The Problem with the ID Argument

Even if that is the case, so what? If the basics of Darwin’s theory had not been confirmed by thousands of pieces peer-reviewed evidence since its publication, it would be remembered as nothing more than a historical curiosity, if was remembered at all.

In the 21st century, significant scientific breakthroughs are not published as books. They are published as journal articles.

I never cease to marvel at your ability to reject carefully conducted science based on your own vaguely expressed intuitions. You must be a stable genius indeed.

His model doesn’t consider that sort of thing, as it deals with the evolution of homologous proteins. But once again you fail to understand the difference between the source of mutation and the pattern produced by its results. What we have here concerns the latter.


I understand you sir. Logic is a gift which i believe is from God. And the reason i believe in God -in particular the God of the Bible- starts with my thinking on the illogical nature of mass energy creating itself and ends with two very definitive apologetics for the Christian faith itself-the historicity of the resurrection of a man named Jesus that altered history and the conversion of a pharisee named Paul who one day was a religious bigot terrorizer/murderer of followers of Jesus then another day after his miraculous conversion, His greatest ally, spokeman and encourager of that same people group! Faith in Jesus who chose to forgive me of my selfishness, pride and sin was the start of my journey as a Christian that has brought such joy. This is like a treasure i found in a field that caused me to buy the field and i can think of no better a gift to give to everyone everywhere! Enjoy the rest of your weekend.

I have never seen one of the latter. Could you offer examples?

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That’s because, partly, you are not looking at the construction from the inside, to see the parts and how they were put together. Your judgement is based on surface detail.

convergent evolution, however, poses an interesting problem for the YEC model: morphology doesn’t dictate genes. Thus lions do not necessarily have to be genetically closely related to tigers, although they are. Hyenas, Wolves, and Tasmanian Tigers, for example, might all appear similar, but there are distinct genetic differences that are strong evidence of common ancestors being quite distant, and of having different evolutionary branches.

Hmm, I don’t think I conflated it, what I’m trying to get at is the process. Here’s an analogy of what these conversations often look like to me:

Question: How did this house get built?
Biologists: A foundation was dug and poured, then the frame was built, roof put on, insulation and drywall, electrical and plumbing, and final painting and finish work.
ID: we know that architects make blueprints

If ID can’t come up with some kind of mechanism (and no, “mind” is not a mechanism, it’s an agent or cause) I have a hard time seeing it as a scientific claim. I could claim “Robots made Stonehenge” as a scientific theory and then when questioned about how they did that, if I simply said “we know robots assemble things” I would be rightly dismissed without a further thought.

Hmm, I think it assumes that there is a common ancestry somewhere, not a single tree. I would maybe also look at the difference between rooted and unrooted trees. I would spend a little bit of time to learn how phylogenetic trees are made. It gave me an appreciation for how grounded it is in solid math and I have a better understanding of how powerful they are and some of the limitations. Again, just in a generalized, I’ve just scratched the surface, sense. If you can’t figure out if tigers and lions share a common ancestor, ask a friendly biologist. That’s what’s so awesome about Peaceful Science, once we get past distrusting each other, I think we’ll find a lot of common ground and lots of really smart people willing to help.

I think it would really be worth your time to dig into @John_Harshman’s Office Hour: John Harshman: The Phylogeny of Crocodiles because we talked about comparing to random sequences. Also, remember that a generated phylogenetic tree is a hypothesis, so if we had more than one starting point I think we should see problems in our phylogenetic trees when we compare them to morphology or the fossil record.

If we can’t tell the difference between one or multiple starting points, then we can basically just assume UCD as a working model and seek other ways (philosophy, etc.) to tell us about the other starting points.


I am not alone here criticizing this paper. The problems are obvious and I am surprised you cannot do critical analysis here.

Koonin and Wolf

The tests described above show that there is currently no formal demonstration of the universal common ancestry of the extant life forms. The likelihood tests of the kind described by Theobald [4] fail to address the problem because they yield results “in support of common ancestry” for any sufficiently similar sequences.

It is what it is at this point. I do think John has done great work with both flightless birds and crocs in looking at data and doing comparative genetic work and comparative morphology work. I just don’t understand the basis of some of his conclusions.

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Another analogy how biologists describe evolution. How did the software get made? Random changes when we copy it and choosing a copy that runs faster than the old one.

ID analogy: Study and test a better algorithm and insert into the code.

Ah, but here’s the difference Bill, we have a decent shot at telling the difference between a model for software developed by optimizing random changes and one that’s been studied and “designed” to run better. If we looked at the previous 10 versions of the code under both models, I’m guessing we could tell them apart. That’s because they have a different mechanism for the change that should be fairly apparent, assuming we have a knowledgable programmer. However, if we have a complete novice, who has no programming skills at all, we may not be able to tell the difference between the random changes and the “designed” ones because the poor programmer would make effectively random changes.

The data we have in the genome looks unmistakably like common descent. That seems to indicate one of the following:

  1. UCD is real, and there is no designer
  2. UCD is real, but set up by the designer
  3. UCD is mostly real, but there could be minimal exceptions outside the “view” of our data
  4. UCD is not real, but we have a “bad programmer” and can’t tell the difference.

If I was a betting man I’d go with 2 or 3. I have outside reasons to think that 1 is insufficient and 4 is just weird.


I would just want to emphasize that “minimal exception” could very well be very important.


Yeah…my analogy not the best. Ironcally, in my humble estimation “convergent evolution” is an apologetic that negates the logic of evolutionism!

I dont get too sweaty palmed about “problems” w the yec model either. If i trusted a model that relied on chance and mutations and energy to concoct eyes, and livers, and reproductive organs and then there were problems with the logic (which i believe is true) then there is no where to turn as a better explanation. But i trust in God, not nature. The universe had a beginning and God is the powerful Designer and Maker of it. With God, all things are possible and the mysteries and transcendence within His being as Creator may be too lofty for the science of man to figure out. I actually feel for the scientist who thinks he has the wherewithall to box in God as well as the nature of His workmanship because they miss out on the opportunity to experience higher levels of enjoyment related to aknowledging the mysteries and awesomeness within His glory. Sometimes it is a good thing to admit that we just dont know and trust in revelation given by God for understanding.

I can agree and say the work ahead is to get a better handle on “mostly”.

I think what is confusing him is that ID books are often written to resemble the idea of some uninformed people of what a scholarly book looks like


Really? You think evoutionary biologists believe someone is choosing the mutations that work best?

BTW, the process you described is actually used in computer programming, and works very well.

The environment is selecting the one that reproduces best. Beneficial mutations are rare but happen.

Right, so that is a mechanism that is regularly observed, and which even you accept.

You do not even have a hypothetical example of even a single one of the mechanisms by which a protein could have been designed.

Genetic recombination is a mechanism as part of the reproduction process. I know it produces variation but how much I don’t know. Art Hunt has an example in plants where a novel gene arose by modifying and existing gene.

If the process is deterministic could it be capable of design? If it is from where did this capability originate?

That does not involve design. Did I really have to tell you that?

How do you know?