Where is the evidence that those transitions were way beyond reproduction?
No, it isn’t. At most it’s evidence against unguided evolution, if indeed the differences are very unlikely to arise naturally. But that has nothing to do with common descent.
The causes of transitions are not relevant to the title subject. Of course reproduction is not the cause of transitions. Mutation, fixation, selection, and conceivably divine nudging would be causes, but the nature of the cause is not relevant to whether the various differences show common descent. I know you will never understand this, but everyone else should, and should stop arguing in this thread about the causes.
No, because that’s not what I said. I did not say that intelligent design cannot explain those features. I said that you must demonstrate that it can explain those features better than evolution can, before your hypothesis of intelligent design can be considered on par with evolution. You cannot just bash evolution and expect everyone to accept intelligent design as a result. That’s a false dilemma.
No, an image is not evidence. A paper is evidence, but only if it actually supports your claims. The only paper you’ve posted is the dependency graph paper, but we’ve repeatedly explained to you why that does not constitute evidence for intelligent design.
Do you honestly believe that those papers say the only function is simply binding?
Maybe read them again.
Your selective amnesia strikes again – I’m afraid that you have not posted anything about the WNT pathway in any of the threads that I have taken part in on Peaceful Science. However, a mere diagram is indeed not evidence. You would need to show quantitatively that evolutionary mechanisms cannot have given rise to the WNT pathway, or at least that intelligent design can explain it better than evolution.
And I don’t think you understand how scientific literature is written. When the authors of that paper say that Prp8 “may have evolved” via those mechanisms, they mean that they now have significant evidence to support that hypothesis. Which is more than you can say about intelligent design explaining the spliceosome, since you have not provided a testable prediction of intelligent design yet. You might want to read the actual paper, it’s very interesting.
Precisely what I said – evolution can explain the spliceosome. That is, evolutionary processes could have given rise to the spliceosome. And don’t go moving the goalposts on me by saying that just because evolution can explain it doesn’t mean that evolution did explain it. Your original claim was that evolutionary processes cannot explain the spliceosome, which is false.
“That which can be asserted without evidence, can be dismissed without evidence.”
For one example, intelligent design proponents claimed that evolutionary processes could not explain the evolution of new functional proteins. That was shown to be false when we literally observed multiple new functional proteins evolving in the wild, as I’ve explained to you several times.
No, no double standards. You asked me for a testable mechanism for the evolution of the spliceosome, and more broadly the diversity of life on earth. So give me a testable mechanism for the intelligent design of the spliceosome, and more broadly the diversity of life on earth.

Did you look at the article I posted?
You mean the one that claims that intron splicing is irreducibly complex, while completely ignoring self-splicing introns? Yeah, not ID’s best work. Or maybe it is, I dunno.
All irrelevant to the supposed thread topic. Bill is wrong about many things that are irrelevant to the topic, and he doesn’t know they’re irrelevant either. But why encourage him?
Good point. @colewd, should I change the thread topic to “genetic evidence against unguided evolution”? Or will you give any evidence related to the thread topic of “genetic evidence against common ancestry”?
Hi Andrew
I think evidence against God guided common ancestry is fine. We can defer discussion about unguided evolution. I was just responding to a claim you made about your belief that unguided evolution explained the diversity of life.
For this we need to review only the hypothesis that the large changes we are observing (such as new genes or new chromosome structures) are due to God making genetic and cellular changes to pre existing structures and implement these changes through the reproductive process.
Note that Bill has nothing whatsoever to say about the actual subject. That’s because he literally has nothing and never has had anything. His preference for separate creation is purely religious.

Your reiterating evolutionist talking points with no independent thinking here. ID is a method of detecting design.
Given that the second sentence is simply the (further) ‘reiteration’ of one of Bill’s handful of (vacuous and debunked) ID-Chatbot-like talking points, I find this quote utterly hilarious – as well as being demonstrative of Bill’s complete lack of self-awareness.
If I say “ID is a method of detecting design” three times will Michael Behe magically appear?
Unlikely, but that would appear to be about the only purpose that this empty incantation might have.

Let me repeat what I said before. Intelligent design is a method for detecting design in nature.
Repeating a falsehood does not make it true.

It was certainly irrelevant to my point.
Weren’t you arguing, rightly, that common descent doesn’t explain gene gain?
Didn’t you take the phenomenon of horizontal gene transfer to illustrate the point?
Doesn’t the piece I referred to provide additional examples of phenomenon illustrating this same point? Since the answer to these questions is yes, the piece was highly relevant to your point.

