This is such a failure of logical thinking it doesn’t even need to be argued against.
I had to pick my jaw up off the floor. In a strong, strong field, this is your dumbest statement yet.
I will just quote this back at you on occasion.
In the words of @John_Harshman your opinion means nothing.
That’s okay. I have long given up the idea that your mind can be changed. I don’t so much argue with you as I just demonstrate how vacuous your ideas are to the observer.
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Time well tell if there is any substance to the theory (UCD) you have been vigorously and passionately supporting.
As far as changing my mind it will take more than speculative papers that assume UCD when the first of many transitions has no real explanation.
My take is your conviction is really based on materialist thinking and has little to do with real evidence and facts.
In the words of @John_Harshman your opinion means nothing.
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That ship sailed so long ago that it was probably a trireme. As has the ship carrying the theory that all deer share a common ancestor, if you recall the topic at all.
Incidentally, your opinion means nothing in at least two senses.
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Indeed, censorship as it was practiced at UD. Or Evolution News, which does not allow comments.
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The question I asked at the beginning of the op was never answered so I guess the support for the theory of deer common ancestry remains the UCD inference.
I agree the theory has been around a long time and supported by methodological naturalism. The problem is naturalism in this case maybe leading to the wrong answers.
There isn’t any question you posed in the OP that hasn’t been answered. There isn’t anything about population genetics that contradicts species with different chromosome numbers sharing common ancestry. We have already given perfectly good evidence that many changes that lead to changes in the number of chromosomes can be either neutral or beneficial and the different species of deer are separated by millions of years of divergence, giving plenty of time to fix neutral and beneficial mutations of all sorts.
This was explained to you numerous times in the thread.
Behe disagrees. He thinks differences of a certain nature can arise by design, and yet species be related by common descent. Naturalism just has nothing to do with this.
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All papers we post are based on the assumption of natural UCD. If this turns out to be false thousands of papers become worthless.
You have inadvertently, and unintentionally, stated something true here.
ID advocates pervasive use of logical fallacies does indeed reveal how weak your position is.
These uses of logical fallacies include:
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Your arguments from authority citing Michael Behe and Gpuccio would be classic examples – neither of them have any apparent expertise in population genetics, and Gpuccio would appear to have no expertise in Logic.
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ID’s repeated use of the Texas Sharpshooter fallacy.
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Your pervasive non sequitors.
I think what you really meant was accusations of logical fallacies, not “use” of them – but that claim would have been wrong. The side with the weaker argument has to employ logical fallacies to ‘shore it up’. This will in turn lead to the side with the stronger argument pointing out those fallacies.
Articulate =/= logical. The problem with Gpuccio would seem to be that he is a rhetorical thinker not a logical one. This is perhaps why he took 9000 words to make his argument on Uncommonly Dense. Most ID arguments seem to be rhetorical rather than logical, and are thus replete with logical fallacies.
The problem with this claim is that Gpuccio never even calculates functional information, so is in no position to show a “jump” in it. What he is showing a jump in isn’t information at all.
It is not uncommon on this forum for a new entrant, particularly an invited one, to be given their own, protected, thread to present their thesis, in the hopes that doing so will reduce the ferocity with which that thesis is shredded.
No, it is rather an implicit admission that the thesis is likely to be sufficiently controversial that it is likely to be exposed to fierce scrutiny. This, if anything, is an indication that it has less credibility.
There is certainly little indication in the contents of that thread that Gpuccio’s ideas were viewed as credible – rather they seem to have been viewed as “not properly filled out or developed” (i.e. vacuous by the OED’s definition).
I would point out that both your claims are no more than bald, unsubstantiated, assertions – but thought it more productive to point out why you were wrong than to simply reply in kind “no it isn’t”. 
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Completely meaningless response to what I write. Once again, Behe supports common descent and that has nothing to do with an assumption of naturalism.
Common descent is definitely a working assumption in many articles, but time and again the data turn out to be consistent with that assumption. It could fail in principle, but doesn’t. The assumption isn’t somehow magically making the data support a tree.
Merely having an assumption that something is true is not somehow going to make, for example, the synthetic chromosomal fusions in mice be neutral or beneficial if they really aren’t.
And by subjecting a collection of gene sequences to a phylogenetic algorithm you are also implicitly assuming there is a tree in the data, but the resulting tree the algorithm spits out could have essentially no consistency. That just isn’t what we find.
Ah, cool. Gpuccio was deemed credible (or possibly just influential?) enough to be offered a chance to defend his stuff, but he failed and so did you and his other resident fans. So whatever credibility was implied by him having had a platform to elaborate on his nonsense is now long gone.
