livescience: Another model

When I set out to do realign the genetic code, it was almost like playing a game of sudoku. The intention was to see if there was a way to simplify the way the code was represented as an answer to some who claimed that the code was too complex to have evolved on its own. Now that it looks so shockingly simple, some might claim that it is so perfectly simple that only a designer could have made it. This I cannot agree with, it's not perfect whatever that may mean, but simple physical and chemical forces appear to sufficiently explain the evolution of the code based on the material that was available at the time. There are countless little and big influences that made me have a go at the code, but Tetris and Calder are sure to have played a role in this...

I would suggest that a three-dimensional representation would be an even better model. All you need if you want to build a model yourself at home is a couple of molecular building block kits. Make sure that you have blocks that allow for tetra- and penta-valent binding (e.g. carbon atoms in normal and transitional state).

Start with a tetravalent-binding block at the centre to get the tetrahedrical base, use the binding elements to represent A, G, C, and U and continue with the pentavalent-binding blocks until you reach the level of amino acids where you then can use different coloured blocks to symbolise the individual amino acids.

This approach lets you bring amino acid codons that seemed at opposite poles into close proximity (e.g. K and R or F and Y). I know, it may look confusing to begin with, but it adds another layer of information. The categories for grouping the amino acid codons on www.rna-game.org are after all somewhat subjective (non-polar, transitional, special, polar), maybe there are other categories that should be used to group the codons.

I guess what I mean to say is, have fun. Of course sincerety and truth remain the essence of science and empirical and rational thinking are the backbone of this line of work, but intuition and a sense of wonder are crucial elements as well.