Did Dr. Dan Make Us Change Our Position on Junk DNA?
Last week, I published a review of Casey Luskin’s recent debate with Rutgers University professor Daniel Stern Cardinale (“Dr. Dan”) of the Creation Myths YouTube channel. I noted that Luskin did a good job during the debate of refuting Dr. Dan’s main arguments that most of our genome is junk — and I also pointed out that after the debate we posted a follow-up article that refuted his claim that “degraded” LINE elements cannot be functional. Now, Dr. Dan is claiming that he forced Discovery Institute to “change” its take on the percent of the genome that is functional. This claim is totally false and it perhaps reflects Dr. Dan’s wish to find a positive spin on the substance of what happened during the debate.
We’ll get to that in a moment, but first, let’s recap what happened during the debate.
Point 1: Luskin Refutes Dr. Dan’s Main Argument
The first of Dr. Dan’s two primary arguments during the debate was that most of the transcribed DNA documented by ENCODE cannot be functional since 70 percent of the coverage is transcribed at a rate of less than one transcript per cell. Luskin refuted this argument during the debate, making two main points. First, this statistic is an average — and, therefore, a mean of one transcript per cell does not imply that every cell has only one transcript or less. Second, there are plenty of examples of cases where there is a low copy number of RNA transcripts that are nonetheless functional. See my previous article for details. I observed that it was curious that, after these rejoinders were made by Casey Luskin, Dr. Dan never revisited this argument throughout the remainder of the debate.
Point 2: We Refute Dr. Dan’s Fallback Argument
After abandoning his first argument, Dr. Dan’s then fell back to a secondary argument — namely that large percentages of our genome are composed of “degraded” repetitive DNA which he claimed are “absolutely not” functional. Well, during the debate Luskin gave examples of “degraded” repetitive DNA that can be functional, and after the debate Richard Sternberg, Luskin, and I co-authored an article that reported over 50 peer-reviewed papers showing that what Dr. Dan calls “degraded” LINE elements can be functional. The only thing that Dr. Dan’s secondary argument showed is that evolutionists continue to assume that if they do not understand what a particular genetic element is doing then this constitutes grounds for thinking that it is functionless.
Did We Change Our Arguments in Response to Dr. Dan?
The short answer is no, we didn’t change our arguments in response to Dr. Dan because he did not raise any points that warranted our changing anything. To appreciate why this is the case, one first must appreciate our position.
In Casey Luskin’s opening statement in the debate — before Dr. Dan had made any arguments — Luskin fully acknowledged that there’s much we don’t know about the genome. He stated the following:
So again we’re going to deep dive into this today but I think it’s good to start with some points of agreement. I fully agree with Dr. Dan, and I’m assuming this is what you think Dr. Dan so forgive me if I’m misrepresenting you, but I thought these are reasonable things — that there is still a lot we don’t know about the genome. And I agree with you that probably some of it is going to turn out to be “junk”. I also agree with you that there’s much transcription going on where we still don’t know what it’s for. Some of it could even be quote-unquote stochastic. But I certainly agree that there’s a lot we don’t know, and that science will reveal much to us in the coming years.
That was from Luskin’s opening statement, before Dr. Dan had made any substantive points. And it was entirely consistent with what Luskin has said in the past. For example in a paper last year in the journal Religions, Luskin stated the following about junk DNA
Junk DNA genetic arguments for common human–ape ancestry have also come under significant critique in recent years due to the discovery of mass-functionality for non-coding or “junk” DNA in the human genome. A major 2012 Nature paper by the ENCODE consortium reported “biochemical functions for 80%” of the human genome (ENCODE Project Consortium 2012, p. 57). Lead ENCODE scientists predicted that with further research, “80 percent will go to 100” since “almost every nucleotide is associated with a function.” (Yong 2012). In the wake of this research, the journal Science published an article titled “ENCODE Project Writes Eulogy for Junk DNA” which stated that these findings “sound the death knell for the idea that our DNA is mostly littered with useless bases” (Pennisi 2012, p. 1159). Evidence of functions for non-coding DNA has continued to mount at a high pace. A 2021 article in Nature reported that over 130,000 specific “genomic elements, previously called junk DNA” have seen specific functions identified (Gates et al. 2021, p. 215), followed by a paper in Genome Biology and Evolution which concluded, “The days of ‘junk DNA’ are over” (Stitz et al. 2021, p. 11). There is still much we do not understand about the genome and there are many specific genetic elements for which no function has yet been discovered. Nonetheless, this evidence suggests a strong trendline in the research literature away from non-functionality for “junk” DNA.
