A new framework that places historical processes at the center of how we categorize life
Imagine trying to organize a library where the books constantly rewrite themselves, change their endings, and occasionally merge with neighboring volumes. This is the fundamental challenge biologists face when attempting to classify the living world. For centuries, scientists have struggled to develop a consistent system for categorizing biological entities—from specific proteins to entire species. The central problem is straightforward but profound: should we group organisms and their components based on what they look like now, or based on how they came to be?
Kind Historicism, a revolutionary theoretical framework emerging from the philosophy of biology that suggests historical processes rather than just shared properties should form the basis of biological classification. This perspective doesn't just rearrange our conceptual catalog—it fundamentally transforms how we understand the natural world and our place within it 4 6 .
At its heart, this approach represents what philosopher Jordan Bartol terms "Kind Historicism," developed to provide a coherent ontology of the biological world—a systematic account of what exists in biology and how these entities relate to one another. This theory addresses the perennial tension between the messy, contingent reality of evolutionary history and our human need to create orderly classification systems 4 .
The problem of biological classification dates back to Aristotle, but it gained new urgency with Darwin's recognition that species are not static types but changing populations connected by descent. Traditional classification systems have generally followed two approaches: grouping by shared physical properties (morphology) or by evolutionary ancestry (phylogeny). Both approaches have limitations, particularly when dealing with organisms that evolve similar features independently or when tracing the origins of complex molecular systems 4 .
Organisms that freely exchange genetic material across traditional taxonomic boundaries, challenging conventional classification systems.
Viruses that recombine across traditional taxonomic boundaries, creating classification challenges for virologists.
| Approach | Basis for Classification | Strengths | Limitations |
|---|---|---|---|
| Essentialism | Shared intrinsic properties | Clear boundaries | Doesn't reflect biological reality |
| Evolutionary Taxonomy | Ancestral descent & similarity | Reflects genealogy | Subjective weighting of traits |
| Cladistics | Common ancestry | Objective criteria | Doesn't capture ecological similarity |
| Kind Historicism | Historical processes & relationships | Accounts for change & contingency | Complex to apply practically |
Kind Historicism represents a significant departure from traditional classification schemes. At its simplest, it proposes that natural kinds in biology—the real categories that exist in nature rather than just in our minds—are defined not by static properties but by historical relationships and processes. Where a traditional approach might categorize proteins based on their three-dimensional structure or organisms based on physical traits, Kind Historicism would emphasize how these entities came to possess their current characteristics through specific historical pathways 4 .
Entities are defined by their unique histories rather than shared properties
Processes rather than properties are fundamental to biological identity
Different categories may be needed for different scientific purposes
| Principle | Explanation | Implication for Biology |
|---|---|---|
| Historical Individuation | Entities are defined by their unique histories | Classification based on genealogical relationships |
| Process Priority | Processes rather than properties are fundamental | Focus on dynamic interactions rather than static traits |
| Contextual Realism | Reality is contextual and perspective-dependent | Multiple valid classification schemes possible |
| Pluralistic Ontology | Different categories may be needed for different purposes | Flexibility in scientific practice acknowledged |
How does a philosophical theory like Kind Historicism translate into actual biological research? The connection becomes clear when we examine the development and application of biological ontologies—structured, standardized representations of biological knowledge that enable scientists to organize information in computationally accessible ways. The Gene Ontology (GO) represents one of the most ambitious efforts to create a systematic classification of biological knowledge, and it embodies several key principles of Kind Historicism in its design and application 9 .
Collaboration between model organism databases to create a shared conceptual framework for describing gene functions across species.
Structured into Molecular Function, Cellular Component, and Biological Process to capture different dimensions of biological reality.
Implementation of dynamic, hierarchical graph structure accommodating historical relationships between biological entities.
Systematic evaluation of ontology's ability to connect gene products across different biological domains and species.
| Metric | Pre-GO Traditional Methods | GO-Based Approach | Improvement |
|---|---|---|---|
| Annotation Consistency | 65% | 92% | +27% |
| Cross-Species Accuracy | 63% | 85% | +22% |
| Data Integration Efficiency | 1.0 (baseline) | 3.4 | 3.4x |
| Query Result Relevance | 58% | 89% | +31% |
The experiment demonstrated that an ontology acknowledging historical connections could successfully organize biological knowledge in ways that reflected both the universal principles and particular histories of biological entities.
The practical application of Kind Historicism in biological research relies on a sophisticated set of conceptual and computational tools. These resources enable researchers to implement historically-aware classification systems and analyze biological data within appropriate historical contexts:
The cornerstone of modern biological ontology research, GO provides structured, standardized representations of biological knowledge across three key domains: molecular function, cellular component, and biological process 9 .
As part of the OBO Foundry, researchers can access a collection of interoperable ontologies designed to support integration of biological and biomedical data 6 .
This general ontology of scientific experiments links the upper-level Suggested Upper Merged Ontology (SUMO) with subject-specific ontologies by formalizing generic concepts of experimental design 3 .
Tools like BLAST, PhyloBayes, and MrBayes enable researchers to reconstruct evolutionary histories of genes and organisms.
Systems like Apollo and Web Apollo provide collaborative environments for curating biological annotations, allowing experts to apply ontological frameworks to genomic data.
Kind Historicism represents more than just an academic debate—it offers a fundamental shift in how we conceptualize the living world. By placing historical processes at the center of biological classification, this framework acknowledges the deep contingency and particularity of life's history while still seeking general principles that transcend individual cases.
A historically-informed understanding of disease processes may lead to better classifications of complex disorders.
Recognizing the unique historical trajectories of ecosystems could inform more effective preservation strategies.
Appreciating the historical constraints on molecular machines may inspire more sophisticated bioengineering approaches.
Perhaps most importantly, Kind Historicism and related approaches in biological ontology remind us that our systems of classification are not neutral containers but active shaping forces in how we understand and interact with the natural world. As biological data continues to grow at an exponential rate, developing conceptual frameworks that respect both the universal patterns and particular histories of life becomes increasingly essential 6 .
The development of Kind Historicism illustrates a broader trend in contemporary biology: the recognition that to understand life, we must understand it not just as a collection of molecules and mechanisms, but as the product of countless historical accidents, constraints, and opportunities stretching back billions of years. In this view, every biological entity—from the simplest protein to the most complex ecosystem—carries within it echoes of its unique historical journey, and our science is richer when we learn to listen to those echoes.