Nils Walter disputes junk DNA: (7) Conservation of transcribed DNA

I'm discussing a recent paper published by Nils Walter (Walter, 2024). He is arguing against junk DNA by claiming that the human genome contains large numbers of non-coding genes.

This is the seventh post in the series. The first one outlines the issues that led to the current paper and the second one describes Walter's view of a paradigm shift/shaft. The third post describes the differing views on how to define key terms such as 'gene' and 'function.' In the fourth post I discuss his claim that differing opinions on junk DNA are mainly due to philosophical disagreements. The fifth and sixth posts address specific arguments in the junk DNA debate.

• Nils Walter disputes junk DNA: (1) The surprise
• Nils Walter disputes junk DNA: (2) The paradigm shaft
• Nils Walter disputes junk DNA: (3) Defining 'gene' and 'function'
• Nils Walter disputes junk DNA: (4) Different views of non-functional transcripts
• Nils Walter disputes junk DNA: (5) What does the number of transcripts per cell tell us about function?
• Nils Walter disputes junk DNA: (6) The C-value paradox

Sequence conservation

If you don't know what a transcript is doing then how are you going to know whether it's a spurious transcript or one with an unknown function? One of the best ways is to check and see whether the DNA sequence is conserved. There's a powerful correlation between sequence conservation and function: as a general rule, functional sequences are conserved and non-conserved sequences can be deleted without consequence.

There might be an exception to the the conservation criterion in the case of de novo genes. They arise relatively recently so there's no history of conservation. That's why purifying selection is a better criterion. Now that we have the sequences of thousands of human genomes, we can check to see whether a given stretch of DNA is constrained by selection or whether it accumulates mutations at the rate we expect if its sequence were irrelevant junk DNA (neutral rate). The results show that less than 10% of our genome is being preserved by purifying selection. This is consistent with all the other arguments that 90% of our genome is junk and inconsistent with arguments that most of our genome is functional.

This sounds like a problem for the anti-junk crowd. Let's see how it's addressed in Nils Walter's article in BioEssays.

There are several hand-waving objections to using conservation as an indication of function and Walter uses them all plus one unique argument that we'll get to shortly. Let's deal with some of the "facts" that he discusses in his defense of function. He seems to agree that much of the genome is not conserved even though it's transcribed. In spite of this, he says,

"... the estimates of the fraction of the human genome that carries function is still being upward corrected, with the best estimate of confirmed ncRNAs now having surpassed protein-coding genes,[12] although so far only 10%–40% of these ncRNAs have been shown to have a function in, for example, cell morphology and proliferation, under at least one set of defined conditions."

This is typical of the rhetoric in his discussion of sequence conservation. He seems to be saying that there are more than 20,000 "confirmed" non-coding genes but only 10%-40% of them have been shown to have a function! That doesn't make any sense since the whole point of this debate is how to identify function.

Here's another bunch of arguments that Walter advances to demonstrate that a given sequence could be functional but not conserved. I'm going to quote the entire thing to give you a good sense of Walter's opinion.

A second limitation of a sequence-based conservation analysis of function is illustrated by recent insights from the functional probing of riboswitches. RNA structure, and hence dynamics and function, is generally established co-transcriptionally, as evident from, for example, bacterial ncRNAs including riboswitches and ribosomal RNAs, as well as the co-transcriptional alternative splicing of eukaryotic pre-mRNAs, responsible for the important, vast diversification of the human proteome across ∼200 cell types by excision of varying ncRNA introns. In the latter case, it is becoming increasingly clear that splicing regulation involves multiple layers synergistically controlled by the splicing machinery, transcription process, and chromatin structure. In the case of riboswitches, the interactions of the ncRNA with its multiple protein effectors functionally engage essentially all of its nucleotides, sequence-conserved or not, including those responsible for affecting specific distances between other functional elements. Consequently, the expression platform—equally important for the gene regulatory function as the conserved aptamer domain—tends to be far less conserved, because it interacts with the idiosyncratic gene expression machinery of the bacterium. Consequently, taking a riboswitch out of this native environment into a different cell type for synthetic biology purposes has been notoriously challenging. These examples of a holistic functioning of ncRNAs in their species-specific cellular context lay bare the limited power of pure sequence conservation in predicting all functionally relevant nucleotides.

I don't know much about riboswitches so I can't comment on that. As for alternative splicing, I assume he's suggesting that much of the DNA sequence for large introns is required for alternative splicing. That's just not correct. You can have effective alternative splicing with small introns. The only essential parts of introns sequences are the splice sites and a minimum amount of spacer.

Part of what he's getting at is the fact that you can have a functional transcript where the actual nucleotide sequence doesn't matter so it won't look conserved. That's correct. There are such sequences. For example, there seem to be some examples of enhancer RNAs, which are transcripts in the regulatory region of a gene where it's the act of transcription that's important (to maintain an open chromatin conformation, for example) and not the transcript itself. Similarly, not all intron sequences are junk because some spacer sequence in required to maintain a minimum distance between splice sites. All this is covered in Chapter 8 of my book ("Noncoding Genes and Junk RNA").

Are these examples enough to toss out the idea of sequence conservation as a proxy for function and assume that there are tens of thousands of such non-conserved genes in the human genome? I think not. The null hypothesis still holds. If you don't have any evidence of function then the transcript doesn't have a function—you may find a function at some time in the future but right now it doesn't have one. Some of the evidence for function could be sequence conservation but the absence of conservation is not an argument for function. If conservation doesn't work then you have to come up with some other evidence.

It's worth mentioning that, in the broadest sense, purifying selection isn't confined to nucleotide sequence. It can also take into account deletions and insertions. If a given region of the genome is deficient in random insertions and deletions then that's an indication of function in spite of the fact that the nucleotide sequence isn't maintained by purifying selection. The maintenance definition of function isn't restricted to sequence—it also covers bulk DNA and spacer DNA.

(This is a good time to bring up a related point. The absence of conservation (size or sequence) is not evidence of junk. Just because a given stretch of DNA isn't maintained by purifying selection does not prove that it is junk DNA. The evidence for a genome full of junk DNA comes from different sources and that evidence doesn't apply to every little bit of DNA taken individually. On the other hand, the maintenance function argument is about demonstrating whether a particular region has a function or not and it's about the proper null hypothesis when there's no evidence of function. The burden of proof is on those who claim that a transcript is functional.)

