# The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree

## TL;DR

This paper discusses how the discovery of archaea, a new domain of life, led to a major restructuring of the phylogenetic tree and highlights the role of anomalies in scientific discovery.

## Contribution

The paper introduces a philosophical analysis of how unexpected anomalies during normal science can lead to the discovery of new biological entities.

## Key findings

- The discovery of archaea led to a tripartite tree of life model replacing the previous bipartite one.
- Anomalies during normal science projects can trigger significant model-changing discoveries.
- RNA splicing and ribozymes were also discovered due to unexpected irregularities in experiments.

## Abstract

Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn’s terminology, this discovery of a major biological entity was made during a ‘normal science’ project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese’s project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.