Phylogeny vs Similarity and Function

Two thumbs up, Joshua! Thanks for patiently answering the questions, and correcting the mistakes, of this tyro.

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Even the tiny number of ID proponents who accent shared ancestry, still reject evolution as an explanation for the diversity of species. If ID proponents really accepted evolution, they would be Evolutionary Creationists, but they take great care to differentiate themselves from that position, precisely because they do not accept evolution. Not only that, but they repeatedly argue that evolution is simply not a valid explanation for the diversity of species.

They say they have no problem with natural selection, but don’t believe it can lead to evolution. They say they have no problem with genetic mutation and gene drift, but don’t believe it can lead to evolution. They say they have no problem with the fossil record, but don’t believe it provides evidence for evolution. They say they have no problem with common descent, but keep raising arguments against it and arguing that it isn’t evidence for evolution. They say they don’t believe evolution is necessarily incompatible with the Bible, but keep raising arguments as to why it’s incompatible. All this is precisely why IDers not only oppose evolution but also oppose evolutionary creationism.

Actually I agree with Ben Kirk on this point. I think he identified the issues very well.

This needs to be filled out a bit more. Even the most staunch atheist agrees that some forms of life appear to be designed. However even the most staunch creationist finds it hard to explain why many forms of life do not appear to be designed; fish with eyes which don’t work, insects with inactive wings trapped beneath a hard carapace, and the hideously dangerous and painful birth process of the spotted hyena (resulting in 60% of cubs being stillborn, and a high death rate among first time mothers), to name just a few.

This is why atheists don’t go around saying life has a “false appearance of design”. Rather, they explain (as you did), that life is generally so well adapted that we interpret some forms as having an appearance of design, because of our personal perspective (very much as you described). The problem for many Christians on the other hand is that since they rightly believe God created the universe then they have to explain why God did so in such a way as to give it a false appearance of age, or the false appearance of evolution. This is not a problem for the atheist.

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There really is no need to turn every thread into a “why ID/YEC folks are the worst” tangential tirade. Please try to stay on topic.


I don’t believe either of our posts could be described in that way. The whole point of this thread is which explanation best describes the evidence. Joshua has explained why evolution explains the evidence better than ID and YEC. Ben and I agree, and have provided additional commentary on the point.

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Your “additional commentary” needs some new material.

[quote=“Christy, post:15, topic:26471”]
There really is no need to turn every thread into a “why ID/YEC folks are the worst” tangential tirade.[/quote]
I don’t see that either of us claimed that “ID/YEC folks are the worst.” We are simply disagreeing with Swamidass’s description of positions regarding evidence.

[quote]Please try to stay on topic.
[/quote]I’m not following you. We were responding directly to Swamidass. Were his comments off topic? His OP was about analyzing evidence.[quote=“Christy, post:17, topic:26471”]
Your “additional commentary” needs some new material.
[/quote]Are you saying that ID people actually do claim that evidence is being suppressed? I’ve certainly never seen anything of the sort.

This point is incredibly important. No one is claiming that similarity simply demonstrates evolution, while the denialists’ straw men rarely go beyond the word “similarity,” used as vaguely as possible. The details of the evidence are where it’s at.


I understand that. It was a defensive, preemptive maneuver on my part, because I could envision where things were headed. It seems to me that we already have three or so open threads with plenty of “ID is not real science” themed content contributed by the two of you and more of the same on this thread would be an unnecessary bunny trail. We are all aware of your views on the topic of how ID folks handle evidence.

Measured by the “heat index” (number of posts), those threads have been by far the most popular. They may not have fared quite so well as measured by the “light index” (understanding advanced), however. :relaxed:


For this thread, let’s focus on the data at hand, and try and explain it clearly. We have a lot we agree on.

I started another thread to discuss the Omphalos argument and ID and YEC. We should continue that conversation there. It is interesting in its own right, and needs its own thread.

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Well, yes, but that’s because the IDers aren’t showing up.


@Chris_Falter, I thought I would check into some of Denton’s thinking. I have to say, it doesn’t seem like he has much conviction to any such belief in common descent.

Let’s look at this chunk of logic and thinking:

"Denton suggested that these data undermined the notion that fish were ancestral to frogs, which were ancestral to reptiles, which were ancestral to birds and mammals. If they were, then wouldn’t the difference in cytochrome C structures be increasingly different from carp to frog, to reptile, to mammal? How could the cytochrome c amino acid sequences for such a wide range of species all be “equidistant” from the sequence for bacteria? "

In the very first sentence, you see Denton challenging something as basic as fish came before amphibians, and amphibeans came before reptiles! If Denton thinks God-Guided evolution is the “main-chance”, he’s got a funny way of making the point!

The paragraphs below is a discussion of why Denton’s criticism didn’t make much of an impact.

“Molecular biologists quickly pointed out the fallacy in Denton’s argument. Just as there is no such thing as a “living fossil”, and all modern species are cousins, so too, the amino acid sequences for all living species have been evolving since the time of their divergence from a common ancestor.” [14]
[Footnote 14: Spieth, Philip T. (June 1987). “Review – Evolution: A Theory in Crisis”. Zygon. 22 (2): 249–268. doi:10.1111/j.1467-9744.1987.tb00849.x.]

