“Creation Myths” Misquotes and Misrepresents Junk DNA Video
A YouTube channel called Creation Myths put up a new offering that claims, “Discovery Institute recently put out a video on junk DNA that contains all the usual lies about junk DNA, plus a few other tricks to make their audience think they’re on the up-and-up. We’re going to talk about it.” This is in reference to our new Long Story Short video:
Sure, Let’s Talk About It
Before I get too far into this, I need to say that it’s probably best to be cautious when dealing with “Creation Myths,” who also identifies as “Dr. Dan” and is a genuine PhD biologist at Rutgers. He’s an anti-ID YouTuber who has exhibited an unfortunate unwillingness to acknowledge black-and-white facts that are in favor of intelligent design. To be specific, two years ago I did a debate on the Unbelievable show, and Creation Myths left a comment stating that the ID research program “Hasn’t advanced past where it was in 2004/2005. Where’s the research program? Where are the papers?” Well, I had already provided this evidence in spades throughout the debate. He was just unwilling to accept these realities.
During the debate I discussed multiple ID 3.0 research projects that we fund, and discussed multiple papers that have been published through this research program. I don’t usually speak like this, but it’s important to get a sense of what we’re dealing with here: Creation Myth’s unwillingness to acknowledge the simple fact that the ID research program has advanced since 2004/2005 — and is publishing papers — does not inspire confidence in his ability to handle this debate fairly. He’s welcome to disagree with ID, but to deny our research program exists or that it’s publishing papers is simply to deny reality. He invited me to go on his channel, but I’m sorry, I don’t think it’s fruitful to dialogue with people who cannot acknowledge unambiguous facts. So it’s important to understand the temperament of debaters and their tactics before engaging with them.
What We Actually Said
With that, my first point provides another disturbing example of how Creation Myths operates. He has now left another comment, this one on our YouTube Channel, which directly misquotes the new Long Story Short video on junk DNA. His comment claims the video says “it was assumed that the other 98 percent was junk.” Those are words that Creation Myths puts in quote marks but they were never stated in the video!
Here’s what we actually said: it was “assumed that it was largely junk.” Words matter and we did not say it was assumed that the entire other “98 percent was junk.”
So did evolutionists say the genome was “largely” junk? Of course they did! Creation Myths recommends Laurence Moran’s book that says “90 percent” of the genome is junk, and then there’s Richard Dawkins who said 95 percent is junk. In other words, “largely” junk. What we said is accurate and defensible.
In fact, had we used the more aggressive language that Creation Myths falsely claims we did, there might even be authorities to support such a claim. As I recently noted, a 2021 article in American Scientist said that “Close to 99 percent of our genome has been historically classified as noncoding, useless ‘junk’ DNA”! So it’s clear that we are accurate in saying that many evolutionists view the genome as “largely” junk — if anything, that may be an understatement.
Creation Myths has overstated our argument in order to make it look unreasonable. This is a common tactic from junk DNA defenders.
Second, Creation Myths wants to have it both ways — he wants to essentially say evolutionists never said DNA was largely junk, but that nonetheless the genome really is largely junk. So there’s an internal contradiction in his framing.
The Bigger Issues
With that, my first point provides another disturbing example of how Creation Myths operates. He has now left another comment, this one on our YouTube Channel, which directly misquotes the new Long Story Short video on junk DNA. His comment claims the video says “it was assumed that the other 98 percent was junk.” Those are words that Creation Myths puts in quote marks but they were never stated in the video!
Here’s what we actually said: it was “assumed that it was largely junk.” Words matter and we did not say it was assumed that the entire other “98 percent was junk.”
So did evolutionists say the genome was “largely” junk? Of course they did! Creation Myths recommends Laurence Moran’s book that says “90 percent” of the genome is junk, and then there’s Richard Dawkins who said 95 percent is junk. In other words, “largely” junk. What we said is accurate and defensible.
