The Autonomous Algorithm

The S&B Blog will be running a series of posts dealing with the rise of the black box and the fall of the foundations of systematics.

The Timetree of Life: A product
of the Autonomous Algorithm?

Presently, the majority of systematic analyses are constructed in the same way - a matrix is assembled and fed into a computer that then produces a branching diagram. Students of systematics are taught how to produce this branching diagram, using the algorithm, without context to the foundations of systematics. The result is a whole new generation of computer users ignorant of the basic fundamentals of systematics, such as theory (i.e., homology, monophyly), history (i.e., why we do what we do) and methodology (i.e., how to find homologs and construct a cladogram by hand). This also results in an increased dependency on algorithms, which in turn creates a new systematic history and theory that revolves around algorithms rather than concepts. The former black box, which implemented basic algorithms to find approximations of cladograms, is now totally autonomous to the theory, method and history that had gone into its creation. We call this the Autonomous Algorithm.


The Autonomous Algorithm is a self perpetuating phenomenon. Many users of phylogenetic software are unaware of the foundations of systematics and are totally reliant on algorithms to do their work. They are also dependent on the developers and programmers, who themselves are dimly aware of the foundations and their relevance to each new published algorithm. The Autonomous Algorithm has created a number of problems which we will attempt to address, namely:

1. Malpractice in Theory: Homologs as Homology
2. Misaligned Methodology: Cladistics as Phenetics
3. A Misconstrued History: Systematics as Phylogenetics

Before we begin, we wish to reemphasise our terminology to avoid any confusion.

Rationale of Terms

Theory herein are the basic fundamental principles underlying what we do. This means defining what we do and its associated logical procedures.

Methodology herein is the practice of what we do. Creating cladograms by hand, finding homologs, understanding the anatomy of an organism etc. are all part of what a systematist does.

Implementation herein refers to the numerical tools we use. These are generally black boxes (i.e., software that uses numerous algorithms that process our data). Most systematists are generally unaware of how these work exactly, but use them by proxy. An implementation is not equivalent to a methodology.

History herein is the history of an idea. This is sometimes referred to as an ‘internalist history’, since we are concerned with the theory and methodology of systematics over time. Whatever external history has occurred generally is irrelevant to how a systematic method works.

A natural classification herein is a hierarchical ordering of organisms based on systematic relationship.

A systematic relationship equivalent to kinship, that is, when two taxa are more closely related to each other than they are to any other taxon (herein systematic Monophyly or sMonophyly). Relationship here means a shared history. In hindsight this shared history is a result of some known or unknown evolutionary process/es. This relationship is only true if the relationship is based on two homologs that are more closely related to each other than they are to any other homolog (sHomology).

The Cladistic Parameter (herein CP) is a hierarchical representation all manifestations of a systematic relationship. Homology, for instance is a systematic relationship of homologs, or the parts of an organism, while monophyly is a relationship of taxa based on homologies. This can be expressed diagrammatically (as branching diagrams) to highlight the dependancy of one relationship within another, that is to say monophyly cannot exist without homology and homology cannot exist without a relationship between homologs, or:

The Cladistic Parameter = Relationship : sHomology : sMonophyly : sTaxon

sTaxa herein are deemed to be relationships between organisms (e.g., their parts, individuals, populations, etc.). We recognize that there are many artificial taxa that share closer relationships to other taxa than they do to themselves (e.g., reptiles, fish etc.). These taxa are not informative and add little to our knowledge of natural classifications. When we refer to sTaxa we refer to natural classifications.

In the next post we will tackle Malpractice in Theory, namely the widespread phenomenon of confusing homologs with homology.