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I found this article on estimating body time using molecular timetable of 168 genes. researchers looked at gene expressions and plotted them to 24 hour cosines curve with some pretty spectacular results.

Unfortunately the techniques discussed required sampling of liver cells, which may be invasive. Are there non- invasive methods of estimating body time/ biological clock/ circadian rhythm time?

An example of body time: at 8:00 real time, a mouse may exhibit gene expressions more appropriate for 9:30, so the body time of the mouse is 9:30.

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metabolism is controlled by circadian cycle. I think certain metabolites/hormones can be measured from a blood sample. –  WYSIWYG Apr 30 '13 at 5:43
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For circadian rhythm, the gold standard is melatonin secretion (blood or saliva). Also, core body temperature.

see: Circadian temperature and melatonin rhythms, sleep, and neurobehavioral function in humans living on a 20-h day

James K. Wyatt , Angela Ritz-De Cecco , Charles A. Czeisler , Derk-Jan Dijk American Journal of Physiology - Regulatory, Integrative and Comparative PhysiologyPublished 1 October 1999Vol. 277no. R1152-R1163

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Don't forget cortisol/corticosterone! –  nico Sep 29 '13 at 17:03
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