Several questions on evolution, and mutation (rate)

Doug Yanega dyanega at denr1.igis.uiuc.edu
Sun Sep 8 21:56:02 EST 1996


I'll respond to Ram and Don Cates both here...

In article <50vl3j$bl5 at hecate.umd.edu>, me at ram.org wrote:

>Because natural selection does not explain how you can get from
> zero frequency to low frequency.  This is what I call evolution.

That is not the only thing that evolutionary biologists call evolution.
Natural selection is evolution also, as is drift.

> Natural selection has nothing to do with origin of a new trait, which
> I call evolution.  Call natural selection a form of evolution is
> confusing and misleading.

No, it is the STANDARD DEFINITION. How many times do I have to BEG you to
open up a textbook on evolutionary biology and READ the definition????

> Yes to the origin of new function (i.e, the new function has
> evolved).  

No. Evolution is a property of a population - "functions" do not evolve,
they arise. Evolution is the underlying change in the genetic material,
not the function that *results* from that change.

>How can you call, a protein that remains the same, that
> simply increases its prescence in the population, evolution? 

Because that is the *definition* of evolution. Look it up, please.

>What is
> evolving?  The protein? 

No, the population. Only populations evolve. Read the definition.

> The protein has stopped changing---it's just
> being spread through the population.

Right. That's what evolution is.

> That's your definition, which I obviously disagree with. 

It's not MY definition, in the sense that I did not coin it or alter it or
twist it in some manner to suit my purposes. I learned it that way 20
years ago, and every text on evolutionary biology I've ever read or taught
from uses essentially that same definition. I can't express how sorry I am
that you have chosen to make up YOUR own definition, which *I* find
"confusing, misleading, and non-illuminating". Show me a textbook that
uses your definition, explicitly, and I'll be content to leave you in
peace. You can't go around coining new definitions based on your own
personal view of what makes sense - unless, of course, you choose to
*publish* your new definition, and get the basking of the scientific
community. 

>Here's a scenario: there's
> a gene duplication, one of the genes becomes inactive (due to
> mutations), one of the genes keeps mutating for a while, and finally
> the protein it produces gains new function.  Would you call this
> entire process "mutation"? 

Yes, by definition. 

> How about: a foreign piece of DNA is
> incorporated into the chromosome, mutates, and the resulting protein
> gains a new function.  Would you call this entire process "mutation"?
> I think that's misleading too!  It's clearly a lot more than
> mutation.

That's lateral gene transfer followed by mutation. All your talk of
*function* is utterly irrelevant unless it affects selection. Otherwise
there is nothing in any definition of evolution I have ever heard in which
the word or concept of "function" appears.

> you
> want to generalise mutation so much that you hide the terms "gene
> duplication", "crossover", etc., all into mutation. 

Actually, all of those ARE types of mutation. Does the term "conceptual
hierarchy" have *any* meaning to you whatsoever?

> This is as
> misleading as calling something like natural selection evolution. The
> point is that natural selection by itself doesn't change the nature
> of the gene/protein being selected.  It spreads that SAME gene/protein
> through the population.  Evolution is the origin of NEW genes/proteins.

In your unique, idiosyncratic, unpublished definition, yes. Try to get it
past a peer review committee that way, and write back and tell us all what
they said, please.

In article <50vle9$cu9 at canopus.cc.umanitoba.ca>, cates at cc.umanitoba.ca
(Don Cates) wrote:

> (Ram Samudrala)
> >>> Well, it's one use of the word.  I'd call the entire process, of a new
> >>> trait arising from zero to non-zero frequency (via mutation,
> >>> crossovers, magic, whatever) as evolution of that trait.  I'd call the
> >>> spread of it through the population natural selection (if that was the
> >>> mechanism of the spread). 
> 
> (Doug Yanega)
> >>I have several texts on evolutionary genetics, not ONE does not call the
> >>latter process evolution. Natural selection is a *subset* of the possible
> >>modes of evolution.
> 
> [snip]
> 
> Let's see if I understand what you mean.  I will give some examples and
> my understanding of what your interpretation woiuld be.  Then I will
> explain why I think you would be wrong. 

If they are the same as Ram's explanations, I can see that it simply comes
down to whether you prefer your own personal defintion of evolution to the
general use of the term in the scientific community, and you should not
bother without giving me a PUBLISHED reference to the definition you are
using.

>If I am wrong about your
> interpretation I am sorry but it is an honest (possibly  flawed) reading
> of your post.
> 
> There is some change in function of a gene. You call this evolution. 

Strike one. As I say above, there are NO definitions of evolution which
relate to function. If there is a change in an allele, then it is
evolution, because a new allele has arisen. If an allele changes in
frequency, whether it started at zero frequency or not, it is called
evolution. Evolution is a term that incorporates ALL modes by which
allelic frequencies change, not just a selected one or two.

> What if the change was not beneficial, but neutral? Would you say that
> evolution took place? For me, it's only evolution if the change gets
> passed on to a new generation.

Close, but not quite. If there is a neutral mutation and a new allele
results, then evolution occurred. If this is not passed on to the next
generation, then the frequency has gone back down to zero, and evolution
has resulted in the loss of that allele. Evolution is not just gain, gain,
gain. It is *change*, whether it is positive, negative, and whether or not
it starts or ends at zero frequency, and it is not change in *function*,
it is change in *frequency*.

> What if the change was lethal? A literal reading of your definition
> would still call this evolution. I  don't *think* that you mean this. I
> certainly don't know anyone who *would* call this evolution.

Any evolutionary biologist familiar with the use of the term. Just because
a new allele doesn't remain long in the population does not mean that for
the brief time it was present, the population did not evolve.

> But then what of the beneficial or neutral change that fails to spread
> because of chance? Do you call *this* 'evolution'.

Yes, it is called "genetic drift" and is one of the other prominent
evolutionary modes besides natural selection. Look it up in any
evolutionary text.

> If so, I don't agree
> and do not believe that many would agree. 

You're entitled, but I really do wish you'd read up on these things before
muddying the waters. For every hour I sit here typing and you sit there
reading, you could be learning a lot more by simply opening a book. Try
virtually anything with the words "population genetics" in the title.
There are far, far more people who agree with me than there are in your
private camp. Like I said above, just try publishing your definition and
see how many reviewers pat you on the back and say you've done biology a
service by challenging the established order. 

> So by my reconning, 'evolution' requires both
> the change and the spread and your definition won't  do.

In what way does "a change in the frequency of alleles in a population
between generations" NOT accomodate either the appearance of a new allele
or its spread? That's precisely the point - it allows for BOTH of them,
whereas you and Ram seem to prefer that it only be restricted to ONE of
these steps. What, pray tell, do *you* then use as an all-inclusive term
for all of the different methods by which a new allele changes its
frequency once it has arisen? For me, the task is simple. You, having
pre-empted "evolution" in your private lexicon to mean something else
entirely, are forced to coin a new word if you want to refer to these
processes in the aggregate.
Sincerely,

Doug Yanega     (dyanega at mail.inhs.uiuc.edu)
Illinois Natural History Survey, 607 E. Peabody Dr. 
Champaign, IL 61820  USA  (217) 244-6817 fax:(217) 333-4949
affiliate, University of Illinois Dept. of Entomology
  http://www.inhs.uiuc.edu:80/~dyanega/my_home.html
"There are some enterprises in which a careful disorderliness is
    the true method" - Herman Melville, Moby Dick



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