Luskin later wrote the following in that paper:
Again, it is true that there is still much we do not know about junk DNA and there are many specific genetic elements (including pseudogenes and ERVs) for which specific functions have not yet been discovered. However, recent trends in research show that far more functionality is being discovered than was anticipated, leading to the possibility of mass functionality for junk DNA. As a 2023 academic book on RNA states:
“While the story is still unfolding, we conclude that the genomes of humans and other complex organisms are not full of junk but rather are highly compact information suites that are largely devoted to the specification of regulatory RNAs. These RNAs drive the trajectories of differentiation and development, underpin brain function and convey transgenerational memory of experience, much of it contrary to long-held conceptions of genetic programming and the dogmas of evolutionary theory.”
(Mattick and Amaral 2023, p. vii)
So Luskin has been very clear that there’s a lot we do not know about the genome — including many specific genetic elements for which we have not yet discovered their specific functions — and much remains to be discovered. But we do have evidence that over 80 percent of the genome is transcribed, and that’s evidence of function. Plus, the numerous scientific papers discovering function for “junk” DNA show the trendline of the research strongly implies the large bulk of the genome is functional.
Does Lack of Knowledge of Specific Function Imply Junk?
Does our lack of knowledge of the specific function for a genetic element imply it is probably junk? Again, the answer is no.
I also noted in my review that “Though Dr. Dan is correct that we currently know of specific functions for significantly less than half of the genome, this is hardly a strong argument for supposing that the ‘dark regions’ of the genome are non-functional ‘junk’ — particularly given the trends in the scientific literature over the last couple of decades — and the fact that the great majority of our genome is transcribed.” Dr. Dan has now put out a video titled “I Made Discovery Institute Change Their Junk DNA Argument.” In the video, Dr. Dan quoted my statement above, together with Luskin’s remark from his concluding statement: “I mean it could be another hundred years before we cross that 50 percent threshold, but I predict we’re going to get there and we’re going to go above that.” Dr. Dan contends that this is a significant shift in our position on the subject of junk DNA.
In support of his contention, Dr. Dan cites a few past articles from Evolution News, which he contends are at odds with this statement. Here is a list of the relevant quotes:
Casey Luskin, on March 28, 2024:
“…the concept of junk DNA — long espoused by evolutionists — has overall been refuted by mountains of data and is no longer even considered valid by many biologists.”
“A major Nature paper by the ENCODE consortium reported evidence of ‘biochemical functions for 80%’ of the human genome. Lead ENCODE scientists predicted that with further research, ’80 percent will go to 100’ since ‘almost every nucleotide is associated with a function.’”
Evolution News, on August 4, 2020:
“Skipper says it was ‘striking’ to find that they were able to assign a ‘biochemical function’ to 80 percent of the genome…”
Casey Luskin, on July 9, 2015:
“I should note that for my part, I think that the percentage of our genome that is functional is probably very high, even higher than 80%.”
“ENCODE critics who say the genome is junky rely primarily on theory. ENCODE proponents who say the genome is functional rely primarily on data.”
