# Conceptual Confusion: The case of Epigenetics

## TL;DR

This paper clarifies the concept of epigenetics by linking it to dynamical systems theory and explaining how gene regulatory networks create stable patterns of gene activity.

## Contribution

The paper provides a mathematical foundation for the 'epigenetic landscape' concept using dynamical systems theory.

## Key findings

- The 'epigenetic landscape' is shown to have specific mathematical foundations in dynamical systems theory.
- Gene regulatory networks produce multiple attractor states that represent self-stabilizing patterns of gene activation.
- This network dynamics approach offers a clearer correspondence than reductionist views of molecular modifications.

## Abstract

The observations of phenotypic plasticity have stimulated the revival of ‘epigenetics’. Over the past 70 years the term has come in many colors and flavors, depending on the biological discipline and time period. The meanings span from Waddington’s “epigenotype” and “epigenetic landscape” to the molecular biologists’ “epigenetic marks” embodied by DNA methylation and histone modifications. Here we seek to quell the ambiguity of the name. First we place “epigenetics” in the various historical contexts. Then, by presenting the formal concepts of dynamical systems theory we show that the “epigenetic landscape” is more than a metaphor: it has specific mathematical foundations. The latter explains how gene regulatory networks produce multiple attractor states, the self-stabilizing patterns of gene activation across the genome that account for “epigenetic memory”. This network dynamics approach replaces the reductionist correspondence of molecular epigenetic modifications with concept of the epigenetic landscape, by providing a concrete and crisp correspondence.