In fact, had we used the more aggressive language that Creation Myths falsely claims we did, there might even be authorities to support such a claim. As I recently noted, a 2021 article in American Scientist said that “Close to 99 percent of our genome has been historically classified as noncoding, useless ‘junk’ DNA”! So it’s clear that we are accurate in saying that many evolutionists view the genome as “largely” junk — if anything, that may be an understatement.
Creation Myths has overstated our argument in order to make it look unreasonable. This is a common tactic from junk DNA defenders.
Second, Creation Myths wants to have it both ways — he wants to essentially say evolutionists never said DNA was largely junk, but that nonetheless the genome really is largely junk. So there’s an internal contradiction in his framing.
The Bigger Issues
Third, and this bring us to the bigger issues, let’s look at the paper he cites, Kellis et al. (2014). It’s authored by quite a few prominent ENCODE scientists, and despite what Creation Myths asserts, this paper does not “walk back” central claims of their major 2012 Nature ENCODE paper. That 2012 paper is cited by our video because it reported evidence that 80 percent of the genome is biochemically functional. As the 2012 paper stated, “These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions.”
And note what our video says — we did not claim that the 2012 Nature paper said 80 percent MUST be functional. Our video correctly states that the 2012 Nature paper from ENCODE “found 80 percent of DNA shows evidence of functional biochemical activity.” That’s absolutely true and totally consistent with what the 2012 ENCODE paper said and what the evidence says. And no one has walked that claim back.
I’d like to ask Creation Myths to provide the exact statement where Kellis et al. (2014) denies or “walks back” ENCODE’s claim that 80 percent of the genome shows evidence of biochemically functionality. He won’t find it because they never retracted that evidence.
Fourth, Kellis et al. (2014) does cite the major 2012 Nature ENCODE paper — not to retract it but rather it cites this paper very affirmatively. But we’ll get to that in a moment. Before we delve into the paper, here’s a revealing question:
If ENCODE was really “walking back” their claims, then why did lead ENCODE researcher Ewan Birney — who is a co-author on Kellis et al. (2014) — say the following just a couple of weeks before the Kellis paper was published: “There is not a single place in the genome that doesn’t have something that you might think could be controlling something else.”
That quote from Birney came from his comments in Bhattacharjee (2014), an article published in the journal Science as a response to ENCODE critic Dan Graur who had claimed that the genome is largely junk. So it’s totally on point and in context.
Birney is effectively saying that the entire genome appears to be functional — i.e., “There is not a single place in the genome that doesn’t have something that you might think could be controlling something else.” And he said what he did around the same time he co-authored the Kellis paper (the statement was published on March 21, 2014, and Kellis et al. came out on April 29, 2014, but was probably submitted months earlier). So Ewan Birney cannot be understanding his own paper to be walking back the claim about 80 percent functionality because clearly he thinks the genome is almost entirely functional.
Creation Myths Is Bluffing. How Do I Know?
Fifth, you have to understand what kind of paper Kellis et al. (2014) is. It’s a perspectives or review paper that compares and contrasts three different methods of investigating genome function: evolutionary, genetic, and biochemical. They set up this framing in the introduction, stating: “Geneticists, evolutionary biologists, and molecular biologists apply distinct approaches, evaluating different and complementary lines of evidence.”
The paper then discusses the strengths and weaknesses of each method, and discusses estimates of function for the genome for each method, offering pros and cons for each estimate and the methods used to infer those calculations. No method is perfect or foolproof, and they look at strengths and weaknesses of the evolutionary method and of the biochemical method. That’s what you do in a review paper. Well, what method do they ultimately favor? We’ll get there in just a moment.
Now, the biochemical method is the method that ENCODE used to find evidence of function for 80 percent of the genome. Kellis et al. (2014) note that the evolutionary method, in contrast, predicts that no more than 20 percent of the genome is functional, and the rest is junk:
The estimated mutation rate in protein-coding genes suggested that only up to ∼20% of the nucleotides in the human genome can be selectively maintained, as the mutational burden would be otherwise too large. The term “junk DNA” was coined to refer to the majority of the rest of the genome, which represent segments of neutrally evolving DNA.
