So how can you say that evolution doesn’t have an explanation when you admit that the mechanisms evolution proposes are observed in the lab and in the wild?
So why can’t the observed mechanisms of evolution produce functional sequence?
Your explanation need to cover differentiated features or you are not explaining the hierarchal structure. Your claim is not simply observed mutations if that was it I agree but it is those mutations making complex features.
There is no proposed mechanism that science can model to produce interdependent protein sequences. Until then your claim is philosophical and almost certainly wrong given that you are dealing with long sequences.
When you’re asking you proponent to prove a negative you essentially have nothing to offer. You need to show how the “mechanism” can produce complex functional sequences.
I am sure this is true. Thanks for your patients.
The explanation does cover those features. The genes associated with those features fall into a nested hierarchy (with noise) as we would expect from evolutionary mechanisms. If evolutionary mechanisms were responsible for those differences then we would expect to see a nested hierarchy, and that is what we see.
Those mechanisms are random mutation and natural selection. Those are the mechanisms that biologists use in their models.
Your argument is based on a universal negative which is the problem.
Bayes is comparison two statistical alternatives. Is design really a statistical solution or a deterministic solution? Bayes may not be the right tool for the job.
Where are the models validated to produce the features claimed?
What you have not established is the cause of the hierarchal structure. You are dead in the water until you establish that evolutionary mechanisms were responsible.
No, the conscious intelligent mechanism (design) solves the problem. It is a positive argument.
The models are based on phylogenetics. For example, the evolution of the bacterial flagellum:
That is very well established. Any simple understanding of how vertical inheritance, random mutation, and selection works will lead to the conclusion that these mechanisms will produce a nested hierarchy. These mechanisms produce lineage specific changes that will necessarily produce a tree-like pattern, with noise introduced by mechanisms such as incomplete lineage sorting and homoplasies.
Your only evidence for these processes is that evolution can’t do it.
How will they test their model? At this point it is a speculation.
Just an assertion with no support. The only long term experiment did not produce a hierarchy (Lenski).
Not at all. I have evidence that you can produce a complex functional sequence as I am forced to answer it 
They tested their model with phylogenetics. Didn’t you read it?
Then please tell me how mutations in one lineage get moved to a different lineage when there is a lack of horizontal genetic transfer.
I can also produce a block of ice. That doesn’t mean all pieces of ice are the product of intelligent design.
In this study we combined phylogenetic, structural, and phenotypic studies to understand by inference possible evolutionary pathways to high torque in the Campylobacter- type ε-proteobacterial motors.
Need a break but something for you to think about. How does the above directly test the proposed mechanism?
Do you possibly see that the claims of “tested science” are not valid. BTW this is the most comprehensive attempt I have seen so far so great citation by you.
I am sure this is true. Thanks for your patients.
Better to understand one another than argue at cross-purposes. 
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This isn’t a question about (or test of) design, it’s an example of how statistical methods are applied. In this case I’m posing a common argument in the form of a Bayes factor to demonstrate that, if the question is posed in a formal mathematical way, it requires a tacit assumption. The form of argument is circular, and therefore wrong.
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BUT, supposing we did have some testable statistical hypothesis about design, we know how to apply Frequentist and Bayesian methods to the problem. There are mathematical proofs of how to go about constructing the best methods for estimates and hypothesis testing, where “best” is defined by certain desirable mathematical properties that would bore you to death (minimum variance, unbiased, uniformly most powerful, etc.). Statistical theory is “finished” in this respect because of proofs showing there is no better way of doing things. There is ongoing work in developing new applications of existing theory, and the best way of applying them, but the theory isn’t going to change**. Statistical Genetics and Phylogenetics, mentioned above, are areas with new methods being developed. To say that we don’t know the right tools to apply to questions about design, is like saying that design is not subject to the same mathematics as the rest of the universe.
** This is one of my complaints about CSI and ASC methods from Dembski, Marks, Ewert, etc… They are trying to construct new tools to detect design, but theory tells us we already have the tools.
From your equation the tacit assumption appears to be there are only two alternative solutions. Your tacit assumption also assumes you know the overall probability given all possibilities.
The fact given all you know that the equation for design is 1 is not trivial.
This is the cause that the math is telling you as you are comparing a highly deterministic process to a highly probabilistic one for being the cause of certain quantities of functional information.
We know conscious intelligence can create large quantities of functional information and mutual information. The mechanism is well known and very effective.
This is an interesting comment and I think I agree. The gap between where we are and increasing certainty of the design inference is empirical and not mathematical. The empirical evidence has been increasing dramatically since I have been following these debates.
If we want to prove that the process is not stochastic it is not setting up horrendous probabilities like 10^150 but showing how sequences break down with odds like 10^3 of deleterious mutations vs beneficial which is clearly inside the functional vs non functional sequence for protein coding genes.
Bill Bassemer and John Sanford wrote an interesting paper recently on this very issue.
The prospect of explaining the principles of statistical inference in an Internet in order to sort sort out what was wrong with all that is quite daunting. I’m gonna go with “I’m not sure you really understood what I meant”, and leave it at that.
This is an interesting comment and I think I agree. The gap between where we are and increasing certainty of the design inference is empirical and not mathematical. The empirical evidence has been increasing dramatically since I have been following these debates.
I think you are misunderstanding again. In statistics it’s the sample that should be random, there is no difficulty with taking random sample from a population that is deterministic.
AND I have to disagree about increasing evidence for ID as well. The only serious attempt at testing design hypotheses was a deliberate nose-thumbing to ID proponents for not testing obvious hypotheses (I think we discussed that topic when I first got here).
So we can agree to disagree. Thats fine I have studied enough statistics (although many years ago) to understand some of its limitations in real world applications.
Again lets agree to disagree. I don’t think you may be familiar with all the work done. The more challenge to the Darwinian paradigm by new discoveries in molecular biology the stronger the ID claim. Have you followed gpuccio’s work at UD?
We are testing the ID hypothesis by these discussions alone. The ability to exchange abstract thought through exchange of arbitrary symbols.
As the ability to transcribing DNA containing introns and exons, alternative splicing of exons and then translating the exon sequence to proteins that perform cellular function.
If there is one specific topic coveered by Guccio you think would be enlightening it might be worth its own thread.
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Believing in evolution and climate change does not effect my politics at all. It would only effect one’s politics if she believes that the only way to deal with problems is to use violence or the threat of violence or force to accomplish her goals. And most people unwittingly believe this. 
I accept the MAIN conclusions of scientists regarding evolution and climate change, but think that ideally, the state should get out of the education business altogether, and I would still not be for stringent regulations regarding climate change. Let one private school use a Dawkins textbook and another use Dembski. I would love to send my future kid to a private Christian grade school that does NOT teach YEC, but other than Catholic schools, I’m not sure these schools exist.
And as insane as it may sound to some, it seems plausible that voluntary rather than compulsive choices to address climate change would be just as effective. Yes, I know I sound like a crazed lunatic, but it doesn’t mean I am one. I’m just a libertarian. Even though some people might automatically equate the two. Haha