I am aware that there is shuffling amongst genes and that for example 100 genes can perform (say)some 300 functions due to the shuffling. However, I do not understand how you arrive at the conclusion that due to this new functions arise or more importantly as to the matter of evolution, how it ends up in the creation of new species. After all, it seems to me that all individuals with the same genetic structure would be able to do these functions so that these functions, though not residing in a particular gene as we commonly think, would still be part of the species and would not result in a new species. In fact, I think it is this "shuffling" that is the cause of what is called micro-evolution - changes caused by the environment to help a species adapt to it.
Actually, it's more or less one gene, one function, unless you are referring to the production of antibodies, which is a completely different matter.
What I was talking about is the physical movement of a piece of DNA from one location to another, either on the same chromosome or another. In lower organisms, this kind of shuffling is quite common; the fruit fly, for example, has enzymes for just this purpose. Where the new functions can arise is this: Proteins are modular, with regions of highly ordered structure. There really aren't that many different structures that occur in proteins--alpha helices, beta sheets, random coils--and protein functions are determined chemically, by the type of amino acid (acidic, basic, hydrophobic, hydrophilic, etc.) predominant at any particular region of the protein. Suppose, by their biochemistries, that Protein X can attach to DNA, and Protein Y can bind to a hormone, and a shuffling event occurs such that a new Protein XY is produced, having both properties. Furthermore, by mutating the DNA binding site, the protein can attach to a different DNA sequence, and by mutating the hormone binding site, the protein will recognize a different hormone. Voilà, new proteins with new functions.
In fact, I think it is this "shuffling" that is the cause of what is called micro-evolution - changes caused by the environment to help a species adapt to it.
You can't embrace the idea of "micro-evolution" while rejecting the idea of "macro-evolution." It is all the same thing.