So which method does Kellis think is the most reliable? You guessed it — they strongly favor the biochemical method. Here’s the conclusion of the paper:
In contrast to evolutionary and genetic evidence, biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act, thus providing a launching point to study differentiation and development, cellular circuitry, and human disease (14, 35, 69, 111, 112). The major contribution of ENCODE to date has been high-resolution, highly-reproducible maps of DNA segments with biochemical signatures associated with diverse molecular functions. We believe that this public resource is far more important than any interim estimate of the fraction of the human genome that is functional.
They are saying that the “biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act” and that ENCODE’s application of this method provides reliable data that “is far more important than any interim estimate of the fraction of the human genome that is functional.” They affirmatively cite five papers in saying this. Guess which citation is #69? It’s the major 2012 ENCODE paper in Nature which said that 80 percent of the genome is biochemically functional. They are citing it to say that the approach taken in that paper gives results that are “far more important than any interim estimate of the fraction of the human genome that is functional.”
So it’s true that in this particular paper they aren’t asserting any particular fraction of the human genome that is functional — but neither are they denying or “walking back” the 80 percent statistic either. They are clearly endorsing the biochemical approach in ENCODE’s 2012 paper. That means they don’t think the evolutionary approach is going to give you the best answer. Instead, they prefer the biochemical method, which uncovered evidence of function for 80% of the genome.
Critical of Evolutionary Estimates
Sixth, also noteworthy is that the Kellis paper is highly critical of evolutionary estimates of the fraction of the genome that is functional. Here’s how it describes the evolutionary view:
[T]he biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Many examples of elements that appear to have conflicting lines of functional evidence were described before the Encyclopedia of DNA Elements (ENCODE) Project, including elements with conserved phenotypes but lacking sequence-level conservation, conserved elements with no phenotype on deletion, and elements able to drive tissue-specific expression but lacking evolutionary conservation. … A high level of sequence conservation between related species is indicative of purifying selection, whereby disruptive mutations are rejected, with the corresponding sequence deemed to be likely functional.
They are saying that the “biochemical data offer clues about both the molecular function served by underlying DNA elements and the cell types in which they act” and that ENCODE’s application of this method provides reliable data that “is far more important than any interim estimate of the fraction of the human genome that is functional.” They affirmatively cite five papers in saying this. Guess which citation is #69? It’s the major 2012 ENCODE paper in Nature which said that 80 percent of the genome is biochemically functional. They are citing it to say that the approach taken in that paper gives results that are “far more important than any interim estimate of the fraction of the human genome that is functional.”
So it’s true that in this particular paper they aren’t asserting any particular fraction of the human genome that is functional — but neither are they denying or “walking back” the 80 percent statistic either. They are clearly endorsing the biochemical approach in ENCODE’s 2012 paper. That means they don’t think the evolutionary approach is going to give you the best answer. Instead, they prefer the biochemical method, which uncovered evidence of function for 80% of the genome.
Critical of Evolutionary Estimates
Sixth, also noteworthy is that the Kellis paper is highly critical of evolutionary estimates of the fraction of the genome that is functional. Here’s how it describes the evolutionary view:
[T]he biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Many examples of elements that appear to have conflicting lines of functional evidence were described before the Encyclopedia of DNA Elements (ENCODE) Project, including elements with conserved phenotypes but lacking sequence-level conservation, conserved elements with no phenotype on deletion, and elements able to drive tissue-specific expression but lacking evolutionary conservation. … A high level of sequence conservation between related species is indicative of purifying selection, whereby disruptive mutations are rejected, with the corresponding sequence deemed to be likely functional.
We will address this objection head-on in a forthcoming Long Story Short video on junk DNA that’s been in production since long before Creation Myths posted its objections. The objection is fallacious because it assumes DNA can only be functional if it is “evolutionarily conserved.” But that view further assumes that evolutionary processes are the only way to produce function in the genome. If you can have function outside of “conserved” regions because evolution isn’t what generated the genome, then the argument falls apart. So this evolutionary argument effectively assumes the truth of evolution and boils down to a circular argument.
