They are direct responses to them.
Your positions change every day and you’ve never supported any of them with evidence. You are evading.
Objectively false. We have chromosomal rearrangements.
Objectively false. They’ve become fixed in isolated populations.
More word salad. You don’t have a model. You just keep spewing words with fungible meanings.
It’s a prediction of the mechanisms we observe.
Evasion.
That’s just you making an excuse to avoid answering. And whatever your real position may be, your expressed positions are highly confused.
You should at least end a question with a question mark. And I see you’re still avoiding any real answers.
You clearly don’t understand the scientific method. Kepler was able to come up with his laws of planetary motion without knowing anything about universal gravitation. Newton was able to come up with his law of universal gravitation without knowing anything about the Higgs boson. And so on. Science always works on incomplete information. You’re just using the common creationist excuse that if we don’t know everything we therefore know nothing. Not true. We have copious evidence of common descent that doesn’t depend on knowing how mutations happen. And anyway we do know how mutations happen. You are just clinging to the notion that not enough of them happen, or not enough of them get fixed. But you have no evidence for that, and your unsupported claim contradicts the historical evidence. If you were actually interested in science, you would have noticed that.
Please explain. Why does that make it a poor alternative? And what do you mean by “muddles” here?
In the first case, that’s just an admission that the chromosome evidence is not relevant, since you need something else instead. In the second case, since some of them are fixed in their local populations (some of them isolated, in fact), that’s more than variation in a population. Further, all that’s needed is that the variants attain a high frequency, which shows that they could become fixed, i.e. that they are not strongly deleterious. These are nothing but excuses to ignore the data.
What evidence do you have of this mechanism? And when did the argument become about gain and loss of function? This is the first time that subject has been mentioned.
The logic is quite simple. We have a phylogenetic tree that puts flying tinamous in the middle of the flightless ratites. Either flight was lost and regained, or it was lost multiple times. We know of a great many cases in which flight was lost in birds (mostly island rails), none in which it was regained. Notice that there’s nothing at all about why or how it was lost. Though you could certainly come up with hypotheses about that, I didn’t in that paper. See? No assumptions about natural variation, and the phylogeny is prior to any inference of events, regardless of their cause.
That’s right. You are determined not to. The basis is that nested hierarchy or, if you prefer, the fit of the data to a particular tree. There’s more than that, data of various other sorts, but that’s what I usually talk about.
Actually, we do. There are variations in gene presence and absence within populations. And between populations, some genes are clearly homologous to non-genic sequences in other populations. What explanation other than alteration of a non-gene into a gene would produce such a thing?
Would I really have to? Is it not exceedingly obvious, if you just think about it for a few moments? Start with a branching tree of species. Now sprinkle changes randomly over that tree. Isn’t it clear that the distribution of characterstics would follow a nested hierarchy, such that you could reconstruct the tree based on that distribution? And it’s even been done in the laboratory, with virus evolution, and the true relationships were reconstructed based on that nested hierarchy of sequence data. How can anyone fail to understand that after so many years?
Better question: why, when we’re talking about one thing, do you change the subject to another?
More deflection.
Great. So we’re all done?
You misunderstand the degree of Bill’s confusion. When he says “gene arrangements” he means the sets of genes that different species possess, not their arrangement. He uses words differently from other people.
Since @colewd keeps talking about the opening post, let’s review.
The opening post only talked about chromosome variation. That’s it. I would say that we have completely demonstrated chromosome arrangement and counts with common ancestry.
The challenge in the opening post has been met in spades.
Not quite. It briefly mentioned “gene family variation” in the second paragraph. I predict that Bill will ignore everything else you said to concentrate on this one error.
Fair enough I will try to be more clear.
Kepler was able to base his inference on the elliptical orbit of Mars and Newton was able to build his model based on the mass of the earth and the object in question. These models were built on direct observations.
With the single origin claim you are making a claim without the benefit of observation. We have observed the reproductive process but have not observed it generating the transitions required to support the single origin theory. Both Newton and Kepler were able to make inferences from direct observation.
Common descent or a single origin depends on radical transitions. This is what we see in the Venn diagrams. You needed to invoke gene gain and gene loss to reconcile the Venn diagram with the tree. You are clinging to the notion that this is a likely scenario.
The possible involvement of God is not being explored. This is simply added as a possible alternative thus preserving a potentially faulty model.
Both of these pieces together are highly relevant. Looking at only one is cherry picking the data.
Some of the evidence for the mechanism existing is the complex arrangements in the cell including DNA and Proteins. Also the complex arrangements of organs that make up Deer including heart, lungs, brains etc.
