In other words, I am saying that, given the evolutionary model, molecules must change positions(vary) in order to adapt biologically functional states. You are saying they don't have to because they were already in such states. Or to put in simply, eyes, ears, lungs, gills, joints, heart, brain, RNA splicing machine... didn't have to evolve, but only change, because they were present from the very beginning.
The problem is you seem to imagine that within the genome are definitions for the structure and position of organs like heart, lungs, brain or even gills. In other words you imagine the genome to be a blueprint. But really, multi-cellular organisms are a colony of cells, a bit like a bacterial biofilm, just with a more diverse range of proteins to form intracellular connections, secreting extracellular matrices, or signalling neighbours to coordinate interactions with each other. This is what our genome handles, from that single-celled fertilised ovum as it multiplies and diversifies.
So for example you have hox genes who's protein products signal to cells their position in this growing colony, which trigger other signalling proteins in a cascade which is dependant on where in the growing colony the cells find themselves. Another example would be the SHH gene (sonic hedgehog) which codes for a protein that diffuses from the neural tube through the colony, affecting cells differently depending on the concentration. By this point the colony will have become a long tube with an opening running it's length that will eventually be the gut, but these networks of regulatory genes continue right through development, differentiating and refining neighbourhoods of cells into different tissues. So for example towards one end of the embryo a series of branchial arches form. Some will go on to form the basis of jaws and in fish others will develop into gills, or be reabsorbed in terrestrial animals. In mammals a small part of the first branchial arch will split off from the developing jaw and migrate towards the ear. Can you see why talking of 'a gene' for gill formation can appear nonsensical, as these structures are the culmination of the interaction of many genes over many generations of cell division? To illustrate this, here is a video of how the face comes together during development:
I know this may appear complex, but when the first regulatory genes developed, the colonies of cells were a lot smaller and more simple to what we have in a human. But a lot of variety can develop with duplication and subsequent mutation of genes. For example, in previous posts responding to Faith's example of hair colour, the MC1R gene was brought up, which codes for a protein that is an example of a G protein-coupled receptor. The interesting thing about this is that this is a large family of proteins which perform many tasks in different tissues, including opsins in the retina as part of the visual system.
Edited by Meddle, : No reason given.
Edited by Meddle, : Fixed youtube video so it displays, removed joke about boards being up and down like Assyrian Empire.