Evolution doesn’t predict a perfect nested hierarchy, and Ewert says as much in the quote I gave you.
Ewert specifically states that if we see a close fit to a tree then the dependency graph is wrong. With design we should see shared genes that clearly violate a nested hierarchy, and this shouldn’t be rare but common.
Just like gravity has to be invoked to explain why people stay stuck to the surface of the Earth.
You can trivially nest planets, flower arrangements, submarines, baseball cards, and anything else in a nested hierarchy by limiting belonging attributes, but it is even more trivial to break the hierarchy by other attributes. The tree of life goes beyond a schema, by procreation it is organic and literally inherent.
Gene loss and gain is generally what accounts for branching. If there were never any alteration to the genes, all life on earth would be one happy species, and there would be a stick of life instead of a tree of life.
This is exactly right.
As Winston claimed the nested pattern may very well be the product of design. There is more evidence that different gene patterns generate different structures. This is evident when you examine the gene structures required to build vertebrate organs.
It is “science’s burden” to discover which hypotheses and theories have the most explanatory power. Common descent and evolution have far more explanatory power than intelligent design, which has exactly zero explanatory power, since it makes no testable predictions.
Obviously, no theory can explain everything, since there will always be things we have not yet fully researched. But it is the epitome of “God of the gaps” to just ignore everything that evolution does explain, and assert that because there are things we aren’t sure of yet, intelligent design must be true. This is why the burden of proof is on you to show that intelligent design explains these features, and all other features, better than evolution. Spoiler alert: it doesn’t.
That is false. I have produced extensive evidence for every one of my claims. On the contrary, it is your claims which are shallow, with no apparent evidence to back them up, since you have not provided any.
That may well be true. I have always been an “all-or-nothing” kind of person.
Also, kind of arguing semantics here, but I am not an “evolutionist believer.” I don’t believe in evolution (or, worse still, “evolutionism”). I believe in God. I accept that common ancestry, and the ability of unguided evolutionary processes to account for the modern diversity of life, are supported by the vast preponderance of the evidence.
We agree, but you don’t know what it means. And your third sentence works quite well as a reference to the second. Again, probably not what you thought you were saying.
Your reiterating evolutionist talking points with no independent thinking here. ID is a method of detecting design. It is limited but it does indicated limitations in what unguided evolution can explain.
You believe the papers to be complete explanations yet I made a challenge to find or generate a model to show feasibility and you ignored this challenge and instead repeated evolutionists talking points.
If there was a tested mechanism that could be modeled and tested to explain what you believe then I would accept that you are not an “evolutionist believer”
You have been sold YEC in the past and know you have been sold on unguided evolution at this point. Could the answer be in-between these extreme views?
He said just the opposite.
This is what he said but what we observe is not " a few minor additions". We see very different patterns where gene gain and loss need to be explained. Its time to drop the label “nested hierarchy” and discuss the actual patterns.
And you’re missing my point. You can bash evolution all you want, but until you show that intelligent design is a better explanation, you’re not doing real science, just wishful thinking.
I will note that you have provided far less evidence – none, in fact – to back up your claims than I have. So until you provide evidence for your unfounded assertions, I have no reason to take you seriously. You also have not provided a “model” for intelligent design despite your repeated insistence that we must provide a “model.” Although I don’t think any of the claims anyone here has made requires a model.
As Hitchens famously said, “That which can be asserted without evidence can also be dismissed without evidence.”
Evolution is not an “extreme.” Perhaps that’s how you see it, but that’s just not the case.
ID has never been used to detect design. It is only a method for concealment and obfuscation.
Just so we are clear, Ewert is saying that his dependency graph is a better fit for the data because the data does not fit a nested hierarchy. Is that correct?
They have been explained, over and over.
You are the one claiming design will produce a nested hierarchy. Did you already forget this?
“As Winston claimed the nested pattern may very well be the product of design.”–colewd
Evolution and intelligent design are not mutually exclusive idea’s both can be true.
This is the my evidence is better the yours. claim 
Do have real evidence that known evolutionary processes explain the diversity of life? Maybe you can explain how nature generated the spliceosome with a tested model?