This brings us to the main point of Walter's objection to sequence conservation as an indication of function. You can see hints of it in the previous quotation where he talks about "holistic functioning of ncRNAs in their species-specific cellular context," but there's more ...

Some evolutionary biologists and philosophers have suggested that sequence conservation among genomes should be the primary, or perhaps only, criterion to identify functional genetic elements. This line of thinking is based on 50 years of success defining housekeeping and other genes (mostly coding for proteins) based on their sequence conservation. It does not, however, fully acknowledge that evolution does not actually select for sequence conservation. Instead, nature selects for the structure, dynamics and function of a gene, and its transcription and (if protein coding) translation products; as well as for the inertia of the same in pathways in which they are not involved. All that, while residing in the crowded environment of a cell far from equilibrium that is driven primarily by the relative kinetics of all possible interactions. Given the complexity and time dependence of the cellular environment and its environmental exposures, it is currently impossible to fully understand the emergent properties of life based on simple cause-and-effect reasoning.

The way I see it, his most important argument is that life is very complicated and we don't currently understand all of it's emergent properties. This means that he is looking for ways to explain the complexity that he expects to be there. The possibility that there might be several hundred thousand regulatory RNAs seems to fulfil this need so they must exist. According to Nils Walter, the fact that we haven't (yet) proven that they exist is just a temporary lull on the way to rigorous proof.

This seems to be a common theme among those scientists who share this viewpoint. We can see it in John Mattick's writings as well. It's as though the logic of having a genome full of regulatory RNA genes is so powerful that it doesn't require strong supporting evidence and can't be challenged by contradictory evidence. The argument seems somewhat mystical to me. Its proponents are making the a priori assumption that humans just have to be a lot more complicated than what "reductionist" science is indicating and all they have to do is discover what that extra layer of complexity is all about. According to this view, the idea that our genome is full of junk must be wrong because it seems to preclude the possibility that our genome could explain what it's like to be human.

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Walter, N.G. (2024) Are non‐protein coding RNAs junk or treasure? An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non‐functional or functional RNAs. BioEssays:2300201. [doi: 10.1002/bies.202300201]

Nils Walter disputes junk DNA: (6) The C-value paradox

I'm discussing a recent paper published by Nils Walter (Walter, 2024). He is arguing against junk DNA by claiming that the human genome contains large numbers of non-coding genes.

This is the fifth post in the series. The first one outlines the issues that led to the current paper and the second one describes Walter's view of a paradigm shift/shaft. The third post describes the differing views on how to define key terms such as 'gene' and 'function.' In the fourth post I discuss his claim that differing opinions on junk DNA are mainly due to philosophical disagreements.

• Nils Walter disputes junk DNA: (1) The surprise
• Nils Walter disputes junk DNA: (2) The paradigm shaft
• Nils Walter disputes junk DNA: (3) Defining 'gene' and 'function'
• Nils Walter disputes junk DNA: (4) Different views of non-functional transcripts
• Nils Walter disputes junk DNA: (5) What does the number of transcripts per cell tell us about function?

Nils Walter disputes junk DNA: (5) What does the number of transcripts per cell tell us about function?

I'm discussing a recent paper published by Nils Walter (Walter, 2024). He is arguing against junk DNA by claiming that the human genome contains large numbers of non-coding genes.

This is the fifth post in the series. The first one outlines the issues that led to the current paper and the second one describes Walter's view of a paradigm shift. The third post describes the differing views on how to define key terms such as 'gene' and 'function.' The fourth post makes the case that differing views on junk DNA are mainly due to philosophical disagreements.

-Nils Walter disputes junk DNA: (1) The surprise

-Nils Walter disputes junk DNA: (2) The paradigm shaft

-Nils Walter disputes junk DNA: (3) Defining 'gene' and 'function'

-Nils Walter disputes junk DNA: (4) Different views of non-functional transcripts

Transcripts vs junk DNA

The most important issue, according to Nils Walter, is whether the human genome contains huge numbers of genes for lncRNAs and other types of regulatory RNAs. He doesn't give us any indication of how many of these potential genes he thinks exist or what percentage of the genome they cover. This is important since he's arguing against junk DNA but we don't know how much junk he's willing to accept.

There are several hundred thousand transcripts in the RNA databases. Most of them are identified as lncRNAs because they are bigger than 200 bp. Let's assume, for the sake of argument, that 200,000 of these transcripts have a biologically relevant function and therefore there are 200,000 non-coding genes. A typical size might be 1000 bp so these genes would take up about 6.5% of the genome. That's about 10 times the number of protein-coding genes and more than 6 times the amount of coding DNA.

That's not going to make much of a difference in the junk DNA debate since proponents of junk DNA argue that 90% of the genome is junk and 10% is functional. All of those non-coding genes can be accommodated within the 10%.

The ENCODE researchers made a big deal out of pervasive transcription back in 2007 and again in 2012. We can quibble about the exact numbers but let's say that 80% of the human is transcribed. We know that protein-coding genes occupy at least 40% percent of the genome so much of this pervasive transcription is introns. If all of the presumptive regulatory genes are located in the remaining 40% (i.e. none in introns), and the average size is 1000 bp, then this could be about 1.24 million non-coding genes. Is this reasonable? Is this what Nils Walter is proposing?

I think there's some confusion about the difference between large numbers of functional transcripts and the bigger picture of how much total junk DNA there is in the human genome. I wish the opponents of junk DNA would commit to how much of the genome they think is functional and what evidence they have to support that position.

But they don't. So instead we're stuck with debates about how to decide whether some transcripts are functional or junk.

What does transcript concentration tell us about function?

If most detectable transcripts are due to spurious transcription of junk DNA then you would expect these transcripts to be present at very low levels. This turns out to be true as Nils Walter admits. He notes that "fewer than 1000 lncRNAs are present at greater than one copy per cell."

