lamoran{at}bioinfo.med.utoronto.ca (Larry Moran) wrote in
news:c92cvu$3te$1{at}darwin.ediacara.org: 

> On Tue, 25 May 2004 23:48:32 +0000 (UTC), 
> William Morse  wrote:

(snip)

>> I know there has been a previous discussion on the definition of
>> evolution, and in many ways I can agree with the definition of any
>> change in gene frequency as evolution, but I'm having difficulty
>> resisting the temptation of playing devil's advocate. 
 
> No problem, playing devil's advocate can be a very effective learning
> tool. Let's see if we can learn something ....
 
>> Now first I would like to clarify something. Bob's original agreement
>> was that drift is unquestionably the main mechanism of change at the
>> sequence level. I also agree with this. However change at the
>> sequence level is not evolution by the generally accepted definition
>> of evolution as change in "gene" frequency, at least not until the
>> change in sequence affects the function of the "gene".  
 
> Evolution is the change in frequency of *alleles*, not genes. Alleles
> are any differences in base sequence at a particular position in the
> genome. This definition of alleles has evolved from the original
> definition since we've learned that lots of DNA isn't part of genes. 

A very wise man has said the following: 

"When biologists say that they have observed evolution 
they mean that they have detected a change in the frequency of _genes_ in a 
population." (emphasis added)

The same wise man also suggested the following definition:

"Evolution is a process that results in heritable changes in a population 
spread over many generations."

(And just in case you get any ideas, if you start quoting things I have 
previously said back at me I'll come and stuff your hard drive full of 
peanut butter. Toronto ain't all that far from Syracuse :-)


Now you may call it quibbling, but in my book an SNP with no change in 
function does not qualify as an allele.It is not "a change". In my defense 
I quote the following definition for allele:

"one of two alternate forms of a gene that can have the same locus on 
homologous chromosomes and are responsible for alternative traits;"

Note the emphasis on traits. Again, a non-functional SNP doesn't qualify.  
 
>> Now as to actual changes in gene function, as far as I know there is 
>> still debate as to the relative importance of  drift vs. selection in
>> gene frequencies,  so I would have to take issue with your 
>> characterization "by far", although you may well be correct about 
>> "majority". 
 
> If you want to redefine evolution so that it only refers to changes in
> the functions of genes then that's a possible way of restoring the
> supremacy of natural selection. I think this is carrying devil's
> advocacy too far but let's see where it takes us. Can you give me a 
> more precise definition of evolution that your devil would like to
> defend?  :-)

Now I can't define evolution only as changes in functions of genes unless I 
can define genes, and I don't really want to try to do that. Furthermore, a 
change in a regulatory sequence would certainly also qualify as evolution 
in my book. However I do not see a substitution of alanine for glycine in a 
region far from the active site of an enzyme as necessarily contributing 
anything to  evolution. So let's try this:

    	Evolution is a heritable, statistically significant change in a     
	population of organisms that  can be detected without using either     
	DNA or protein sequence data.

This sort of definition gets away from the problem of trying to define a 
gene and from assuming that "junk" DNA is actually junk. It has the 
advantage of including non-morphological changes, since I can presumably 
detect say a 5% difference in Km for a dehydrogenase even if it doesn't 
affect morphology. 

Now under this definition, I am guessing that while the combination of 
neutral mutations and sampling error may still comprise the majority of 
evolutionary change, it will be a tight race with natural selection.  

 
>> But in either case:
>> 
>> Since the extent of drift due to sampling error is dependent on
>> effective population size, and since effective population size is
>> dependent on the niche, and since selection pressure is also governed
>> by the niche, it is clear to me that ecological niche development is
>> the main mechanism of evolutionary change.
 
> The overall rate and extent of evolution by random genetic drift is
> independent of population size. Your devil seems to be redefining
> random genetic drift as well as evolution. Can you give me his new
> definition of random genetic drift and the new population genetics
> equations that support his statement?

I had a rant about this subject recently, and it seems to be rearing its 
ugly head again. Are you including sampling error as part of drift, or 
defining drift as just neutral mutations? My statement on population size 
dependence only applies to sampling error - which is in fact exactly what I 
said ;-) The population genetics equation for this type of drift is:

 delta q = pq/2N

(note that my reference for this is Wilson (1975), so I am risking putting 
foot in mouth, but that won't be anything new)(And also note that this is 
based on the definition of an allele to include SNP's :-(  )

Last time I checked my basic algebra textbooks this equation would indicate 
that drift is in fact inversely proportional to population size.


> Niches are vastly overrated but they are popular among the adaptionist
> crowd who believes that environmental change drives evolution. Can
> your devil give me an estimate of the total amount of evolution that
> is "driven" by niche development as opposed to evolution that occurs
> in the absence of any significant change in niches? Does your devil
> believe that natural selection can only occur when species move into a
> new niche? 

Apparently you are accusing adaptationists of being niche-pickers :-)

But I am going to put this back on you. Since in fact sampling error is 
dependent on population size, which is determined by the niche, all of this 
form of evolution is dependent on niches. It still may not be "driven" by 
niche development, since a stable niche that results in a small effective 
population size will still yield evolution due to sampling error drift. 
This was the original thrust of my statement - which was admittedly bait to 
get a comment from you - that even though drift is the proximate cause of 
the change in "effective allele"  frequency, the ultimate cause is the 
niche that results in a low N. What I would ask you is, what is the total 
amount of sequence change  that is due solely to neutral mutation, and of 
this change, what is the likelihood that a cumulative series of  SNP's that 
are individually neutral will result in an effective change in a trait. 

I would like to spend more time on the subject of niches, but this is 
getting long and that subject might be better treated in a new thread.


Yours,

Bill Morse
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