Kellis et al. (2014) offers some additional arguments against the “evolutionary approach” to discerning function:
has limitations. Identification of conserved regions depends on accurate multispecies sequence alignments, which remain a substantial challenge. Alignments are generally less effective for distal-acting regulatory regions, where they may be impeded by regulatory motif turnover, varying spacing constraints, and sequence composition biases (17, 49). Analyzing aligned regions for conservation can be similarly challenging. First, most transcription factor-binding sequences are short and highly degenerate, making them difficult to identify. Second, because detection of neutrally evolving elements requires sufficient phylogenetic distance, the approach is well suited for detecting mammalian- conserved elements, but it is less effective for primate-specific elements and essentially blind to human-specific elements. Third, certain types of functional elements such as immunity genes may be prone to rapid evolutionary turnover even among closely related species. More generally, alignment methods are not well suited to capture substitutions that preserve function, such as compensatory changes preserving RNA structure, affinity-preserving substitutions within regulatory motifs, or mutations whose effect is buffered by redundancy or epistatic effects. Thus, absence of conservation cannot be interpreted as evidence for the lack of function.”
That’s a potent critique. It says some sequences cannot be compared or aligned because they are TOO different, and those differences might in fact encode functions! The evolutionary approach might be missing some of the sequences that encode differences between species. And it notes that “absence of conservation” does not mean “lack of function.”
So Kellis et al. (2014) gets the logic right: while conservation strongly implies function, the converse is not necessarily true: absence of conservation does not necessarily mean lack of function. In other words, they blew the “If it ain’t conserved you can’t say it’s functional” objection out of the water.
Seventh, there are additional noteworthy statements from the Kellis et al. (2014) showing they did not walk back the claim about 80 percent of the genome:
“[T]he noncoding regions of the human genome harbor a rich array of functionally significant elements with diverse gene regulatory and other functions.”
They still see the non-coding genome as having a “rich array of functionally significant elements.” This is NOT the traditional evolutionary view.
“[F]unction in biochemical and genetic contexts is highly particular to cell type and condition, whereas for evolutionary measures, function is ascertained independently of cellular state but is dependent on environment and evolutionary niche.”
This suggests that something can still be functional in a biochemical context, though in an evolutionary sense it can be hard to determine if it’s “functional.”
“The methods also differ widely in their false-positive and false-negative rates, the resolution with which elements are defined, and the throughput with which they can be surveyed.”
So genetics and molecular biology, on one hand, and evolutionary measures on the other have different rates of “false negatives” for function. This is a polite way of saying that the evolutionary approach often wrongly says things aren’t functional.
But the junk DNA advocate will say that the biochemical approach might lead to false positives of function. The paper acknowledges this: “[A]lthough biochemical signatures are valuable for identifying candidate regulatory elements in the biological context of the cell type examined, they cannot be interpreted as definitive proof of function on their own.”
That’s fair. We haven’t studied in detail every single time that the genome is transcribed to see what it’s doing, and there could be some “transcriptional noise” — the “junk RNA” view. We’ve also addressed this in the earlier Long Story video. Is this tantamount to “walking back” the 80% statistic? Not in the lease.
Random Noise or “Reproducible Biochemical Activity”
To defeat the 80 percent statistic, junk DNA defenders need there to be a huge amount of random noise in transcription. It’s possible that some transcription is random noise. But if much or most or nearly all of this transcription is noise, then cells are wasting colossal resources, and that would be highly deleterious to an organism, and would likely be selected against. So we have good reason off the bat to doubt that this transcription is largely random.
