is this also a made-up cartoon?:
(image from https://www.quora.com/Is-it-true-that-all-apes-are-monkeys-but-not-all-monkeys-are-apes)
(image from https://www.quora.com/Is-it-true-that-all-apes-are-monkeys-but-not-all-monkeys-are-apes)
Yes, unless you can point to the data itâs based on. Now in fact thereâs plenty of data to back up that particular topology, though the time scale is less clear. But I can safely say that you know nothing about any of that. This is just a picture you pulled off a random place on the web, nothing more.
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Maybe to fine tune cytochrome C to the particular physiology of each kind?
Even supposing there is some tuning on the sequence of cytochrome c to fit it to some particular organisms physiology that would make it a bit better than some other variant, why should that tuning result in the sequences of cytochrome c from different species yield a similar branching topology when subjected to a phylogenetic algorithm, to the trees derived from the sequences of other genes, or some intronic or intergenic region?
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Maybe because more similar kinds with more similar physiologies would need more similar cytochrome c?
Phylogenies arenât derived by similarity, so that explanation doesnât work.
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Well, I have to admit my ignorance in phylogenetic science. Iâam just asking questions for my education here. BTW, I have ordered « Tree Thinking », the book @John_Harshman recommended to me to better understand these phylogeny issues. Hope it will help me!
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It should. In the meantime, to reiterate some of the basics: phylogenetic analysis is not based on just ordering similarity. Anyway, absent real nested hierarchy, thereâs no reason to suppose that similarity should be consistent among data sets or that distances should fit a tree at all. One popular creationist expectation is a star tree, in which all branches converge on a single internal node with no other branching at all. Of course, that isnât what we see.
here are two papers about primates phylogeny:
you can see that the phylogeny is basically the same (at least for human, chimp, gorilla and others).
You exceed my expectations. Now, have you actually read either of those papers? Have you looked at the data and analyses, even a little bit? If you did, you would see that theyâre nothing like what you would need for any of your little cartoons of creation and trucks/jet fighters to make sense.
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in any case, if we can get a nested hierarchy by difference/similarity comparison on designed objects, it means that we can get a nested hierarchy without common descent.
Regardless of whether or not you can, you have never managed to do so. All youâve done is hand-pick the data for the purpose of achieving a result and then applied the hand-picked data in misunderstood ways to get your tree. Or sometimes you havedispensed with data and just drawn the cartoon you want. Neither is valid, and lately itâs all been the latter.
Now, is it valid to use simple distance measures in phylogenetic analyses? Yes, given certain assumptions. But you have to show that those assumptions hold true. And you further have to show that the tree you produce is strongly supported by some measure. Just piling up distances isnât good enough. This gives me an opportunity to plug an old paper that explores this question: Harshman J. Reweaving the Tapestry: What can we learn from Sibley and Ahlquist (1990)? Auk 1994; 111:377-388.
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if you agree that a car is more similar to a truck than to a bicycle then you should accept this comparison and the data that this comparison was base on:
You canât just keep drawing cartoons as if theyâre evidence. You have no data.
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the data is the fact that a car share more parts in common with a truck than with a bicycle. are you rejecting this fact?
But you havenât shown that any designed objects fall into natural, well supported nesting hierarchies. You can certainly impose a hierarchy (you can just nest folders within folders within folders on your hard drive, for example). But what you need to show it is that the attributes of objects (for example the attributes of folders) naturally sort into an objective nested hierarchy.
As has been attempted by others to exlain to you numerous times before, including myself, in multiple different ways. For example here - or here - or here - or here - or here. And those are just my own attempts at this that I can remember of the top of my head.
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Why is it that you never show any sign of even wanting to find out if what you are saying is really true? You just say stuff without a care in the world.
That really isnât data; itâs an impression. But letâs assume you have assembled some real data and it does come out that a car is more similar to a truck than to a bicycle. Is this a nested hierarchy? No. What you now have is an unrooted 3-taxon tree, which will always result from putting 3 taxa together. To turn it into a nested hierarchy you must add a root, as you did in your cartoon. The problem is that you have no basis for the root. You need either an outgroup, which you donât have, or an assumption that the tree is clocklike, which you could certainly try to assert if you didnât mind people snorting through their keyboards.
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Could you explain what you mean by a tree being âclocklikeâ?
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It means that change ocurs at a constant rate on all branches. This would have the effect of all paths from root to tip having the same length, as in @scdâs cartoon. If that assumption is true, the tree roots itself (often referred to as âmidpoint rootingâ).
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