This is a problem for those who advocate that many of these low abundance transcripts must be functional. We are familiar with several of the ad hoc hypotheses that have been advanced to get around this problem. John Mattick has been promoting them for years [John Mattick's new paradigm shaft].

Walter advances two of these excuses. First, he says that a critical RNA may be present at an average of one molecule per cell but it might be abundant in just one specialized cell in the tissue. Furthermore, their expression might be transient so they can only be detected at certain times during development and we might not have assayed cells at the right time. I assume he's advocating that there might be a short burst of a large number of these extremely specialized regulatory RNAs in these special cells.

As far as I know, there aren't many examples of such specialized gene expression. You would need at least 100,000 examples in order to make a viable case for function.

His second argument is that many regulatory RNAs are restricted to the nucleus where they only need to bind to one regulatory sequence to carry out their function. This ignores the mass action laws that govern such interactions. If you apply the same reasoning to proteins then you would only need one lac repressor protein to shut down the lac operon in E. coli but we've known for 50 years that this doesn't work in spite of the fact that the lac repressor association constant shows that it is one of the tightest binding proteins known [DNA Binding Proteins]. This is covered in my biochemistry textbook on pages 650-651.¹

If you apply the same reasoning to mammalian regulatory proteins then it turns out that you need 10,000 transcription factor molecules per nucleus in order to ensure that a few specific sites are occupied. That's not only because of the chemistry of binary interactions but also because the human genome is full of spurious sites that resemble the target regulatory sequence [The Specificity of DNA Binding Proteins]. I cover this in my book in Chapter 8: "Noncoding Genes and Junk RNA" in the section titled "On the important properties of DNA-binding proteins" (pp. 200-204). I use the estrogen receptor as an example based on calculations that were done in the mid-1970s. The same principles apply to regulatory RNAs.

This is a disagreement based entirely on biochemistry and molecular biology. There aren't enough examples (evidence) to make the first argument convincing and the second argument makes no sense in light of what we know about the interactions between molecules inside of the cell (or nucleus).

Note: I can almost excuse the fact that Nils Walter ignores my book on junk DNA, my biochemistry textbook, and my blog posts, but I can't excuse the fact that his main arguments have been challenged repeatedly in the scientific literature. A good scientist should go out of their way to seek out objections to their views and address them directly.

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1. In addition to the thermodynamic (equilibrium) problem, there's a kinetic problem. DNA binding proteins can find their binding sites relatively quickly by one dimensional diffusion—an option that's not readily available to regulatory RNAs [Slip Slidin' Along - How DNA Binding Proteins Find Their Target].

Walter, N.G. (2024) Are non‐protein coding RNAs junk or treasure? An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non‐functional or functional RNAs. BioEssays:2300201. [doi: 10.1002/bies.202300201]

Nils Walter disputes junk DNA: (2) The paradigm shaft

I'm discussing a recent paper published by Nils Walter (Walter, 2024). He is trying to explain the conflict between proponents of junk DNA and their opponents. His main focus is building a case for large numbers of non-coding genes.

This is the second post in the series. The first one outlines the issues that led to the current paper.

Nils Walter disputes junk DNA: (1) The surprise

Walter begins his defense of function by outlining a "paradigm shift" that's illustrated in Figure 1.

FIGURE 1: Assessment of the information content of the human genome ∼20 years before (left)[110] and after (right)[111] the Human Genome Project was preliminarily completed, drawn roughly to scale.[9] This significant progress can be described per Thomas Kuhn as a “paradigm shift” flanked by extended periods of “normal science”, during which investigations are designed and results interpreted within the dominant conceptual frameworks of the sub-disciplines.[9] Others have characterized this leap in assigning newly discovered ncRNAs at least a rudimentary (elemental) biochemical activity and thus function as excessively optimistic, or Panglossian, since it partially extrapolates from the known to the unknown.[75] Adapted from Ref. [9].

Reference #9 is a paper by John Mattick promoting a "Kuhnian revolution" in molecular biology. I've already discussed that paper as an example of a paradigm shaft, which is defined as a strawman "paradigm" set up to make your work look like revolutionary [John Mattick's new paradigm shaft]. Here's the figure from the Mattick paper.

The Walter figure is another example of a paradigm shaft—not to be confused with a real paradigm shift.¹ Both pie charts misrepresent the amount of functional DNA since they don't show regulatory sequences, centromeres, telomeres, origins of replication, and SARS. Together, these account for more functional DNA than the functional regions of protein-coding genes and non-coding genes. We didn't know the exact amounts in 1980 but we sure knew they existed. I cover this in Chapter 5 of my book: "The Big Picture."

The 1980 view also implies, incorrectly, that we knew nothing about the non-functional component of the genome when, in fact, we knew by then that half of our genome was composed of transposon and viral sequences that were likely to be inactive, degenerate fragments of once active elements. (John Mattick's figure is better.)

The 2020 view implies that most intron sequences are functional since introns make up more than 40% of our genome but only about 3% of the pie chart. As far as I know, there's no evidence to support that claim. About 80% of the pie chart is devoted to transcripts identified as either small ncRNAs or lncRNAs. The implication is that the discovery of these RNAs represents a paradigm shift in our understanding of the genome.

The alternative explanation is that we've known since the late 1960s that most of the human genome is transcribed and that these transcripts—most of which turned out to be introns—are junk RNA that is confined to the nucleus and rapidly degraded. Advances in technology have enabled us to detect many examples of spurious transcripts that are present transiently at low levels in certain cells. I cover this in Chaper 8 of my book: "Noncoding Genes and Junk RNA.

The whole point of Nils Walter's paper is to defend the idea that most of these transcripts are functional and the alternative explanation is wrong. He's trying to present a balanced view of the controversy so he's well aware of the fact that some of us interpret the red part of the pie chart as spurious transcripts (junk RNA). If he's wrong, and I am right, then there's no paradigm shift.

You don't get to shift the paradigm all on our own, even if John Mattick is on your side. A true paradigm shift requires that the entire community of scientists changes their perspective and that hasn't happened.

In the next few posts we'll see whether Nils Walter can make a strong case that all those lncRNAs are functional. They cover about two-thirds of the genome in the pie chart. If we assume that the average length of these long transcripts is 2000 bp then this represents one million transcripts and potentially one million non-coding genes.

