Common Ancestry and Nested Hierarchy

[John_Harshman]

@colewd

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?

One gets so tired of word salad. What do you mean by “the gene that is being tested”? Who is testing anything? Splitting, inheritance, and changes are all necessary to create the pattern. A tiny little bit of thought should be enough to show why this produces a nested hierarchy. Common descent with splitting makes a tree. Inheritance and changes produce the content of taxa on the tree. After all this time, you ask questions like that? Disturbing, though not surprising.

@colewd

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.

Why would species created at similar times group together? Does God change his mind on what the similar parts ought to look like through time? But even if that were true, all we would have would be two levels of star tree, in other words a star tree of star trees. Not a nested hierarchy.

@colewd

Both common design and common descent are not generating random sequences.

But common design would not produce a nested hierarchy. The sequences may not be random, but the differences among kinds should approximate random differences. Again, a star tree.

[misterme987 (Andrew P.)]

@John_Harshman

What do you mean by “the gene that is being tested”?

@colewd seems to think that phylogenetics tests one gene at a time. He probably got this misunderstanding from the DI and other ID sources, since they sometimes make it sound as though different genes produce entirely different trees.

Edit: For the record, a real scientific study (Galtier and Daubin 2008) has been done on the amount of incongruence between gene trees. What they found is that incongruence is remarkably rare – only 1% within metazoans (animals) – and that the amount of incongruence correlates with the amount of horizontal gene transfer, implying that incongruence is caused by natural means, and not by special creation.

[colewd (Bill Cole)]

@John_Harshman

Why would species created at similar times group together?

If you are measuring genes that are reused based on common design and created at similar times they would likely group together.

[John_Harshman]

@colewd

If you are measuring genes that are reused based on common design and created at similar times they would likely group together.

That’s just a repetition of the original claim. It doesn’t say why. Why should they group together, and why should similar times be relevant? And, again, even if this were true, it would not result in a nested hierarchy. You still don’t know the difference between similarity and nested hierarchy.

[Rumraket (Mikkel R.)]

@colewd

If you are measuring genes that are reused based on common design and created at similar times they would likely group together.

Prove it.

[misterme987 (Andrew P.)]

Edit: this post originally came after post #47

@colewd, since you continue to falsely claim that kinds created with identical genes at different times would create a nested hierarchy, I think you need a demonstration. With a few modifications to my original evolutionary algorithm, I created another program which models Bill’s hypothesis.

This program generates a new taxon with the same, identical sequence every generation, and mutates it from that point on. In this way, it models the ‘identical genes’ hypothesis with different, identical ‘kinds’ being created at various points in time.

Here is the tree produced by 10 taxa from this program (visualized at iTOL: Interactive Tree Of Life):

In what should be an unsurprising turn of events for everyone except Bill, these sequences produce… (drumroll please)… a star tree! As expected, the ‘kinds’ which were ‘created’ earlier in the simulation have longer branches, while the newer ‘kinds’ have shorter branches, reflecting the time since their ‘creation.’

Now, I was unable to properly view the bootstrap values on the unrooted tree, because the branch lengths at the center were too small (on account of it being a star tree). So I uploaded the tree to PRESTO and viewed it in “Dendrogram” format. Here are the bootstrap values:

Disclaimer for @colewd: the branch lengths on this tree do not reflect the actual number of mutations along each branch, since it is in “Dendrogram” format. Do not falsely claim that this diagram shows a nested hierarchy.

The bootstrap values are extremely low (3-24; avg. 11) as expected from a star tree, and are not nearly as high as the bootstrap values on a phylogeny of real living organisms.

Therefore, Bill’s ‘identical genes’ model cannot explain the nested hierarchy of living organisms (not that anyone except Bill thought so in the first place). But kudos to him for at least advancing a testable hypothesis, even if it was a terrible one. @colewd, would you like to provide another testable hypothesis for how ‘common design’ can explain nested hierarchy without common ancestry?

[misterme987 (Andrew P.)]

