Catabolic biochemistry extracts free energy from food. Core catabolism arose early in evolutionary history. Modern microbes express many design variants around the basic catabolic core.208
Design variants arose for several reasons. Alternative food sources require specialized processing. Disparate environments alter the redox flow of electrons. Different catabolic products provide alternative precursors for building new molecules.
Biochemical innovations change opportunity, leading to novel forces that further alter design. Diversity also arises because different biochemical designs accomplish the same function.
Core catabolism sets a primary challenge in the study of biological design. If we cannot explain design variants in the most basic aspects of microbial biochemistry and energetics, we are not going to succeed for the diverse physiological and behavioral adaptations of life that build on core energetics.
This second part of the book analyzes the design of microbial metabolism. What are the great puzzles in understanding metabolic design? How do we go about solving puzzles of biological design?
To address those questions, I synthesize current knowledge about microbial catabolism and its consequences for microbial fitness. That synthesis highlights puzzles of biochemical design. I then go after my primary goal: solving puzzles of design in biology.
To achieve that goal, I build on the principles in Part 1. My primary method for analyzing design is comparative prediction. Can we predict how a change in some environmental attribute alters metabolic design?
To say that we understand design, we must formulate such comparative predictions and test those predictions. This second part lays the foundation for generating comparative predictions about microbial metabolism. Along the way, I develop many specific predictions.
The methods of approach and the listing of comparative predictions light the way forward in the study of metabolic design. The same approach illuminates design throughout life.