I suggest Meerkat_SK5 gets to stay in his own thread where his nonsense has already been, and is still being discussed at length. No reason for him to take the same stuff into every thread about common descent.
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If you think that would form a nested pattern, you must still have some serious misunderstanding about what nested hierarchies are and how they form in biology. If each ‘created kind’ started out with the exact same sequence and diverged from there (regardless of if they diverged at different times), the result would be a star tree, since they all diverged from the same point. The time since divergence would of course be reflected in the branch lengths, not the pattern.
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Mod comment: Please do not derail this thread irrelevant arguments.
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Sadly, all he does there is repeat the same few non sequiturs, some of which he’s trotted out here already. So don’t waste your time.
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How is this different then when two populations become isolated and lose the ability to reproduce with each other?
Again, what is causing the nested pattern according to the common descent hypothesis?
Using the “mock character-trait matrix of wheeled vehicles” produced by creationist John Woodmorappe (found here), I generated a morphology-based phylogeny using IQ-TREE (thanks, @davecarlson!). Here is the result, both unrooted and outgroup-rooted* (visualized at iTOL: Vehicles):
This tree actually displays the same strange topology as the ‘random’ trees, as all of the vehicle ‘taxa’ fall along a single line rather than creating a branching pattern. The bootstrap values are high, but I suspect that this is only because Woodmorappe purposely cherry-picked features of these vehicles that fall along such a pattern. If we did a comprehensive morphological analysis of these vehicles, the tree would undoubtedly have more ‘noise’ and less ‘signal.’
Ideally, this should put to rest the creationist claim that vehicles produce a nested hierarchy like common ancestry (cough @scd cough) but sadly it’s very likely that this myth will continue to be perpetuated. At least now, when creationists make this claim, I can direct them to this post which shows that even in the best-case scenario (using Woodmorappe’s cherry-picked morphological data), the topology of the vehicle phylogeny is actually far closer to ‘random’ trees than the branching pattern produced by common ancestry.
* The outgroup is “unicycle.”
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Before moving on in this discussion, let’s just all try to agree on one simple fact: that nested hierarchies are far more complex and robust than creationists often make them out to be. All three of the major creationist organizations claim that nested hierarchies are merely different levels of similarity between extant organisms. But biological nested hierarchies are much more than this. Biological phylogenies have:
- Nested hierarchy in sequences where function does not change between organisms.
For example, in the OP, I constructed a phylogeny based on CYT B, CYT C, and COX1 proteins. These are all proteins that operate in the electron transport chain, and so they do the exact same thing in all of the taxa from that phylogeny. In fact, life quite literally depends on them doing the exact same thing in every organism; if they did not, then our mitochondria could no longer make ATP.
- Nested hierarchy in unconstrained sequences.
There are certain places in the genome (including functional sequences, so this isn’t a “junk DNA” argument) where changes in sequence do not effect a change in function. For example, at ‘silent sites’ in protein-coding genes, mutations do not affect the protein that is transcribed from the DNA, and many studies have shown that such mutations are functionally neutral. Yet these sites, too, exhibit nested hierarchy, as do other unconstrained sequences like ERVs.
(Note: this is not the same as the “shared ERV” argument, this is referring to the sequences within the ERVs rather than the placement of the ERVs themselves.)
- Ancestral convergence.
We can use ancestral sequence reconstruction (which has been experimentally proven to be highly accurate) to phylogenetically reconstruct ancestral gene sequences for a group of organisms. When we do this on large groups of organisms (for example, comparing all deuterostomes to all protostomes), the ancestral sequences are more similar to one another than the extant sequences, to an insane degree of statistical certainty (p-value: 2.59 x 10^-132). This shows that nested hierarchies are not merely an artifact of similarities of modern organisms, but actually represent divergence in the past.
- Functional ancestral proteins.
