But that doesn’t stop them from misinterpreting them! Here’s a classic example of Evolution News & Views completely missing the point of an article to claim it supports their beliefs about junk DNA.
I am so punchy and tired today that I wrote out a script. I had to. So transcript below the fold:
Hey, friends —
I got a question in my email, asking me a simple question…or maybe not so simple.
May I please ask you a last question? It is regarding an article I read recently. Intelligent Design proponents often use “junk DNA” functions as evidence for ID. I know that they are dishonest and advocate nonsense, but if you have time to have a look at the article below, may I ask for your opinion?
I’m reading it and realized that the Discovery Institute was pulling an Otto. You know what I mean, the assassin in the movie A Fish Called Wanda, who was so incredibly stupid yet also pretentious, thinking he was an intellectual. You may recall the exchange:
Wanda says, “you think you’re an intellectual, don’t you, ape?”
Otto replies, “Apes don’t read philosophy!”
Wanda fires back with “Yes, they do, they just don’t understand it!”
That’s my summary. The Discovery Institute reads papers in Cell, they just don’t understand them. They ought to be embarrassed, if they weren’t so shameless.
There’s a problem, though. I have to provide a fair bit of technical background, so you can see what’s wrong with their take. They rely on that — they provide a bunch of complicated technobabble and emphatic confidence to make you think they’re super smart. Don’t be fooled!
This particular article is titled “Caltech Finds Amazing Role for Noncoding DNA”; it’s a summary of a real, genuine science article published in the journal CELL, and what it’s doing is taking a legit science article and putting a creationist spin on it. It’s not clear who wrote it, but whoever it was didn’t actually understand the article. Here’s the introduction:
Scientists at Caltech may have sounded the final death knell for the “junk DNA” myth. If only Dan Graur had known this years ago, it might have saved a lot of wasted rhetoric. ENCODE, readers recall, found that 80 percent of the genome is transcribed, even if only a small part codes for proteins. The functions of those non-coding regions were only hinted at. Now, the windows are opening on organization so all-encompassing for all those non-coding RNA transcripts, it is truly mind-boggling what goes on in the nucleus of a cell.
This is very strange. What the Discovery Institute article is is yet another attempt to debunk the idea of junk DNA, but the CELL article is not about junk DNA, and says nothing relevant to the creationist arguments about junk DNA. For some reason, creationists detest the idea that not all DNA has a specific function, and I’m not certain why. After all, their designer can do anything, why not just say that He intentionally left lots of room in the code, for expansion, maybe? Why not just call it the white space around the important content? Call it the artistic filigree He put there because He, in his unknowable ways, found it beautiful? It really would be that easy. But instead, they have to insist that it is all biologically functional.
It’s almost as if they fear we might notice that their sacred holy books are maybe 5% good art and humane advice, and 95% flaming demented useless inconsistent junk, too.
They do love that awful ENCODE study, which claimed that at least 80% of the genome was functional by an odd definition of functionality that no one accepts. The ENCODE studies argued that any bit of DNA that was transcribed into RNA counted as functional, no matter how short or rare it was, and ignored the possibility of spurious transcription. There are very few biologists who accept that nonsensical idea, but the creationists ate it up. If you mention junk DNA to them, they immediately bring up ENCODE in a kind of spastic kneejerk reaction.
They also have a special loathing for Dan Graur, who has been particularly eloquent and historically literate in his arguments against every scrap of the genome being functional. There are limits to how many genes there can be based on the mutation rate and the ability of recombination to purify deleterious alleles — we’ve known since Haldane and Wright that humans ought to have approximately 20,000 genes, as confirmed by the human genome project, and that making any greater proportion of the genome functional would impose an excessive genetic load on the species. It is mathematically impossible for the claims of the ID creationists to be true.
But now they’re claiming that they’ve got a Graur-killer paper in their hands. It’s almost embarrassing how irrelevant this paper is to their claim.
So here it is, “RNA promotes the formation of spatial compartments in the nucleus” by Quinodoz and others.
RNA, DNA, and protein molecules are highly organized within three-dimensional (3D) structures in the nucleus. Although RNA has been proposed to play a role in nuclear organization, exploring this has been chal- lenging because existing methods cannot measure higher-order RNA and DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the spatial orga- nization of RNA and DNA. These maps reveal higher-order RNA-chromatin structures associated with three major classes of nuclear function: RNA processing, heterochromatin assembly, and gene regulation. These data demonstrate that hundreds of ncRNAs form high-concentration territories throughout the nucleus, that specific RNAs are required to recruit various regulators into these territories, and that these RNAs can shape long-range DNA contacts, heterochromatin assembly, and gene expression. These results demonstrate a mechanism where RNAs form high-concentration territories, bind to diffusible regulators, and guide them into compartments to regulate essential nuclear functions.
It’s not light reading. There’s a lot of quantitative molecular biology, and detailed analysis, and I’ll be honest, MY eyes glazed over here and there in the manuscript. To distill it down to the important points, though, they’re saying a couple of things. One, nuclear DNA is organized and shows a specific functional arrangement. This is not entirely new — I was reading about the 3 dimensional structure of folded DNA in the nucleus way back in the 1980s, but this does provide better methods of imaging it. The second point is that one of the agents of this structure is long non-coding RNA — that is, RNA that isn’t translated into protein, but functions to link DNA and proteins into loops of associated active regions. This RNA works like little bungee cords to tie related elements together.