Are you inferring ancestry from the phylogenetic tree? If the flightless ratites were inferred to have separate origins due to different gene/chromosome arrangements do you agree that no loss of flight would be inferred?
What type of gene variations do we see within populations?
The nested hierarchy we are observing has radical genetic differences. It is not obvious at all that reproduction is capable of these type of differences. It’s also not obvious that God would use the reproductive mechanism to make these different species.
Both gene and chromosome arrangements are a critical observation in determining the correct model. They both have been the subject of the op from the beginning. The only reason you object is that together they are a powerful challenge to the single origin of deer hypothesis.
Yes, and so is common descent.
You misunderstand the nature of observation. We don’t have to observe the phenomenon we’re trying to hypothesize directly. We just have to observe its effects. Kepler did not in fact observe an elliptical orbit. He observed the positions of the planets with respect to Earth on a number of dates and was able to explain them by elliptical orbits. And this is another change of subject on your part: one objection (no mechanism) refuted, you retreat to a new objection. Do you even know you’re doing this?
No it doesn’t. There’s another subject irrelevant to the question. And it’s false anyway. Gene loss isn’t all that radical, and neither is gene gain. And I remind you again that even if radical transitions were required, you can always resort to divine guidance, which saves the fit of data to nested hierarchy and so works better than your preferred hypothesis.
Again, we don’t have to explore that involvement when investigating common descent, because the nested hierarchy doesn’t depend on knowing the causes of variation. But if we needed such a cause, I have to ask why you aren’t considering it.
When I deal with one, you go to the other one. This is whack-a-mole. And once again you ignore most of what I say. Deflection is your only defense.
That’s not evidence for a mechanism. But it does make up some of the evidence for common descent. All these complex arrangements can be shown to arise gradually in the history of life, at particular places on the tree.
Of course I am. What other inference is possible?
Yes, of course. But that would require ignoring all the data. This is also getting away from the original issue, your claim that I’m assuming a particular cause of loss of flight. I can’t tell whether you’re deflecting on purpose or whether you just forget what we’re talking about.
First, let’s consider expectations. What type would you expect to see under your hypothesis? What would you not expect to see?
That’s another tangent that evades the question. I have to assume that one was on purpose. I could respond but I would like to start discouraging you from changing the subject.
I’ll take this opportunity to ask again why you prefer separate creation to divinely guided evolution.
One, you do not “reconcile” Venn diagrams with trees; they are just different ways of visualizing the groupings of traits in common and traits which are unique. You could use columns in Excel if you wished. Two, while gene gain and loss are biological realities, that has nothing to do with alternate visualizations of the data.
And we are directly observing the sequence evidence. You refuse to.
This is a misunderstanding.
Kepler saw a finite set of data points. There are infinitely many possible curves that fit those data points. An ellipse is only one of those possible curves. Furthermore, his data did not exactly fit an ellipse.
I don’t know how Kepler came up with that idea. I have long assumed that he was partly guided by the mathematical simplicity of the ellipse.
Newton could not possibly have based his model on the mass of the earth. The mass of the earth was not known, until determined by Cavendish more than 100 years after Newton came up with his theory of gravity. And, in order for Cavendish to measure the mass of the earth, he had to presuppose Newton’s theory.
All of science is based on clever guesses which fit the data very well, even if not perfectly.
What direct observations is common descent built on?
John, you brought up the subject of Newton and Kepler and now you are dropping Newton from your argument. Why?
If it is not radical then we should have a model that makes sense of these changes.
To avoid this problem you invoke God to save the model by insisting this is His method.
How do you know the nested pattern is a result of common descent or a single origin event? The weakness in your argument is it depends on a naked assertion. “The only explanation for the nested hierarchy is common descent”
The op is about dealing with both issues. You are making excuses for cherry picking.
It is evidence for the mechanism. We don’t know of any other mechanism responsible for functional arrangements that are not associated with physics and chemistry as a direct cause.
When did the heart arise gradually independent of the brain or other critical organs? When did the beta catenin protein arise independent of the wnt, frizzled and APC proteins that it interacts with today? Is there any real evidence of this proposed gradualism?
Separate origin of flightless birds.
In response to your claim that you could only come to the conclusion of separate origins if you ignored all the data. Maybe you mean the data available when you wrote the paper.
Do you have gene Venn diagrams for flightless birds? Do you have chromosome counts for the various species?
This is not a claim I made.
What you think is deflection is you not realizing that you are the source of the claim and not me. I never asked you to explain the cause of the loss of flight.
My argument was always about you using loss of flight as a conclusion based on common descent as an inference. This is the same case as you using gene gain and loss to explain the various Venn diagrams. If common descent of flightless birds in not true then your analysis fails.
I would expect variations that we can explain with population genetic models.
