I have written about the relationship between circadian clocks and food numerous times (e.g., here, here and here). Feeding times affect the clock. Clock is related to hunger and obesity. Many intestinal peptides affect the clock as well.
There is a lot of research on food-entrainable oscillators, but almost nothing on the possibility that there is a separate circadian pacemaker in the intestine. It is usually treated as a peripheral clock, entirely under the influence of the SCN pacemaker in the brain, even when it shows oscillations in clock-gene expression for several days in a dish.
But why not have a true pacemaker in the gut? The intestinal nervous system is large and semi-autonomous. It makes sense that there would be a circadian clock in there. After all, all the GI functions follow daily rhythms.
I remember that there was a paper – a VERY old paper – that showed that an isolated intestine in a dish shows circadian rhythms of motility. I could not locate that paper. If you can, please let me know.
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What do we know about establishment (or lack thereof) of natural clocks (particularly the food one) when the calibrating events fluctuate (e.g. irregular timing of meals)?