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[Phys-L] Re: ultrametricity +- evolution



I wrote:

We can very precisely quantify "how far back" by counting the number of
mutations in the DNA; less precisely that corresponds to _time_ back in
history.

R. McDermott wrote:

So I presume, then, that some assumption has to be made as to a "mutation
versus time" ratio?

1) Any such assumption is optional.

2) Any such assumption is approximate, i.e. less than precise, as I stated.

Do you know how that has been determined?

Calibrate the number of mutations against radioisotope dating of the fossil
record.

I'm just trying to understand the
process here. The tree diagrams seem to me to be based on the assumption of
what some refer to as macroevolution; ie, there is a common ancestor,

Absolutely not. That's my point. The ultrametric structure would have
told you there was a tree structure even if you hadn't been expecting
it -- let alone assuming it.

so
genetic "distance" equates to the passage of time,

No. Mutation distance is primary; time is secondary, optional, and
approximate.

therefore if we diagram
the genetic distance it is also a diagram of speciation over time.

Optionally and approximately.

We know absolutely that different species mutate at different rates.
The rate of mutation is under biological control, due to DNA proofreading
enzymes and the like. To say the same thing more pointedly: the
rate of evolution is under evolutionary control.

My
question, then, is: What if that basic assumption is not correct?

Re-read what I said about what is precise and what is not precise.


I'm inclined to agree that this is the best scientific
explanation we have for what we see,

:-)

I'm simply concerned about
categorically stating that no other possibility exists (which is the general
implication).

I have no idea how to respond to that. I am responsible for what
I said. I am not responsible for what other people may have said,
whatever that is. I didn't state that no other possibilities
exist; I didn't "imply" that no other possibilities exist; indeed
I quite explicitly left that door open. How is it possible for me
to say one thing and "imply" the opposite?

I'm concerned that in an attempt to understand, we may have
IMPOSED an order on nature that is an illusion, if only in part.

But I didn't impose any such thing. The ultrametricity is there. Anyone
with eyes can see it. It is not a matter of opinion; you can write a
computer program to check it impartially.

Would a broad base set of coexisting and evolving organisms
remote in time also generate what we observe? If not, why not?

Be careful: I very explicitly said that all _extant_ species
shared a common ancestor. I also explicitly said that for all
I know, there may at one time have been multiple independent
lineages but all of the Others died out.

I repeat (again) that there may have been a "base set" but that
evidently only one member thereof contributed to the _extant_
species. The Others (if any) died out.

The evidence for this, as previously mentioned, includes the
chiral sugars and other chiral biomolecules.

Every time you introduce an independent lineage, you have a 50/50
chance that it will be based on right-handed (as opposed to left-
handed) sugars. Handedness is preserved by inheritance, but there
is no reason to expect correlation across _independent_ lineages.

If you imagine there are N independent lineages all of which
"accidentally" have the same handedness, that's implausible by
a factor of at least 2^(N-1). (I imagine the factor is actually
much larger than that, if you consider other inherited quirks.)

I say again that although this issue is fascinating, and is consistent
with the main ideas of evolution, it is not a necessary part of the
discussion of evolution, and if it were disproved tomorrow there
would be little if any disruption of modern biology.

The bottom line remains:

1a) From time to time, new species evolve from pre-existing species.
This is true and important.

1b) From time to time, old species go extinct.
This is true and important.

2) Many of the observed facts about biology can be understood in
terms of evolution and not otherwise.
This is true and important.

There is overwhelming DNA evidence and macroscopic evidence of this.
There is a comprehensive logical framework for understanding this.
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