@colewd

@John_Harshman

Why would species created at similar times group together?

If you are measuring genes that are reused based on common design and created at similar times they would likely group together.

First, and most importantly, you just repeated the assertion without answering the question “why.” That’s disingenuous, and a mere assertion is not going to convince anyone.

Second, that’s also false. If each ‘kind’ were created with some identical genes, then those genes would produce a star tree, since all of the ‘kinds’ would begin with the same sequence and split off from there. The time that they were created wouldn’t create a nested hierarchy, since the number of genetic changes is reflected in the branch lengths of a phylogeny, not in the relationships themselves.

I just don’t understand how you can be so ignorant about phylogenetics after it has been explained to you so many times…

[colewd (Bill Cole)]

@misterme987

This program generates a new taxon with the same, identical sequence every generation, and mutates it from that point on. In this way, it models the ‘identical genes’ hypothesis with different, identical ‘kinds’ being created at various points in time.

Hi Andrew

Here is the basic logic I used for my claim. If you look at a common gene:

If two or more species split and become isolated that is the same as two different species being created at the same time with the same gene sequence. Both origin methods will diverge in the same way depending on the rate at which mutations get fixed. The divergence is based on reproductive isolation of the populations. A tree pattern can be formed by the timing of these events.

@misterme987

The time that they were created wouldn’t create a nested hierarchy, since the number of genetic changes is reflected in the branch lengths of a phylogeny, not in the relationships themselves

I have assumed that species are paired based on sequence similarity as that is what happens with the trees generated by uniprot. Is this different in your simulations?

@misterme987

@colewd, would you like to provide another testable hypothesis for how ‘common design’ can explain nested hierarchy without common ancestry?

After this discussion is resolved there are other possibilities of causes of the observed pattern.

[misterme987 (Andrew P.)]

@colewd

If two or more species split and become isolated that is the same as two different species being created at the same time with the same gene sequence. Both origin methods will diverge in the same way depending on the rate at which mutations get fixed. The divergence is based on reproductive isolation of the populations. A tree pattern can be formed by the timing of these events.

I literally just proved this claim false by modelling your hypothesis and showing that it did not generate a nested hierarchy. Nothing more needs to be said.

@colewd

I have assumed that species are paired based on sequence similarity as that is what happens with the trees generated by uniprot.

No, nested hierarchy is not the same as differing levels of similarity. As I also proved by modelling this hypothesis, in the OP.

@colewd

After this discussion is resolved there are other possibilities of causes of the observed pattern.

It’s obvious you have no idea what you are talking about, and at this point you’re just repeating claims that I already falsified, without even acknowledging that I tested them.

[John_Harshman]

@colewd

If two or more species split and become isolated that is the same as two different species being created at the same time with the same gene sequence. Both origin methods will diverge in the same way depending on the rate at which mutations get fixed. The divergence is based on reproductive isolation of the populations. A tree pattern can be formed by the timing of these events.

That last sentence is where it all falls apart. The timing of what events? Pairs of species being created? But that doesn’t form a tree pattern unless the created pairs start with the genomes of a previous species that has diverged over time from a previous creation, etc. In other words, what you seem to have described there is simulated common descent. But why would God use the genome of a previous species as a starting point for new ones? If instead he just used the same starting point at different times, you would get a star tree. The only ways to get a nested hierarchy are common descent or creation that purposely simulates common descent.

@colewd

I have assumed that species are paired based on sequence similarity as that is what happens with the trees generated by uniprot. Is this different in your simulations?

This again shows that you have no idea how phylogenetic analysis works.

@colewd

After this discussion is resolved there are other possibilities of causes of the observed pattern.

I’d be interested to know what your other possibilities are, but don’t wait for this discussion to be resolved, because that would require you to learn and understand.

[Dan_Eastwood]

Declaring a unilateral cease-fire on @colewd. I think the point has been made.

[John_Harshman]

If a point is stated in the forest and no one is there to hear it, is it actually made?