Re: Pitman numerology

On 8 Dic, 18:54, Seanpit <sean...@xxxxxxxxx> wrote:
On Dec 8, 9:30 am, Vend <ven...@xxxxxxxxxxx> wrote:



How do you get from Ala-Ala-Ala-... to Met-Met-Met-... in a single
mutational event?
It would require an inserition or substitution of a large sequence.

Or a frame-shift mutation - all of which can happen.

I don't thin there is any frame-shift mutation that allows such
chance, and large insertions and substitutions must copy dna from
somewhere else thus they are not arbitrary.

Given a repeating DNA pattern, a frame shift mutation can indeed
produce a completely different repeating sequence using a different
residue in the sequence.

Alanine can be coded by GCT, GCC, GCA, GCG
Methionine can be coded only by ATG.
No shift can transform a repeating string of Alanine-coding codons
into a string of ATG.

 And, although large insertions and
substitutions must copy DNA from somewhere else, the copying process
itself, as far as the location to copy, is indeed arbitary.  That is
why it can be classified as a truly "random" mutation.

It's random but the inserted or substituted sequences are not
equiprobable and are not sampled from a complete sequence space.

That's the whole problem here . . .  There is an exponential drop in
the likelihood that a small mutation will be able to cross a linearly
increased Hamming Distance in sequence space.

A small mutation crosses a small mutation distance, by definition.
The Hamming distance in aminoacid sequence space crossed can range
from 0 to N.  What is the point?

I meant to say a small number of mutations.  The odds that a
particular Hamming distance between seqeunces A and B will be crossed
by one or two mutations drops exponentially as the Hamming distance
increases linearly.

Proof?

You see, the odds of success vis RM are very much dependent upon the
ratio of targets vs. non-targets in sequence space.

No it depends on their location and the shape of the fitness landscape
around them.

A target island is defined by everything on the island - the whole
landscape of sequences that make up the beneficial island.  Each and
every sequence on the island is defined as a "target".

Now, island clusters of beneficial sequences in sequence space have an
unknown location.  That's the whole point here.  Sure, if the island
was closer, it would be easier to find.  But, what are the odds that
the actual location of a target with an unknown location are going to
be "favorable" to discovery in a given amount of time?

It depends on their location.

Yep - except the actual location is unknown.

Since we know that assuming that they
are uniformly distributed is unrealistic, we can't predict anything
without a realistic estimate of their distribution.

You can't assume anything else when it comes to finding targets with
unknown locations.  The best you can do is assume a uniform
distribution.

If the targets were uniformly distributed and scarce, we wouldn't
observe evolution.
We observe evolution in action and historical data which is best
explained by evolution, therefore it's reasonable to assume that they
aren't uniformly distributed (or they aren't scarce).
The assumption is falsifiable.

If you deny that assumption then the burden of falsifying it is on
you.

(Hint: get a large database of protein sequences, possibly with
corresponding DNA sequences.
Run conventional statistical tests for uniform distribution on them.)

 Could the reality be that the actual location is closer
than the uniform distribution assumption?  Sure, but it could also be
farther away just as easily.

 Those odds
depend upon the ratio of targets vs. non-targets. . .  just as you
originally noted yourself.

I don't think I did.

You did mention the fact that you have to include a factor for the
likelihood of a certain number of mutations being able to do the job -
- did you not?

Please elaborate.



.

Relevant Pages

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