Dear TB,
Interesting questions and I have given them a thorough thought for many years.
Fred already responded to the major part and I will respond to:
"2. Something I have wanted to know for years - blue/brown eyes - what are the allele amino-acid sequences/differences/SNP(s)?"
The genetics of eye colour of humans is pretty intricate. It cannot be explained by the application of simple Mendelian genetics. It is more likely that epigenetics determines the differences in colour.
Ever met a person with two distinct eye-colours (eg David Bowie)? In my opinion this can best be explained by epigenetics (=beyond genes). It is known that every individual has several alleles for eyecolour (in fact eye colour genes are completely redundant since they serve "no" function). The expression of the genes that determine the ultimate colour are stringently regulated. The regulation of genes strongly depends on DNA elements in the vicinity of the gene. On has to imagine the DNA spatially; elements within 10-100 kb can easily affect the expression of the genes because of spatial folding of the DNA molecule. In this way, transposable DNA elements are able to affect eyecolour. These elements are thought to be (retro)transposons and Alu-sequences. I think it will soon be discovered that these sequences -- that have always been regarded as junk DNA -- have a crucial function in generating the differences within species. In contrast to what everyone beliefs (=paradigm), I belief that genes -- although the contribute -- do not determine the phenotype of an organism. Gene expression and (thus gene regulation) does!!!!
Best wishes,
Peter
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