OK, I'm going to write my friend who is an immunologist and see what SHE thinks. She is in no way an expert on animal nutrition (though her current research has to do with how proteins are absorbed and survived post absorption - my made up totally lame-o amatuer terminology) - but she might have some insight since she also feeds raw to her, um I think six performance dogs.
It's holidays so it may take a couple days, be patient!
As to the cell lining - that was actually just a theory of mine although I was surmising that it was something to do with the GI, not specifically the small intestine.
I'll tell you what I've seen and heard directly from reliable friends (scientifically disciplined, either biologists, veterinary specialists, nutritionists, or trained in human medicine - when it comes to nutrition, I tend to trust people who combine both scientific discipline and experience similiar to mine in feeding performance animals - sometimes I make a boo-boo and it's almost always because I've absorbed some internet factoid without following it up).
The time frame is always the same. Detox may happen
before 21 days but rarely after, and usually the major "events' happen around that time. Detox is also
short - never longer than a couple days, never severe more than a few hours.
Detox is self-correcting. I do, as I say, rest the tummy if there's a real crazy reaction, but that's a "Just in case" thing - standard operation when I have a dog with tummy upset symptoms.
The greater the difference is between the two food types, the greater the chance for a more dramatic event. Similiarly, the longer the dog was on a grain-based food, the greater the chance for a more dramatic event. Oddly, it does not seem to matter how gradually you switch, so my theory about the intestinal flora which sounded so good at 2 am kind of gets blown away there. [

] Therefore, I would not expect a young dog switching from Science Diet to Cal Natural to have any major detox event. But from Science Diet to EVO I might be suspicious. Science Diet to raw, especially grain free, I'd almost expect something in any dog older than, say, 18 months.
What detox looks like (presentation - but I hate to use pathological terminology since I'm not convinced it's an abnormal process) varies widely. It can be very subtle - I'm sensitive to changes in coat and smell since I'm a real hands on person with my dogs and HATE the smell of dog - so at around twenty one days for a new dog I see that harsh staring coat, weird smell, and may or may not see a change in stool - I rarely miss it. I ought to start collecting this inforamation formally because it would help, I know, if this sort of thing were documented. We holistic types have too well deserved a reputation for being undisciplined. [

] I'll see whether my friend who also feeds raw and does a lot of rescue, would be willing to join me. She is an RN with an MS, working on her PhD (or whatever the nursing equivalent is).
What it is not, but often I suspect is often claimed to be:
Anytime the dog is affected with symptoms such as lethargy, dehydration, anemia, fever, severe or prolonged colitis, inappetence - basically if the dog is
sick, that's not detox in my experience.
Prolonged mild symptoms, especially if they start within hours or days of switching.
Itchiness, skin lesions, yeast infections. Anal glands CAN be affected but it would have to be at the same time as typical detox stuff for me to believe it was detox.
Respiratory symptoms, or any change in major system function. I heard someone say her dog's liver values elevated because her dog was "Detoxing". Poppycock. If detoxing is a natural process, I'd hope my dog's liver could handle it. I do support older dogs with milk thistle on the recommendation of my vet, after my experience with Greg, but that's different. That's like saying my pancreatic levels are high because I ate bacon for breakfast. They'd better not be abnormally high or something is not doing its job right!
So those are the assumptions I operate under. I've got a new dog coming tonight so I'll start a diary for him. He looks really well taken care of, from his pictures, I think he was an owner turn in to the shelter. His diet has been shelter food du jour, from donations and whatever's cheapest, but he's also quite young. It would be nice if he'd do the coat thing so I could document it in pictures. Maybe by then I'll have an answer from Polly, too.