees, whose DNA is not so compressed, and if I recall correctly, comes in around 2.5 or so. With onions, I think it is a safe bet that the fractal dimension is < 2.0.

What does this changing dimension mean for DNA size? Well the information in DNA is proportional to the volume of phase space, so if humans have dimension 3.0, then the volume ~ (3.2 GB)^3 = 27 GB. This dwarfs the 15 GB of the onion, but then I don’t know the fractal dimensionality of onions.

Now admittedly, the ENCODE papers don’t do the entire genome — they look at little subsets, so I may be generalizing too much to say that I know the dimension of information packing. But if the genome had junk DNA in it, it would drive the number lower, not higher, because junk DNA is uncorrelated to everything else. This is categorically what is not found, and so even without the ENCODE results, it is manifestly obvious that human DNA is not mostly junk.

The “fRaCtAl dImEnSiOnAlIty” of DNA? And he’s just making up numbers. Literally just making stuff up. Onions “it is a safe bet” is < 2.0
Chimps, “if he recalls”, is ~2.5

This is pure cargo-cult science.

This guy is a total fraud. Also, he seems to have totally missed the whole point that the Onion is just one example, and that even within different species of Onions, genome sizes vary five-fold. So one onion has higher “fractal dimensionality” than another, because it has more complex embryonic development too? Or what? Is he going to concoct a new and unique, ad-hoc hypothesis for ALL individual genomes?


That would require knowing the context - and everything about @Giltil’s presentation suggests he cribbed it from a creationist website where no context was provided.

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I am suggesting it should be Gil’s responsibility to verify the quote AND the context of that quote.

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I’m setting a 15 minute Slow Mode until 6 PM today, because my time is limited.

An article that begins by misunderstanding what the onion test is might not be a good reference for you. Apparently you don’t know what the onion test is either. It’s not a comparison of humans and onions; it’s a comparison of closely related species of onions. You probably shouldn’t cite Evolution News, or any creationist web site, really.


You will find the same quote in Science

It’s Ptolomy’s epicycles again.

So rather than a single overarching hypothesis that actually explains something about the sequences we find in living organisms that make up the differences in genome size, we’re going to need 10 million different hypotheses, one for each individual species that has to do with some obscure and unique relationship between their complexity, development, life-challenges and so on?
Also from that EN&V article:

Crude, but why do that at such a high cost to the genome of every cell?

Perhaps there is a plant virus that hijacks the “clock” to crank out tumors. This onion solution would then be impervious to such a virus. It might even give it an “evolutionary advantage.”

Perhaps this, perhaps that. If I recall that Y, it is a safe bet that X. And we’ll know some time in an unspecified future why things we already have a single very good - in practice easily falsifiable hypothesis to explain - is better explained by some baroquely complex replacement.


If you don’t know the difference between something being in Science, and something being on someone’s blog that is hosted by Science.org, you really shouldn’t be making any comments at all.


No, you will not. That’s a very good blog on the Science web site, not Science itself.

You don’t seem to look very carefully before claiming to have evidence. Why is that?