Here is support of my claim.
https://ui.adsabs.harvard.edu/link_gateway/2000SHPSA..31..691O/doi:10.1016/S0039-3681(00)00016-9
I don’t agree at all.
You are claiming a direct test of a transition is irrelevant on one of the trees transition is where the problem is. You have an untested hypothesis being treated as an axiom for almost all papers I have read.
Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of…
Exhaustive analyses of DNA sequence data from 20 unlinked nuclear genes provide strong evidence that ratites are polyphyletic. We have discovered a robust genome-wide signal that is not associated with any known phylogenetic artifact. We believe this phylogeny resolves a debate on ratite origins that began in the time of Huxley and Owen (3–5). Our phylogeny implies that the numerous striking similarities associated with flightlessness (1) had independent origins in various ratite lineages. Thus, the flightless ratites are living evidence of parallel evolutionary trajectories from flighted ancestors. The possibility that multiple, unique developmental genetic pathways underlie the ratite form should be tested in light of this new phylogenetic hypothesis. Finally, our phylogeny removes the need to postulate vicariance by continental drift to explain ratite distribution. Although that theory seemed to represent a consilience between evolutionary biology and geology, it was never completely consistent either with any published phylogeny or the existence of paleognath fossils in the Northern hemisphere (45, 57). Perhaps the impact of our phylogeny should be viewed as yet another example of the phenomenon that Huxley called “the great tragedy of science—the slaying of a beautiful theory by an ugly fact.”
Hi John
What was your method to test whether all ratites share a common ancestor? How would this test fail?
Obviously, the paper was not intended as such a test, but it works as one nevertheless. The evidence of common ancestry is the pattern in the data, i.e. that they fit a particular tree much better than they fit others. Common ancestry is the only reasonable explanation of that fit. You could consider separate ancestry the null model in that test, and failure to reject the null model would result from data that didn’t distinguish among trees. There are of course thousands of papers that conduct similar tests on these and other taxa. Howe et al. conduct no formal test, but the data are decisive enough that none should be required.
Essays are not evidence.
That’s OK, but don’t pretend that your position is supported by evidence when all you have is hearsay and a misunderstanding of the most basic terms:
I’ll ask again: how can a method also be a hypothesis, Bill?
Parallels do nothing to disprove common descent. The hypothesis of common descent makes testable empirical predictions about parallel evolution.
Have you considered working from real evidence instead of trying to twist words into knots?
How wonderfully ironic that you should offer a paper discussing Bayesian Inference to support your claim, but refuse to recognize the Texas Sharpshooter Fallacy.
… Common Descent was more parsimonious then special creation.
That is the form of argument (I checked!) but no one considers Special Creation as a scientific hypothesis.
Your source goes on to conclude this is not a very good form of argument …
According to van Fraassen, when IBE is scrutinized carefully, its credentials are found seriously wanting. By scrutinizing van Fraassen’s own arguments, we see that this conclusion can be resisted. Van Fraassen’s point of departure was the ‘bad lot’ argument. That argument forced the defender of IBE to retrench, and talk the language of degrees of belief. Van Fraassen then argued that IBE conflicts with Bayesian rationality constraints; this argument was shown to depend on an idiosyncratic way of representing IBE in probabilistic terms. (Okasha 2000)
So if you want to claim Darwin was arguing against Special Creation, go ahead, but that’s a bad argument too.
[Emphasis mine]
Irony strikes again, because just a few hours ago you wrote …
So which is it?
Finally,
You [Dan] are claiming a direct test of a transition is irrelevant on one of the trees transition is where the problem is. You have an untested hypothesis being treated as an axiom for almost all papers I have read.
WHAT untested hypothesis? Not Common Descent, that’s a confirmed prediction, remember??
Hmmm… I’m getting two things here.
Can you share your thoughts on the difference between these two concepts? From my view, these are the same thing.
So you are looking for human design in nature?
So what do you think explains the discrepancy in the signal strength?
Do you think ideally they would have the same strength? Why or why not?
Hi Dan
I would indeed be ironic if you could establish a valid connection. The evidence that continues to be collected should work fine with Bayesian statistics. The assignment of the TSS to Behe and Gpuccio is suspect as no one is “drawing a circle” around the target or data. The specification in Gpuccio’s case is based on historic sequence alignments that are NOT following the expectations of neutral mutations.
Sure. Maybe this is a problem that needs to be worked out. So far you have an axiom being followed and no direct test of transitions that would confirm the axiom. The theory is inferred based on the fit to a tree.
Inference to the best explanation and disqualifying the alternative on a technicality. 
This is your confirmed assertion not mine. When I ask you to confirm, by test, the assertion you dismiss it as not important. If testing a hypothesis is unimportant how would you falsify common descent?
I asked you to state the “untested” hypothesis for clarity, because you are being evasive. The only clear statement I can find is this:
Here you are asking for a test of Common Ancestry, which we have already covered. You even provided the methods for testing this hypothesis yourself, as @John_Harshman notes (#310).
