Computer programs as theories in biology.

Area of Science:

• Computational Biology
• Theoretical Biology
• Bioinformatics

Background:

• Computer simulations offer a powerful method for developing, refining, and testing complex biological theories.
• Existing programming languages often result in incomprehensible code, hindering the use of programs as definitive theory statements.

Purpose of the Study:

• To advocate for computer programs as the definitive statement of biological theories.
• To introduce a methodology for abstraction and a language for representing abstractions to improve communication.

Main Methods:

• Utilizing computer science techniques to develop an abstraction methodology.
• Creating a language for representing abstractions.
• Illustrating the approach with a recently published biological theory.

Main Results:

• Programs, when executed, act as models of biological theories, providing a means for rigorous examination.
• Abstraction techniques and a specialized language can make complex biological theories represented by programs more comprehensible.

Conclusions:

• Computer programs should be considered the ultimate, irrefutable statement of complex biological theories.
• The integration of programs with abstractions facilitates effective communication and understanding of intricate biological concepts.