Sorry to take a while, but my sleepy little town has suddenly become a thriving metropolis and I'm flat out keeping up.
Anyway, haven't had a really good look into it. Most searches turn up sites making unsubstantiated claims. The best I could find was this:
Neither Ganong nor thousands of scientific writers on the subject of digestion make mention of any value of intrinsic food enzymes in human digestion. There is one exception: Prochaska LJ; Piekutowski On the synergistic effects of enzymes in food with enzymes in the human body. A literature survey and analytical report. Med Hypotheses (ENGLAND) Jun 1994. In this article the authors mostly repeat the well understood effects of heat in breaking down vitamins, amino acids, and producing undesirable cross-linkages in proteins, particularly in meat. They do not produce a surfeit of evidence in support of the "enzyme theory", although they do point out that cooking beans increases their digestibility by destroying the trypsin inhibitors therein and they cite this as evidence that these enzymes can survive the digestive enzymes at least long enough to cause negative effects. They also present tentative evidence that there is some degree of synergy between some food enzymes and human digestive enzymes, a concept that would at least seem plausible. However they admit: "In the absence of active enzymes in food, the foodstuffs are still able to be digested and the nutrient release from food still occurs, but not at maximum efficiency." This is a far cry from "the enzymes present in raw foods take priority over secreted enzymes."
A search of Medline and the American Journal of Clinical Nutrition, however, failed to turn up a single additional article in support of this thesis and four physiology, biochemistry, and nutrition textbooks, while elaborating on human digestive processes to the point of tedium, also did not mention any useful predigestion of food by the food's own enzymes.
Fairly damning, and not really interesting unless you can see exactly what constitutes 'tentative evidence'.
On a related note though I thought these studies were interesting:
All animals in the wild eat raw food. Various studies have been performed comparing extensively animals eating cooked versus raw foods. As early as the beginning of the last century, it had already been noted that animals in captivity eating cooked foods had a much higher mortality rate than those kept on raw foods. One such study was done at the Philadelphia Zoo and described in Disease in Captive Wild Animals and Birds in 1923 by Dr. H. Fox. Animals kept on cooked foods not only died earlier but also bred poorly. When their diets were changed to natural, raw foods, the health, life-span and breeding of the animals improved greatly.
Another well-known study was performed by Dr. Francis M. Pottenger through a 10-year research project and published in the American Journal of Orthodontics and Oral Surgery in 1946. Dr. Pottenger fed 900 cats the same food, except that one group ate it raw, while the other cooked. Cats eating raw, living food were seldom sick and gave birth to healthy kittens year after year with no health problems or pre-mature deaths. But cats eating the cooked version of the same food developed heart disease, cancer, kidney and thyroid disease, pneumonia, paralysis, loss of teeth, arthritis, birthing difficulties, diminished sexual interest, diarrhea, irritability, liver problems and osteoporosis. It was also noted often that the first generation of kittens from cats eating cooked food were more prone to sickness, the second generation were often born diseased or dead, and by the third generation, the mothers were sterile.
I can't remember now if we were already feeding the dog raw foods before adding the alfalfa or not. I think we were though. Anyway, like I said something quite obviously improved both his arthritis (which was diagnosed) and hot spots. Whatever it was occurred fairly dramatically about a week or two after the change in his diet, so unless it was related to that either arthritis isn't actually a degenerative disease or something random happened to change his physiology.