Nowhere do I find this “axiom” other than your circular thinking about Common Descent. If I am wrong, then please clearly state this axiom in your own words , so that I might address it directly.
AND in anticipation, I don’t think you will be able to state this axiom, but will be pleasantly surprised if you can. Please do not divert into discussion about Behe or GPuccio, I want to know exactly what you think this axiom is, and I want it from you.
The Texas Sharpshooter question I will reserve for a new thread when I have time to start it. For the moment it is enough to note that neither Behe nor GPuccio have a theory to guide them. They are making post hoc claims with no means to make predictions and falsify a hypothesis.
Hi Matt
You are changing what was said in the second case. This is a straw man argument. The first case is correct based on the something vs nothing argument.
One is a statement of factually designed. The second is a statement of our ability to make that judgement based on Behe’s method.
Human designs have been discovered in nature such as the statues at Easter Island.
In a case (design detection in a rock) I can think of it is the possible resolution of what we can detect. Again, Behe’s criteria is a purposeful arrangement of parts.
At this point we can detect this arrangement in biology easier then in matter as cells are larger then atoms.
Hi Dan
The axiom is that reproduction and natural variation explains life’s diversity.
@colewd ?
We can add transitional birds and transitional mammal fossils to that of course to show that, yes indeed, paleontologists have been able to find extinct species that are morphologically intermediate between groups, of the correct ages.
There is no explanation on special creation for the existence of fossils of extinct organisms with their special mix of ancestral and derived characters, while common descent absolutely demands that such organisms should have once existed if extant life evolved from from common ancestors.
Hey Bill, do you remember that series of posts on the vitellogenin pseudogene on this forum?
Evograd wrote this nice blog post on it:
Explain to me why you carry around a gene encoding a nonfunctional egg-yolk protein?
Thanks, Bill. So what I hear you saying is that having more than one particle in the universe does not mean it’s undesigned? Did I get that right?
If I did get that right, is there any attribute you can think of that an undesigned thing has and a designed thing does not?
So the first is the actual state of affairs and the second is the ability to detect the actual state of affairs. Would you say that’s an accurate summary?
Sorry, I didn’t see an answer to my previous question. Are you saying in an ideal scenario, the rock would return an equally strong signal as the cell?
And a couple more questions to finish off:
1. (A) By what method does one detect purpose in an arrangement of parts? (B) How can we rule out a faulty determination of purpose?
2. What happens when we apply this method to the rock?
The point I am making is that our ability to build all we are observing with a single structure (atoms) is evidence of design.
Your discussion of undesigned is interesting and I will have to think about it.
I agree.
The “ideal scenario” is an interesting case let me think about it.
By direct observation and using our mind to interpret what we see based on experience. I don’t think we can rule out faulty determination of purpose however with a large number of coordinated parts with a easily identified function the odds of proper design detection are pretty good.
Using human designs this can be tested.
Thank you, Bill, you have met my expectation …
AND in anticipation, I don’t think you will be able to state this axiom …
… by making a statement that clearly is not an axiom. It’s very demonstrable hypothesis that reproduction and natural variation creates diversity (for starters, we differ from our parents). No assumption here. Would you like me to cite some source of new variation discovered from the literature, or are you satisfied with looking up examples for yourself?
More, evolution is a far more successful theory that any of it’s competitors which attempted to explain the diversity of life (Great Chain of Being, Vitalism, Theistic Evolution, Orthogenesis, Lamarckism, Catastrophism, Saltationism). There is no current competing theory in this respect. Design can neither predict how variation occurs nor be falsified for variations we already observe - it’s not a theory at all.
So, once again I ask: There is no assumption of Common Descent. Do you agree?
Thanks for a abandoning the pretense that there’s any scientific testing of hypotheses involved!
But once you have atoms, in principle nature has all it needs for the rest.
Hi Dan
What you cannot show is a testable model that gets you to the Howe diagram or the WNT developmental pathway. Until you can you have a bunch of people writing papers using the axiom that reproduction and natural variation explain the diversity of life.
Inference to the best explanation without a solid competing theory may only lead you to a bad explanation.
This is true.
Some of the variations are natural mutations…
The problem is natural mutations do not explain the WNT pathway, the Howe diagram and many more Venn diagrams that have recently surfaced. We don’t need to invoke design to explain all the observations. If we see differences and can model their fixation in the population then natural variation can indeed be the cause.
When we see a purposeful arrangement of parts then the conclusion of design can be considered.
Bill likes to use big fancy words he does not understand to try give the impression that he is capable of engaging in this sort of discussion. “Axiom” is one such word, I would guess.
Thanks for reposting that, reading it was a nice blast from the past. I sure did have have a lot of spare time to write blog posts a few years ago…
Oh no you don’t! You have already moved the goalposts twice, first with CD and then axioms. I see no need to rehash Howe and WNT given that you have gained zero traction with others on the topic.
That paper you cited to me says otherwise. Did you read past the introduction?
SCREENCAP TIME! 
IF ONLY there were a theory of Design to consider.
So, once again I ask: There is no assumption of Common Descent. Do you agree?
Please respond.