Weren’t you arguing, rightly, that common descent doesn’t explain gene gain?
Yes, but it’s irrelevant to the category of “Genetic evidence against common ancestry.”

Didn’t you take the phenomenon of horizontal gene transfer to illustrate the point?
I won’t speak for John, but I strongly suspect that he’ll agree that it doesn’t.

Doesn’t the piece I referred to provide additional examples of phenomenon illustrating this same point?
The existence of HGT does not falsify common ancestry. Note that HGT was not discovered, and has never been studied since its discovery, by anyone who disputes common ancestry. What does that tell you?

Since the answer to these questions is yes, the piece was highly relevant to your point.
Since the answer to all of them is no, it was irrelevant. HTH.

Weren’t you arguing, rightly, that common descent doesn’t explain gene gain?
Didn’t you take the phenomenon of horizontal gene transfer to illustrate the point?
Doesn’t the piece I referred to provide additional examples of phenomenon illustrating this same point? Since the answer to these questions is yes, the piece was highly relevant to your point.
No, I didn’t use the phenomenon of horizontal transfer to illustrate that point. The point was that the source of new genes is not relevant to evidence of common descent. The larger point was that talk of gene gain and loss is irrelevant to the supposed topic of this thread, and so is horizontal transfer.
Indeed. “Horizontal gene transfer happens. Therefore, common ancestry is not true.” I am not seeing the logic, sorry. @Giltil, what do you think I am missing?

Note that Bill has nothing whatsoever to say about the actual subject.
Hi John
Until common ancestry is clearly defined we will be talking over each other. Without a clear definition the current post does not make any sense.
If common ancestry is simply represented as explaining the pattern of the changes (tree) this explains very little.
The fix here is maybe to start evolutionary theory assuming the existence of populations and don’t try to explain their origin as physics is not trying to explain the origin of matter.
Starting with populations takes away the problem of trying to explain the dramatic observed differences in the diversity of life.

Weren’t you arguing, rightly, that common descent doesn’t explain gene gain?
Didn’t you take the phenomenon of horizontal gene transfer to illustrate the point?
Doesn’t the piece I referred to provide additional examples of phenomenon illustrating this same point?
Let’s say I streak out a strain of E. coli on a plate and get a bunch of colonies that look like this.
Those isolated colonies would have grown from a single bacterium, so all of the bacteria in that colony share a common ancestor. I pick some of those bacteria from an isolated colony and grow a liquid culture of bacteria. At some point I stick in a different species of bacteria into the culture. Lo and behold, the different species of bacteria get their Barry White on.
We get HGT, a transfer of DNA from one species to another.
Does this event erase the history of what happened? Did we not see these E. coli descend from a common ancestor?

The fix here is maybe to start evolutionary theory assuming the existence of populations
Once you get past abiogenesis, isn’t that already the case?

Until common ancestry is clearly defined we will be talking over each other. Without a clear definition the current post does not make any sense.
Universal common ancestry is the theory that all life on earth descended from a single ancestor (which could be either an organism or population of organisms). That’s a clear definition, and I’m pretty sure you already knew that, so your insistence on a clear definition is merely sealioning.

The fix here is maybe to start evolutionary theory assuming the existence of populations and don’t try to explain their origin as physics is not trying to explain the origin of matter.
Universal common ancestry does start with the existence of living organisms, since it is merely the theory that all life descends from a single ancestor, saying nothing about where that ancestor came from.

Starting with populations takes away the problem of trying to explain the dramatic observed differences in the diversity of life.
Nope – you’re going back to arguments against unguided evolution again. For all that common ancestry is concerned, the differences in the diversity of life could be caused by God or anything else. What common ancestry explains is the patterns of those differences. Your task in this thread is to show that the patterns of those differences are explained better by separate ancestry than common ancestry.

Until common ancestry is clearly defined we will be talking over each other. Without a clear definition the current post does not make any sense.
So you still do not know what is meant by “common ancestry.”
Words fail.

The fix here is maybe to start evolutionary theory assuming the existence of populations and don’t try to explain their origin as physics is not trying to explain the origin of matter.
Starting with populations takes away the problem of trying to explain the dramatic observed differences in the diversity of life.
I wonder if we will ever reach the point where the extent of your ignorance and incomprehension can be overestimated. Clearly we are not yet there.
Edit post

Universal common ancestry is the theory that all life on earth descended from a single ancestor

What common ancestry explains is the patterns of those differences.
Can you help me understand why you think these two statements are consistent. What do you mean descended from a single ancestor or a population of ancestors?
How would the pattern of differences test for this?