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1. The term "paradigm shaft" was coined by reader Diogenes in a comment on this blog from many years ago.

Walter, N.G. (2024) Are non‐protein coding RNAs junk or treasure? An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non‐functional or functional RNAs. BioEssays:2300201. [doi: 10.1002/bies.202300201]

Nils Walter disputes junk DNA: (1) The surprise

Nils Walter attempts to present the case for a functional genome by reconciling opposing viewpoints. I address his criticisms of the junk DNA position and discuss his arguments in favor of large numbers of functional non-coding RNAs.

Nils Walter is Francis S. Collins Collegiate Professor of Chemistry, Biophysics, and Biological Chemistry at the University of Michigan in Ann Arbor (Michigan, USA). He works on human RNAs and claims that, "Over 75% of our genome encodes non-protein coding RNA molecules, compared with only <2% that encodes proteins." He recently published an article explaining why he opposes junk DNA.

Walter, N.G. (2024) Are non‐protein coding RNAs junk or treasure? An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non‐functional or functional RNAs. BioEssays:2300201. [doi: 10.1002/bies.202300201]

The human genome project's lasting legacies are the emerging insights into human physiology and disease, and the ascendance of biology as the dominant science of the 21st century. Sequencing revealed that >90% of the human genome is not coding for proteins, as originally thought, but rather is overwhelmingly transcribed into non-protein coding, or non-coding, RNAs (ncRNAs). This discovery initially led to the hypothesis that most genomic DNA is “junk”, a term still championed by some geneticists and evolutionary biologists. In contrast, molecular biologists and biochemists studying the vast number of transcripts produced from most of this genome “junk” often surmise that these ncRNAs have biological significance. What gives? This essay contrasts the two opposing, extant viewpoints, aiming to explain their basis, which arise from distinct reference frames of the underlying scientific disciplines. Finally, it aims to reconcile these divergent mindsets in hopes of stimulating synergy between scientific fields.

John Mattick's new paradigm shaft

John Mattick continues to promote the idea that he is leading a paradigm shift in molecular biology. He believes that he and his colleagues have discovered a vast world of noncoding genes responsible for intricate gene regulation in complex eukaryotes. The latest salvo was fired a few months ago in June 2023.

Mattick, J.S. (2023) A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs. BioEssays:2300080. [doi: 10.1002/bies.202300080]

Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non-functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein-coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information.

This paper is promoted by a video in which he explains why there's a Kuhnian revolution under way. This paper differs from most of his others on the same topic because Mattick now seems to have acquired some more knowledge of the mutation load argument and the neutral theory of evolution. Now he's not only attacking the so-called "protein centric" paradigm but also the Modern Synthesis. Apparently, a slew of "anomalies" are casting doubt on several old paradigms.

This is still a paradigm shaft but it's a bit more complicated than his previous versions (see: John Mattick's paradigm shaft). Now his "anomalies" include not only large numbers of noncoding genes but also the C-value paradox, repetitive DNA, introns, enhancers, gene silencing, the g-value enigma, pervasive transcription, transvection, and epigenetics. Also, he now seems to be aware of many of the arguments for junk DNA but not so aware that he can reference any of his critics.¹ His challenges to the Modern Synthesis include paramutation which, along with epigenetics, violate the paradigm of the Moden Synthesis because of non-genetic inheritance.

But the heart of his revolution is still the discovery of massive numbers of noncoding genes that only he and a few of his diehard colleague can see.

The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the majority of the mammalian genome is differentially and dynamically transcribed during development to produce tens if not hundreds of thousands of short and long non-protein-coding RNAs that show highly specific expression patterns and subcellular locations.

The figure is supposed to show that by 2020 junk DNA had been eliminated and almost all of the mammalian genome is devoted to functional DNA—mostly in the form of noncoding genes. There's only one very tiny problem with this picture—it's not supported by any evidence that all those functional noncoding genes exist. This is still a paradigm shaft of the third kind (false paradigm, false overthrow, false data).

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1. There are 124 references; Dawkins and ENCODE make the list along with 14 of his own papers. Most of the papers in my list of Required reading for the junk DNA debate are missing. The absence of Palazzo and Gregory (2023) is particularly noteworthy.

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

John Mattick's new dog-ass plot (with no dog)

John Mattick is famous for arguing that there's a correlation between genome size and complexity; notably in a 2004 Scientific American article (Mattick, 2004) [Genome Size, Complexity, and the C-Value Paradox ]. That's the article that has the famous Dog-Ass Plot (left) with humans representing the epitome of complexity and genome size. He claims that this correlation is evidence that most of the genomes of complex animals must have a function. He repeats this claim in a recent paper (see below).

Mattick, J.S. (2023) RNA out of the mist. TRENDS in Genetics 39:187-207. [doi: 10.1016/j.tig.2022.11.001,/p>

RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long ‘intergenic’ and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed ‘enhancers’, which marshal generic effector proteins to their sites of action to control cell fate decisions during development.

John Mattick's paradigm shaft

Paradigm shifts are rare but paradigm shafts are common. A paradigm shaft is when a scientist describes a false paradigm that supposedly ruled in the past then shows how their own work overthrows that old (false) paradigm.¹ In many cases, the data that presumably revolutionizes the field is somewhat exaggerated.

John Mattick's view of eukaryotic RNAs is a classic example of a paradigm shaft. At various times in the past he has declared that molecular biology used to be dominated by the Central Dogma, which, according to him, supported the concept that the only function of DNA was to produce proteins (Mattick, 2003; Morris and Mattick, 2014). More recently, he has backed off this claim a little bit by conceding that Crick allowed for functional RNAs but that proteins were the only molecules that could be involved in regulation. The essence of Mattick's argument is that past researchers were constrained by adherance to the paradigm that the only important functional molecules were proteins and RNA served only an intermediate role in protein synsthesis.

Chapter 8: Noncoding Genes and Junk RNA

I think there are no more than 5,000 noncoding genes but many scientists claim that there are tens of thousands of newly discovered noncoding genes. I describe the known noncoding genes (less than 1000) and explain why many of the transcripts detected are just junk RNA produced by spurious transcription. The presence of abundant noncoding genes will not solve the Deflated Ego Problem.

