New Paper Demonstrates Superiority of Design Model

(Cornelius_Hunter) #27

Well, it sounds like statistical significance counts in the one case (when it supports evolution), but not in the other case (when it demolishes evolution). You are certainly correct that it has been argued there is a strong, statistically significant phylogenetic signal. But those methods entailed silly (strawmen) models to compare against. What Ewert shows is a more interesting comparison of models.

I think what is happening is you are resistant to contemplating a new model, even though it is evaluated using standard methods and practices.


There is a strong, statistically significant phylogenetic signal. Even Ewert admits as much.

Also, Ewert’s model doesn’t even include sequence data. That makes it far less interesting, by a country mile. Ewert’s model can’t explain the patterns in sequence divergence which is a massive piece of evidence that needs to be addressed.

(Cornelius_Hunter) #29

No, I can’t. Guess that’s it huh?


I can point to such a gene. There are mice that carry the GFP gene from jellyfish, and that gene got there through intelligent design (on the part of human designers). Humans move genes between distantly related organisms all of the time. We can find yeast species with human genes, E. coli with mouse genes, mice with human genes . . . on and on and on we see massive departures from the expected phylogeny due to intelligent design on the part of humans. That is what design looks like.

What design doesn’t look like is small incongruencies between closely related lineages. What design doesn’t look like is more divergence in introns than in exons. What design doesn’t look like is genetic equidistance. What design doesn’t look like is DNA sequence following lineages instead of environments and niches. If design is true then we shouldn’t see anything close to a nested hierarchy, but we do. We don’t see species with feathers and mammary glands. We don’t see species with three middle ear bones and feathers. We don’t see species with fur and flow through lungs. There are all of these different modules that could be swapped in and out, BUT THEY AREN’T. Instead, we see a nested hierarchy.

(Cornelius_Hunter) #31

Yes, when compared to silly, strawmen, alternatives. Please be aware that statistical significance is a tricky commodity. You need to understand the underlying method used. Every evolutionary study that has found such “statistical significance” has relied on these meaningless alternative models, in order to gain such “statistical significance.”

I realize Ewert’s new model is a radical departure in thinking, and requires an entirely different way of looking at systematics. But I would encourage you and others to try to keep an open mind about it. What you don’t want to be doing is to reject a new, superior, model, because it doesn’t “fit.”


What “meaningless alternative models”?

The problem is that it doesn’t even attempt to explain the sequence data which is what it would have to do if it wants to replace evolution and common descent as an explanation. On the face of it, Ewert’s model is completely falsified by the sequence data since we don’t see a mixture of modules when we look at the sequence of genomes. We don’t see a species with a module from rodents, a module from fish, a module from birds, and a module from jellyfish. Instead, we see the pattern of sequence conservation and divergence that we would expect from evolution and common descent.

(Matthew Pevarnik) #33

Here’s a more recent paper on the yeast study:

(Cornelius_Hunter) #34

Oh thanks for that. It is a good example of the failure of sequence comparisons.



“We first used our improved approach MLWD (refers to the third point of the Methods) to construct the phylogeny for the first yeast genomes dataset with 11 species, which are available in YGOB (Version 3 April 2009). Five of them are post-WGD species under four genera. Six of them are non-WGD species under other four genera. This was the same dataset that used in Gordon’s ancestor reconstruction study43. _As shown in Fig. 1(a), we correctly classified all yeast species into their corresponding genera, and also into their corresponding groups, post-WGD and non-WGD. We compared this phylogeny with the recent studies and publications. Our phylogeny agrees with NCBI taxonomy ( on all 11 species. Our phylogeny also matches the phylogeny that was used in Gordon’s ancestral reconstruction study_43.”

(Cornelius_Hunter) #36

They are using genome-wide events, gene-order, etc. (non sequence data, like Ewert !!). Obviously, you are unfamiliar and resistant to the empirical evidence that does not bode well for evolution and CD. You are claiming “statistical significance” while ignorant of the flawed method. You claimed the big evidence for evolution / CD is the congruence of molecular and morphological phylogenies, ignorant of how those have failed. You were ignorant of the prefiltering that is routine. You are ignorant of the failure of sequence comparisons (e.g., in the yeast studies). So you are operating under the false impression that the data confirms and fits evolution / CD. And you are rejecting out of hand an alternative model which is far superior to CD, based on the same methods used by evolutionists!


Do you realize you are basically saying “all the literature is wrong, except the few papers from my biased sources?”. The editors and reviewers of all the other scientific journals are ignorant as well?


How is the method flawed?

They haven’t failed. That’s the point. There is still a statistically significant phylogenetic signal. For 20 species in two trees, incongruencies for two nodes has a p value of 3.00 x 10^-17. That’s a really, really tiny p value, in case you were wondering. You can check out the statistics here:

(Cornelius_Hunter) #39

Oh my. Again, you are making my point, and to the extreme. This is just phony, junk, science–terms which I do not use lightly. And here you are citing it. Do you not understand how these numbers are derived?

Tell me, how do you explain it when a quarter of the genes in an organism are not found in the other species in the genus? And how do you explain it when identical, long stretches of DNA without selective constraint in distant species?

(Cornelius_Hunter) #40

Hmm, very interesting. I guess I was wrong after all.


Irony aside, I would honestly like to hear your argument for that. Are most scientists in the area idiots? It is a naturalistic conspiracy to promote atheism? Ewert is the new incomprehended genius of evolution which will show everyone else wrong? There is gotta be some kind of explanation for why these ideas are not accepted outside of publications specialized in ID.

(Randy) #43

wow, good insight! (sorry, posted same above without the quote and realized it would be hard to tell what I was referencing).


I understand it just fine. Why do you say that it is phony, junk science?

That can be due to many reasons, from gene deletion to poor annotation. Do you have a specific case you would like to look at?

I am unaware of any such stretches of DNA that have 100% DNA sequence identity without selective restraint. Even in regions with selective restraint in the human and chimp genomes there is still a mutation every thousand bases or so between the two genomes. Do you have an example you would like to discuss?

(Cornelius_Hunter) #45

Well I suggest you take a look at the paper. Ewert uses a new model, yes, but beyond that the paper uses best practices and methods all around. There is nothing incomprehensible, or otherwise controversial in the approach.

As for your inquiry, I don’t always have time to address fallacies (in this case, your argument from authority, and ad hominem). Fallacies are false arguments that attempt to rebuke an argument, or in this case a model. The fact that evolutionists use these so often says more about evolutionists than anyone else. If you are looking for conspiracies, perhaps that is where to start. As for your question about atheism, I’m afraid I don’t understand where that came from.

(Cornelius_Hunter) #46

OK, so how would you describe the null hypothesis is that is being used in the test?

(Randy) #47

Wow, Dr Hunter. You’re written a lot of articles (Evolution News):

Welcome, by the way. God bless. Can you introduce yourself to get some background? I am not a Biologos employee but I enjoy discussing with them and their congenial humor. I’m a family physician (not a scientist) from Michigan, but a missionary kid born in Nigeria (grew up in Niger).

Hopefully we can learn from each other. Thanks.