A car and a truck sharing the same exact engine is not equivalent to convergent evolution. With convergent evolution you get different adaptations for the same function, such as the very different wings on bats and birds.
What data? Show your data. I don’t believe you actually have any.
the first step: do you agree that a bicycle is more similar in general to other bicycle then to a car?
and what about convergent loss like in the alx3 gene example i gave? its basically the same.
The lack of a gene is not a shared feature. It isn’t the same thing.
Yes. Where does that get you? Nowhere. You appear not to understand what a nested hierarchy is.
How do phylogenists handle gene loss? I had always thought shared derived features were used instead of a lack of a feature, but I am more than willing to be corrected on this point.
The way phylogenetic analysis works is by coding characters with multiple states, and an evolutionary event is represented by a change in state of one or more characters. To represent gene loss, you would code a character for the gene as “present” or “absent”. A change from absent to present is an event, and a change from present to absent is an event. And of course after that event happens on some branch of the tree, the descendants of that branch would retain that state. So yes, absence of a gene is a feature that’s amenable to phylogenetic analysis.
Now of course there are two possible reasons for a gene being absent: it was lost or it was never there. But that’s a question for the phylogenetic analysis to resolve.
(Incidentally, the term is “phylogeneticist”; @swamidass has misspelled my title.)
this gene is shared between far species but we cant find it in some specues between. so its like a truck with a trait that is shared with a bicycle but not with a car.
First problem: you haven’t presented any data at all. Second problem: that isn’t even a tree, since it only has two taxa. Third problem: you’re still just clustering by overall similarity, if anything, and that isn’t how nested hierarchy works.
but you just said that you agree that a bicycle is more similar to another bicycle then to a car in general. so you should accept the first step above. right?
No, because it’s a step to nowhere. You’re making a claim that vehicles display nested hierarchy, just like life does. “More similar” is not a first step to that.
here is the second step:
again: very similar to this tree:
so where do you see a problem?
I’ve already explained your problem several times, at length. You have ignored all of it. At the very best, you are merely clustering on intuitive feelings of similarity. That’s not how phylogenetic analysis works.
I am amazed that this conversation continues. @scd look, even if designed objects fit into a nested hierarchy that doesn’t mean a nested hierarchy (NH) isn’t evidence for common ancestry (CA) Common ancestry predicts such a pattern. Design (D) does not. P(NH|CA) > P(NH|D). You’re fighting a losing battle.
This appears to be an assertion. His tree is constructed from data: Functional similarity and parts similarity.
This appears to be an assertion. He is showing you that design does predict a pattern of similarities and differences where similarity of function will correlate with similarity of components. ie bicycle wheels will be look alike and car wheels will look alike.
What parts? I can’t find any reference to any parts on the phylogeny.