Posted by: dacalu | 10 March 2016

The Naming of Organisms

Here is an essay I prepared for the Center of Theological Inquiry on the history of how we name organisms.

 

What’s in a name? that which we call a rose / by any other name would smell as sweet.[1]

 

Concepts of names and knowledge within science have deep roots. Just as a genome bears the imprint of many generations of environment, so scientific naming bears the imprint of millennia of arguments about how we know about the universe. These imprints may no longer be useful – or adaptive – but they still impact the way we speak about nature. Such a brief overview can only touch on historical highlights, so I have chosen to focus on the natural-ness of names and how they reflect on the relationship of humans to other things.

Modern nomenclature rests on a foundation of Greek natural philosophy, particularly concepts of “natural kinds” and “differentiae.” Plato introduces the first concept in Phaedrus, oddly enough speaking about kinds of passion. “This, in turn, is to be able to cut up each kind according to its natural joints, and to try not to splinter any part, as a bad butcher might do.” (265e) A hope persists that scientific categories might represent real divisions in nature, rather than arbitrary categories imposed by particular authors. In this way, it is hoped that one truth can be converged upon, from a variety of beliefs. There has been much controversy over whether these “natural kinds” are possible, but I will side with Christopher Shields in saying that some kinds are more natural than others; they are more likely to be useful for a broad range of researchers.[2] Aristotle introduces the second concept when speaking about sciences in Metaphysics (IV). He introduces the idea that we reason with broad categories (genera, sing. genus) in which types (species, sing. species) are distinguished using fixed characters (differentiae). Genera, species, and differentiae have been foundational to scientific naming at least since the eighteenth century.

Aristotle divides sublunary things (imperfect beings, contrasted with the perfect, eternal heavens) into two categories – elements, moved by necessity to their proper region (fire above air above water above earth), and living things, moved by necessity and a soul.[3] The nature (physics) of souls rests in their activity of nutrition and reproduction (vegetable souls), sensation and motion (animal souls), and reason (human souls). Seeking perfection and being unable to live eternally below the heavens, they make copies of themselves, but the types or species of souls remain the same eternally. Thus offspring look like parents. These types and species were common in biology through the Renaissance.

In the eighteenth century, Carl von Linné, picks up on this Aristotelian typology in a particularly Enlightenment way. Aristotle has an etiological nomenclature – based on first principles; Medieval and Renaissance scholars have a relational and anagogical nomenclature – based on the moral import for people; but Linné (or Linnaeus) introduces a systematic taxonomy – intended as a universal and natural ordering. Michel Foucault (The Order of Things 1966) and Margaret Osler (Reconfiguring the World 2010) set forth the metaphysical and epistemological shifts that make this possible. In short, the intrinsic purpose, organization, and order of Aristotle’s souls have been exported to the mind of God, a move that simultaneously promises a comprehensive, well delineated, and replete universe and human comprehension thereof. In his grand work on systematics, Linné states “The Earth’s creation is the glory of God, as seen from the works of Nature by Man alone.”[4] Adam’s role as namer in the garden is extended to scientists in the current day. “The first step in wisdom is to know the things themselves; this notion consists in having a true idea of the objects; objects are distinguished and known by classifying them methodically and giving them appropriate names. Therefore, classification and name-giving will be the foundation of our science.”[5]

Within this frame, Linné divides the world into minerals, plants – which are organized and have life – and animals – which are organized, have life, sensation, and locomotion. He roughly follows Aristotle’s designations according to the vegetable and animal souls. He also speaks of humans as rational animals “endowed with a portion of intellectual divinity.”[6] Our divinity allows us, and us alone (under heaven), to perceive the divine order. (Aristotle makes a similar move with the intellectual soul.) These “kingdoms” of animal, vegetable, and mineral are subdivided into classes, orders, genera, and species, though Linné is quick to point out that “classes and orders are arbitrary; [only] the genera and species are natural.” (ibid.) The last two categories come to be what we call the “Latin binomial” the official scientific name for a species. With Aristotle, Linné was convinced they were eternal, though later in his life careful thinking about hybrids made him question this.

