DNA, Genes, Proteins revisited

DNA: collection of genes

Gene:
    proteinCode: byteString which specifies the particular protein produced by this gene
    activator: proteinCode(s) which turns this gene on
    silencer: proteinCode(s) which turns this gene off


Protein:
    code: unique byteString id
    desc: short description of what the protein does
    functions: [
        {
            key: hard-coded string linking to a function,
            value: how strongly the protein does whatever it does
        },
        ...
     ]

Some protein codes are hard-coded to UI and environmental functions, but most are not. That is, some proteins have "functions" external to the cell, but most do not. Those which are not hard-linked are free to be used as activator/silencer proteins to control genetic expressions. Hard-links represent imaginary physical properties of the produced proteins. Color, for instance is a protein function. Proteins can (should?) have multiple functions.

Hard-coded protein codes can represent input or output. Inputs are used by becoming activators for other proteins, outputs are used when a Gene produces the output protein.

HARD-CODED PROTEIN CODES (INPUT):

these proteins are hard-coded into the environment

* onclick: when the cell has been clicked (within last few generations?)
* onmouseover: when the cell is hovered over (within last few generations?)
* overcrowded: the cell has > certain # of neighbors
* undercrowded: the cell has < certain # of neighbors
* allwaysOn: 

HARD-CODED PROTEIN FUNCTIONS (OUTPUT):

these protein functions are hard-coded into the environment

* color: color display is changed by given val [-FFFFFF, +FFFFFF]
* move: cell moves to neighbor # given by val [1,2,3,4, 6,7,8,9]
* suicide: cellular sepukku in {value} generations
* spread: protein spreads out to neighbors and stays there for {value} generations
* silence: silences proteinCode specified by {value}

onCellRun:

CellObj:
    proteins_present: [protCode1, protCode2]  # list of proteins present and not silenced

1. produce proteins

foreach "activated" gene (foreach activator prot. present, foreach gene activated by this protein)
    if silencer not present:
        produce_protein # add protein to proteins_present

    execute protein function(s)

#EXAMPLES:

colorProtein:
    desc: adds 123 to the hex color value
    code: COLOR_UP_PROT
    functions: [
        {
            key: increaseColor
            val: 123
        }
    ]

doNothingProtein:
    desc: does nothing
    code: RANDOM_STUFF_HERE
    functions: []

crowdedBehaviorGene:
    desc: this Gene produces a protein when crowded
    activator: OVERCROWDED_PROT

linkGene:  # creates a protein in presence of other protein
    activator: ACTIVATOR_PROT_CODE
    proteinCode: RESULTANT_PROT_CODE