Where to start... I agree that DNA and RNA are pretty amazing and that the life is complex. But, when it comes to 'atrophy of this chemical coding' I have no idea what you are talking about. DNA and RNA genomes accrue mutations through the process of molecular evolution. This can be slow, eg by accruing single point mutations over long periods of time, or it can be fast, eg by horizontal gene transfer (especially think of microorganism here). Any mutation may be neutral (no effect on phenotypic trait), positive (gives some selection advantage) or negative (is deleterious). The study of population genetics is basically the mathematical study (probabilities) than any given genotype will persist in a population and become either more or less prevalent within the population, causing genetic drift over time (usually very long periods of time, but as mentioned before, you can get a relatively rapid change in some circumstances such as through horizontal transfer or a mutation of larger size, eg Deletion of a gene function, or substantial modification of protein function).
I think part of your problem is trying to draw a line between natural selection and this so called macro evolution. What you don't seem to appreciate is that within the scientific community, it is not always clear what distinguishes one species from another. For example, one definition is that different species cannot interbreed. But this does not always hold true, look for example at the wolf and domestic dog. They were once considered different species, but now the domestic dog is considered a subspecies of the wolf (Canis lupus familiaris) and genetic studies indicate that the domestic dog diverged from the wolf around 30,000 to 40,000 years ago. Think also of the mule. Taxonomists are often arguing about whether a particular organism is a certain species, or if it should be allocated a new species. Hence, I don't understand what the 'transitionals' are supposed to be. Maybe the 'fronkey'?, the famed half frog half monkey that is supposedly missing from the fossil record.
Essentially, genetic evolution is a function of biochemistry, which in turn is driven by physical processes (the physicists say that everything comes down to physics) over time. Intelligent design to me is a way of saying "I don't understand these processes, they are too complex, therefore someone smarter than us must have done this". Bit of a cop out and not what science is all about.