In the 19th century, the eternal taxonomy gave way to a historical and once again etiological theory of biological naming (Foucault, again). Jean-Baptiste Lamarck (Philosophie Zoologique 1809) popularizes theories of evolution and the changeability of species. Charles Darwin (On the Origin of Species by Means of Natural Selection 1859) provides a mechanism, by which such changes could occur, and suggests a single tree of life, through which all organisms might be related. Darwin sets the stage for a new kind of taxonomy, in which organismal names are consistent with their place on such a tree. Willi Hennig (Phylogenetic Systematics 1950) argues that all biological nomenclature should be based on the historical relationships between individuals and groups – not just on similarity, but on evolutionary homology. Important phylogenetic traits are those that two individuals share because they arose once in a common ancestor. The earliest such “phylogenetic trees” tracing common ancestry were based on phenotypes – physical features and behaviors – and parsimony – the rule that simple family trees (fewer changes along branches) are better trees. More recent phylogenies are more likely to use genotypes – gene sequences – and statistical models of mutation.

This shift to “molecular phylogenetics” was facilitated by the discovery of nucleic acid structure and the small subunit of ribosomal RNA.[7] This SSU rRNA is required by all organisms to express genes, resulting in very slow mutation rates. Organisms literally cannot live without it. Nor will they easily suffer changes; the one gene does so much, that small changes can have big effects on fitness. We can identify it in all cellular organisms, making it an ideal molecule for creating universal trees of (Earth) life. Such a tree revealed a vast diversity of life as yet unrealized. The category of vegetable has always covered such a range, but we usually identify it with multicellular photosynthetic organisms, or plants. We now speak of three Domains: the Archaea, the Bacteria, and the Eukaryotes. The kingdoms of Animalia, Plantae (plants in the narrow sense), and Fungi all possess cells with membrane-bound nuclei; thus, they are all within the Domain Eukaryotes. The domain also includes a wide variety of unicellular organisms.

Modern biological nomenclature follows a number of basic rules regulated by international professional societies composed of prominent scientists within their fields. The goal is consistent communication. All require unique Latin (and Greek) binomials composed of a genus and species and the two always come together. Many species may belong to a genus, but no species is genus free. Genus and species must be published in a peer refereed journal with a type specimen – a concrete example of the organism or group – along with specific differentiae allowing other scientists to identify the species. Higher level groupings may also be proposed. Though they are not regulated as tightly as genus and species, the higher level groups also require a type specimen. When conflicts arise, the oldest attribution is considered authoritative. Thus if two organisms have received different names, but are found to be of the same species (or higher level group), the older name is assigned to both. Common Latin binomials include Homo sapiens (humans), Oryza sativa (rice), and Escherichia coli (gut bacteria). The most common groups are, in increasing specificity: Domain, Kingdom, Phylum, Class, Order, Family, Genus, and species. (E.g., Eukaryota, Animalia, Chordata, Mammalia, Primates, Hominidae, Homo sapiens.) Attempts are made for each such group to be monophyletic – comprising all and only descendants of a single common ancestor. Ideally groups also correspond to a clearly identified, adaptive trait. (E.g., humans are in the groups of organisms that possess true nuclei, are multicellular and motile, have notochords, produce milk, Resemble humans, ditto, ditto, and are intelligent. Admittedly the last four groups are very human focused.)

There are formal codes of nomenclature and regulatory committees for naming Animals, naming algae, fungi, and plants, and for naming Bacteria and Archaea. (Note that algae, fungi, and plants do not warrant capital letters; they reflect common names but not accepted monophyletic taxa.) Some unicellular Eukaryotes may fall under the jurisdiction of multiple or no groups. Much debate has arisen in the late 20th and early 21st century on how inclusive or exclusive groups should be. Even at the species level, questions can be difficult. Ernst Mayr made one of the most popular proposals, the “biological species concept.”[8] The BSC holds that a species comprises all and only those individuals of sexual species that can mate with one another. Intuitively helpful and largely successful for animals and plants (restrictive definition), it fails in a few cases (e.g., lions and tiger can mate but their offspring are sterile), and does not apply at all for the vast majority of organisms, which reproduce asexually. Genotypic similarity has been proposed, with a 3% cut-off for species. The solution is logical, but fails to operate as desired. Humans and chimpanzees have less than 3% difference, while E. coli have diversity up to 40%. Some level of arbitrariness remains. The regulatory committees remain emphatic that they regulate the usage of names and how they refer to groups but do not “infringe upon taxonomic judgment” concerning whether the groups are natural or, in any way, objective.

