In response to their environment, algae in the wild may use an approximation to optimality of resource allocation in cellular structures, photosynthetic pigments, enzymes, transporters in membranes and RNAs and in their genetic material. However, under controlled conditions, when algae are grown for biofuel (lipid) production for example, some of these processes can be altered to increase the efficiency of photosynthesis and therefore, lipid yield. This suggests that there is scope for selecting mutations and for genetic engineering at various levels in the photosynthetic apparatus with the aim of increasing efficiency of photon use and the rate of transformation of resources per unit biomass to improve biofuel yields. More specifically, the wavelength range covered by photosynthetic pigments and photochemical reaction centres could be increased, the number of protons transported from the thylakoid lumen to the stroma per unit ATP synthesised by the ATP synthetase could be decreased, the fluctuating light effect could be utilised and photosynthetic pathways changed, e.g. replacing part or all of the current machinery for autotrophic fixation of inorganic carbon. There are also possibilities for decreasing carbon loss by decreasing 'wasteful' aspects of dark respiration and of dissolved organic carbon loss. Provided that the environmental fluctuations to which algal growth conditions are constrained, there are possibilities for decreasing the resource costs of protection from ROS, and by down-regulating photoprotective mechanisms, as well as limiting the capacity to repair processes related to photoinhibition. Decreased protein turnover is also a potential energetic saving. These interventions apply to individual processes; however, this may not be immediately incorporated into the optimal allocation of resources by the alga, and further intervention using a system biology approach may be required.