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As deeply as I value and respect the expertise and accomplishments to be counted among our merry band, I am not so certain that the Peaceful Science Forum is in the elite position to bestow credibility were we to engrave a trophy, particularly to someone otherwise nearly unknown.
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Is the problem with naturalism or with methodological naturalism? They seem to be synonymous to you, I’m not sure why. Also, may it, in fact, be the case, that naturalism (or methodological naturalism, which ever it is you mean) is “leading to” any answers? May it, in fact, be the case, that it is leading to “the wrong” answers? What indication, over and above ‘me no likey’, is there, that the answer arrived at by scientific means is either incorrect (by some for now unspecified measure of correctness) or inadequate for some purpose?
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Hence the heavy moderation and frequent banning at Uncommon Descent and the disallowing of comments at ENV. Meanwhile, @gpuccio has not been censored or deplatformed here. His account remains available but unused.
Also, you should learn the difference between not providing a platform versus censorship.
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Clearly, with this astonishing claim, it can be seen that it’s you who have a problem with logic, not Gpuccio.
Well, to my comment that Gpuccio was allowed to express his view on this site in a special, very unusual way, ie through a dedicated thread only open to the scholars frequenting this site, you first reply by saying that it was hardly unusual on this forum. As far as I can tell, it is unusual for since I participate in this forum, it has happened only for two guests, namely Gpuccio and Winston Ewert. I may be wrong. If so, I would welcome any correction on this matter.
You also added that it is certainly not an indication that the individual so ‘honored’ is worthy of any credibility. I think your statement here is illogical and that the special way Gpuccio was allowed to express his view is evidence that he was considered here as as a knowledgeable and articulate person with interesting views worth being debated by the best experts on this forum. Here are some quotes that make this point taken from the thread where Gpuccio expressed his view on this forum:
Swamidass at 17
Gpuccio, it is great to see a starting point of a response from you. We aim to key the conversation substantive and professional. It doesn’t always go that way perfectly, but that is our goal. I hope that we would all understand each other, and science, better through exchanges like this.
…….
It is an interesting hypothesis, and it deserves to be received with seriousness and rigor. Good ideas come from all over. The beauty of how science works is that we can, if we are humble to the data, come to common understanding through engaging hypotheses like this. Even failed hypotheses have value for this reason.
……
I really love that you are looking at the data yourself. You clearly have the ability to run much of these anlayses yourself. Great!
Art at 99
Thanks again, @gpuccio. I would like to commend you for broaching this subject, as it stands in contrast to the approaches used by the ID vanguard. I have long been of the opinion that the relevant metric that ID proponents should be measuring is something akin to informational work, which may be like what you describe here. I suspect that there are serious issues with the approaches one may take to estimate this property, but the concept seems to make sense to me.
“Clearly” your astonishment is both idiosyncratic, and misplaced.
“It can be seen” that your conclusion is a non sequitor and thus fallacious.
Consider yourself corrected then – most recently, this thread was created for discussion of Rope Kojonen’s book, and then restricted to exclude “anonymous/non-academic participants” when he turned up. This did not, in fact, stop Kojonen from getting eviscerated by many of the non-anonymous academic participants.
Your fallacious argument rests on two false premises:
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That having a moderated-thread is in some way “special”. Heck, even I got a moderated (“curated”) thread once – for a discussion that I eventually came to the conclusion was a complete waste of bandwidth and time.
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That being “allowed to express his view” is in some way an indication that his views are credible. Heck, even @colewd is “allowed to express his view” on this forum, and even the replies to him on this thread should give you an indication of how little credibility he has here.
These comments are simply boiler-plate ‘welcomes’, and confer no credibility. If you want to see how credible he is here, you need to read further down the thread to see how his ideas held up under scrutiny. It would seem that they were viewed with skepticism that Gpuccio was unable to dispel:
Etc, etc.
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Back to the original subject, as Bill requested. Yes, we can, and no, it isn’t. I presented a very simple model of the former quite some time ago, and “separate points of origin” is incompatible with the phylogenetic data. Of course those are two quite separate questions, and one major problem is that Bill is unable to separate them.
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The passages you refer to are from scholars who expressed some objections or incomprehensions toward some methodological aspects of Gpuccio’s analysis, to which IMO he responded convincingly most of the time. I invite those really interested by this debate to carefully read the whole piece and decide by themselves whether Gpuccio is interesting and credible, knowing that being credible doesn’t necessarily means being right but rather being knowledgeable and articulate on the matter being discussed.