Dr. Dan contends that my (and Luskin’s) statements that we do not know the functions of significantly more than half of the genome are incompatible with the statements given above. This is not the case because, as noted, not knowing the specific function does not mean we don’t have evidence of function. Indeed, Luskin clearly stated during the debate that we are well over the 50 percent threshold” when it comes to evidence of genome function. As Luskin argued, over 80 percent of the genome is known to be transcribed into RNA, and it has long been our contention that the fact that over 80 percent of the genome is transcribed is prima facie evidence of function. (ENCODE only studied about 147 cell types, leading to the prediction Luskin quoted that as more cell types are studied “80 percent will go to 100.”) This does not mean that we know the specific function of all of the sequences that are transcribed, but again we don’t need to know the specific function to have evidence for some real function. Assigning specific functions to DNA sequences is not the only sort of evidence that may be adduced for functionality. Transcription itself is evidence that there is a function. Indeed, as Luskin noted during the debate, an ID-friendly RNA biologist at an Ivy League school told him that in their field, the dominant thinking in the field holds: “If it’s transcribed, it has a function.”
Moreover, the trends in the scientific literature — documenting more and more function of the dark regions of the genome — give us strong reason for confidence that those trends will continue. Thus, it’s not at all hard to envision virtually all of these transcribed regions have a specific function that is just waiting for us to discover.
The only statement listed above that might be construed as being at odds with this is the quote from the 2020 Evolution News article. However, here is the statement in context:
Skipper says it was “striking” to find that they were able to assign a “biochemical function” to 80 percent of the genome: striking, because “not such a long time ago, we still considered that a vast proportion of the human genome was simply junk.” Birney comments, “It’s very hard to get over the density of information” in the genome. They found places that are “much more complex” than expected, and loci thought to be completely silent are actually “teeming with life, teeming with things going on; we still really don’t understand that…”
Neither Casey Luskin nor I wrote those words, nor did any Discovery Institute author. Indeed, those quotes are pulled from a video from Nature. Skipper’s comment that they are “able to assign a ‘biochemical function’ to 80 percent of the genome” is clumsily worded. However, Birney’s statement (also quoted in the Evolution News article) adds more nuance: “It’s like a jungle of stuff out there. There are things that we thought we understood and yet it’s much, much more complex. And then places of the genome that we thought were completely silent and they’re teeming with life. They’re teeming with things going on. We still really don’t understand that.” Thus, Birney appears to agree that we do not know what is going on in many of these regions, though we nonetheless have evidence of function. This supports what we are saying about the genome, not Dr. Dan’s view.
Of course, Dr. Dan objects to our contention that transcription constitutes prima facie evidence of function, since the mean level of transcription for much of the transcribed regions is less than a single transcript per cell. But we rebutted that argument during the debate, and it is curious that Dr. Dan still (even in his latest video) has not addressed, nor even remarked on, our rebuttal to his objection — that this is only an average and that even low copy number transcripts can be functional.
Dr. Dan Should Stop Projecting His Own Views Upon Us
To conclude, we have not changed our position on junk DNA as a result of Dr. Dan’s debate with Casey Luskin. Luskin’s comment about the “50 percent threshold” pertained to our not having yet identified the specific function for 50 percent of the genome — he was NOT claiming that there is no evidence of function for 50 percent of the genome, and he was certainly NOT conceding that there is evidence that 50 percent of the genome is junk. Instead, as we have noted, because over 80 percent of the genome is transcribed, this provides prima facie evidence that at least 80 percent of the genome is functional even if we have not yet identified the specific function. In fact, Luskin stated this upfront in his opening statement — fully acknowledging that there is much we have yet to learn about the genome.
In this debate, Dr. Dan is the only party who is arguing that if we have not identified the specific function, then even if it is transcribed, we are safe to assume it is probably junk. He seems to think that if we concede that we don’t know the specific function, that therefore this means it is junk. Dr. Dan must be projecting his own views upon us because he is the only party here who thinks like that. We certainly don’t. We are not arguing that way because it is a science-stopping argument. We believe that the evidence of mass-transcription of the genome plus the trendline of the research indicate that the vast majority of the genome is functional. Dr. Dan is welcome to disagree with us, but he should not impose his own science-stopping views upon us
No comments:
Post a Comment