So here’s their model. non-coding RNA (ncRNA) aggregates around RNA polymerase as it works, and forms a mass that can bind to other regions of DNA and to proteins, binding them together into a compartment that promotes further synthesis of mRNA.
This isn’t a surprising idea to biologists. We’ve known for a long, long time that DNA is organized in the nucleus, for example: there are structures called nuclear pore complexes, where arrays of proteins in the nucleus bind to newly synthesized RNA and expedite its export directly to pores in the nuclear membrane, and then to the cytoplasm for translation.
But, I ask you, what does this have to do with the proportion of junk DNA in the genome? It doesn’t. Whatever hack wrote the Discovery Institute article didn’t understand the paper. I think they saw nothing but that it was about a novel function for non-coding RNA, and they leapt to the conclusion that this was about junk DNA. “Non-coding” is not a synonym for “junk DNA”, although creationists think so.
So let’s take a look at a comprehensive review of non-coding RNA. This is an excellent review article by Palazzo and Lee that I recommend highly if you want to figure out what the real story is about ncRNA.
Starting with the discovery of transfer RNA and ribosomal RNA in the 1950s, non-coding RNAs (ncRNAs) with biological roles have been known for close to 60 years. Even in the late 1970s and early 1980s the existence of other functional ncRNAs was known, including RNAse P, snRNAs, and 7SL [the RNA component of the signal recognition particle].
Note that the Discovery Institute wants to claim that the idea of functional non-coding RNAs was derived from Intelligent Design thinking, but actually, it has been common knowledge in the biology — that is, the real biology — community for decades. It’s so old that it’s what I learned as an undergraduate, which was ages ago.
Palazzo and Lee go on to point out that this notion of pervasive transcription has also been around for a long time, and that there are a few people, like John Mattick, who still promote this idea that every bit of the genome is transcribed and therefore functional, which is absurd.
This idea was epitomized by the ENCODE consortium, which claimed to have assigned “biochemical functions for 80% of the genome”. Others have disagreed, pointing out that the vast majority of these novel transcripts are present at low levels, and that the term “function” had been misappropriated.
Yeah, that’s what I think. It’s pretty hard to argue that RNA polymerase is flawless and perfect and never errs in RNA transcripts. Palazzo and Lee again:
It is important to recognize that the pervasive transcription associated with the human genome is entirely consistent with our understanding of biochemistry. Although RNA polymerases prefer to start transcription at promoter regions, they do have a low probability of initiating transcription on any accessible DNA. Indeed it has been observed that most nucleosome-free DNA is transcribed in vivo and that many random pieces of DNA can promote transcription by recruiting transcription factors
But let’s focus on the implied claims of the Discovery Institute. Is this discovery by Quinodoz and others of a role for some ncRNAs represent a revelation that shows the human genome is mostly, or even entirely functional? I don’t think so. Here’s the key point from Palazzo and Lee — long non-coding RNAs are only a tiny fraction of the genome, so identifying a few lncRNAs that have a function cannot tell you that the whole genome is functional.
As of spring 2014, the LNCipedia website has compiled a list of ∼21,000 human lncRNAs, with an average length of about 1 kb. These would originate from <1% of the human genome. Needless to say, this is a very small fraction of the total. Even if we compiled all of the putative lncRNAs using the most optimistic analysis, all the putative lncRNAs would still be transcribed from at most 2% of the genome.
They go on, in brief:
In summary, our best candidates for novel functional ncRNAs (lncRNAs, eRNAs) arise from only a minute fraction of the genome. Again it appears that the vast majority of the genome that falls outside of these loci is transcribed into junk RNA that is present at very low levels at steady state.
lncRNAs are less than 1% of the genome. Even if every single one of them was demonstrated to be performing an essential function, they are a small drop in the bucket of the entire genome. And that functionality has not been demonstrated, except in a few examples.
Thus far, only a small minority of lncRNAs have been shown to be important for organismal development, cell physiology, and/or homeostasis. As of December 2014, the LncRNA Database, a repository of lncRNAs “curated from evidence supported by the literature,” lists only 166 biologically validated lncRNAs in humans. Additionally there are so called eRNAs, which according to FANTOM5 come from an additional 43,000 loci. However, at an average length of ∼250 nucleotides they would be made from ∼0.34% of the human genome. Again, these are very small numbers.
So the Discovery Institute article concludes by saying:
This is a paper to remember. It shows in hindsight the fruitfulness of the ID perspective over the evolutionary one. Evolutionary thinking dismissed these non-coding RNAs as junk. ID thinking would have approached the unknown with the premise, “If something works, it’s not happening by accident.”
The second and third sentences are outright lies. The Quinodoz paper was not inspired by Intelligent Design creationism — it builds on prior work on molecular and evolutionary biology that emerged out of the 1950s. Evolutionary biology does NOT dismiss non-coding RNAs as junk. Evolutionary thinking approaches these scraps of RNA with the premise that function can’t be assumed, it must be demonstrated.
That’s it. That’s all I’ve got to say. The Discovery Institute mangled and misinterpreted an article in a science journal to twist it to support their silly agenda. News at 11.
DI — Caltech Finds Amazing Role for Noncoding DNA
Quinodoz and others — RNA promotes the formation of spatial compartments in the nucleus
Palazzo & Lee — Non-coding RNA: what is functional and what is junk?