I directly answered the question discussing the problems with both common descent by reproduction and natural variation and God guided evolution.
It’s a more clear alternative to common descent than God guided evolution which presumes the method God used. I do not think there is a good argument other then naked assertion that God guided evolution explains the observed nested hierarchy better then separate origin events.
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This question merely exposes your ignorance of both the data and practice of science. I can’t bring myself to dignify it with an answer. Maybe later.
It was just an example to illustrate a point. Focus.
I’m not sure of the connection between “not radical” and having a model. Bet you aren’t either. And again you ignore my question. Why do you reject common descent with divine guidance? Doesn’t it fit the data better than separate creation?
Because we expect such a pattern from common descent but not from anything else we know of. We certainly don’t expect it from separate creation.
I’ve dealt with both issues. When I do, you just change the subject.
I have no idea what you were trying to say there. On the surface, it seems to argue against God as a source of functional arrangements, but that presumably isn’t what you intended.
Clearly you know nothing about the history of life. Try looking at a textbook on comparative vertebrate anatomy. Yes, there is evidence of this proposed gradualism, both in the fossil record and in comparisons among living species.
So you’re claiming that each species of island rail was created separately on its own island, only coincidentally resembling the still-flying rails present on the mainland and larger islands? But what about that nested hierarchy? How does your separate creation explain that?
If you know of any data that contradict my claim, please cite it now.
I’ve never looked. I assume that chromosome counts are available, but you would need annotated whole genomes for the Venn diagram, and I doubt that enough species have been sequenced for that. None of that is relevant, though I predict that both of those would fit nicely into a nested hierarchy if you looked.
Here you are wrong. You didn’t ask, you merely assumed that my paper had done it, and by appealing to natural causes. You have no idea what you’re talking about.
If that was your argument, you never managed to state it. But what you say this time is true. It’s exactly the same. Notice that there is no assumption of what caused either the loss of flight or the loss or gain of genes, contrary to your previous claims.
True. But if pigs had wings we’d need big umbrellas.
Well, that was opaque. And since it’s your claim that there are variations we can’t explain with population genetic models, isn’t your hypothesis falsified?
I will admit the possibility that you think you did. Not the same thing.
What do you mean by “more clear”? And doesn’t separate creation also presume a method?
That presumes that you expect to see nested hierarchy from separate creation, yet you have never been able to give a reason. Fail.
Way to miss the point.
Kepler did not(nor has any single human being) observed the entire orbit of all the planets in the solar system. He just observed micro-increments of most of these orbits and inferred an overall pattern from what little he observed. He could then use this pattern to make predictions about other planets who’s entire orbits he had not observed.
There’s a law or process(branching descent with modification, planetary motion), it leads to predictions(a tree/nested hierarchy, elliptical orbits), these predictions can be observationally confirmed on new data(novel types of data fit the tree, new planets also have elliptical orbits).
You still don’t get it. We are NOT saying that the only explanation for the nested hierarchy is common descent. What we are saying is that a nested hierarchy is exactly what we would expect to see with common ancestry. At the same time, there is absolutely no reason why we would expect to see a nested hierarchy from separate origins.
Could an intelligent designer create species so that they look exactly like they have common ancestry just to mess with us? Yes. In the same way, this same designer could plant fingerprints at crime scenes or fossils for species that never lived. However, we never entertain the idea that this designer plants fingerprints and fossils. For the same reason, we don’t entertain the thought that this designer just made life so it looks evolved on a whim.
I do not think that it fits the data better and it has the problem of being a misleading claim.
A pattern that includes dramatic gene differences? There is no logical connection between a branching pattern from reproduction and a nested pattern with dramatic differences.
Here you are evading my challenge which has nothing to do with the history of life. How did parts that are meant to fit together evolve in a step by step process? This is the problem with the gradualism claim.
Separate origin explains it by a common design strategy of reusing parts.
I have found some Venn diagram’s for birds and like deer they have different gene arrangements,
Chromosome counts of all birds are quite diverse ranging from 40 to over 100.
Where did I say I assumed it? This has never been a subject I have broached.
Again I think you are mistaken here.
It appears you never question this axiom. You are not alone here.
If there are variations in two different populations we cannot explain then I think common descent between the populations is suspect. If we look at the house mouse data I believe we can explain the observed variation with population genetic models.
It clearly demarcates the difference between reproduction and natural variation and God’s involvement.
Separate creation (origin events) cannot identify a specific method.
Winston showed a nested pattern from human design of software programs. The nested hierarchy is a logical product of design. It is not necessarily a logical product of common descent which has limited evidence of generating large variations.
This is still a naked assertion. I would not expect the dramatic nesting from common descent as reproduction generates highly similar species.
