Rule-Based Biology

Constraint-Based Reconstruction

Modern biology accumulated extensive data without establishing the governing constraints that define necessity. When unconstrained observations diverge, interpretation expands while mechanism remains unresolved.

Systematic evaluation of large-scale biomedical data reveals multiple overlapping constraints. These constraints operate in parallel and limit what biological processes can and cannot do. Their application produces internally consistent reconstruction across molecular, cellular, and systemic levels.

This reconstruction differs structurally from prevailing descriptive models. Mechanisms become derivable rather than inferred. Ambiguities that persist under correlation-based interpretation are resolved through constraint.

The rules themselves are not enumerated publicly. What is presented here reflects their application.

Biology as a Physical System

Biological systems are physical systems. They obey the same fundamental constraints as all matter: conservation of energy, structural stability, and lawful interaction between components.

Yet biology has historically been treated differently from other sciences. Rather than being grounded in governing principles, it has evolved as a largely descriptive discipline—cataloguing components, pathways, and effects without establishing the rules that determine how those components must behave.

This absence of foundational structure has shaped how biological knowledge has been accumulated, interpreted, and applied.

The Missing Foundation

In mature sciences, understanding arises from constraints. Laws determine what is possible, what is forbidden, and what must follow from given conditions.

Biology developed without such constraints. As a result, explanation has relied heavily on correlation, context, and post hoc interpretation rather than necessity.

This has produced a field rich in data but poor in unifying structure.

Rules as the Basis of Biological Order

Biological behavior is not arbitrary. Molecular interactions, cellular processes, and physiological states occur within strict limits imposed by energy, structure, and reaction dynamics.

These limits are not conventions or models. They are governing rules.

When such rules are identified, biological systems become intelligible. Mechanisms can be derived rather than inferred. Outcomes become constrained rather than probabilistic.

From Description to Principle

Descriptive biology records what happens.

Foundational biology explains why it must happen that way.

The transition from description to principle marks the difference between a catalog of observations and a coherent science.

Implications of a Rule-Based Foundation

When biology is grounded in rules:

• mechanisms become derivable
• contradictions dissolve
• prediction becomes possible
• complexity becomes structured

Biology becomes comparable to other foundational sciences in rigor, coherence, and explanatory power.

A Basis for Reconstruction

The purpose of establishing foundations is not philosophical. It is practical.

A rule-based foundation allows biological knowledge to be reorganized, tested for consistency, and extended without ambiguity.

It provides the basis for understanding disease, designing interventions, and integrating biology with computation and artificial intelligence.

What follows from this foundation is not speculation, but structure.

Learning the Method

Rule-Based Biology is not a collection of claims. It is a method for identifying and applying governing rules.

The method cannot be conveyed through examples alone. It must be learned systematically.

A structured course is now available for those who wish to study the method directly.

Learn more →