This chapter covers the misconceptions about the Central Dogma and how they are incorrectly used to try and discredit junk DNA. The views of John Mattick are explained and refuted. I end the chapter with a plea to adopt a worldview that can accommodate messy biochemistry and a sloppy genome that's full of junk DNA.

Click on this link to see more.

Chapter 8: NoncodingGenes and Junk RNA

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ChatGPT lies about junk DNA

I asked ChatGPT some questions about junk DNA and it made up a Francis Crick quotation and misrepresented the view of Susumu Ohno.

We have finally restored the Junk DNA article on Wikipedia. (It was deleted about ten years ago when Wikipedians decided that junk DNA doesn't exist.) One of the issues on Wikipedia is how to deal with misconceptions and misunderstandings while staying within the boundaries of Wikipedia culture. Wikipedians have an aversion to anything that looks like editorializing so you can't just say something like, "Nobody ever said that all non-coding DNA was junk." Instead, you have to find a credible reference to someone else who said that.

I've been trying to figure out how far the misunderstandings of junk DNA have spread so I asked ChatGPt (from OpenAI) again.

Junk DNA, TED talks, and the function of lncRNAs

Most of our genome is transcribed but so far only a small number of these transcripts have a well-established biological function.

The fact that most of our genome is transcribed has been known for 50 years but that fact only became widely known with the publication of ENCODE's preliminary results in 2007 (ENCODE, 2007). The ENOCDE scientists referred to this as "pervasive transription" and this label has stuck.

By the end of the 1970s we knew that much of this transcription was due to introns. The latest data shows that protein coding genes and known noncoding genes occupy about 45% of the genome and most of that is intron sequences that are mostly junk. That leaves 30-40% of the genome that is transcribed at some point producing something like one million transcripts of unknown function.

Nature journalist is confused about noncoding RNAs and junk

Nature Methods is one of the journals in Nature Portfolio published by Springer Nature. Its focus is novel methods in the life sciences.

The latest issue (October, 2022) highlights the issues with identifying functional noncoding RNAs and the editorial, Decoding noncoding RNAs, is quite good—much better than the comments in other journals. Here's the final paragraph.

Despite the increasing prominence of ncRNA, we remind readers that the presence of a ncRNA molecule does not always imply functionality. It is also possible that these transcripts are non-functional or products from, for example, splicing errors. We hope this Focus issue will provide researchers with practical advice for deciphering ncRNA’s roles in biological processes.

However, this praise is mitigated by the appearance of another article in the same journal. Science journalist, Vivien Marx has written a commentary with a title that was bound to catch my eye: How noncoding RNAs began to leave the junkyard. Here's the opening paragraph.

Junk. In the view of some, that’s what noncoding RNAs (ncRNAs) are — genes that are transcribed but not translated into proteins. With one of his ncRNA papers, University of Queensland researcher Tim Mercer recalls that two reviewers said, “this is good” and the third said, “this is all junk; noncoding RNAs aren’t functional.” Debates over ncRNAs, in Mercer’s view, have generally moved from ‘it’s all junk’ to ‘which ones are functional?’ and ‘what are they doing?’

This is the classic setup for a paradigm shaft. What you do is create a false history of a field and then reveal how your ground-breaking work has shattered the long-standing paradigm. In this case, the false history is that the standard view among scientists was that ALL noncoding RNAs were junk. That's nonsense. It means that these old scientists must have dismissed ribosomal RNA and tRNA back in the 1960s. But even if you grant that those were exceptions, it means that they knew nothing about Sidney Altman's work on RNAse P (Nobel Prize, 1989), or 7SL RNA (Alu elements), or the RNA components of spliceosomes (snRNAs), or PiWiRNAs, or snoRNAs, or microRNAs, or a host of regulatory RNAs that have been known for decades.

Knowledgeable scientists knew full well that there are many functional noncoding RNAS and that includes some that are called lncRNAs. As the editorial says, these knowledgeable scientists are warning about attributing function to all transcripts without evidence. In other words, many of the transcripts found in human cells could be junk RNA in spite of the fact that there are also many functional nonciding RNAs.

So, Tim Mercer is correct, the debate is over which ncRNAs are functional and that's the same debate that's been going on for 50 years. Move along folks, nothing to see here.

The author isn't going to let this go. She decides to interview John Mattick, of all people, to get a "proper" perspective on the field. (Tim Mercer is a former student of Mattick's.) Unfortunately, that perspective contains no information on how many functional ncRNAs are present and on what percentage of the genome their genes occupy. It's gonna take several hundred thousand lncRNA genes to make a significant impact on the amount of junk DNA but nobody wants to say that. With John Mattick you get a twofer: a false history (paradigm strawman) plus no evidence that your discoveries are truly revolutionary.

Nature Methods should be ashamed, not for presenting the views of John Mattick—that's perfectly legitimate—but for not putting them in context and presenting the other side of the controversy. Surely at this point in time (2022) we should all know that Mattick's views are on the fringe and most transcripts really are junk RNA?

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The Function Wars Part XI: Stefan Linquist responds to my critique

Stefan Linquist is a philosopher at the University of Guelph (Guelph, Ontario, Canada). He recently published a paper on function that I discussed [The Function Wars Part IX: Stefan Linquist on Causal Role vs Selected Effect]. This is his response.

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Hi Larry,

First, thank you for giving my paper a careful read. The intended audience is the community of biologically-minded philosophers who seem largely convinced that:

1) Genes are so passé. More specifically, when it comes to explaining phenotypic development and evolution, such non-genic factors as noncoding RNA, maternally inherited methylation patterns, repetitive elements, etc. are equally if not more significant than genes. It is a short step to the view that most of these elements are somehow functional for the organism. Stated pejoratively, thinkers like John Mattick and Evelyn Fox-Keller have had a significant intellectual founder-effect on my discipline. My paper attempts to push back against this trend.