As I previously demonstrated to you, this claim is false Bill.
Yes, Ewert was able to algorithmically force-fit a nest hiearchy to the data. But he then immediately stated:
Figure 6 shows a simplified version of the true dependency graph for these same applications.
This is Ewert’s “simplified version of the true dependency graph”:
This is clearly nothing like a nested hierarchy.
You have provided neither logic nor evidence supporting this contention.
Let me correct that last phrase:
… as reproduction generates initially highly similar species.
There is no reason to believe that those initially “highly similar species”, and their descendant species, will not diverge substantially in the millions of years after their initial speciation.
In what way is it misleading? And how does separate origins fit the nested hierarchy better than divinely guided common descent?
Once more: the nature of the differences is not relevant to the pattern. Please stop confusing this.
Gradually. As you can see from the history of life. Hearts begin as a contractile bit in an artery and a one-way valve. Some taxa with minimal hearts don’t even have brains. The gradual changes don’t even have to happen at the same time. One system has time to adapt to a change in another. If you look at that comparative anatomy text you will find a lot of that. Or you could of course choose to remain ignorant, if that would make you more comfortable.
Sorry, but reusing parts doesn’t explain nested hierarchy. Try again.
How does that contradict my claim? But do cite those Venn diagrams.
That’s nice, but how is it relevant?
I can’t be responsible for your inability to remember your past claims.
Why can’t the same models explain the differences between populations? Remember that there are multiple populations of house mice, and yet you think population genetics can explain their differences. How does that suddently change if you call the populations different species?
Still opaque. Please try to explain what you’re trying to say, even if it takes more than one or two sentences. Assume that nobody will get your point unless you actually say what it is and why it makes sense.
None of these sentences is true, and the reasons have been explained to you on many occasions, all of which you ignore. I’m about ready to give up on this futil attempt to communicate with you.
Just my usual statement that software in no way follows a nested hierarchy. This has been demonstrated in many threads already. Carry on.
While it is of minimal import what you in particular would expect, still, I wonder why you would not. If a parent - be it an individual, or a population - has several offspring, all of whom are similar but not identical to the parent, then those offspring will share a majority of characteristics by which we can classify them as related: the similarities you are happy to acknowledge. If now those children each or mostly have children of their own, those grand children now share with their parents about as much as the parents did with one another, and as they do also among each other. However, cousins will share less in common than siblings, or parent-child pairs, and parent-grandchild pairs will also share less in common than siblings or parent-child pairs. They will still be highly similar, but the differences will stack up, since it is unlikely that the changes between one parent and its child will be reversed between said child and the grand child. As generations pass, each generation will be typically less similar to the common ancestor, but most similar to its immediate siblings and first cousins, than to any more distant cousin.
That is the expectation we have from the basic assumption that reproduction yields descent with minimal modification: We expect, that if organisms share ancestry, that the differences in their genes will have these structures, where some change happens early, gets inherited, and sometime down the line new changes happen, usually in other loci, and, too, get inherited. We do not need to assume common ancestry, or particular familial relations at all, but when we see genetic markers form exactly this sort of pattern where one can classify which variants are modified versions of which other ones in a single direction, this is perfectly consistent with common ancestry, not least of which because genes are the literal substance of inheritance by definition.
Common design, on the other hand, has no reason to yield any patterns of such kind at all. It is free to make changes that are in no way at all based on the immediate parent, but can go back and reverse all arbitrarily old changes for any reason, or introduce de novo designs completely foreign to the entire family at will. Common design, while not impossible given the data - as no data could hope to falsify common design; a weakness of that model, I should opine - is in no way positively indicated by it. We would not expect the data to be as it is assuming the model, since the model does not entail the data being as it is. Our experience with design patterns, if anything, would lead us to suspect otherwise. We could of course also speculate that part of the designer’s intent is to deceive us into thinking descent was a better account of his design, by making said design look exactly what we would expect to look like and nothing like what any known design looks like. Personally, I find this excuse rather reaching. If that is how far we are willing to go to defend the idea of design, then there is no reason that can reach us on this subject.
Why would generating highly similar species from one generation to the next not produce a nested hierarchy?
There is no reason why this would produce a nested hierarchy. Humans do the same thing, and their designs do not fit into a nested hierarchy.
Just as we would expect from evolution and common ancestry. Genomes change. Those changes stay on branches, just as we would expect from common ancestry.
Chromosomal fusions, chromosomal fissions, insertions, and deletions are all observed and known processes. It is explained.
So we can’t explain it, except when we can. What a joke. If it can happen in mice it can happen in deer.
He said just the opposite.
Why do you keep lying about this?
And what, exactly, constitutes a “dramatic nesting”? 
