I made an embarrassing mistake and managed to confuse myself. Let me try again.
How do you get a tree from the fact that most trucks and vans have mudflaps(say), while most cars don’t? It’s not clear to me why that should yield a tree.
Your just asserting here. How do you know a nested hierarchy is the fingerprint of common descent? When in doubt circular reasoning will convince someone 
Quantity of gene loss and the pattern. You only get one why question the ball is now in your court
By directly observing common descent take place. It is readily evident from even a few generations of reproduction.
This does not eliminate other causes of the observed pattern as SCD is trying to articulate. Very impressed you immediately corrected your argument a few posts ago.
That’s literally a repeat of the same assertion Bill.
First you say: “Gene loss occurring is not an issue it is the pattern of gene loss that looks troubling.”
Rumraket: “Why? What looks troubling about it?”
colewd: “Whats troubling is the quantity of gene loss and the pattern.”
Rumraket: “Why is that troubling? You’ve now repeated that it is troubling, but have yet to explain why.”
And now you come back with what you wrote above: “Quantity of gene loss and the pattern.”
Okay, so you think the quantity of gene loss, and the pattern of gene loss, is troubling. And?
Why? I understand that you think it is troubling. I understand what you think is troubling. I now want to understand why you think it is troubling. Please proceed to actually explaining in what way it is a problem.
Your trying to shift the burden Rum. I showed you a pattern where there are lots of genes not following a strict inheritance pattern. This is troubling to me as it is not just a few genes and not just a single node on the tree. This type of diagram has been out there since our 5000 post discussion with Sal and Harshman.
Show how it matches the phylogenetic and morphological trees. If it doesn’t you have a significant failure to your hypothesis.
Ahh so your question was actually how do we know that something else doesn’t produce a nested hiearchy, not just how do we know that common descent produces a nested hiearchy? That’s what you meant by a fingerprint, I get it.
Well basically because no other process has been observed to produce an objective nested hiearchy, and it is easy to just pick another character that completely conflicts with any hiearchy you can come up with. You sort vehicles by wheels or mudflaps (or wings, or rocket engines), I can sort them by leather vs synthetic fabric interior, or by carbonfiber vs steel plates (and so on and so forth), and get a completely different nesting pattern.
Very impressed you immediately corrected your argument a few posts ago.
Thanks. I’m sure we’ll see more of that, I make plenty of mistakes.
Assertion Rum and Scd is showing you this is nonsense. The design process produces a nested pattern. The objective nested hierarchy canard is not the issue. The specific pattern we are observing is the issue. Common descent alone does not explain it as Harshman concedes common descent does not explain new features and new features are part of the pattern.
You are the one making the claim that something is troubling. OBVIOUSLY I want you to explain what is troubling about it. You took on that burden yourself when you said it was troubling.
Anyone can just point to something and say “I think this is troubling”. If you wish to persuade that there is a problem, you need to be willing to expain and argue why and how. If you can’t be bothered doing any kind of work then why should anyone care to discuss this with you? At the very least you could try to explain your own position, not just state what that position is.
He isn’t showing anything. He puts labels at the ends of lines, picks a single character to define clades, and then stops. He needs to try to construct a tree based on a collection characters using real, actual data from the real world, and show that it reproduces his subjective nesting hiearchy of vehicles (cars ((trucks)(vans)). He hasn’t even begun to do that.
Make a tree based on mudflaps presence/absence, leather vs synthetic interior, number of seats, number of wheels, tire manufacturer and so on, the more characters the better, and make sure to use lots of different cars (pick, say, five car models from five different manufacturers), vans (pick 5 vans from 5 different manufacturers) and trucks (again, pick 5 trucks from 5 different manufacturers). That should provide a good “taxon sample”.
Now, his(and yours?) claim is that if he does that, he will get a neat tree with all the cars in a clade, and then vans and trucks will nest within that clade in two different groups. But he hasn’t actually shown that this result will emerge from such an analysis. He has basically just asserted that it will, but haven’t done the actual work that shows this.
Do you now understand how he isn’t actually doing what you think he is doing?
The design process produces a nested pattern.
Prove it. Stop claiming it does when neither you nor anyone has not even begun to show this is true.
The same way that we know a fingerprint at a crime scene came from a finger.
Nope. All of those vehicles can be found with extra wheels and mud flaps.
And we know of a mechanism that would produce that pattern: gene loss. We also know that gene loss is overwhelmed by genes that are still shared which gives us the expected statistically supported phylogeny.
You don’t have any mechanism that produces the pattern in Sal’s flower. Gene loss can produce subtle changes. How do you explain 76 genes appearing in zebra fish and not re appearing until humans in the venn diagram I posted.
This question has been answered for you many times, and yet you have learned nothing. It’s the fingerprint of common descent because it’s the exact pattern we expect from common descent but not from anything else. Unless you want to present an alternative.
I have no idea what you are referring to.
What Venn diagram?
I did it a TSZ with Macs. You continue to ignore arguments on this subject so I am not going to repeat myself as I made the same argument here. What you continue to ignore is that nested hierarch is just an abstract description of the data. What matters is the real data and common descent does not explain it because new features are part of the data.