The Center for Science and Culture (sic) and the Discovery Institute (sic) have published another propaganda video on junk DNA. The emphasis is on their claim that ID predicted a functional genome and that prediction turned out to be correct! The difference between this video an previous attempts to rationalize their failures is that I now get a personal mention and a caricature in this latest video.
I think I understand the problem. The ID creationists are getting worried about junk DNA as they realize that more and more scientists are beginning to understand the real problems with the ENCODE data and previous claims of function. This is why they are attempting to rebut the science behind junk DNA. But the real problem is that they simply don't understand the science as you can see in the video.
Once again, we are faced with a question about whether Intelligent Design Creationists are stupid or lying (or both).
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10 years after ENCODE, creationism still doing same-old, same-old on junk DNA: they have an inch but they pretend it's a mile. With vast amounts of unused DNA lying around, it is only to be expected that evolution will opportunistically enlist small amounts to do something, especially as yet another regulator of some gene. They continually gloat over some tiny bit of "Junk DNA" that has been shown to be useful (by mainstream biologists, of course). But they still ignore the vast amounts of DNA with no known function, and the arguments why most of it is almost certainly useless. Also, the function of the non-coding DNA is often not nearly as "information rich" as coding DNA is.
Lying. They have had this explained to them before so many times. It's actually not THAT complicated. One can't accidentally misunderstand the case for junk DNA in a misleading way so many times, over and over and over again. They're lying.
If the Christian God exists then everything is permitted, including lying, because all they have to do is repent and they'll go to heaven.
-César
There's also a bit of cognitive dissonance. IDer's claim over and over that function requires a highly specific sequence, and yet they think 90% of the "functional" DNA in the human genome can mutate freely without selection and still maintain function. Those two concepts don't match up.
If IDers are of the opinion that transcription = function, then I believe it is useful to reflect on the roles of the transcripts they are using to infer function. Many (most?) of the transcripts derived from repetitive DNA and transposons are small RNAs that work to prevent the expression of these DNA elements as polII transcripts. This in turn reduces the deleterious consequences of expression of these elements. This in turn promotes the persistence of these elements by "shielding" them from natural selection (that would otherwise promote their deletion).
In other words, the function of all of this DNA (and RNA) is to survive. Which means that IDers are all agog about selfish DNA.
I have not heard about that one -- that these sorts of junk DNA have a bit of transcription that protectively act as negative regulators of their own transcription.
@Arthur Hunt: Genes take up about 45% of the genome so that accounts for transcription of 45% of the genome. ENCODE claimed that about 80% is transcribed so what about the 35% of the genome that isn't accounted for by genes?
You are suggesting that a good part of this is due to production of regulatory RNAs that block the production of spurious transcripts from repetitive DNA. Since these regulatory RNAs have a function, they must be genes. They are not junk.
Let's assume that the functional part of these small regulatory RNA genes is about 1kb. They must be subject to purifying selection if they are functional but there's no evidence that a substantial number of these presumed regulatory RNA genes exist from looking at constrained sequences. Furthermore, if they account for 35% of the genome then that would amount to about one million of these genes.
How many of these hypothetical genes do you think there are in the human genome?
The other explanation is that there are lots of spurious transcription promoters scattered throughout the genome. Some of these are due to chance and some are leftover promoters from now defunct viruses and transposons. These spurious transcripts give rise to junk RNA and those rare, rapidly degraded RNAs are easily detected by modern techniques. That accounts for the extra 35% of the genome that's transcribed.
We should also keep in mind that introns account for almost 40% of the genome and almost all of this is junk DNA. Introns are transcribed but the RNA is rapidly degraded. What this means is that typical eukaryotes don't seem to under significant pressure to reduce the amount of junk RNA that is produced so it's unlikely that they would evolve sequences to suppress the transcription of each degenerate virus or transposon.