Again, ancestral sequence reconstruction has been experimentally shown to be highly accurate. When we conduct ancestral sequence reconstruction on proteins from modern groups of organisms, the resulting ancestral protein sequences are actually functional. This has been done dozens of times, and has been used to reconstruct the evolutionary history (mutation by mutation) of different proteins, for example, hemoglobin. This, like ancestral convergence, shows that nested hierarchies aren’t merely an artifact, but represent real histories of organisms. If a common ancestor didn’t exist, why would its proteins be functional?
If we tried to apply these four features to human-designed objects, like the oft-used ‘vehicle phylogeny,’ it should be obvious that it doesn’t work. Finding nested hierarchy in unconstrained sequences would be like trying to build a phylogeny of vehicles based on features that don’t affect their function, like paint color or the presence of a sunroof. You couldn’t do it, and even if you could, the resulting phylogeny wouldn’t agree with the phylogeny of, for example, engine parts.
Trying to find ancestral convergence in vehicles would be like finding that the ‘bicycle ancestor’ is more similar to the ‘car ancestor’ than extant bicycles and cars are to one another. This would be a meaningless endeavor since vehicles don’t have ancestors anyway, but even if you tried, it would fail since cars have been cars, and bicycles bicycles, as long as they have existed. They never transitioned from bicycles to cars or vice versa. And trying to conduct ancestral sequence reconstruction on vehicles would be like discovering that the ‘ancestor’ of bicycles and cars is a working vehicle – also a meaningless endeavor that is doomed to fail.
For the creationists here, I hope this helps you to see that nested hierarchies are much more robustly supported than the creationist organizations make them out to be, even if you still don’t think that they represent real evolutionary histories.
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Then you don’t understand von Neumann’s universal constructor model. A simple search on Wikipedia shows that von Neumann’s universal constructor model is the same as common ancestry, just applied to mechanical rather than biological systems. The “universal constructor” isn’t a reference to some ‘universal common designer,’ it’s von Neumann’s name for the mechanical ‘universal common ancestor’ which self-replicates. So the fact that von Neumann’s model shows the same nested hierarchy pattern as biological lifeforms doesn’t help your case, it hurts it.
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It doesn’t seem that you do, as you are misrepresenting Andrew testing a hypothesis as improving his own models, two very different things.
The analysis has nothing to do with molecular clocks. That’s some pretty good salad to go with your sealioning, though.
More salad!
This is one of your most impressive salad creations to date, Chef Bill! You go to truly amazing lengths to avoid understanding the concept of nested hierarchy.
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Then what is a common design scenario? We see this same complaint every time, but we’re never told how to create sequences by “common design” in such a way that they consistently produce the same branching topology simply as a byproduct of how the sequences are each designed for their specific tasks.
Your position is resting on some nebulous idea none of you actually know what really is or how to put into practice. It is just a fantasy. It’s actual contents seem to stop at merely uttering the words.
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Wouldn’t that just be generating a nested hierarchy on purpose, though? That’s not how design works, as actual engineers here can tell you (paging @RonSewell). Instead, design works like a web, and designers often intentionally violate nested hierarchy by using shared technology.
Like, bikes, cars, and trucks might at first glance seem to be on different branches of the ‘vehicles tree’; but electric bikes, cars, and trucks are more similar to one another in the way that they are powered than they are to other bikes, cars, and trucks. And what about this bike with car wheels? Or what if two different brands of car and truck use the same engine?
In contrast, we don’t see this in biology. Sure, homoplasy exists, but whenever we look under the hood of analogous structures we find that they always have different underlying mechanisms. For example, both sharks and whales have flippers, but sharks (which are chondrichthyans) have cartilaginous flippers with fin rays, while whales (which are mammals) have the typical tetrapod limb motif, just modified into a flipper.
For this reason, it just wouldn’t be an accurate representation of design to intentionally create a nested hierarchy in the way that you describe.