Viral nomenclature follows the pattern of biological nomenclature, though species are even harder to define. Thus strains, identified within a particular lineage of descent and environmental niche, are more commonly named than genus and species. Beyond biology, celestial bodies, geological time periods, and minerals likewise have their own nomenclature, code, and committees. Below the notes, I’ve provided a list of the officials responsible for monitoring each of the codes.

[1] William Shakespeare, Romeo and Juliet II.ii

[2] Shields, C. (2012) The dialectic of life. Synthese, 185, 103–124.

[3] Studtmann, Paul, “Aristotle’s Categories”, The Stanford Encyclopedia of Philosophy (Summer 2014 Edition), Edward N. Zalta (ed.), URL = <http://plato.stanford.edu/archives/sum2014/entries/aristotle-categories/&gt;.

[4] Linné, Carl von (1758) Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. 10th ed. Stockholm: Holmiae. p. 3

[5] Linné, Carl von (1964) Systema Naturae. Nieukoop: B. De Graaf. P.19

[6] Linné (1758) p. 3

[7] Watson, J. D. & Crick, F. H. (1953) Molecular structure of nucleic acids. Nature, 171(4356), 737-738. Woese, C. & Fox, G. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences, USA, 74, 5088–5090.

[8] Mayr E. (1942) Systematics and the origin of species from the viewpoint of a zoologist. New York: Columbia University Press.

Animals

Int’l Code of Zoological Nomenclature

Int’l Commission on Zoological Nomenclature

Int’l Union of Biological Sciences

Plants etc.

Int’l Code of Nomenclature for algae, fungi, and plants (Melbourne Code)

Int’l Association for Plant Taxonomy

Int’l Botanical Congress

Cultivated Plants

Int’l Code of Nomenclature for Cultivated Plants (see here)

Int’l Commission for the Nomenclature of Cultivated Plants

Int’l Union of Biological Sciences / Int’l Society for Horticultural Sciences

Archaea & Bacteria

Int’l Code of Nomenclature of Bacteria (see here)

Int’l Committee on Systematics of Prokaryotes

Int’l Union of Microbiological Societies

Viruses

Int’l Code of Virus Classification and Nomenclature

Int’l Committee on Taxonomy of Viruses

Int’l Union of Microbiological Societies

Attempts to Unify Biological Nomenclature

Int’l Committee on Bionomenclature

Geological Time

Int’l Commission on Stratigraphy

Int’l Union of Geological Sciences

Minerals

Commission on New Minerals Nomenclature and Classification

Int’l Mineralogical Association / Int’l Union of Geological Sciences

 

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Responses

  1. Animal Taxonomy is pretty straight forward. Plants on the other hand get messy. Jalapeno peppers and tomatoes (all types) are different cultivars the same species. Same thing with are all roses. Grasses on the other hand have 3, 4, or 5 orders depending on where you got your Ph.D. but they still can occasionally hybridize with each other to form fertile, but unstable offspring. As I said, messy.

    • Plants are certainly more challenging, but animals have issues as well. Mostly this is a problem with the species concept. So far we don’t have any perfect definition for species. Under the popular (for animals) “biological species concept,” you have sterile hybrids and ring species. Sterile hybrids happen when A can mate with B, but their offspring are infertile. For example, offspring of (M) donkey and (F) horse are mules, (M) horse and (F) donkey are hinnies, (M) tiger and (F) lion are tigons, (M) lion and (F) tiger are ligers. Dogs and frogs and guppies all have sufficiently murky “species” that cross breeding and intermediate non-sterile hybrids arise. Ring species are cases where members of “species” A can mate with B, B with C, and C with D, but B can’t mate with D and A can’t mate with C.


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