Hi Puck
This is a diagram introduced at TSZ by @stcordova many years ago based on a discussion between common design and common descent. Latter John asked me not to post it until he had a chance to address it. Out of respected I waited for Johns counter argument. He then posted a gene gain and loss diagram.
I know this is the standard evolutionary explanation and under methodological naturalism it is the most parsimonious.
Yes, I’m amply familiar with the diagram, with your prior references to it, with your inability to understand it, and with John’s patient and gracious attempts to explain it to you. I think that pretty much everyone here is.
I am also familiar with your rhetorical technique. I fully expect that, now that John has explained it to you AGAIN, you’ll say something like:
“That could be true if we assume methodological naturalism. Until you have a hypothesis for how the gene loss and gain happens in the reproductive process, the inference of design is very strong.”
Nobody will think that changes the game at all. AT ALL.
P.S. the above was posted before I saw your response. Your response was even less responsive than my prediction. There are some things so awful that they defy prediction.
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As far as we have scientific method based on methodological naturalism I agree with you.
Under supernatural assumptions about where mutations come from it’s also the most parsimonious. Under a hypothesis of separate creation it’s unexpected and makes no sense.
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@sfmatheson The Argument Morgue is looking better and better. 
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Under certain hypothesis of special creation it may not make sense. Under a hypothesis of how systems are designed reusing parts for new designs it does make sense.
No, sorry. Makes no sense at all even under that hypothesis. You’re assuming functional reasons that have not been demonstrated for the genes in the diagram. And you’re also ignoring the vast amount of other data in addition to gene presence/absence that also fit the standard tree, very little of which can have any functional significance at all. This is your ignorance talking again.
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If I knock out 20 genes from a mouse randomly which is .1% of its genes according to Grok it will have a less than 1% chance of survival.
The probability of a mouse embryo surviving to adulthood after randomly knocking out 20 genes is <1%, likely 0.1-1%, with a ~99% or higher chance of embryonic or perinatal lethality or severe developmental failure. This estimate accounts for redundancy, interactions, and the high likelihood of disrupting essential processes
This is pretty strong evidence that most genes are not only functional but mission critical to allow the embryo to achieve adulthood.
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Putting aside that Grok isn’t a reliable source, so what?
Of course most genes are functional. If they weren’t we would call them pseudogenes. And there are of course plenty of pseudogenes, yet their inactivation didn’t cause death. The problem here is with your thought experiment of randomly deleting 20 genes. Gene loss is of course not random. Only genes whose loss is not selected against are lost. Mutations that inactivate functional genes are selected against and do not generally become fixed in a population.
Nor does this have anything to do with the point you were supposedly responding to. This is all elementary, and a fine example of something you refuse to understand.
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It really is inappropriate to call MechaHitler “Grok.” It’s made its preferences in the matter quite clear.
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Now my assumption of the genes being functional is reasonable?
No, this is not “pretty strong evidence” that most mouse genes are functional - 1% is what the math predicts if the mouse genome is 20.6% “functional”, which is considerably lower than the actual ~28% “functional” suggested by Google Search Labs AI for the mouse genome.
If anything this example leans towards the mouse genome being less than 28% functional, not more, and definitely not most.
If it’s any consolation, this is the same equation Dembski should have used in his 2005 paper:
P[“event” with probability p occurs at least once given N trials] =
1-(1-p)^N
Check my math, please.
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I wonder what method those who rejects “methodological naturalism” use to assess the strength of a hypothesis. As far as I know, there is none. What they do, instead, is treat a completely unfalsifiable idea like “God did it with his magic” as if it was an idea that could be tested, but without actually testing it (because it can’t be).
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You can’t read or understand what you read. Just know that your response here once again demonstrates your ignorance. I could explain but I’m tired of trying, at least for now.
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I agree with your point statistically. The lethal genes in this case however point to mission critical genes in development.
These raise a challenge for change in the gene make up and about 30% of the changes will kill the embryo.
John is right they will be purged from the population.
You should admit when you contradict yourself.
Again, tired of trying to explain your ignorance to you.
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Your problem is you don’t know what a gene is. Your ignorance is quite prolific.
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I have agreed that the tree is evidence for common descent. What you have not shown is that the deviations can be attributed to standard evolutionary mechanisms.