Forms of Life part 1: Intro to Bionomenclature

Part one of what I hope will be series of at least two articles on how different lifeforms differ.

To start off, this article will give an overview of the hierarchical classification of biological life, with a focus on the nomenclature of biological nomenclature.

Taxonometric Methods

Or, ways of deciding what species are in the groups and what are not. A Taxon, plural Taxa, is any group of organisms considered to form a defined group by any biological characteristic.

Grades: Morphology and Physiology

Morphology is the study of the form of living things. This includes eidonomy, study of the external form (size, shape, structure and colour) and anatomy, the internal form (position, size and shape of bones, organs and other internal structures). The set of all observable traits of an organism is called its phenotype.

Morphology is notably distinct from physiology, the study of the function of the organs and other internal components and how they work together to allow for metabolism and other functional activities such as digestion, cognition, movement etc.

Morphology and Physiology provides an obvious way to differentiate lifeforms by their observable physical attributes. For example, in a purely morphological system, a simple top level division might be single-celled vs multicellular life forms. Distinct taxa can be defined within these (e.g. plants vs animals), which can be further divided (e.g. number of legs, or diet - herbivores vs carnivores vs omnivores) and so on.

Example Taxonomy using Morphological Classification

These type of morphological and physiological taxa are sometimes called "grades", in contrast to "clades", described below.

This method of classification might seem straightforward, at least at the top levels - however, some forms of life may straddle categories in ways that make them difficult to define. For example. slime molds can thrive as single-celled organisms, but can form multicellular structures which function as a body, moving around and forming stalks to release spores. This breaks the clear unicellular/multicellular division at the top of the system above.

Clades: Grouping by Ancestry

Since DNA analysis has become widespread, the use of phylogenetic taxa or "clades" to classify lifeforms has become more common.

Clades are defined as a group of species that shares an exclusive common ancestor (or alternatively, a group containing all descendants of a common ancestor). Clades can be thus treated similar to mathematical sets, with superclades sharing a more distant ancestor and subclades sharing a more specific one

To count as a clade the group must be monophyetic, i.e. include all descendants of an ancestor, not excluding any. A group which would be a clade but excludes a small number of species may be described as paraphyletic. For example, the clade "Amniote" includes the subclades "Mammaliaformes" (mammals) and "Ornithurae" (birds), as well as Reptiles, which form the paraphyletic group "Reptilia" from the remaining species of Amniote which are morphologically similar (and neither mammals nor birds).

Conversely, a polyphyletic taxa contains members from many clades with varied ancestry; Algae and Protists are notoriously polyphyletic.

As well as being more useful for analysis of evolution and genetics, clades have a significant taxonomic advantage in that they can be determined based on the purely objective factor of genetic ancestry, whereas division by grades becomes increasingly subjective at finer divisions.

Clades sometimes have the disadvantage that some species that are useful to group together because of common traits may be distant ancestors, whereas species that are radically different may be genetically close ancestors.

For example, Archea are in most ways similar to Bacteria, especially in terms of their cells, with all other lifeforms having a radically different cell structure to Archea and Bacteria. However, all the other forms of life seem to have evolved from Archea, making Bacteria a clade, and all other life forming another clade.

Fortunately, grade-based divisions often do correspond exactly to a specific clade, making the approaches equivalent, such as the examples of mammals and birds used above.

Species, Subspecies and Morphs

A species is typically the lowest and most basic unit in taxonomy, defined generally as a grouping of organisms of which any two (of appropriate sexes if necessary may produce fertile offspring.

The qualifier that offspring must be fertile means for example that horses and donkeys are distinct species despite being able to interbreed to produce infertile mules and hinnies. Hybrids which are nearly always infertile (such as mules) are not classified as a distinct species, instead being classified by their parent species (i.e. "donkey x horse").

The definition of speciation is further complicated by ring species, a set of species which can interbreed with nearby groups on the abstract "ring" but not with groups too far away on the ring. Many bacteria and birds form ring species. An example is the gull species within genus Larus - several species of Herring Gulls can breed with each other, including the East Siberian Herring Gull; the latter can breed with other Siberian Gulls, but Siberian Gulls cannot breed with the European or American Herring Gulls.

