On Thu, 27 May 2004 16:40:43 +0000 (UTC), 
Anon.  wrote:
> Larry Moran wrote:
>> On Tue, 25 May 2004 23:48:33 +0000 (UTC), 
>> Anon.  wrote:

[snip]

>> Why not give it a try? We already have an effective and quantitatvie way of 
>> measuring evolution by looking at changes in DNA sequence. If you want to 
>> find a more effective measure then let's see what you come up with. 
> 
> The first eigen value of the transition matrix for the changes in the 
> phenotypic traits?  You can define the process in either discrete or 
> continuous time.  You can even use a hierarchical model so that you can 
> include discrete traits.

Damn! I wish I thought of that. It's so sbvious.

> It's not clear to me that simply looking at changes in DNA sequence is a 
> good measure of evolution - how do you deal with polymorphism?

Polymorphisms are evolution in progess. How do you deal with them?

> Hmm, Actually, you can use the same sorts of models as I've suggested 
> for phenotypic traits.
> 
> So
>> far, all I've seen is some warm fuzzy feeling that
"phenotypic change"
>> should get a higher score in order to restore the supremacy of natural
>> selection as a mechanism of evolution. Can you turn that subjective
>> feeling into a scientific definition that we can examine?
>> 
> That's a mis-representation - I'm not arguing that phenotypic change 
> should get a highe score, but rather that there is no obvious single 
> score, so whatever measure you use is subjective.  Why remove phenotypic 
> traits from evolution?

Because nucleotide changes are mutations and because phenotypic traits are 
the result of, not the cause, of (some) mutation?

>> Let's take the evolution of humans and chimps as an example. We already
>> know that they differ by about 2% in DNA sequence. How would you evaluate
>> the "phenotypic changes" along each lineage in order to
arrive at some
>> quantitative measure of the amount of evolution in each species from
>> the time of the last common ancestor? How much of that is due to natural
>> selection?
>> 
> That's actually something I'm starting to work on.  Over short time 
> scales, one can compare Fst and Qst (e.g. Palo et al. 2003 Molecular 
> Ecology, 12: 1963-1978) but some more work needs to be done to find a 
> more quantitaive formulation.  I've started work with a colleague on the 
> variation between species, but I'm not sure how that will pan out.

Let me know if you get anywhere and we'll see if the scientific community
will agree to change the definitions.



Larry Moran
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