Well, my intention was to test the claim that differing levels of similarity, caused by ‘common design,’ can produce a nested hierarchy pattern sans common ancestry. This is the official position of CMI, AiG, and ICR, and as far as I know, no other hypothesis has been advanced to explain nested hierarchy without common ancestry.
The only feasible way to test this is to use random sequences, since (as should be self-evident) any set of more than 2 random sequences will necessarily have some sequences that are more similar to one another than they are to the other sequences. In this way (and only in this way) random sequences are the same as ‘commonly-designed’ sequences according to creationists. However, this is really the only similarity that matters, until someone else advances another hypothesis about how ‘common design’ can explain nested hierarchy without common ancestry.
Frankly, I don’t know what @colewd is saying, and I’m not sure he does either. Very little of what he says actually makes sense in the context of biology and phylogenetics.
Typically, different genes do recover the same phylogenetic relationships, but that’s beside the point. I was referring to the branching pattern with high bootstrap values, which is what we see in real biological organisms, and we don’t see this in just any sequences with differing levels of similarity.
The problem with those quotes is that they conflate similarities with nested hierarchy. This is best seen in the ICR quote:
They are saying that a tree with the same branching pattern as that produced by common ancestry could be produced if you just have different levels of similarity between organisms, or in this case, vehicles. That is false, as I have shown, and yet this seems to be a general misconception about nested hierarchy shared by most creationists.
I appreciate the honesty. 
You have also been very nice, much nicer than the other creationists I have encountered here and elsewhere.
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Two species do not demonstrate nested hierarchy. It takes at least three, preferably four (one as outgroup). You still don’t know what nested hierarchy is, after all these years. Words fail.
Common descent, splitting of lineages, inheritance, and changes in characters within lineages are sufficient to explain the nested pattern. Not only sufficient but expected.
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If you don’t understand the difference between a nested hierarchy and a star tree, why are you even trying to argue against phylogenetics as evidence for common ancestry? Shouldn’t you have at least a basic understanding of something before you try to refute it?
Here are two very simple explanations of how the branching pattern and nested hierarchy are produced by common ancestry:
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How is ‘two’ different from ‘all’? That’s your question?
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Maybe, haha, but after reading lots of papers, that seems to be a common theme - many sequences shared among most, some shared among some, many private mutations. Like this one I read recently - that I guess isn’t fully initially created design, but creates the same pattern. Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes | Nature (After looking into this topic for a few years, I was surprised to find out mtDNA insertion happens, and I hadn’t come across that in my reading before or had forgotten it. Super cool.)
Anyway, I was just picking out the design that I’ve noticed along the way. I wasn’t actually sure whether it would create a nested hierarchy or not. This topic confuses me, and I’m too sleep deprived most of the time to know how logical what I’m saying is. 
But it seems like your reply is - well, that makes a nested hierarchy so that doesn’t count; common design has to look like a web. Why? It still looks like design to me if there’s a pattern - we as humans could show God’s image by creating much like he does, but there may be a brilliance there in biology we don’t yet understand. God especially loves trees AFAIK (also a favorite biblical theme of mine). 
Not surprising created things form trees. (Random aside, it’s funny to me scientists have to go to great lengths to explain how and why trees evolved.)
Aren’t these examples the same thing as your whale and shark example? Similar looking flipper, tire, engine; different mechanism or transportation branch?
Ok, I think I can agree with you on that narrow point.
I’m not saying that common design has to result in a web. Purposely generating a nested hierarchy as a model of common design is begging the question, because that’s the very thing that I’m testing, whether or not ‘common design’ apart from common ancestry results in a nested hierarchy. Don’t you see that it would be circular reasoning to generate a nested hierarchy on purpose as a test of whether common design generates a nested hierarchy?
I’m not questioning whether there is design. I think there is certainly design involved, whether direct or indirect guidance from God. I’m testing whether or not design, apart from common ancestry, can generate the same branching structure and nested hierarchy as common ancestry.
