In an earlier post, I discussed functions for disease-associated junk DNA. That subject isn’t of just academic significance. Reports have recently come to my attention that some critics (unfriendly and more ID-friendly alike) have taken issue with certain of the papers that we listed in our “far from exhaustive” bibliography of papers reporting function for junk DNA. We’re not inerrant and it’s entirely possible that some papers were included in the list that did not belong. But after looking at some of these complaints, I consider them to be overall very minor, They really don’t do anything to diminish our overall point. And that point was, as we said in our original bibliography, to provide…

[A] far from exhaustive (but nonetheless exhausting) list of papers documenting function for various classes of non-coding DNA — including transposable elements, endogenous retroviruses, pseudogenes, and more — all of which were called “junk DNA” in the past.  The list contains over 800 papers… given that we only took about a day and a half to put this list together, we think it’s an impressive showing. It must be re-emphasized that this list is nowhere close to comprehensive. Indeed, we could have multiplied the list many times over. Nonetheless, we hope that it gives the reader a sense of how vast the literature is that has accumulated in recent years that has served to significantly undermine the paradigm that much of our genome (and those of other organisms) is nonfunctional debris that has accumulated over evolutionary history.

A Huge Body of Literature 

Some key phrases are “we could have multiplied the list many times over,” “this list is nowhere close to comprehensive,” and “we only took about a day and a half to put this list together.” The point is: There exists a HUGE body of literature reporting, describing, and discovering function for non-coding / junk DNA. It’s not for no reason that a paper last year in BioEssays reported that the scientific community has experienced a Kuhnian paradigm shift against the idea of junk DNA, and it’s not for no reason that many papers and authorities now speak of junk DNA as if it were an idea of the past. If we had unlimited time, thousands upon thousands of papers finding function for junk DNA could have been documented and listed. So if a handful of papers on our list could potentially be deleted, this doesn’t negate the huge body of literature that does in fact belong in our bibliography. 

What exactly are the concerns about our list? Based upon my understanding, most of the complaints can be summarized into five categories: (1) Some papers are review papers, not original research papers. (2) In some cases there are multiple papers discussing the same functional genetic “junk DNA” element. (3) Some papers report roles that junk DNA plays in causing disease. (4) Some papers report evidence of biochemical activity rather than a specific function. (5) Some papers don’t affirm function for junk DNA. While I appreciate the time that these critics (both friendly and unfriendly) have taken in evaluating our list, I believe that only those in the fifth category really indicate the paper doesn’t belong on our list. Let’s discuss these briefly:

Category 1: Review Papers, Not Original Research Papers

Response: I don’t think this category should count against our list. The purpose of the list is to highlight functions that have been discovered for junk DNA and to showcase how this has led to a major shift in thinking about “junk DNA” in the scientific community. Review papers may not represent original research, but they are frequently useful summaries of the precise kind of evidence that we’re discussing. The fact that the papers were solicited and / or published to review function for junk DNA shows how the scientific community is becoming, or has become, far more open to the idea that junk DNA really is functional. So this is evidence of the prevalence of function for junk DNA.

Category 2: Multiple Papers Discussing the Same Functional Genetic Element

Response: I would argue that this category also belongs on our list. Labs often publish multiple papers from of a long-lasting project that may span multiple years. Each successive paper may build upon or refine previous findings, and they’re all relevant to the overall discovery of function for junk DNA. Alternatively, multiple labs may be studying similar genetic elements, coming to similar conclusions in different papers. In any case, it’s not unusual, weird, or problematic for our present purposes if there are multiple papers covering the same genetic element. In most cases, multiple papers covering the same genetic element just shows accumulating evidence over multiple aspects of a study showing function for some genetic element, and/or it may show multiple labs coming to similar results of functionality (i.e., repeatable results) for some genetic element, further reinforcing the functionality of that element.

Category 3: Papers Reporting Roles in Causing Disease — i.e., Pathogenic Functions

Response: This category also belongs on our list. I addressed the science of this objection in my previous post, where I explained that the “role” in some genetic element causing disease is actually usually evidence that it has a beneficial function under normal circumstances, but that function has gone awry due to mutation. So, finding a disease that correlates with mutations in some non-coding / junk DNA element is normally evidence that that element has a useful function. This objection poses no threat to our argument.

Category 4: Papers Reporting “Activity” but Not Identifying the Specific Function

Response: As we have seen with ENCODE, evidence of biochemical activity is generally prima facie evidence of some useful function. So, identifying biochemical activity is a useful in indicating function for junk DNA and can spur on future discoveries of the specific function of a genetic element. Indeed, this activity often correlates with gene expression, strongly suggesting we already have evidence of specific function. So this class of evidence most certainly counts in favor of function for junk DNA and should not be excluded from our list. 

Category 5: Papers That Don’t Affirm Function for Junk DNA

Response: The only papers that might potentially deserve to be removed from our list would be those in Category 5 — those that don’t affirm function. However, I’m not aware of any papers on our list that fall into this category, though it’s possible that there might be a couple that slipped in by accident. If there are any, I’d love to know about them and I will gladly remove them from the list. 

If we were to remove any papers under Category 5, I suspect the size of our list would barely change. Indeed, if you were to remove every paper that critics are concerned about, it would not change the fact that there are many thousands of papers uncovering function for non-coding / junk DNA. 

As we stated about our review, our list only scratches the surface of the literature, and you can’t negate the existence of that body of literature through a few complaints — some of which hold merit, and many of which, in my opinion, are a bit nitpicky. If you’re looking to argue that there is not a large body of scientific literature finding, reporting, and discovering function for non-coding / junk DNA, I would humbly suggest that your limited time and energy are best spent doing something else.