Re: Non-beneficial Gaps

On Feb 17, 8:38 am, Seanpit <seanpitnos...@naturalselection.
0catch.com> wrote:
On Feb 16, 11:11 am, Glenn <GlennShel...@xxxxxxx> wrote:

http://en.wikipedia.org/wiki/Neutral_mutation

In other words, in must cases this particular substitution would not
have any appreciable effect and would therefore be a functionally
neutral mutation. On rare occasions such a substitution *may* have an
appreciable functional effect and therefore would NOT be a neutral
mutation. This is actually what the author of the Wiki article is
trying to say.

There really is no suggestion here that a neutral mutation can
actually have an appreciable functional change. That's contrary to
the very definition of a neutral mutation. And, that is Richard's
basic misunderstanding of the concept of a neutral mutation here.

Richard is actually right about this. Neutral mutation includes that
which result in phenotypic changes with no effect on fitness.
Hopefully you haven't totally relied on Wiki for your information.

Of course neutral mutations include those that have no signfiicant
result on repreductive fitness. That's one of the definitions of a
netural mutation. The Wiki article does not really suggest
otherwise. The problem here is that the majority of mutations that do
actually affect protein function also affect reproductive fitness to
at least some detectable degree - i.e., they are under the influence
of natural selection. And, of those mutations that change function
without significantly falling under the affect of natural selection,
the vast majority reduce functionality.

Well from above it appears one problem is settling on a definition of
"appreciable". If you consider that means "detectable", then your
claim "If the protein's function has been changed to a detectable
degree, that change is not functionally "neutral" - by definition." is
wrong, and Richard is right. I can easily detect eye color, Sean.
Now your claim that some so called neutral mutations might be under
some selective pressure, yet that doesn't change the meaning of
"neutral mutation", which is what the dispute here is about.

A change in eye color is not invisible to natural selection. In fact,
the vast majority of functionally detectable changes to a protein are
also detectable to natural selection. Very functional changes that you
can detect are completely immune from natural selection. In fact,
some scientist argue that the percentage is essentially zero.

I'll assume you meant very *few* functional changes. Eye color was
just an example, whether really an example of neutrality or not. I may
not easily be able part of an immune system which would defend against
some pathogen that doesn't currently exist in my environment, but
changes as a result of the responsible gene(s) mutations are at least
in principle "detectable". I can't just accept your word for multiple
eye colors having a "fitness value" either, absent some references,
anymore than I can accept Richard's word for 95% of mutations being
neutral without evidence. But you seem to be arguing against the
validity of neutral mutation more than for a "correct" definition,
which has been my concern. I happen to share your scepticism, however
functional changes are not automatically under the gun of natural
selection, or "adaptive".
Richard seems to have thrown a new twist into the definition today
though, including "fixation" in the definition, from his referenced
PNAS article. Curious to see the abstract state: "The prediction,
however, has not been verified by observation.", although the article
is from 2000. I don't think much has changed in the neutralist world
since then, though. From the Wiki http://en.wikipedia.org/wiki/Neutral_theory_of_molecular_evolution,
"Thus such tests contribute to the ongoing investigation into the
extent to which molecular evolution is neutral (Leigh 2007)", which
leads me to think that you, Richard and the Wiki on that most
mutations are neutral may not be based on as firm a ground as some
would like.

Leigh 2007 is an interesting read, by the way:
http://www.blackwell-synergy.com/doi/pdf/10.1111/j.1420-9101.2007.01410.x

And from the 2003 textbook "Evolution"
http://www.blackwellpublishing.com/ridley/tutorials/Molecular_evolution_and_neutral_theory3.asp
"Most mutations are deleterious".

http://www.niaid.nih.gov/dait/cross-species/page5.htm
"Neutral allele theory proposes that "most mutations are deleterious"

http://jb.asm.org/cgi/content/full/182/11/2993 (2000)
"However, since most mutations are deleterious, random mechanisms that
increase mutation rates also result in genomewide DNA damage"

http://www.science.org.au/future/hilton.htm
"Most mutations are deleterious, reducing protein function."

http://www.genetics.org/cgi/content/full/167/2/1031 (2004)
"As the number of mutations increases, average homozygous viability
will decrease, because most mutations are deleterious, but average
heterozygous viability may increase, due to the increasing number of
partially dominant beneficial mutations."

http://biology.plosjournals.org/perlserv?request=get-document&doi=10.1371/journal.pbio.0030381
(2005)
"However, because most mutations are deleterious, mutation
accumulation experiments tend to cause reduced fitness"

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1617134
(2006)
"It is widely believed that most mutations are deleterious, that is,
they harm the organisms in which they occur."

http://www.bio.indiana.edu/facultyresearch/faculty/Lynch.html
"Although mutations provide the ultimate material upon which natural
selection depends, most mutations are deleterious, and in certain
population settings, can lead to a substantial fitness load."

http://www.emunix.emich.edu/~rwinning/genetics/mutat.htm
"On the other hand, most mutations are deleterious to the individuals
in which they occur."

http://www.sciencemag.org/feature/data/pharmacia/1999/Cascalho.dtl
http://www.nature.com/hdy/journal/v84/n4/abs/6887250a.html
http://www.genetics.org/cgi/reprint/167/2/1031.pdf (2004)
"most mutations are deleterious"


.

Relevant Pages

  • Halting NS experiment
    ... None of them can halt natural selection within one population. ... the proposition I have provided for Total Darwinian Fitness ... effectively neutral mutations and positively selected mutations. ... then remove the control from stasis and do the measurements including ...
    (sci.bio.evolution)
  • Re: Non-beneficial Gaps
    ... Read "A neutral mutation may or may not affect the resulting protein" ... mutations to *all* mutations. ... neutrality" is relative reproductive success. ... function are allowed to pass through the filter of natural selection ...
    (talk.origins)
  • Re: Non-beneficial Gaps
    ... mutations being essentially neutral. ... A different protein does not necessarily translate into an appreciably ... Neutrality basically means that natural ... do *not* affect function, yet at the same time accepting that they ...
    (talk.origins)
  • Re: On the Origin of a Species
    ... If isolation results from drift, we expect equal change in each ... population will continue to fix neutral mutations at the mutation ... Another way of looking at it is that, assuming neutrality, the number ... the number of fixed differences ...
    (talk.origins)
  • Halting NS experiment
    ... > one population over many generations can natural selection be halted. ... > the proposition I have provided for Total Darwinian Fitness ... > effectively neutral mutations and positively selected mutations. ...
    (sci.bio.evolution)
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