2) Molecular biology can and should ignore evolution. The idea here is that when it comes to the search for molecular mechanisms, it doesn’t matter if genomes are the product of multi-level evolution or if they had been created by God. When you work on mechanisms, you do experiments, and evolutionary considerations are irrelevant to how those experiments are conducted and interpreted. Or, so the thinking goes.

Many of your blog posts present counter arguments to these ideas with a level of understanding and precision that exceeds my efforts in this paper. Nonetheless, I want to take issue with your one suggestion (if I understand correctly) that biochemists tend to operate with a sophisticated understanding of the genome. My position is that biochemistry might be necessary, but is not sufficient for an informed view of genomics. Without Darwinian reasoning, biochemistry leads down unnecessary blind alleys.

Obvious to whom?

Let me be upfront that I am something of an academic bumpkin in comparison to fancy city-folk like you, or Palazzo, or Graur, or Doolittle, or Haig. My knowledge of molecular genetics is largely self taught. This is partly why I am perplexed by statements like the following. In a special collection of Chromosome Research entitled, “Transposable elements and the multidimensional genome” (2018), P.A. Larson (the collection editor) opens with this doozy:

“There is no such thing as “junk DNA.” Indeed, a suite of discoveries made over the past few decades have put to rest this misnomer and have identified many important roles that so-called junk DNA provides to both genome structure and function…”

Is it me? Or is it him? It’s him, right? My point is simply that it can’t be obvious to everyone within the molecular biological community that not every binding site or repetitive element is somehow functional for the organism. This is to say nothing of the hype surrounding lncRNA.

My argument in the paper is that the missing piece of information is an understanding of where the majority of eukaryotic DNA comes from: a byproduct of coevolutionary interactions between parasitic TEs and the cell. Indeed, I provide evidence in another publication, Transposon dynamics and the epigenetic switch hypothesis, that over the past two decades or so, within the fields of molecular biology and biomedicine, interest in TEs has steadily declined. This trend is surprising given that over the same period we have come to learn just how prevalent TEs are in most genomes. I think that I can show, in another forthcoming paper, that this trend toward ignoring TE coevolutionary dynamics is associated with the increased biomedicalization of molecular biology as a discipline (more on that another time, perhaps). Whether this decline of interest in TEs is responsible for the tendency to interpret junk DNA as somehow functional is a further question.

Another factor that I find perplexing is the trickle of molecular biology majors who attend my philosophy of biology undergraduate seminar. I'm not surprised that they show up at all, rather I'm surprised about their conviction that any biochemically active region of the genome simply must be functional for the organism. "Functional until proven otherwise" seems to be the mantra that one must memorize in order to pass the med-school admissions exam. When I suggest to them that Darwinian reasoning leads to an alternative hypothesis about most of the DNA in eukaryotic genomes, they balk. Some just leave my class: “What does he know, just a philosopher.” Such is the life of an academic bumpkin from the intellectual sticks.

This is all to say that, yes, you are correct that my paper presents no new biological data. In a sense, it is old news. But it is news that many people –even some academic city slickers-- seem not to have absorbed.

I like to think of philosophy journals as a clearing house for discussions that are extremely important, but would be unlikely to elbow their way into the pages of most scientific journals. Aside of helpful blogs such as yours, where else are we to debate the theoretical framing and interpretation of junk DNA?

What’s with the philosophical obsession over functions?

It’s true that my article focuses on this longstanding debate over CR vs SE functions. I can imagine that from the perspective of a molecular biologist (with such a rich ontology to draw from, and so many fine grained distinctions at your disposal) this binary must appear ham-fisted.

Let me say two things. First, I repeat that my main audience is the community of biological philosophers. In this context, these basic categories of function and the debates that surround them provide a lingua franca. To have this discussion without connecting it to function concepts would seem odd. Second, I think that you and I would both be happy if the word “function” in genetics were restricted to what I elsewhere call maintenance functions. That is, to elements that have been maintained by purifying selection. However, many of my colleagues are so convinced of point 2 (above) that this proposal is essentially a non-starter. That is, they maintain that since molecular biology doesn't investigate causal role functions (a big assumption, but let it go for now), then this discipline can ignore Darwinian reasoning. My argument is that this inference is too quick. A problem with CR functions is their permissiveness: any old strand of DNA can have some CR function or other. What we need is some way to sort the functional wheat from the junky chaff. To do that, thinking about selective history is your best bet. In effect, you can deny entrance to Darwin at the front door if you want, but eventually you’ll have to let him in through the back.

A final note on the term “selective history.” You suggested that I should have instead used “evolution” in order to discourage a Panglossian view of the genome. The issue I see with your suggestion is that “evolution” is too vague –it really just means change over time. My contention is that one needs to do more than just consider historical (e.g. phylogenetic) details in order to take a biologically informed view of the genome. In addition, one needs to think about how the cell coevolves with parasitic TEs. Maybe “coevolutionary dynamics” would have been a better choice.

Finally, a plug. The paper you read is part of a special collection in Biology and Philosophy that I co-edited with Ford Doolittle entitled, “Function, junk and transposable elements: contested issues in the science of genomics.” As I write, I see that three papers have so far appeared and the other two (including mine and one coauthored by Alex Palazzo) should see the light of day soon:

Function, junk and transposable elements: contested issues in the science of genomics

Hopefully some of these will provide additional fodder.
Cheers,
Stefan

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Most lncRNAs are junk

A hard-hitting review will be published in Annual Review of Genomics and Human Genetics. It shows that the case for large numbers of functional lncRNAs is grossly exaggerated.

A long-time Sandwalk reader (Ole Kristian Tørresen) alerted me to a paper that's coming out next October in Annual Review of Genomics and Human Genetics. (Thank-you Ole.) The authors of the review are Chris Ponting from the University of Edinburgh (Edinburgh, Scotland, UK) and Wilfried Haerty at the Earlham Institute in Norwich, UK. They have been arguing the case for junk DNA for the past two decades but most of their arguments are ignored. This paper won't be so easy to ignore because it makes the case forcibly and critically reviews all the false claims for function. I'm going to quote a few juicy parts because I know that many of you will not be able to access the preprint.

