I think this is a pretty important observation!
Except for the very few known ID supporters who accept the premise that Intelligent Design is tied to a Very Old Earth scenario (which essentially makes them a BioLogos supporter) - -
- - the vast majority of ID supporters have to conclude that God started creating (aka “Poofing”!) thousands of new species every year since the landing of Noah’s Ark, in order to arrive at the current period’s species count in the Millions!!!
Who can be named in the I.D. “camp” that accepts “Common Descent” in a very old earth context?
That’s something I totally agree with.
Per a source I don’t consult often, RationalWiki:
“Denton does not deny common descent which distinguishes him from most intelligent design proponents.”
Michael Denton is a senior fellow at the Discovery Institute’s Center for Science and Culture.
Hugh Ross doesn’t accept common descent with respect to homo sapiens sapiens, and he would generally be described as an ID proponent. But he argues vehemently that the earth is 4.6B years old and the universe is 13.8B years old. He has publicly debated Jason Lisle of Answers in Genesis on the age question many times.
Cheers,
Hi Joshua -
I am hoping to pull the thread back to your original post, which still fascinates me. Based on your latest post, here’s my understanding of the process:
The goal is to determine which method of projecting relationships yields better predictions: straightforward genetic similarity (method a) vs. phylogeny (method b).
The results show that phylogeny yields far more accurate predictions. Thus we infer that phylogeny is a better description than simple genetic similarity of the relationship between the species.
Aside from the fact that some of the steps are grossly oversimplified – in particular the final step – have I accurately depicted the research?
Critics of evolution often state that genetic similarity has no bearing on the question of biological origins and common descent because we expect similar functionality to be supported by similar genetic sequences. The implication of the research, however, is that phylogeny is more important than pure genetic similarity in predicting function; therefore we can confidently accept the reality of a phylogeny (i.e., common descent).
Again, thanks! And please feel free to clarify anything I might have misunderstood or explained poorly.
Godspeed,
Thanks. It really is a fascinating study.
So your summary is incorrect in a couple points.
First, the algorithms we are discussing operate on genes, not species. It traces the phylogeny inferred from the sequences of these genes. Therefore duplication events give rise to different leafs in the tree, and most species therefore map to multiple leaves in the tree. The phylogeny algorithm can make inferences about exactly when in the tree the duplications occur.
Second, the analysis does not pick sequences based on the species. Instead, it starts by finding all similar sequences, including those that are only remotely similar, that have been observed in nature. It is a 100% sequence based approach. As long as there is enough sequence similarity, the gene is included in the analysis.
Third, your language about “projecting” relationships is a reasonable analogy. It matches closely what is happening in the similarity case, but it isn’t exactly what is happening in the phylogeny case. Still, your schematic is about right.
In the phylogeny case, we try and reconstruct the history of the genes. We first do this by using the genetic similarity to give us the ancestry relationships between genes. Next, we infer the points (with careful attention to uncertainty) in the tree where specific functions are gained and lost. So we now have an inferred history of all the genes in the phylogeny and the gain and loss of function in these genes. Of course, this model makes predictions about the function of genes that are not annotated.
They key point is that the reconstruction of history does change the predictions we make on the function of unknown sequences. And the predictions improve dramatically. If the reconstructed history was just a false reality, this just does not make sense. Of course, there is still real uncertainty in the history, and even errors, But there seems to be enough correct inferences in it to improve predictions of function dramatically.
As you put it…
That is correct.
Exactly.
Well I would be more circumspect.
I would say: this is strong evidence for the “similarity caused by shared history” hypothesis over the “similarity caused by common function” hypothesis, whether or not evolution is ultimately true.
Moreover, this directly tests the adequacy of a design principle in explaining biology. It is absolutely true that proteins/machines/etc that have the same function often show similarity to one another. It also true that very similar thing have different functions, and very different things have similar functions. In the end, we need to see how well this principle explains the data over alternatives. We find that phylogeny really does systematically improve our predictions of function, over that of just using the “common-function causes similarity” design principle.
I think this is an important body of work for those that dismiss evolutionary theory as useless, or assert that similarity data captures everything we get from phylogenies. Something real and useful is being inferred by phylogenetics.
Thanks for the questions, and I hope that clarifies things!
Two thumbs up, Joshua! Thanks for patiently answering the questions, and correcting the mistakes, of this tyro.
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.
@benkirk
@Jonathan_Burke
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.
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. 
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.
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.
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?
[/quote]
All fine questions!
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.
Cheers,
@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:
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 …
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