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Counter-proof against the molecular clock hypothesis

Grumbler popa0206 at po-box.mcgill.ca
Wed Jul 12 18:02:49 EST 1995

I had written
>> So to make a long story short molecular clocks with such a basis are invariably inaccurate!
>> Graham
>Strange then that myoglobin changes in such a clock-like manner when you
>actually LOOK AT THE DATA.   Something is wrong somewhere, methinks.
Perhaps, off the top of my head I chose a poor example...  but the concept
of the genome as complex "ecology" of interelated structures (3D and 2D;
origins, domains, loops etc.)- in which not just the linear sequence of DNA
may encode vital information for the accessing (transcription) and organization
of DNA but the overal structure of the genome itself (both local and global)- 
is becoming more and more accepted.

SO, in support for a possible reason why in some cases a molecular clock may
be wrong, I provided an example of a mechanism (DNA  repair) which is intimately
involved in mutation rate(basis of molecular clocks) and may be strongly affected by 
chromosome context.

I have not studied the case of myoglobin (or the data used to determine the 
dating scheme) so I may be indeed in error, I can not determine that on the spot
as you have.  

Perhaps the averaging among several organisms (which does happen in the development 
of molecular clocks) may reduce the source of error introduced by differences
in genome context... i.e. ends up in the error analysis.   Since these
clocks are based on fitting a known divergence of two proteins (amino acid differences or
on the nucleotide level) to a "best Guess" of the actual divergence by fossil record, they
work reasonable well in retrospective...but predicative value for determing
possible evolutionary changes in the future is very low. 

So in conclusion accessibility of the genome is a "real" phenomenon which should
be taken in account when molecular clocks are developed... perhaps simply
as a caveat when they are used, or in the extreme a reason to refute a particular
molecular clock.

All is well "methinks"


>> _______________________________________________________________________ 
>> Graham Dellaire			    Snail Mail:
>>                                     Red Cross, Research		
>> McGill University                   Montreal Blood Services	  	
>> Faculty of Medicine                 3131 Sherbrooke St. East         
>> Div. of Experimental Medicine       Montreal, QC, Canada           
>> E-mail: popa0206 at po-box.mcgill.ca   H1W 1B2			   
>> B2XE at musicb.mcgill.ca							   
>> WWW Page: http://www.medcor.mcgill.ca/EXPMED/expmed.html	

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