Genetic evidence *against* common ancestry

[misterme987 (Andrew P.)]

@colewd

I think you need to look at actual data to confirm your assertion. Over deep evolutionary times we are seeing different patterns depending on the conditions. There is a lot of variation depending on the conditions.

Just look at any phylogenetic analysis. It’s extremely evident that we don’t see a star tree with different ‘kinds’ splitting off of the same ‘starting point.’ For one, based on my very limited understanding of phylogenetics, the bootstrap values would be much lower for nodes above the ‘kind’ level if they weren’t related. That’s not what we see.

@colewd

If we selected 6 living organisms that theoretically split from a common ancestor 400 million years ago and selected a mutationally tolerant gene would we predict a star tree based on comparing that genes sequence?

No. You seem to be purposely misunderstanding what I and others have been saying. If each ‘kind’ immediately diverged from an identical starting point, then we would see a star tree. In contrast common ancestry does not predict a star tree, but a nested hierarchy, because that reflects the actual relationships between organisms if common ancestry were true.

[colewd (Bill Cole)]

@misterme987

No. You seem to be purposely misunderstanding what I and others have been saying. If each ‘kind’ immediately diverged from an identical starting point, then we would see a star tree. In contrast common ancestry does not predict a star tree, but a nested hierarchy, because that reflects the actual relationships between organisms if common ancestry were true.

I think you clarified what a star tree is. Thanks. I also think you clarified what is causing it: Independent divergence from a single starting point.

What we don’t yet agree on is that comparing certain nodes under the common descent model could produce a star tree. These nodes would be something like comparing a common protein found in fish, reptiles, birds and primates.

Since the star tree is caused by the same starting point and independent divergence I propose if we go back in time and compare mutationally tolerant sequences that diverged a long time ago the nested pattern should look more like the star pattern then more recent sequences. We can test this hypothesis.

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[Faizal_Ali]

@colewd

Since the star tree is caused by the same starting point and independent divergence I propose if we go back in time and compare mutationally tolerant sequences that diverged a long time ago the nested pattern should look more like the star pattern then more recent sequences. We can test this hypothesis.

Wow, what a great idea. I can’t believe no one has ever thought of this until you did, just now.

[Faizal_Ali]

We should start a betting pool on how many posts until Bill again completely forgets what a star pattern is.

[T_aquaticus]

@colewd

Since the star tree is caused by the same starting point and independent divergence I propose if we go back in time and compare mutationally tolerant sequences that diverged a long time ago the nested pattern should look more like the star pattern then more recent sequences.

Let’s say we find an orthologous intron shared by humans, chickens, and chimps. Would you expect the human and chicken sequence to have about as many differences as the human and chimp sequences?

[T_aquaticus]

More for kicks since it will sail above @colewd’s head.

People can check out the pairwise alignment scores for cytochrome c at Homologene:

HomoloGene - NCBI

The pairwise alignment scores can answer a lot of questions about whether there is a nested hierarchy or a star phylogeny. For example:

human v. mouse = 90.5% similarity
human v. chicken = 81.6% similarity

What would the mouse v. chicken similarity be, and why? What kind of arrangement of species could we use to make this kind of prediction?

[misterme987 (Andrew P.)]

@T_aquaticus

The pairwise alignment scores can answer a lot of questions about whether there is a nested hierarchy or a star phylogeny. For example:

human v. mouse = 90.5% similarity
human v. chicken = 81.6% similarity

What would the mouse v. chicken similarity be, and why? What kind of arrangement of species could we use to make this kind of prediction?

I’m not sure this goes against @colewd’s hypothesis, actually.

His “created with identical genes” hypothesis is rather odd in that it allows each kind to be created with the same sequence, but at different times. So, for example, the “human” and “chimp” kinds might have been created with identical cytochrome c 6 mya, whereas the “chicken” kind was created with the same cytochrome c sequence but 12 mya. In that case, human and chimp cytochrome c would be twice as different from the chicken sequence than they are from one another.

The hypothesis is still falsified by the fact that these sequences form a nested hierarchy. But this particular piece of evidence doesn’t actually seem to contradict it.