Optimality In Biology
Optimality In Biology – a comprehensive collection of annotated examples
General Description
Optimality – the property of a system to maximize or minimize some function under given constraints – has been a central concept in many fields such as physics, computer science and engineering. In the realm of biology, natural selection leads to exquisite functional life forms all abiding to the laws of physics and chemistry yet show remarkable adaptation to the surrounding conditions. One manifestation of this process is that some characteristics of organisms can be shown to be close to optimally adapted to the constraints of their environment. This website and annotated collection aims to serve as a source of examples that will help discuss and disseminate this form of studying biological processes and inspire the analysis of other biological phenomena using these tools and perspectives.
In many respects the emphasis is on the constrains rather than on the issue of optimality per se, as eloquently framed by Parker and Maynard-Smith: “Optimization models help us to test our insight into the biological constraints that influence the outcome of evolution. They serve to improve our understanding about adaptations, rather than to demonstrate that natural selection produces optimal solutions.” (Parker & Maynard-Smith, Nature 1990). We encourage everyone interested in this fascinating subject to add examples, comments and join the discussion either by directly editing these pages or by communicating them through email (ron_milo@hms.harvard.edu) and we will add them.
Examples (we aim to have a short paragraph of description on each):
- Level of protein expression – lac system [1]
- Growth rate on different carbon sources - experiments reproduce FBA optimality predictions (Palsson, Nature biotechnology 2001)
- The genetic code (Refs.)
- Age of reproductive maturity, number of eggs in a clutch, foraging strategy etc. (Stearns 1992)
- Codon usage and biases (Ref.)
- Shapes that minimize drag (Ref. fish, fungi spores, birds?)
- Prey interception strategy of bats (Ghose et al., PLOS Biology 2006)
- Optimal virulence level (Jensen et al., PLOS Biology 2006)
- Neural information transmission (Bialek 1997)
- tRNA levels
- morphogen gradients
- photosynthesis wavelength
- enzymes near the diffusion limit
- Optimal metabolic network operation (“Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli” Robert Schuetz, Lars Kuepfer1 & Uwe Sauer Also Jens Nielsen, 2007)
References:
- Dekel E and Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature. 2005 Jul 28;436(7050):588-92. DOI:10.1038/nature03842 |
General references:
- Optimality theory in evolutionary biology, GA Parker, JM Smith - Nature, 1990,
- The evolution of life histories. Stearns, Stephen C., Oxford University. 1992
- An Introduction to Systems Biology: Design Principles of Biological Circuits, Uri Alon, Chapman & Hall/CRC; 1st ed. 2006.