It’s impossible to say whether unstated hypotheses are right or wrong. A hypothesis must be stated and tested before it can even be considered a viable option, let alone on par with such an explanatorily powerful theory as common ancestry. So although there could be, as you say, “a brilliance… we don’t yet understand,” no one is under any obligation to take that seriously until we do understand it. As it is, common ancestry appears to be the only existing hypothesis that can explain this consistent branching pattern.
Not at all. In biology, analogous structures appear superficially similar, but if you look under the hood (so to speak), they are in fact very different and reflect the true nested hierarchy. Sharks and whales occupy the same ecological niches, but have very different structures that do the same things, reflecting their separate ancestry (sharks are chondrichthyans whereas whales are tetrapods/mammals).
In contrast, in the realm of human design, such shared structures aren’t merely analogous, they’re homologous, in that they use the same principles and work the same way. A car and a truck can use the exact same engine, or a car can have a helicopter engine, etc. These violate nested hierarchy and make it a web instead.
So, if God used human design principles to create living organisms, then that doesn’t explain the nested hierarchy structure of life, with phylogenies that have a branching structure and high bootstrap values. If this is the case, then we need common ancestry in addition to design to explain the diversity of life. And if God didn’t use human design principles, then we have no basis for comparison, which means we have even less reason to believe that separate ancestry is true, since such a design hypothesis is untestable. By explaining anything, it explains nothing.
Great, because that’s really the main point I am trying to make in this thread; that the current creationist hypothesis for how design explains nested hierarchy (differing levels of similarity) actually fails to explain it.
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Why is inheritance creating the pattern? Is it because it copies the gene that is being tested? If so how is this different then common design that is using a strategy of reusing parts?
After the species is designed then the gene may diverge. If new groups of designs (mammals, birds etc) designs are occurring at different times then the nested pattern forms as species that were created at similar times will group together.
I would not expect random sequences to form a nested pattern. Both common design and common descent are not generating random sequences.
That is false. You still clearly don’t know what nested hierarchies are or how they form. Which is frankly mind-boggling considering that this has been explained to you dozens of times over several years, and at least three times just since I joined this forum a few weeks ago.
You’re not understanding why I used random sequences. The claim is that merely differing levels of similarity form nested hierarchy. (There are no other currently existing ‘design’ hypotheses for nested hierarchy, at least none that don’t invoke common ancestry, which is the point I’m trying to make.) Since random sequences also exhibit differing levels of similarity, the fact that they don’t form a nested hierarchy with a branching pattern and high bootstrap values (like real organisms do) falsifies this claim.
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Because re-using parts does not produce a consistent nested hierarchy. Pay special attention to the word ‘consistent’ in that sentence, it is key. That is to say, between independent loci(or attributes) you do not expect to inadvertently produce the same tree topology as a byproduct of re-using the parts over and over again.
To elaborate, suppose you create two different genes A and B, each with different functions. You re-use these two genes in all the different species you create.
Now you infer a tree from the sequences of gene A, which was re-used in all your different species, and you get a particular tree. Now you infer a tree from the sequence of gene B, which was also re-used in all your different species, and you get … another tree.
Now, why would those two trees be essentially the same? There is no reason why they would be.
Nobody has shown that re-using parts will mean trees inferred from different parts will be the same. And in fact there is no reason to suppose they will be. Ewert hasn’t shown they will. His paper simply doesn’t deal with a consistent nested hierarchy. He tried to show that design CAN produce a nested hierarchy, he didn’t at all deal with why design would produce a consistent one. That is to say, that design produces the same(or highly similar) tree inferred from the attributes of different parts as a byproduct of simply re-using them.
You know why he didn’t? Because he couldn’t. It doesn’t work. It does not, in fact, produce a consistent nested hierarchy. You can re-use gene A, re-use gene B, and re-use gene C, for each different species, and yet you do not have reason to think this will make the tree from A, be similar to the tree from B, or to C, or anything.
Can you fathom this now? Will there come a future where you at least understand it, never mind accept?
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