I'm an old earth creationist, and have generally agreed with this series of videos on origin of life by Long Story Short. However, in this case, I posted this critical comment on YouTube: "Appreciate this series, but giving the impression that the c-value paradox is explained by polyploidy is misleading: “Some organisms with large genomes are not polyploid. For example, lungfish and salamanders have enormous genome sizes but are not consistently polyploid. Their large genomes are attributed more to the accumulation of repetitive elements and other non-coding sequences.” (Oddly, the comment is not visible when I'm not logged to a specific Google account)
Regarding this topic, thoughts on this paper? It challenges Dan Graur's position, but allows for a low f for other reasons.
"Mutational Load and the Functional Fraction of the Human Genome"
https://academic.oup.com/gbe/article/12/4/273/5762616?login=false
@MarkE: Graur refereed that paper and he now agrees with the general conclusion that the mutation load argument does not put a severe constraint on the fraction of functional DNA in the human genome. The calculations and the assumptions are too complex for me to evaluate.
@Larry Moran, you said that, for eukaryotes, “it's unlikely that they would evolve sequences to suppress the transcription of each degenerate virus or transposon.” It may seem unlikely, but it is a fact that such systems do exist. Plants possess, in addition to the “standard” complement of DNA-dependent RNA polymerase (Pol I, Pol II, and Pol III) two additional related enzymes (Pol IV and Pol V). These two enzymes collaborate with each other and with the RNA silencing system (AGOs, DCLs, RDRs, etc.) to produce small regulatory RNAs that in turn direct modifications of the transcribed loci so that they are not transcribed by Pol II. The Arabidopsis genome has tens thousands (or perhaps more) of loci that are targets of Pol IV/Pol V, and these are typically repetitive DNA and transposons. (I don’t recall if anyone has counted up the numbers of analogous targets in other plant genomes, but they likely number in the thousands-millions). Because of their origins and the ways they work (by homology-directed targeting and recruitment), these different RNAs will be under the same selective constraints as the loci they are transcribed from. If the loci are junk DNA, there will be no indication of positive (or negative) selection.
If one is going to be of the opinion that junk DNA cannot encode functional RNAs, then I am inclined to respectfully disagree. In my opinion, junk DNA can and does give rise to functional RNAs whose functions are (in part) to protect genomes from the deleterious consequences of the presence of the junk DNA. In a manner of speaking, they “allow” junk DNA to persist (and, I suppose, to grow and shrink over evolutionary time). Hence my suggestion that junk DNA may be viewed as selfish.
One should not construe that I am discounting the existence of the products of aberrant or inappropriate transcription by Pol II. Rather, I am stating that self-silencing via production of functional RNAs is yet another reason that pervasive transcription is most definitely NOT a refutation of the existence of junk DNA.
I find it ironic that Luskin et al. are cast, by these considerations, as promoting the existence of parasitic, selfish DNA. I rather suspect that they haven’t entirely thought through their arguments.
@Larry Moran This is a bit OT for this thread but maybe of interest to Larry.
Coyne is at it again on the lab leak stuff:
https://whyevolutionistrue.com/2025/01/27/monday-hili-dialogue-502/
“First the FBI and Department of Energy admitted that the Covid pandemic was more likely the result of a lab leak than a wet-market contamination by the virus, though neither agency had huge confidence in their conclusions. Now, as the WSJ reports. the CIA has also given a higher probability to a lab leak.
[…Coyne quotes WSJ article…]
The fact that the Chinese won’t cooperate with the investigation, which after all can help us understand worldwide epidemics, always makes me think that something fishy is going on, and by that I don’t mean “wet market”. My friend Luana has always been a big booster of the lab-leak hypothesis, and while I used to be pro-wet-market, I’m not somewhat agnostic leaning towards lab-leak. What cannot be denied is that both Facui and Francis Collins did their best to discourage the lab-leak hypothesis, and not solely on the grounds of science! They simply demonized those who suggested it, which is not a scientific attitude.”
The preponderance of evidence says that Coyne is wrong about the lab leak hypothesis. He is not the only academic who has been swayed, though, and that is presumably from learning about the lab leak argument from sources who omit details for a wet market origin.
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