Intelligent Design and Common Descent


(T J Runyon) #178

Yep. And this could be due to reasons I listed above and the reasons listed in the papers I linked to. And I guess if ID is true the gene could also be a special, direct creation. But I think you would have to rule out all other explanations to come to that conclusion.

(S. Joshua Swamidass) #179

That is what I am saying. Though, if we allow for God’s guidance, it obviates all the discussion about functional information. It just does not follow. Even if the FI argument against evolution was valid, it would not be an argument against common descent. Even if the isolated protein function argument against evolution (from Axe) was valid, it would not be an argument against common descent.

It just doesn’t make sense to raise arguments like FI/Axe as if they cast any doubt on CD. In no way do they cast doubt on common descent. At best, they just indicate God intervened at times, if they were valid arguments.

(Ann Gauger) #180

This is very interesting. I think some terms have been conflated or misunderstood. ID implies only the necessity of an intelligent designer, not how he acts. It could be by guided evolution, special creation, or a combination of unguided evolution, guided evolution, and special creation. Mix and match.

Swamidass has a point. He sees the signal in the genome for common descent as incontrovertible. Examples of de novo genes or incongruent gene trees or the extremely rare distribution of proteins in sequence space don’t matter. They would merely be acts of intervention against a background of common descent in Josh’s view. Correct, @Josh? Even functional information translates to guided evolution on a background of common descent. Is there a point when the intervention outweighs common descent?

I don’t know how many of those potential interventions you would actually grant, but it appears to me that agreement on common descent is fundamental to you.

(S. Joshua Swamidass) #181

We’ve covered this here: Would God’s Guidance Be DNA-Detectable?. Given what we know of population genetics, a priori we do not expect it would be detectable, even if we allowed every selectable mutation to have been inspired by God.

In principle, I agree with you. However, in practice, the immense amount of effort invested in arguing against common descent speaks something different with DI’s actions.

You basically have it it right, though I wouldn’t say “incontrovertable.” Remember, I have also made the case for a de novo Adam. Rather, I’d say it is very clear that God made us in a way that we looks like we share common ancestry with the great apes.

Given the evidence, the only viable argument against CD have to engage with theology. Not finding any contradiction between CD and Scripture, even if see teaching of a de novo Adam, there are no theological grounds for rejecting common descent. It looks like we share common descent with the apes, because we in fact did. Of course, I’m open to hearing other arguments, and I am happy to legitimize people taking different views, as long as they don’t justify themselves with anti-scientific arguments.

As for scientific evidence alone? The evidence, at most, could suggest God’s involvement. However, as I explained, we do not expect this would be detectable a prior. God could have been clear in the evidence. Imagine a world where humans-chimps had very different genomes, and archaic humans (e.g. Neanderthals) did not exist. Such a would would very much trouble or even disprove an evolutionary interpretation. That, however, is not the world we find. Instead, we see gobs of evidence that suggest common descent that need not exist unless we really did share ancestry with the apes.

That, in my view, is part of why the Genealogical Adam is so important. It makes space for the traditional account in the evolutionary story. It takes back ground that was lot. That should change the calculus for everyone.

(Ann Gauger) #182

I didn’t participate in that discussion, but I didn’t find it particularly convincing. Are you speaking of detecting guided point mutations? No, of course that can’t be detected. Even rearrangements or insertions and deletions can’t be individually identified as the result of design. But what about de novo genes? If it can be shown that non-coding DNA really doesn’t make functional protein without guidance, and that the probability of developing a promoter is exceedingly small, that would imply something unusual is responsible for all these de novo genes we are finding. And in that case we would have specific DNA changes to point to.

(S. Joshua Swamidass) #183

In the human genome, can you show any evidence of de novo genes that do not also have homology to non-coding DNA? @T.j_Runyon recently pointed to a paper on this, showing that the “de novo” genes in humans have such homology. Also, these genes are skewed to smaller proteins, consistent with random drift anyways.

I can grant if we found a large number of de novo genes that did not have an obvious mechanism, it would be suggestive. However, keep in mind that deletion in the great ape lineages will produce the appearance of a de novo gene, so that has to be ruled out too.

Though, keep in mind, we do not actually see de novo genes arises out of nothing. They all seem to arise out of homologues in non-coding DNA.

That being said, we agree here.

I’m just saying there does not appear to be any evidence that anything else was needed to produce the human genome from our common ancestor with the great apes. If you can show me evidence, that might be interesting. However, as I said, de novo genes in humans have homology to non-coding regions in apes. They are not really “de novo,” in that critical sense. If one or two have no homology, that could be explained by gaps in the ape genomes, by deletions in the ape genomes, or possibly a rare horizontal transfer. There are not, however, many genes at all that this applies too.

It could have been another way. There could have been 100s or 1000s of de novo genes in the human genome, with no homologues in ape sequences. This would have been very clear evidence of something outside normal processes. This, however, is not what we find in our genomes.

(Ann Gauger) #184

I never said they had to arise out of nothing. In fact, what I said was, “If it can be shown that non-coding DNA really doesn’t make functional protein without guidance”, implying that de novo genes can come from non-coding DNA. It is the extreme unlikelihood of that that is in question.

Gosh, I never restricted it to humans and apes. The strongest evidence is in other taxa.

(John Harshman) #188

Not if you follow the evidence, which pretty much rules out special creation of any species. So we are left with guided and/or unquided evolution, period.

Now Joshua’s scenario is a special case, in which a couple of individuals of a previously existing, evolved species are specially created. That would be undetectable. But an entire specially created species would be undetectable only if god were being intentionally deceptive.

(John Harshman) #189

Strongest evidence of what, exactly? And in what other taxa. Are you referring to bacteria?

(Ann Gauger) #190

That’s an assumption about how God should create. But I do not mean to argue for special creation here.

(Ann Gauger) #191

I am talking about orphan genes. Here’s a recent reference.

(Ann Gauger) #192

And another.

(Blogging Graduate Student) #196

That paper has a rather nice discussion of the origin of their orphan genes, with 80% showing hints of how they evolved.

(John Harshman) #197

No, it’s an inevitable inference from the idea of special creation that’s indistinguishable from common descent. There’s no other credible motive than deception.


What do you mean by “realistic conditions”?

That is just the Texas Sharpshooter fallacy. What you need to do first is determine how many such adaptations are possible before you determine what is probable or improbable. This means finding all beneficial changes that are possible in any genome with respect to epistatis.

(Bill Cole) #200

T, I think her assumption is an adaption that requires 4 specific mutations.


The other assumption is that such an adaptation is improbable. In order to make such a claim you have to know how many adaptations that require 4 specific mutations are possible. If there are billions and billions of such adaptations that are possible then such adaptations can easily occur through random changes to the genome.


Be careful of confusing “gene” with “DNA”. Two species can lack a homologous gene but they can still have homologous DNA for that gene.


It would appear that no ID researcher has determined how likely it is that beneficial proteins can emerge from non-coding DNA, so why is the ID community pushing orphan genes as a problem for evolution? Why is it even being brought up?

(Bill Cole) #204

Not true. Bill Bessemer and John Sanford wrote a paper that could be applied here as it addresses the high probability of DNA breaking down with random change given the real ratio of deleterious mutations vs beneficial ones. This paper was discussed at TSZ.