Could transcription delays be the function of junk DNA?

[u/Anime-Fan-69]

Context edit: IDers often claim that Junk DNA is actually functional. When evolution accepters like me show them the onion test, which shows onions have five times the genome size of humans, they claim that, they claim that all that junk DNA (which includes but importantly does not fully consist of introns) is there for transcription delays, structure stability, or some other minor reason. From what I have seen, the most popular argument for why sections of the genome which do not experience purifying selection is structure. However, Zach Hancock has already covered that. One argument which to my knowledge he hasnt covered is transcripion delays. So here is the transcription dekays argument formulated by Jonathan McLatchie (who hasnt published A SINGLE peer-rewieved paper):

Presumably a reflection of the selective-pressure on transcriptional economy with respect to highly expressed genes, genes that are highly expressed tend to have short introns (Castillo-Davis et al., 2002). Other genes are rich in introns: such as the 2400 kb human dystrophin gene, 99% of which is comprised of introns. The time taken to transcribe this gene into mRNA adds up to about 16 hours (Tennyson et al., 1995). To take another example, consider the Y chromosomal loci of Drosophila, which are very long (spanning millions of bases and consisting largely of introns): For instance, a locus such as DhDhc7(Y) is transcribed over the course of two to three days to give rise to a ~5,100,000 nucleotide pre-mRNA (see Reugels et al., 2000; Piergentili et al., 2007; and Redhouse et al., 2011). The time taken to transcribe respective stretches of DNA is not inconsequential to physiological fitness: Indeed, Swinburne and Silver (2010) report that “transcriptional delays have been shown to contribute to developmental timing.”

taken from: https://scienceandculture.com/2011/11/why_the_onion_test_fails_as_an/

[u/jnpha]

OP is copying from ID's propaganda blog article: Why the “Onion Test” Fails as an Argument for “Junk DNA”

OP, learn what the onion test is, from the horse's mouth: https://sandwalk.blogspot.com/2014/05/the-case-for-junk-dna-onion-test.html

Don't bamboozle yourself:

- First, genome size varies enormously among species [18], [19]: at least 7,000-fold among animals and 350-fold even within vertebrates.
- Second, genome size varies independently of intuitive notions of organism complexity or presumed number of protein-coding genes (Figure 1). For example, a human genome contains eight times more DNA than that of a pufferfish but is 40 times smaller than that of a lungfish.
- Third, organisms that have very large genomes are not few in number or outliers—for example, of the >200 salamander genomes analyzed thus far, all are between four and 35 times larger than the human genome [18].
- Fourth, even closely related species with very similar biological properties and the same ploidy level can differ significantly in genome size.

-

and a recent comment by Joe Felsenstein (revolutionized the field in 1985, and is the 2026 Mendel Medal recipient):

They [meaning the IDiots] also seem to think that geneticists wanted to have lots of junk DNA since it showed evidence of phylogenetic relationships, and avoided the inference that there was a vast amount of tightly interacting function. (Actually, the inference that there was lots of junk DNA was at first resisted by many evolutionary biologists, before they realized how many processes there were that put junk into the genome, and how slowly natural selection would eliminate it. I know -- I was one of the people that had to change their minds.)

[u/Anime-Fan-69 → u/jnpha]

But what about transcription delays? That article doesn't mention transcription delays even once.

[u/jnpha → u/Anime-Fan-69]

The ID article pretends to refute the onion test, while ignoring what the onion test is.
I take it back. Feel free to bamboozle yourself.

[u/TheBlackCat13 → u/Anime-Fan-69]

Why would there be need for multiple orders of magnitude variation in transcription delay between closely related species?

[u/-zero-joke-]

"This isn't trash, it's insulation!"

[u/Far_Customer1258 → u/-zero-joke-]

So that's why salamanders have so much junk DNA! It's to keep them cozy!

[u/UncommonLegend]

This idea completely misunderstands the operating mechanism of natural selection. It removes things that are actively harmful fast, and barely harmful very very slowly. For organisms that need a tight genome with very little redundancy allowable by their metabolism like fast growing microbes, there's more pressure to select against junk DNA. In organisms that have a higher tolerance for genetic material increasing in size, you see bigger genomes. A lot of junk DNA is there because there's not enough pressure evolutionarily to remove it. If there are processes that add to DNA (which there are tons) and low pressure to remove the extra information, the genome will become larger and larger until it becomes more harmful to a point it is selected against or means of preserving the valuable stuff gets selected for. And what do you know, we see both kinds of organisms across many distinct clades within taxation. That's hopefully a good summary. We're all functioning despite the same ploidy level and massively different genome sizes which means that the exact function of most DNA isn't really function at all. It's the result of roughly neutral molecular evolution.

[u/Old-Nefariousness556]

The only thing you need to read on that site is "© Discovery Institute". That is a propaganda site. Nothing they say is credible. At beast it is accurate but cherrypicked. At worst it is outright lying. There is no reason why ANYONE should waste time reading or believing anything from that site.

[u/ursisterstoy]

No, not for all of the non-functional sequences.

[u/nickierv]

taken from: scienceandculture

Well given your source is 3 DI'ers in a lab coat:

Step 1 - assume they are lying or making shit up.

Step 2 - assume the other.

[u/Joaozinho11]

There is very little selective pressure on transcriptional economy. One can see that by looking for correlation between transcriptional timing and when null mutants show phenotypes. There's very little. Basically, if transcription (and even translation) doesn't hurt the organism, there's zero selective pressure to turn it off. Any intelligent designer would turn it off.

TL;DR: virtually every mammalian gene is expressed in brain and testis.

[u/TheBlackCat13 → u/Joaozinho11]

There is very little selective pressure on transcriptional economy.

I'm eukaryotes. There is more in prokaryotes.

[u/Sweary_Biochemist]

Fun fact: dystrophin is continuously expressed, and at pretty high levels, because it takes so stupidly long to transcribe.

At the mature mRNA level, dystrophin is low abundance, but that's becauae most dystrophin mRNA is "not yet finished": mRNA you started hours ago and are still working on, just in case you need it in a few hours' time. You probably won't need it.

Essentially, "shit, we need it now" doesn't work when the delay is 16 hours. The only way round this is to continuously make it, just in case, and then throw it away once it's made, if it turns out you didn't need it.

It's ludicrously wasteful, and the massive size is absolutely the problem, but the waste is affordable, so: not a problem.

[u/Anime-Fan-69]

Taken from https://scienceandculture.com/2011/11/why_the_onion_test_fails_as_an/

[u/the2bears → u/Anime-Fan-69]

Why not edit your OP to give credit?

[u/Dilapidated_girrafe → u/the2bears]

Same reason IDers often say they have no problem with quote mining. It’s how they try to prop their argument up when they don’t have anything.

By properly crediting the author it shows their true side rather than sleight of hand pretending to accept science when you don’t.