John Mattick's new book

John Mattick and Paulo Amaral have written a book that promotes their views on the content of the human genome. It will be available next August. Their main thesis is that the human genome is full of genes for regulatory RNAs and there's very little junk. A secondary theme is that some very smart scientists have been totally wrong about molecular biology and molecular evolution for the past fifty years.

I pretty much know what's going to be in the book [see John Mattick presents his view of genomes]. I also know that most of his claims don't stand up to close scrutiny but that's not going to prevent it from being touted as a true paradigm shift. (It's actually a paradigm shaft.) I suspect it's going to get favorable reviews in Science and Nature.

John Mattick presents his view of genomes

John Mattick has a new book coming out in August where he defends the notion that most of our genome is full of genes for functonal noncoding RNAs. We have a pretty good idea what he's going to say. This is a talk he gave at Oxford on May 17, 2019.

Here are a few statements that should pique your interest.

• (0:57) He says that his upcoming book is tentatively titled "the misunderstandings of molecular biology."
• (1:11) He says that "the assumption has been very deeply embedded from the time of the lac operon on that genes equated to proteins."
• (2:30) There have been three "surprises" in molecuular biology: (1) introns, (2) eukaryotic genomes are full of 'selfish' DNA, and (3) "gene number does not scale with developmental complexity."
• (4:30) It is an unjustified assumption to assume that transposon-related seqences are junk and that leads to misinterpretation of neutral evolution.
• (6:00) The view that evolution of regulatory sequences is mostly responsible for developmental complexity (Evo-Devo) has never been justified.
• (8:45) A lot of obtuse theoretical discussion about how the number of regulatory protein-coding genes increases quadratically as the total number of protein-coding genes increase in a bacterial genome but at some point there has to be more protein-coding regulatory genes than total protein-coding genes so that limits the evolution of bacteria.
• (13:40) The proportion of noncoding DNA increases with developmental complexity, topping out at humans.

• (14:00) The vast majority of the genome in complex organisms is differentially transcribed in different cells and different tissues.
• (14:15) The whole genome is alive on both strands.
• (14:20) There are two possibilities: junk RNA or abundant functional transcripts and that explains complex organisms.
• Mattick then takes several minutes to document the fact that there are abundant transcripts— a fact that has been known for the better part of sixty years but he does not mention that. All of his statements carry the implicit assumption that these transcripts are functional.
• (20:20) He makes the boring, and largely irelevant, point that most disease-associated loci are located in noncoding regions (GWAS). He's responding to a critic who asked why, if these things (transcripts) are real, don't we see genetic evidence of it.
• (24:00) Noncoding RNAs have all of the characteristics of functional RNAs with an emphasis on the fact that their expression is often only detected in specific cell types.
• (31:50) It has now been shown that everything that protein transcription factors can do can be done by noncoding RNA.
• (32:15) "I want to say to you that conservation is totally misunderstood." Apparently, lack of conservation imputes nothing about function.
• (41:00) RNAs control phase separation. There's a whole other level of cell organization that we never dreamed of. (Ironically, he gives nucleoli as an example of something we never dreamed of.)
• (42:36) "This is called soft metaphysics, and it's just come into biology, and it's spectacular in its implications."

• (46:25) Almost every lncRNA is alternatively spliced in mice and humans.
• (46:30) There's more alternative splicing in human protein-coding genes than in mice protein-coding genes but the extra splicing in humans is mostly in the 5' untranslated region. (I'm sure it has nothing to do with the fact that tons more RNA-Seq experiments have been done on human tissues.) "We think this is due to the increased sophistication of the regulation of these genes for the evolution of cognition."
• (48:00) At least 20% of the human genome is evolutionarily conserved at the level of RNA structure and this does not require any assumptions.
• (55:00) The talk ends at 55 minutes. That's too bad because I'm sure Mattick had a dozen more slides explaining why all of those transcripts are functional, as opposed to the few selected examples he picked. I'm sure he also had a lot of data refuting all of the evidence in favor of junk DNA but he just ran out of time.

I don't know if there were questions but, if there were, I bet that none of them challenged Mattick's main thesis.

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The biggest mistake in the history of molecular biology (not!)

The creationists are committed to proving that most of our genome is functional because otherwise the idea of an intelligent designer doesn't make a lot of sense. They reject all of the evidence that supports junk DNA and they vehemently reject the notion that 90% of our genome is junk.

I was recently alerted to a video on junk DNA produced by Creation Ministries International in which they quote John Mattick.

A leading figure in genetics, Prof. John Mattick said ...'the failure to recognize the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology'.

The creationists are making the common mistake of equating noncoding DNA and junk DNA but the quotation sounded accurate to me since John Mattick makes similar mistakes in his publications. I decided to try and find the exact quotation and reference and the closest I could come to a direct quote was in a paper by Mattick from 2007 (Mattick, 2007). He's referring to introns—here's the exact quotation.

It should be noted that the power and precision of digital communication and control systems has only been broadly established in the human intellectual and technological experience during the past 20–30 years, well after the central tenets of molecular biology were developed and after introns had been discovered. The latter was undoubtedly the biggest surprise (Williamson, 1977), and its misinterpretation possibly the biggest mistake, in the history of molecular biology. Although introns are transcribed, since they did not encode proteins and it was inconceivable that so much non-coding RNA could be functional, especially in an unexpected way, it was immediately and almost universally assumed that introns are non-functional and that the intronic RNA is degraded (rather than further processed) after splicing. The presence of introns in eukaryotic genomes was then rationalized as the residue of the early assembly of genes that had not yet been removed and that had utility in the evolution of proteins by facilitating domain shuffling and alternative splicing (Crick, 1979; Gilbert, 1978; Padgett et al., 1986). Interestingly, while it has been widely appreciated for many years that DNA itself is a digital storage medium, it was not generally considered that some of its outputs may themselves be digital signals, communicated viaRNA.

However, the idea of the biggest mistake in molecular biology predates that reference. Mattick is quoted in a Scientific American article by W. Wayt Gibbs where Gibbs is discssing the "suprising" fact that regulatory sequences are conserved and that some genes are noncoding genes (Gibbs, 2003).

“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.”