Indeed, the paper has an opinion on this and it prefers the view that transcription is non-random and functional. Kellis et al. (2014) note that even if there is some transcriptional noise, there’s far more going on in cells than we would expect if most of the genome were genetic junk:
Thus, unanswered questions related to biological noise, along with differences in the resolution, sensitivity, and activity level of the corresponding assays, help to explain divergent estimates of the portion of the human genome encoding functional elements. Nevertheless, they do not account for the entire gulf between constrained regions and biochemical activity. Our analysis revealed a vast portion of the genome that appears to be evolving neutrally according to our metrics, even though it shows reproducible biochemical activity, which we previously referred to as “biochemically active but selectively neutral” (68). It could be argued that some of these regions are unlikely to serve critical functions, especially those with lower-level biochemical signal. However, we also acknowledge substantial limitations in our current detection of constraint, given that some human-specific functions are essential but not conserved and that disease-relevant regions need not be selectively constrained to be functional. Despite these limitations, all three approaches are needed to complete the unfinished process of inferring functional DNA elements, specifying their boundaries, and defining what functions they serve at molecular, cellular, and organismal levels.
The key words there are “reproducible biochemical activity.”
ENCODE’s results suggest that a cell’s type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As another Kellis et al. co-author, John Stamatoyannopoulos, observed in a 2012 paper, ENCODE found that “the majority of regulatory DNA regions are highly cell type-selective,” and “the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types” studied increases. Or, as two other ENCODE researchers explain in a 2013 paper, “Assertions that the observed transcription represents random noise … is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell-and tissue — specific transcription in human cells.”
Stamatoyannopoulos (2012) further finds that repetitive DNA (often called “transposable elements”), which comprises over 50 percent of our genome, is active only in specific cell types. This nonrandom transcription of repetitive DNA into RNA suggests that transposable elements have functions whose importance are on par with other gene regulation mechanisms. He writes:
In marked contrast to the prevailing wisdom, ENCODE chromatin and transcription studies now suggest that a large number of transposable elements encode highly cell type-selective regulatory DNA that controls not only their own cell-selective transcription, but also those of neighboring genes. Far from an evolutionary dustbin, transposable elements appear to be active and lively members of the genomic regulatory community, deserving of the same level of scrutiny applied to other genic or regulatory features.
The vast majority of our genome — including repetitive DNA — is transcribed into RNA in nonrandom, cell-type-specific ways. These non-random processes strongly point against transcription being noise and provides strong evidence of function.
Indeed, individual RNA molecules then form networks in a cell, interacting with DNA, proteins, and other RNAs to control which genes are turned on and off, and which genes are expressed as proteins, thereby playing a crucial role in determining the cell’s type. As Stamatoyannopoulos puts it, this complex system exudes function:
More of the human genome sequence appears to be used for some reproducible, biochemically defined activity than was previously imagined. Contrary to the initial expectations of many, the overwhelming majority of these activities appear to be state-specific — either restricted to specific cell types or lineages, or evocable in response to a stimulus. … [B]iochemical signatures of many ENCODE-defined elements exhibit complex trans-cellular patterns of activity. … Together, these observations suggest that the genome may, in fact, be extensively multiply encoded — i.e., that the same DNA element gives rise to different activities in different cell types.
These consistent and predictable cell-type-specific patterns of RNA expression, and stimulus-specific patterns of transcription, show that mass genomic transcription of DNA into RNA is not random, but has important functional purposes.
In other words, transcription isn’t random — it happens over and over again in predictable patterns — and there’s a lot more non-random transcription going on than what you would expect from an evolutionary view of “constrained regions” of the genome. We may not yet have definitive proof of what every genomic element that’s transcribed is doing, but this evidence tells you that ENCODE’s data shows real evidence of function. Organized, reproducible, predictable transcription across the vast majority of the genome is far more compatible with the mass-functionality view of the genome, and highly incompatible with the “transcriptional noise” view promoted by junk DNA defenders. And the Kellis et al. authors think this biochemical evidence of function is more important than evolutionary predictions.
Bottom line: As for the rest of what Creation Myths has to say, there’s really not much there. Our video backs up what it says with clear quotes and references. We’ve provided more documentation here. Creation Myths, in contrast, is inventing quotes. Whether you celebrate Easter or not, may you enjoy this weekend and spend it quoting people carefully and accurately — not inventing quotes to suit your own purposes.
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