Here is a labor-saving figure:
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Just to make sure I am understanding the diagrams correctly: The numbers on the trees to the right indicate the number of genes lost or gained after the green line, or between the green and red lines when both are present?
Not exactly. The numbers are from particular cells in the Venn diagram. The trees explain the simplest combination of gains (green) and losses (red) that would produce the distribution of genes represented by that cell. For example, there are 1602 genes present in human and mouse but not chicken or zebrafish. The simplest explanation of that is a gain of those genes on the branch leading to human and mouse. Then again, there are 48 genes shared between human and chicken but not mouse or zebrafish. The simplest explanation of that is a gain of genes on the branch leading to chicken, human, and mouse and a loss on the branch leading to mouse.
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OK, got it. Thanks!
And, Bill, your belief is that it is not reasonably possible that, say, 1602 genes could have been gained thru evolution over the time represented by the branch to humans and mice. Correct?
There you go again. We never eliminate non-material reasons. We can’t, that’s pretty much the definition of non-material. The best we can do is make non-material reasons unnecessary through material discovery.
Also consider that “non-material reason” might be an oxymoron, at least so far as material events. If you have an examples of “non-material reasons” that offer insight to how the world worlds, I will consider them.
Common descent alone does not explain it.
Common descent is a prediction of evolution, not an explanation of anything. We’ve been over this before (twice, I think), and you are confusing a really basic concept. Words have meaning, and when you abuse words this way no one understands you. I’m not convinced you even understand yourself sometimes. I suspect what you are really trying to do is express a feeling.
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So they’ve told you what the model is? Pretty sure they haven’t, and I suspect aren’t actually working on one.
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I agree your statement is better.
What I consider that may require non material explanations is the origin of unique living organisms.
You appear to be splitting hairs with this claim.
Semantics, I realize, but wouldn’t it be correct to say that common descent is the explanation for the branching tree pattern we observe in phylogenies?
But those numbers are dependent on one’s definitions of homolog and ortholog, no?
It’s not a claim, it’s defining a hypothesis. Prediction and observation are fundamental to the scientific method - this is NOT splitting hairs. You have a tendency to conflate these things (I’ve called you on this multiple times before), leading to nonsensical questions.
Semantics, yes, and Common Descent is practically synonymous with evolution. Most people will understand that, but look at how Bill uses it:
How have you eliminated non material reasons? There is no mechanistic model that reconciles the pattern. Common descent alone does not explain it. John_Harshman needed to add gene gain and loss to explain it. The adaption gain model that Lynch offered is very limited in how many changes it explains yet this Venn diagram shows thousands of unique genes in the different vertebrates.
Bill is correct that CD does not explain adaptation, but he is leaving out everything about adaptation we expect from evolution. I think Bill probably means something like, “how could all those new genes evolve?”, and remains unconvinced that any genes evolve at all.
@colewd Sorry to talk about you like you are not in the room. 
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John Harshman From TSZ
Ignored
on September 24, 2017 at 5:18 pm said:The differences are explained by different function. When I have looked at the substitution differences there is data that shows certain reptiles with closer sequences (13 different) than certain primates (14 different).The same situation occurs with birds and primates.In order to make the tree work you need to invoke the different molecular clock claim which is untestable.
You persist in making claims that have already been shown to be false. Trees do not make any assumptions about molecular clocks, so nothing needs to be invoked. Looking at individual sites should clear up any confusion.
Differences can’t be explained by different function. Even the apoptosis pathway you mention is possessed by many different organisms with different cytochrome c sequences and thus can’t account for those differences. And your explanation can’t account for the nested hierarchical nature of the differences, while common descent can.
Here John Harshman appeals to common descent as an explanation for the nested hierarchal nature of the differences.
Common descent maybe a prediction of evolution but it is also being used as an explanation for the pattern in the data.
I can’t even anymore.
All true, but are you trying to say this is a problem?
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The problem is clarity of the explanations. This appears to contradict @Dan_Eastwood claim that common descent is a prediction and explains nothing…
That’s true. Perhaps he will explain what he meant or else retract the statement.
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@colewd The problem is your understanding and usage of terms. You also persist in saying “the differences” cannot be explained, when it appears that you simply cannot accept any explanation for a difference. You rarely offer any specific reason why differences are unexplainable other than incredulity. There are people here who would like you to understand, but no one can help you overcome incredulity - that’s up to you.
I don’t understand the argument you cited about phylogeny and molecular clocks, but I think I see the problem. It is most likely that some non-evolution source of adaptation/variation is causing differences, yes?
With differences introduced through evolution/adaptation, changes are inherited (common descent) and a nested hierarchy pattern is a necessity consequence. Not so with design - a designer is not limited to introducing changes that will result in a nested hierarchy. A mischievous designer could do this, mimicking the pattern required by evolution, but then the designer might as well BE evolution, because there is no way the mischievous designer can ever be detected.
To summarize - CD does not explain how differences came about. CD does explain why the NH pattern is a prediction of evolution and not of design.
Does that satisfy the critics? 
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One interesting thing I have learned in these discussions is that there are people in this world who believe that if they declare themselves unconvinced, they have effectively “won” the argument – because the object of argument is to convince them. I think it must have been very difficult to be a teacher when these people were students.
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Are you agreeing that your claim that common descent explains nothing is incorrect and misleading?
I have articulated why the explanation of merely claiming gene gain and loss is inadequate as the magnitude of changes is beyond current mathematical models such as Behe and Lycch offered to explain complex adaptions such as new genes/proteins. The lack of a change mechanism adequate to show the different gene patterns is a limitation of the current models.
Winston showed conditions where humans designs generate a nested pattern. The existence of this pattern is a trivial observation.
This statement is much more clear then your previous claims and is consistent with what John Harshman has claimed over the last 5 years.
Yeah I’ve also lost interest in rebutting the same braindead nonsense over and over again.
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