Evolution explaining the diversity of life by known natural mechanisms is the extreme position as far as I can tell. Maybe you can cite a more extreme position.
Evolution is extreme like biology is extreme.
I totally agree. What is extreme is the claim that evolution explains the diversity of life.
Yes, but you are claiming that specific features require intelligent design. For those features, you need to not only show that evolution cannot explain them, but also that intelligent design can explain them better. That’s not going to happen, since intelligent design does not make quantifiable predictions.
No, it is the “my evidence is better than literally none” claim. 
Yes. In this thread alone, I have provided many studies showing that new functional proteins are not uncommon in sequence space, and we have also shown you several examples where we have observed de novo proteins evolving in real time, in the last few decades.
In addition, @evograd linked a recent literature review that summarizes the evidence, from recent experiments, that monomeric proteins can rapidly evolve into multimeric protein complexes, often with only one or two mutations (Pillai et al. 2022).
Altogether, this shows that unguided evolutionary processes can explain the origin of large protein complexes. And, as it happens, there has been research on the evolution of the spliceosome. We now have a fairly good idea of at least how the main catalytic protein of the spliceosome, Prp8, evolved from earlier transposable elements (Dlakic and Mushegian 2011).
Now, I know that you’re just going to move the goalposts again and name other parts of the cell that you don’t think evolution can explain. And maybe we haven’t yet figured out how evolution can explain those protein complexes, or metabolic pathways, etc.
But the main point is, evolution has a great explanatory power, whereas intelligent design has no fulfilled predictions. The only prediction of intelligent design is that “evolution won’t be able to explain insert feature here,” but every prediction of that type has failed so far.
Now, let me ask you: “Do you have real evidence that [intelligent design] can explain the diversity of life? Maybe you can explain how [God created] the spliceosome with a tested model?”
Indeed. The moderate position between flat earth and round earth is not bagel shaped earth or some such. It’s round earth.
Similarly, the moderate position between evolution and creationism (in all its guises) is evolution. Anything else is fringe pseudoscience.
Once more, none of the argument here has anything to do with the thread title. Until Bill (or someone) presents some genetic evidence against common ancestry, there is nothing to talk about. And since Bill is unfamiliar with what evidence even looks like, nothing on-topic will ever happen.
Is it ok for me to ask you to demonstrate that intelligent cause cannot explain those features?
When I post a paper or image it is not evidence?
Do you honestly believe you accounted for all vertebrate proteins in a paper the says function is simply binding? Did you look at the diagram of the WNT pathway I posted or did you dismiss it because anything an evolutionary skeptic posts is not evidence?
I don’t think you understand the difference between a detailed description and speculation. From the abstract.
Prp8 may have evolved by acquiring nucleic acid–binding domains from inactivated retroelements, and their present-day role may be in maintaining proper conformation of the bound RNA cofactors and substrates of the splicing reaction. This is only the second example—the other one being telomerase—of the RT recruitment from a genomic parasite to serve an essential cellular function.
What is you criteria for “can explain”? Does it mean does explain or does it mean a partial explanation that could indeed be wrong?
We don’t have to move at all until you get past PRP8 which I don’t think you can get past without appealing to a speculative explanation that does not account for the new functional information required to build this protein. This is highly preserved protein which means it does not tolerate mutation well. It contains well over 1000 bits of functional information as measured by its length and its lack of tolerance to mutational change.
What is your criteria of failed so far?
Let me repeat what I said before. Intelligent design is a method for detecting design in nature. It is not mutually exclusive to evolutionary theory especially the areas where you can create a tested model of the claims.
Did you look at the article I posted?
The differences between the prokaryotic cell and eukaryotic cell is evidence against common ancestry. This is the begging of many difficult to explain transitions that appear to be way beyond reproduction.
Andrew just posted a speculative paper that claims some clues to the evolutionary origin of PrP8. Like most papers all new biological function is assumed to have evolved.
Andrew made the claim that the diversity of life could be explained by natural evolutionary processes Lets see if he can get past the first of 170 proteins involved in nuclear intron splicing. The origin of the eukaryotic cell is step one in the claim of universal common descent.