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Rulebooks of taxonomic nomenclature, in biology

Nomenclature codes or codes of nomenclature are the various rulebooks that govern the naming of living organisms. Standardizing the scientific names of biological organisms allows researchers to discuss findings (including the discovery of new species). As the study of biology became increasingly specialized, specific codes were adopted for different types of organism. To an end user who only deals with names of species, with some awareness that species are assignable to genera, families, and other taxa of higher ranks, it may not be noticeable that there is more than one code, but beyond this basic level these are rather different in the way they work.

In taxonomy, binomial nomenclature ("two term naming system"), also called binary nomenclature, is a formal system of naming species of living things by giving each a name composed of two parts, both of which use Latin grammatical forms, although they can be based on words from other languages. Such a name is called a binomial name (which may be shortened to just "binomial"), a binomen, name, or a scientific name; more informally it is also historically called a Latin name. In the ICZN, the system is also called nomenclature, "binomi'N'al" with an "N" before the "al", which is not a typographic error, meaning "two name naming system". The first part of the name – the generic name – identifies the genus to which the species belongs, whereas the second part – the specific name or specific epithet – distinguishes the species within the genus. For example, modern humans belong to the genus Homo and within this genus to the species Homo sapiens. Tyrannosaurus rex is likely the most widely known binomial. The formal introduction of this system of naming species is credited to Carl Linnaeus, effectively beginning with his work Species Plantarum in 1753. But as early as 1622, Gaspard Bauhin introduced in his book Pinax theatri botanici (English, Illustrated exposition of plants) containing many names of genera that were later adopted by Linnaeus. The introduction of two part names (binominal nomenclature) for species by Linnaeus was a welcome simplification because as our knowledge of biodiversity expanded, so did the length of the names, many of which had become unwieldy.

There are also differences in the way codes work. For example, the ICN (the code for algae, fungi and plants) forbids tautonyms, while the ICZN, (the animal code) allows them.

These codes differ in terminology, and there is a long term project to "harmonize" this. For instance, the ICN uses "valid" in "valid publication of a name" (=the act of publishing a formal name), with "establishing a name" as the ICZN equivalent. The ICZN uses "valid" in "valid name" (="correct name"), with "correct name" as the ICN equivalent. Harmonization is making very limited progress.

There are differences in respect of what kinds of types are used. The bacteriological code prefers living type cultures, but allows other kinds. There has been ongoing debate regarding which kind of type is more useful in a case like cyanobacteria.

A more radical approach was made in 1997 when the IUBS/IUMS International Committee on Bionomenclature (ICB) presented the long debated Draft BioCode, proposed to replace all existing Codes with an harmonization of them. The originally planned implementation date for the BioCode draft was January 1, 2000, but agreement to replace the existing Codes was not reached. In 2011, a revised BioCode was proposed that, instead of replacing the existing Codes, would provide a unified context for them, referring to them when necessary. Changes in the existing codes are slowly being made in the proposed directions. However, participants of the last serious discussion of the draft BioCode concluded that it would probably not be implemented in their lifetimes.

Many authors encountered problems in using the Linnean system in phylogenetic classification. In fact, early proponents of rank based nomenclature, such as Alphonse de Candolle and the authors of the 1886 version of the American Ornithologists' Union code of nomenclature already envisioned that in the future, rank based nomenclature would have to be abandoned. Another Code that was developed since 1998 is the PhyloCode, which now regulates names defined under phylogenetic nomenclature instead of the traditional Linnaean nomenclature. This new approach requires using phylogenetic definitions that refer to "specifiers", analogous to "type" under rank based nomenclature. Such definitions delimit taxa under a given phylogeny, and this kind of nomenclature does not require use of absolute ranks. The Code took effect in 2020, with the publication of Phylonyms, a monograph that includes a list of the first names established under that code.

Some protists, sometimes called ambiregnal protists, have been considered to be both protozoa and algae, or protozoa and fungi, and names for these have been published under either or both of the ICZN and the ICN. The resulting double language throughout protist classification schemes resulted in confusion. Groups claimed by both protozoologists and phycologists include euglenids, dinoflagellates, cryptomonads, haptophytes, glaucophytes, many heterokonts (e. g., chrysophytes, raphidophytes, silicoflagellates, some xanthophytes, proteromonads), some monadoid green algae (volvocaleans and prasinophytes), choanoflagellates, bicosoecids, ebriids and chlorarachniophytes. Slime molds, plasmodial forms and other "fungus like" organisms claimed by both protozoologists and mycologists include mycetozoans, plasmodiophorids, acrasids, and labyrinthulomycetess. Fungi claimed by both protozoologists and mycologists include chytrids, blastoclads, and the gut fungi. Other problematic groups are the Cyanobacteria (ICNP/ICN) and Microsporidia (ICZN/ICN).

The zoological code does not regulate names of taxa lower than subspecies or higher than superfamily. There are many attempts to introduce some order on the nomenclature of these taxa, including the PhyloCode, the Duplostensional Nomenclatural System, and circumscriptional nomenclature. The botanical code is applied primarily to the ranks of superfamily and below. There are some rules for names above the rank of superfamily, but the principle of priority does not apply to them, and the principle of typification is optional. These names may be either automatically typified names or be descriptive names. In some circumstances, a taxon has two possible names (e. g., Chrysophyceae Pascher, 1914, nom. descrip. ; Hibberd, 1976, nom. typificatum). Descriptive names are problematic, once that, if a taxon is split, it is not obvious which new group takes the existing name. Meanwhile, with typified names, the existing name is taken by the new group that still bears the type of this name. However, typified names present special problems for microorganisms.