No Junk DNA vs. Rarity of Function



You don’t have to look far to find ID articles supporting the claim that the vast majority of the human genome has function (e.g. here). At the same time, there are ID articles claiming that function is exceedingly rare in DNA sequence space. That is, there are a very limited number of DNA sequences that can have function.

These two concepts are in serious contradiction to each other. Whatever your feelings are towards the ENCODE study or similar research, there is one unavoidable fact: the vast majority of the human genome is accumulating mutations at a rate consistent with neutral drift. This is true if you compare just human genomes or compare genomes between multiple species. This means that there is a lack of selection against deleterious mutations in the vast majority of the human genome. This can mean one of two things: 1) the function in those stretches of DNA are not affected by changes at any base within that DNA, or 2) the vast majority of the human genome does not have function that is being selected for (what ID supporters and creationists would call microevolution).

If we accept the ID claim that these sections of DNA have function then it leads to the unavoidable conclusion that function is found in almost any DNA sequence. Function is not rare in DNA sequence space. Instead, function is found in almost every random DNA sequence, and no mutation can do away with that function.

As far as I can see, ID has to pick between “no junk DNA” and “function is rare”. They can’t have both.


In my most humble opinion you either misunderstand or misrepresent the ID argument. It would perhaps be helpful if you could quote an actual argument. I would be very interested to see where any high profile ID figure makes the argument that function is rare in DNA sequence space.

(S. Joshua Swamidass) #3

I’m pretty sure that is Axe’s and @Agauger’s argument. That is exactly what they have been arguing.


Here are a few quotes:

Compare this to what Jonathan Wells writes about junk DNA in the human genome:

(Dan Eastwood) #5

Pretty much any argument that the probability of genetic sequence XXX is “small” should fit that description.


She’s talking about genes, so she is probably talking about protein function. IOW, a specific category of function. Would you agree?

To cite the ENCODE results and conflate that with the function that Axe and Gauger are talking about is a bit disingenuous. I hope that clears up for you how the two positions are not contradictory.

One sort of function may be rare while another sort of “function” may not be rare.


So we have coding DNA and non-coding DNA. and The “function” of one is not the same as the “functions” of the other. It’s important to not equivocate in these matters.


Orphan genes include non-coding genes that are not translated. More generally, it is argued by ID supporters that only an intelligence can create DNA sequences that have function. If random DNA can have function this contradicts their argument. It is also argued that mutations in functional DNA will mostly be deleterious which is contradicted by the fact that most DNA in the human genome is accumulating mutations at a rate consistent with neutral drift.

(Arthur Hunt) #9

My take on this is: ID proponents will look at the vast quantities of functional DNA (“no junk”) and reason that, since function is extremely rare in sequence space (or by some other metric), then design must have factored into the appearance and maintenance of all this function.


Then how do they explain the fact of neutral drift in the vast majority of this functional DNA compared to sequence conservation in known functional genes, including known promoters and RNA genes?

(Dan Eastwood) #11

I mentioned this discussion on FB, where this book was suggested as relevant:

(Arthur Hunt) #12

I am assuming, to understand their position (and avoid contradictions), the validity of their perspective about the absence of junk DNA and prevalence of function. I don’t agree with this, but I can see how, if this is granted, then their positions may not be contradictory.

(S. Joshua Swamidass) #13

I agree. It is not self contradictory, but it is a totally different view of biology that that of mainstream science. I was actually fairly shocked when I first realized this from some conversations with ID leaders. I had thought that it was a minor tweak to biology that they were proposing. That is not the case at all. I found that many see the function of DNA in the cell as very different than did most biologists.

What is the difference? It is hard to explain precisely, but we are pointing in the right direction here. It is, sometimes, as if there is a intuition that the final form of humans (for example) fix the precise details of the genome, down to synteny and non-coding DNA, and GC content. I could be wrong, and I am sure there is variation in views on this, but if we were to take all the appeals to “design” to explain biology seriously, this is where it seems to lead, and it seems that some have arrived here.

I am not talking about specific people here. I’m not sure this applies, for example, to @Agauger. It is, however, what appears to be how some see things.

(S. Joshua Swamidass) #14

As I understand it, this a central argument in ID, as expressed here:

I can see why people dispute this, but regardless, that seems to be all that we are saying here. They argue that functions in sequence space are rare and isolated. If I am missing something here, I hope that @Kirk and @Agauger and @pnelson would correct us.


Their model would have an intelligent design continually guiding each and every mutation in a way that makes it look like neutral drift, for no apparent reason. At the same time, the same designer would be changing other genes at a much slower rate for no apparent reason. This doesn’t even get us into introns.

In trying to have no junk DNA and rarity of function it requires a very convoluted and unfalsifiable model.

(Arthur Hunt) #16

I for one would be glad to know of any high profile ID figure who would agree that function is not rare in sequence space.

(Arthur Hunt) #17

It just requires, indeed, demands design. As you describe.

That is, I suspect, the entire point of their positions.

(S. Joshua Swamidass) #18

I don’t think that is right. I doesn’t seem that there has been wide appreciation of neutral theory in ID. I do not think most of them have actually considered carefully how population genetics interacts with their claims.

Rather, they are saying an alternate explanation for all the observations consistent with neutral theory is design. However, not really having a good handle on what we mean by “all the observations”, they haven’t yet appreciated how strange of a claim that is. Most of these predictions arise from assuming no function, so why would we think that functional constraints would be a valid explanation? They, usually, cannot actually enumerate the observations we are referring too.

Populations genetics, in my opinion, is the key to cracking the log jam on this.


I view it a bit differently. It’s as if they are saying each raindrop is intelligently guided to hit a specific spot on the Earth, and the result is a pattern that is indistinguishable from a random pattern. It’s almost an Omphalos type argument.


Are there examples of how this model works, or how it differentiates itself from actual neutral drift? Or are they reflexively claiming that it is design and hoping that people don’t dig into it too far?