Abstract

Organisms typically contain thousands of functional protein molecules with diverse and complex evolutionary histories. In recent years we have gained unprecedented knowledge of the structure and evolution of these proteins, particularly with the use of machine learning innovations such as AlphaFold. Through massive databases and rapid search tools we are now starting to get a sense of the overall arrangement of the protein universe, including some potential general principles of gene origin and evolution. The possibility of long-term trends, undergirded by natural laws, is reminiscent of some older “structuralist” views of evolution over against the functionalism and adaptationism of the modern synthesis. Considering both the possibility of long-term trends and the extreme intricacy of protein complexes also helps to resurrect ancient questions about the place of teleology in biology.