The discovery of introns in the mid-1970s was definitely a surprise but it's not true, as Mattick implies, that they were immediately assumed to be junk. In fact, as he points out, there was a lot of debate over the possible role of introns in the evolution of protein-coding genes where they could stimulate exon shuffling. Later on, the presence of introns was recognized to be an essential component of alternative splicing.

Once more and more sequences were published it became apparent that neither their size nor their sequences were conserved except for the spliceosome recognition sequences. It soon became obvious that their sequences were evolving at the neutral rate demonstrating that they were mostly junk. Mattick assumes that this conclusion—that introns are mostly junk—is one of the biggest mistakes in molecular biology. I think the opposite is true. I think that the failure of most molecular biologists to understand junk DNA is a huge mistake.

The creationists are misquoting Mattick when they say that the classification of all noncoding as junk is the biggest mistake in molecular biology. In the quotations above, Mattick is specifically referrring to introns but I'm sure he won't be upset to be misquoted in that manner since he firmly believes that most noncoding DNA is functional.

There's a bit of an ironic twist here. If it were true that knowledgeable scientists in the 1970s actually believed that all noncoding DNA was junk then I'd have to agree that this would have been a big (biggest?) mistake. But they didn't and it wasn't a big mistake. As I've said many times, no knowledgeable scientist ever said that all noncoding DNA was junk since they (we) all knew about noncoding genes, regulatory sequences, centromeres, and origins of replication, all of which are functional noncoding DNA. We now know that about 1% of our genome is coding sequences and about 9% is functional noncoding DNA. The other 90% is junk.

[Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]

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Mattick, J.S. (2007) A new paradigm for developmental biology. Journal of Experimental Biology 210:1526-1547. [doi: 10.1242/jeb.005017]

Gibbs, W.W. (2003) The unseen genome: gems among the junk. Scientific American 289:46-53.

On the misrepresentation of facts about lncRNAs

I've been complaining for years about how opponents of junk DNA misrepresent and distort the scientific literature. The same complaints apply to the misrepresentation of data on alternative splicing and on the prevalence of noncoding genes. Sometimes the misrepresentation is subtle so you hardly notice it.

I'm going to illustrate subtle misrepresentation by quoting a recent commentary on lncRNAs that's just been published in BioEssays. The main part of the essay deals with ways of determining the function of lncRNAs with an emphasis on the sructures of RNA and RNA-protein complexes. The authors don't make any specific claims about the number of functional RNAs in humans but it's clear from the context that they think this number is very large.

The "standard" view of junk DNA is completely wrong

I was browsing the table of contents of the latest issue of Cell and I came across this ....

For decades, the miniscule protein-coding portion of the genome was the primary focus of medical research. The sequencing of the human genome showed that only ∼2% of our genes ultimately code for proteins, and many in the scientific community believed that the remaining 98% was simply non-functional “junk” (Mattick and Makunin, 2006; Slack, 2006). However, the ENCODE project revealed that the non-protein coding portion of the genome is copied into thousands of RNA molecules (Djebali et al., 2012; Gerstein et al., 2012) that not only regulate fundamental biological processes such as growth, development, and organ function, but also appear to play a critical role in the whole spectrum of human disease, notably cancer (for recent reviews, see Adams et al., 2017; Deveson et al., 2017; Rupaimoole and Slack, 2017).

Slack, F.J. and Chinnaiyan, A.M. (2019) The Role of Non-coding RNAs in Oncology. Cell 179:1033-1055 [doi: 10.1016/j.cell.2019.10.017]

Cell is a high-impact, refereed journal so we can safely assume that this paper was reviewed by reputable scientists. This means that the view expressed in the paragraph above did not raise any alarm bells when the paper was reviewed. The authors clearly believe that what they are saying is true and so do many other reputable scientists. This seems to be the "standard" view of junk DNA among scientists who do not understand the facts or the debate surrounding junk DNA and pervasive transcription.

Here are some of the obvious errors in the statement.

1. The sequencing of the human genome did NOT show that only ~2% of our genome consisted of coding region. That fact was known almost 50 years ago and the human genome sequence merely confirmed it.
2. No knowledgeable scientist ever thought that the remaining 98% of the genome was junk—not in 1970 and not in any of the past fifty years.
3. The ENCODE project revealed that much of our genome is transcribed at some time or another but it is almost certainly true that the vast majority of these low-abundance, non-conserved, transcripts are junk RNA produced by accidental transcription.
4. The existence of noncoding RNAs such as ribosomal RNA and tRNA was known in the 1960s, long before ENCODE. The existence of snoRNAs, snRNAs, regulatory RNAs, and various catalytic RNAS were known in the 1980s, long before ENCODE. Other RNAs such as miRNAs, piRNAS, and siRNAs were well known in the 1990s, long before ENCODE.

How did this false view of our genome become so widespread? It's partially because of the now highly discredited ENCODE publicity campaign orchestrated by Nature and Science but that doesn't explain everything. The truth is out there in peer-reviewed scientific publications but scientists aren't reading those papers. They don't even realize that their standard view has been seriously challenged. Why?

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John Mattick's latest attack on junk DNA

John Mattick is the most prominent defender of the idea that the human genome is full of functional sequences. In fact, he is just about the only scientist of any prominence who's on that side of the debate. His main "evidence" is the fact that genomes are pervasively transcribed and that most of the transcripts are functional. Let's look at his latest review paper to see how well this argument stands up to close scrutiny (Mattick, 2018).¹

As you read this post, keep in mind that in 2012 John Mattick was awarded a prize by the Human Genome Organization for proving his hypothesis [John Mattick Wins Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research].

The Award Reviewing Committee commented that Professor Mattick’s “work on long non-coding RNA has dramatically changed our concept of 95% of our genome”, and that he has been a “true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.”

Mattick follows his usual format by giving us his version of history. He has argued for the past 15 years that the scientific community has been reluctant to accept the evidence of massive amounts of regulatory RNA genes because it conflicts with the standard paradigm of the supremacy of proteins. In the past he has claimed that this paradigm is based on the Central Dogma which states, according to him, that the only real function of DNA is to make proteins [How Much Junk in the Human Genome?]. As we shall see, he hasn't abandoned that argument but at least he no longer refers to the Central Dogma for support