Since that’s the only known way of doing science, what’s the problem?
Let’s see if this analogy helps you understand what you are missing.
Imagine we have two scientists. Scientist One hypothesizes the existence of a force called “Gravity”. According to his hypothesis, if a rock is held above the ground then released, it will fall to the ground.
Scientist Two hypothesizes the existence of a force he calls “Schmavity.” According to his hypothesis, when the rock is released Shmavity will act on it in a random way such that it will either fall to the earth or be repelled up into the air.
They test their hypotheses by conducting one million trials. In every single one, the rock falls to the earth.
Scientist One says "I guess the data supports the existence of Gravity, and not of Schmavity.
Scientist Two replies "Not at all. According the my Schmavity Hypothesis, every time the rock is released, it could fall down to earth. And, every time, it did. So the data supports Schmavity just as strongly as it does Gravity.
Common descent is Gravity.
Creation is Schmavity.
Does that help?
The dependency graph was modeled after a software tool. Your most astute comment was those tools show real dependency between between modules. This can be tested for in @Winston_Ewert model.
Under the constraint of methodological naturalism I agree.
There is no problem with methodological naturalism as long as it is applied properly and does not repeatably lead to faulty conclusions.
The problem is that you think opinions somehow falsify scientific conclusions.
A good example of an organism that would seriously challenge a nested hierarchy is a species with a mixture of derived bird and mammal features. For example, a species with teats, feathers, flow through lungs, and a placenta would be a serious problem. Can you tell us why such a species could not be a “seeded” organism in your model?
Phylogenetic signal is a measurement of how well the data fits a tree. It isn’t a label. It is a scientific measurement. Like any measurement in science, there will be noise, but the real question is if there is a phylogenetic signal that overwhelms the noise (i.e. the genes that don’t fit the tree) and that is exactly what we see.
They don’t fit into a dependency graph. Ewert states that if there is a tree-like structure then the data does not fit the dependency graph, and that tree-like structure is there.
Where are these modules?
So why isn’t any creationist trying to test it? How would you test it, incidentally?
Meaningless. What can you do without that constraint?
What’s supposed to supplant this? Methodological supernaturalism? What even is that?
Good questions.
It would open up science to explore models that would require God or an Intelligent Creator as an explanation. Accept @Winston_Ewert model as a new idea to explore and understand why 70 plus genes can share in building a human and a zebra fish but are not required to build a fellow mammal (mouse). The ideas for driving genetic understanding are numerous from this model.
If people on the site would agree to this @swamidass @glipsnort I will try to engage the ID guys in. a productive dialog w @pnelson @Winston_Ewert @AJRoberts and others.
Wave-function collaspe and proton-tunneling
Wrong, we just need to explain and demonstrate why our model is right .
We are still waiting for that explanation.
The problem with it is that scientists are using it as a Trojan Horse for philosophical naturalism where only material causes ,made-up of matter and energy or space-time, exists. Therefore, any mention of an intelligent designer or mind is prohibited by default.
Your complaint would have more weight if you had a hypothesis that actually met the requirements of the scientific method.
BINGO!!!
This is what I have been trying to argue the whole time in the other topic, but you have constantly tried to steer it in the direction that you wanted to focus on that ultimately leads us nowhere.
I will break it down to you what I said to you on the other topic.
If Universal common descent is true, we should observe very few (if any) conflicts between the phylogenetic and paleontological trees that they construct.
If Universal common design is true, we should continue to find more conflicts between those two.
Could you quantify how many conflicts we should expect from common descent and evolution?
Yes I have done this already. Please read post 326 in this source for more to get the lastest revised summary of my hypothesis: Can God be a useful “scientific” hypothesis? Yes - Peaceful Science
At the moment, No. But, it is a good question.
Yes. You should provide good answers, or at least ponder why you don’t have answers.
How would that help? Ewert’s model appears to be untestable and to explain nothing. So far there is no indication of what it would correspond to in the real world, as a tree corresponds to a branching history.
Note your equivocation between “can share” and “required” within a single sentence. The explanation is simple: genes are gained and lost all the time.
You will have to name some of those ideas if you want to convince anyone. They would have to be ideas that haven’t already been falsified too.
Warp factor 5 and dilithium crystals right back atcha.
We are still waiting for that model.

Wave-function collaspe and proton-tunneling
What about 'em?
Be specific.
There’s nothing supernatural about wave function collapse and proton tunneling per se.