“A modern carp is not an ancestor to a frog; frogs are not ancestors to turtles; turtles are not ancestors to rabbits. Similarly, the variations in eukaryotic cytochrome c structure with respect to bacteria are all due to mutations taking place since divergence from the common ancestor of these different organisms. It thus is not surprising that they show a similar level of divergence and equidistance of this type was even predicted and confirmed by researchers as early as 1963.” [15]
[Footnote 15: A Tale of Two Crocoducks: Creationist Misuses of Molecular Evolution, James R. Hofmann ]

As recently as 2014, Denton has fired off another frontal assault on the fundamental premise of Evolutionary science … that a lot of little changes can frequently lead to Speciation - - launching his verbage against the darlings of Darwin - - the finches of the Galapagos!:

“From the emerging developmental genetic picture, it is now relatively easy to envisage how gradual adaptive fine-tuning of the expression patterns of a handful of genes could result in the different beak forms of the Galapagos finches we see today.”

“The evolution of finch beaks requires no causal agency beyond natural selection. Some finch beaks proved advantageous; others, not. The lesson of the Galapagos, and all such cases of microevolution, is that cumulative selection will work its magic just so long as there is an empirically known or plausible functional continuum, at the morphological or genetic level, leading from an ancestral species or structure to a descendent species or structure.”

What is ironic about Denton’s opposition is that he seems to genuinely believe that God has created life forms through his direct intervention - - and yet simultaneously rejects the idea that God would use evolution to create new Species!

How does one pursue both lines of reasoning simultaneously? How does God guide evolution if when God spends a million years to create a brand new life form - - he has to do it WITHOUT creating a new species? How is this even logically sensible?

If God guides evolution … there has to be Speciation!!! Unless you are going to argue that Whales are just a degenerated branch of the same species of Amphibians!

If God’s intelligent design is in use to create new forms of life … unless God is “POOFING” these life forms into existence … then speciation is STILL required.

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Indeed. Denton falsely portrayed the evolution he was attacking as a ladder instead of a tree, which is why his first book was howlingly bad. He has quietly abandoned that view and does not promote it in his second book.[quote=“gbrooks9, post:23, topic:26471”]
How does one pursue both lines of reasoning simultaneously? How does God guide evolution if when God spends a million years to create a brand new life form - - he has to do it WITHOUT creating a new species? How is this even logically sensible?
All fine questions!

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Hi George,

Last February, Biologos published Sy Garte’s review of Denton’s latest book. Yep, right here at Biologos. Denton’s views have evolved considerably since his first book, the one which you are mostly citing. While no one would mistake him for a mainstream biologist (as @benkirk notes), Denton does believe in common descent.

As for ENV, I would not expect them to present unbiased reporting with scientific depth. I recommend giving more credence to Sy’s review.



@Chris_Falter, I read Sy’s review of Denton’s book. Maybe @Sy_Garte could step in and explain his explaination a little more?!

Let me show you what I mean when I ask if Denton has really examined his various positions systematically:

  1. He cites the Finches of Darwin.
  2. He points to the small changes in the Finches.
  3. He says that this is micro evolution.

Sy provides this quote from Denton’s work:

“Descent with modification implies a pattern of descent through time, where extant forms have descended with modification from common ancestral forms, right back to the last common ancestor of all extant life. But the fact of descent with modification cannot be taken as…. support for any sort of gradualism." [emph. added] (p. 195)

So… Denton places all his marbles on the idea that there IS Evolution … that any time there is speciation … it has to be a DRAMATIC jump… Of course he means by this that the dramatic jumps are guided by God.

But if there were any human observers during these jumps… he wouldn’t see a giant ghostly hand waving around in the air … there would still be life forms mating … and creating new generations … but with giant jumps in the genome… not little ones.

I have to wonder if @deliberateresult would agree with Denton on this …

I will try to do that.

I dont think that is quite right. Actually what Denton says in more recent book (the one I reviewed) is that evolution probably proceeds by saltational “jumps” or large scale and dramatic changes not just in genomic structural genes, but in control circuits that regulate gene expression. He quotes a number of the key findings of people like James Shapiro, and the Wagners and others associated with the EES. In no part of this book does he attribute any part of evolution to God. His ideas in this regard are actually quite mainstream, and the whole concept of evolutionary jumps goes back to Gould, and even Mayr, with punctuated equilibrium.

I havent read this entire thread, but I thought I would correct this one point you raised. It might be worthwhile taking a closer look at this book, since as @Chris_Falter says, it is very much “evolved” from the original one.

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Alright… I’m game to try to make more sense of it all …

Thanks, @Sy_Garte… and to you as well, @Chris_Falter !

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My memory is that Gould toyed with saltationism and promoted punctuated equilibrium, but that he never the former as an explanation for the latter.

I think your memory is right. But then he tragically did not live to see (or at least to see wider acceptance of) some of the newer ideas of Shapiro and the related concepts and data on mechanisms for saltation. I believe for example that some recent findings of transposon insertion at the origin of pregnancy came long after his death. I would love to know Gould’s views on how all of the molecular data might fit into PE. l plan to ask him that as soon as we meet again. :slight_smile:

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I wonder what would happen if you apply the same algorithm to the evolution of LEGO or less sarcastically to the evolution of languages as basically the genetic as well as the spoken language fulfill the task of transmitting a will to control the movement of matter or energy. The critical question is why the process of evolution should allow anyone to conclude that it has nothing to do with intelligence


Are you sure you speaking to the right audience? Look at the very syllables of the name BioLogos. “Logos” has everything to do with intelligence.

Maybe an easy way to remind ourselves of the difference between Intelligent Design and the processes that BioLogos supporters frequently discuss is:

The former is usually discussing Instant processes of Intelligence (or Divine Intelligence for most ID folks)… while the later is discussing "Divine Intelligence in Slow Motion" !