[Taxacom] Molecules vs Morphology

[Jason Mate]

An initially simple argument is becoming increasingly complicated. It seems that we are arguing over the dichotomy 
of the organism: the expression of the information (phenome) versus the information and its transmission (genome).
If my email is slightly disjointed I apologise but some of the ideas are not easily conceptualised in writing (or
I am incapable).

("respond" here stands as change under Darwinian Evolution of a panmictic population)

The "environment" (the combination of all the forces acting on the organism)
acts on the "organism" (=phenotype) and therefore in an indirect manner over
the genome. The genotype, being the respository of information "responds" indirectly (changes in the phenotype)
to the "environment" through variation of the information it contains. 
Hence there is the possibility of mismatch, of evolution of the genome but not
the phenotype (that we can detect of course) or viceversa, where the phenotype
changes but not the genome. Also there is chance involved of course (drift, meteors...). 

Phenotypic plasticity is illusory evolution (heritable change at any level of the organism) 
as it represents the variable expression of the genotype. I can vaguely recall research regarding epigenetic effects
(in humans but it is probably widespread). Alas they appear to pertain to the expression  of the genome and since the 
cellular machinery is  conveniently supplied by the parents this sort of information transmission is neither suprising
nor important for phylogenetics. In the end the phenome´s full range of possibilities are encoded in
the genome and expressed more or less accurately (this is where Richard´s "envirome"comes in most likely)
more or less effectively, by the genotype. Alas part of the phenome may be encoded in memes (as mentioned by Kip).
However memes are not "fixed" in the organism but have a "life" of there own. Hence they can be transmitted horizontally
replaced or lost, often many times within the life of a single organism. Their use in infering phylogenies is fraught with risks.

Richard regards "genetic change through generations without any obvious change in 
morphology . . . yes that is evolution" a step too far. I too am uncomfortable calling, for example, random mutations
in a microsatellite (totally useless probably) as evolution. But the problem is that it is heritable 
change and we can´t really say if it influences the organism or not. After all the physical genome is also part of the 
phenome and changes in its structure might be important to the organism´s (ergo its information) ability to endure.
As for a definition of evolution I work under the assumption that evolution (="change") produces biodiversity (=more information) through 
divergence (="speciation") by the constant action of the "environment" and it is fed by variation (pot luck changes). 
So, although the interface of the organisms in all their variation (biodiversity) is interesting from the point
of view of understanding divergence it doesn´t susbtitute the role of studying the changes in the genome to infer relationships.

So, going back to our peppered moth. If our intergalactic phylogeneticist only came to earth only to "do a tree", 
he wasted his time, for what is the use of a tree? It is the information we append on it and try to understand via the phylogeny that
matters. Same goes for barcoding.

Best

Jason

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