Macro vs Microevolution: side comments on Phylogeny

A cursory search finds that there are gorillas with white sclera as a naturally occurring variation.

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Iā€™d say species selection is a form of natural selection, just at a much higher level than individuals. The difficulty with invoking it is that the entities being selected die and are born much less often than do individuals.

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And Iā€™d say itā€™s analogous to natural selection. Sometimes it can operate very quickly, as in the first 20 minutes of the Cenozoic.

It IS silly, but thatā€™s just the point.

Human language is a monster apomorphy (unique character), doubtless distributed over many hundreds or thousands of protein-coding genes and non-coding regulatory elements.

The color of sclera? A VERY minor phenotypic difference, subject to natural variation overlapping the human character (white), at least within gorillas. Probably a simple matter of downregulating pigment deposition during eye development. Maybe a single regulatory locus?

So I was offering a spectrum of open evolutionary puzzles: one big, one tiny and approaching the silly limit. The tiny puzzle appears no easier to solve than the big one, however. My main claim? Similarity of nucleic acid, if one wants to explain descent with modification of phenotypes, is exactly the wrong place to look.

To those who expressed shock that I appear to deny a genetic basis for differences between humans and chimps ā€“ you are misreading my skepticism. There exists an organismal basis for the differences, of which DNA is certainly part of the story.

But only a part. Saying ā€œDNA is the only thing that matters,ā€ however, begs the question in ways which are ultimately destructive of biological knowledge. A dispute for another day. Over and out, thanks for the discussion.

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Iā€™ll pop in to this thread to note that Paulā€™s statement here is eminently reasonable and also wholly consistent with macroevolutionary change being merely the result of accumulated microevolutionary change.

As long as we agree that the differences in the ability to use language is due to genetic differences then we are once again back to asking which mutations you think microevolution could not produce.

They both have the same solution. Mutations. Why do we have big brains that can use language? Mutations.

Organisms are different because the DNA sequence of their genomes are different.

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I think what @pnelson is trying to say is that that is overly reductive. I recall reading of an experiment where they took the nucleus from the zygote of one fish species and used it to replace the nucleus in the zygote of a different fish species (or something like that). The resulting individual developed and had some features of both species. So it isnā€™t just DNA; the other parts of the organism affect how the DNA is expressed and how the organism develops.

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Is it? It seems more like vague nonsense to me. If it means anything, itā€™s alluding to some means of inheritance other than DNA. But he refuses to identify that other means. What is the ā€œorganismal basis for the differenceā€ if it isnā€™t a difference somewhere in the genome? This seems just another version of ā€œwe donā€™t know everything, therefore Godā€.

All true, but the other parts of the organism arenā€™t inherited over the long term and therefore canā€™t be the cause of differences among species. Now of course the cytoplasm has a genome all its own, the mitochondrial genome, which must be taken into account. But otherwise all its contents are either proteins produced by translation of the nuclear genome, RNAs produced by transcription of that genome, or other molecules produced by metabolic processes that themselves result from proteins encoded by the nuclear genome. Long-term inheritance is the crucial point. All else is obfuscation.

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What happened in that example is the cytosolic proteins and RNAā€™s from the nucleus which was removed interacted with the new nucleus. What you got was the interaction of products from two genomes, and all of those interactions do reduce down to the DNA sequence of those two genomes. Environmental cues also play a role, but once again the reaction to those cues are determined by the sequence of DNA in the genome. Sunlight may cause us to tan, but the ability to tan is a direct result of the DNA in our genome.

@John_Harshman also mentions, you need to figure in inheritance and reproduction. You start out as a single cell. Just one cell.

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Are you serious? Just because we havenā€™t studied the developmental basis of sclera colour in enough detail to identify the relevant loci, that means itā€™s just as difficult as the question of human language?

If weā€™re interested in understanding the genetic basis of phenotypic differences, of course we go looking for dissimilar sequences. That is completely unrelated to the idea that we can support common descent using patterns of similarities.

The existence of apomorphies doesnā€™t somehow negate the existence of synapomorphies.

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As @T_aquaticus explained, it really isnā€™t.

I agree with everything @T_aquaticus wrote on this, but just to emphasize this important point: obviously, a nucleus alone doesnā€™t do anything, but everything cytoplasmic in that zygote was at some level, the product of the nuclear DNA that was removed.

One exception to that is the mitochondrial genome, as @John_Harshman noted. Since most mitochondrial proteins are encoded by nuclear DNA and imported, there will be differences there that would undoubtedly affect development. This and the above reason are why the premise of Jurassic Park, in which frog egg nuclei were replaced with dinosaur nuclei, was unlikely to yield anything viable.

There also are components in the zygoteā€™s cytoplasm that are the product of the motherā€™s, not the fatherā€™s, DNA, including some from maternal alleles that didnā€™t make it into the eggā€™s nucleus during meiosis.

Thereā€™s also what we used to call imprinting and now understand to be methylation, in which thereā€™s sex-specific repression of chromosomal sections.

The point Iā€™m trying to reinforce here is that what you initially presented as an exception, and three other exceptions, can still be reduced to DNA and ā€œprove the rule.ā€

This is also why ā€œhuman life begins at conceptionā€ is ironically overly reductive.