Thanks for your thoughtful response.
It used to be that we associated one gene per one trait. With increasing genetic knowledge, we have found that there are an incredible number of factors involved in traits, and that the inter-relationships of various genes are involved in most traits, as well as the timing of expression.
It is true that when we knock out one gene in experiments on mice and such, that we can knock out a trait. However the opposite is not something we can guarantee -- that by adding one gene we will get a trait. In fact, that is being shown not to be true at all. We can induce modifications by genetic manipulation, but not totally new traits. We can produce eyes on legs, but not on plants, for instance, which have no eyes to begin with. That is a far-fetched example, but I wanted to make the point that unless the basic material is already there for a trait, it cannot be put there by the simple addition of a gene.
We have found that some genes are expressed only at certain times and in certain ways: maybe during early development; maybe only during stress, etc. And these genes interact with others in the development and expression of traits.
So, to make this part short, simply counting alleles is not enough. Even out of two human beings -- especially two with no mutations to damage their genetic packages -- almost an infinite variety can emerge as different combinations trigger different timing mechanisms and amounts of expression, etc.
As far as the animals go, it seems that Genesis indicates creation by population, so we would have much, much more variability there. Plants even today have something referred to as 'plasticity' genetically, so that we can graft a plum onto a peach or a lemon onto an orange, and we can do enormous genetic manipulations -- and even watch some pretty significant speciation happen naturally. Plants are fascinating that way.
But animals are quite different. The plasticity is missing and only the initial variation is possible. This can be quite extensive at times, and therefore impressive, but variation is all it is.
Backing up through your post to order and disorder, I would prefer quoting from a couple of people far more educated than I am in their respective fields, both of whom are 'rabid' evolutionists (in other words, they would rather die than admit to creation!)
If organisms are ever to be understood as material physical entities, physics will first have to be transformed into a science of complex systems. This metamorphosis is already under way, but has proven neither quick nor painless: after half a century, the thermodynamics of erreversible processes (those that predominate in the real world) has chalked up few concrete achievements and remains largely outside the main stream of both physics and biology.
...Thermodynamics and evolution, the two branches of science that revolve around order and time, started out in opposite directions: one views the world as running down, the other as building up, and we are still striving to close the circle.
...A more persistent conflict stems from the prime characteristic of living organisms: their ability to grow, develop and evolve, generating mounting levels of order in apparent defiance of the second law of thermodynamics. That most basic of natural laws mandates that all real processes be accompanied by the degradation of energy and the dissipation of order...
Franklin M. Harold, The Way of the Cell, 2001, Oxford University Press, pp 224, 227
The natural tendency of energy to disperse -- that is, to spread through space, to spread the particles that are storing it, and to lose the coherence with whch the particles are storing it -- establishes the direction of natural events...Natural processes are those that accompany the dispersal of energy...As energy collapses into chaos, the events of the world move forward...Entropy must therefore be a measure of chaos. Moreover, we have seen that the natural tendency of events corresponds to the corruption of the quality of energy.
...The descent into universal chaos is not uniform, but more like the choppy surface of rapids. In a local arena, there may be an abatement of chos, but it is an abatement driven by the generation of even more chaos elsewhere...
There is also another important point. The products of the reaction have less energy than the reactants. The energy in the bonds binding the product is less than was in the bonds binding the reactants: the excess has been carried away in thermal motion... That is the cause of chemical change: in chemistry as in physics, the driving force of natural change is the chaotic, purposeless, undirected dispersal of energy.
P.W. Atkins, The 2nd Law, 1994, Scientific American Library, pp 62-63, 82, 112
Both Atkins and Harold take great pains to show how evolution overcomes these universal processes, and in order to be fair to both authors, that has to be stated. But both make the presumptions that local increases in order also imply the arise of specified complexity, and that is nowhere seen in the natural world.
But yes, the natural state of the universe, according to both physics and biology, is that of a downward trend into disorganization. Bicycles rust. They cannot be rebuilt from rust. Bodies run down and die, and all the science in the world is not stopping that. I think the picture is relatively clear. I hope it is, for we spend most of our waking moments fighting this decline in both ourselves and in our surroundings.
And finally, as far as star formation goes, again it is not really important whether or not we see them form in terms of theology. In terms of what we have observed, we have not seen one form (but that's OK!). However the issue I would have with your comments is that you are presuming very old ages based on the rate of processes we see today. Is there anything you are aware of that guarantees these processes have not, in the course of time, slowed down?