Some subspecies or intraspecifc terms are used in taxonomy, for example strains of a species are genetically uniform and a kind of clade; a morph is a grouping within a species based on any kind of morphological characteristic, such as hair or eye colour.

"Official" Taxonomy Ranks

The International Committee on Bionomenclature (ICB) manages a series of subcommittees of taxonometic specialists within subfields of biology (zoology, botany, etc) to decide how lifeforms are classified. The modern (as of 2019) ICB system has eight levels or ranks, which are mostly traditional; some taxonomies (especially zoology) also use super-ranks and sub-ranks within each level.

The original systems were based purely on morphological characteristics, but clade-based divisions are used more recently; notably the top-level division used to be "Empires", based on the morphological division between lifeforms with prokyarotic cells vs eukaryotic cells; it has recently been changed to three "Domains" of Bacteria, Archea and Eukaryota as they form distinct clades as well as having unique morphological characteristics.

Rank Name Example Main Discriminant
1 Domain Eukaryota Cell Type
2 Kingdom Animalia Gross Morphology
3 Phylum Chordata Specific Anatomical Elements
4 Class Mammalia Organs / Arbitrary
5 Order Primates Arbitrary
6 Family Hominidae Arbitrary
7 Genus Homo Arbitrary
8 Species Sapiens Can reproduce with same species

Different subfields within biology have increasingly different approaches to classifying taxa in the lower ranks, and varying terminology. Botany in particular has its own jargon, such as using "Division" as a synonym for "Phylum" and the use of "cultivar" for some cultivated plants.

Subspecies Classification

Zoological classification allows for two or more subspecies to be defined; Algae, fungi, and plants may have specific varieties within a species. Generally, groups of organisms which could interbreed but do not because of geographic location or similar factors and have different morphological traits are considered a subspecies or variety.

Biological Types

In traditional taxonomy, when a species is defined it is considered important to provide a specimen which is a clear example of the unique characteristics of a species; this specimen is called a type. Many museums contain collections of preserved types.

Types of types include Holotypes which are considered original, definitive examples, Neotype which are definitive types used after an original holotype has been damaged or lost, and Paratype which are additional specimens considered inferior examples to the holotype/neotype.

Binomial Species Names

Species are referred to officially by using both the genus name and species name (e.g. "Homo sapiens"); most ICB committees encourage keeping this binomial name unique for each species and in some it is a hard requirement.

The practice of drawing the names of a genus from a specific type, especially in zoology, means that many binomial names consist of the same name repeated; examples include Gorilla gorilla, Rattus rattus, and Vulpes vulpes (the red fox).

The Catalogue of Life

The Catalogue of Life <https://www.catalogueoflife.org> is a public database of all taxa across all domains of life, plus viruses (see the following section). The catalogue is the most complete database of species available, including nearly 2 million species as of 2019.

As well as the dynamic database, a reference version is made once per year, which can be used in academic and legal environments to provide a reference which will remain unchanged and can be referred to by others at a later date.

Note on Things that Aren't Proper Lifeforms

Viruses, Viroids, Virusoids and Prions - these are merely bits of RNA or misfolded proteins (Prions) which are not capable of metabolising anything or growing, and so do not qualify as forms of life. The ICB does have a subcomittee for things in this category , the "International Committee on Taxonomy of Viruses". However they are still classified separate to "proper" biological life.

Viruses and virus-like structures likely do not share a common ancestor with biological life, although due to horizontal gene transfer some viruses contain genes received from lifeforms. Prions are mutations of proteins; they can be classified by the lifeforms where that prion originated, such as the Bovine Spongiform Encephalopathy prion which causes "Mad Cow" disease.

The terms "Pathogens" and "infectious agents" are often used to include viruses, prions as well as infectious bacteria, amoebae etc. They do not imply that the pathogen is a true lifeform, merely that it it may cause some kind of infection.