As for your other point, that new functions cannot arise by chance: proteins only contain a handful of structures. It is by mixing and matching the structures that are there that new functions arise. Proteins that act as environmental sensors of oxygen, of "xenobiotics" (environmental compounds ingested or absorbed by the organism), or light sensors have a common structure and are present in organisms as varied as plants, insects, bacteria, and animals. Organisms are constantly shuffling genes and parts of genes; it is how we believe that novel functions arise. Now, as to how the proteins originally arranged themselves into functional structures, or how thousands of proteins work together to sustain life... these are questions which make many scientists wonder about intelligent design. If there was a creation event, it had to happen billions of years ago, and involved simple organisms such as viruses (which are not truly alive) or bacteria.
Ever notice the women from the Mothers' March of Dimes out collecting money for research? Ever notice that they're ALWAYS asking for money for research to prevent mutations, and not for research to cause them? Think there might be a reason for that?
I would suggest to you that an equivalent event happened two thousand years ago in a place called Jerusalem when a crucified man in a tomb rose from the dead. That event will be celebrated worldwide in just a few days.
Last time I heard, Darwin is still dead. Couldn't he just spontaneously regenerate and settle this once and for all?
In the paragraph above the only major point we disagree on is the effect of mendellian genetics on evolution. At the time "On Origin of the Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life" was published, Mendellian genetics had not been discovered. Darwin made the assumption that the traits of each parent 'melded' in their progenitors and that therefore a favorable mutation would be easily passed throughout a whole species in a short time. This made his theory very viable. This was proven untrue because like the rest of his book it was not science but a bunch of assumptions without scientific basis strung together to prove a theory. What mendellian genetics shows is that it is very difficult, if not impossible to pass on a new trait throughout an entire population. Here's why. For each gene we have a reciprocal gene called an allele. During reproduction only one of these paired genes gets passed on to the next generation. This selection is totally random. So right from the start a new gene has only one chance in two of being passed on to the next generation. Being a new gene, no one else in the population has it. Therefore the chances of its being passed on to each succeeding generation are cut in half with each generation. This makes the spread of a new mutation almost impossible. It can happen, but it will take numerous favorable mutations to die in the genetic abyss before one will finally make it throughout the whole population. Now evolutionists thing that there has been enough time for all these new genes to spread throughout all these different species, but that is not the case. The two-three billion years since life began on earth are insufficient time for the numerous mutations that were necessary to spread throughout all living things when the delays caused by Mendellian genetics are taken into account. Darwin realized quite well that the amount of time to spread these traits was critical for the viability of his theory. Mendellian genetics extends the time far too much for his theory to be viable.
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.