We're talking about excess protein in the manure...
Thanks for sharing these articles, georgeto. It gave me a brief sweep over how proteins are converted, and how excess proteins are handled. But the second and third articles leave a gap in your argument because we're switching between talking about birds and mammals (humans more specifically in the wiki article)... where the birdpee article says there's a big difference in that humans produce urea while birds produce straight ammonia. I suppose if the livers of humans and chickens function the same otherwise, then we could assume that excess protein intake for a chicken results in the same effect that humans experience, but without converting the ammonia to urea; "Deamination converts nitrogen from the amino acid into ammonia, which is converted by the liver into urea in the urea cycle." And that may be right that it's the same process for humans and chickens. All I'm trying to say is that these articles don't directly link excess protein intake in chickens to excess ammonia excretion in their droppings.
On another note, I've always heard that only a ridiculously low amount (like 30%) of nutrients in chicken feed are bio-available to the chicken eating it. I don't have any real research to back that claim, but it makes sense to me considering that grains have a high level of "antinutrients" (like phytic acid) which are known to block absorption in humans (yes, I see I'm comparing humans and chickens, but like I said, I don't have the research, this is just a very underdeveloped theory). If this is the case, then wouldn't it be possible that the chicken isn't even getting the whole 16% of protein in the layer pellets?