The main purpose of this research is to strengthen and exploit the link between engineering thermodynamics and both experimental and theoretical biology. Historically, biothermodynamics studies have often resulted in misrepresentation of thermodynamic quantities and in discrepancies between experimental results and restrictions imposed by the first and second laws of thermodynamics. Analyses performed in this research reevaluate experimental results and measured physiological parameters which are then translated into proper thermodynamic quantities and definitions;This approach begins with the development of comprehensive forms of material and energy balances for open, periodically supplied, growing systems operating far from equilibrium. The re-definition of efficiency and efficacy and the classification of physical work forms is shown to be conducive to the re-interpretation of apparently anomalous experimental results;Generalized material and energy balances are successfully implemented in the analysis of energy flows of growth and development in avian egg and microbial culture systems. The direct relationship between oxygen consumption and heat loss of the egg and microbe systems facilitates the understanding of changing energy flows, energy storage, and energy conversion efficiencies during periods of growth and development;The physiological interpretation of the thermodynamic terms of the energy balance leads to the evolvement of an entropy account which facilitates the rigorous calculation of the entropy production rate and minimal system entropy of living systems. The minimal entropy production rate is determined by comparing heat loss and metabolic energy conversion rates. The calculated rate of specific system entropy production is positive but decreasing during periods of growth and development. The estimated minimal system entropy is increasingly positive during this period. The results of these estimations agree with Prigogine's hypothesis;Additional analyses in muscle physiology result in a cyclic representation of muscle contraction both at microscopic and macroscopic system levels. These representations are used as a guide to the design of muscle experiments and muscle-testing apparatus. Oxygen uptake requirements of muscle are written as a state function dependent upon muscle length, muscle tension, and the work performed. This model produces direct physiological interpretation of nonequilibrium phenomenological expressions for muscle contraction.