Updated: May 4
1.1 Natural vs Artificial Classification
There are many ways one could use to group living organisms but not all of the classification methods are significant in biology, at least not to the people who wanted to study how individual species become the way they are today (a.k.a. evolutionary biologist). Let's take a look at the following examples. Do you noticed any patterns?
You are right, this is a trick question. Although it might be tempting for you to sort these animals based on their unique pigmentation, it is important to realize animals of all shapes and sizes can exhibit similar coloration without being evolutionarily related to one another. Therefore, this form of classification might not be very meaningful to someone who wanted to study evolutionary history. However, this form of classification might be very meaningful to someone who study black-and-white pattern distribution in an art class. It's all about context.
The sorting of organisms based on generic, trivial features (e.g., color, body size) or other non-evolutionary features (e.g., sky animal, land animal, sea animal) is known as artificial classification whereas the sorting of organisms based on and supported by biologically meaningful features (e.g. morphology, anatomy, genetic) is known as natural classification.
Even the most widely accepted organism classification method is not without controversial. After all, Earth’s life is vast and individual complexity can be highly unpredictable. As our technology advances and knowledge in sciences deepen, new evidence might appear someday in the future to overwrite parts or even replace the entirety of existing classification methods. It is therefore important to realize that methods in sciences are constantly evolving. Well-supported theories that are widely accepted during this time period can still change in the future, as illustrated by examples in the next section.
1.2 History of Organism Classification
An accomplished Swedish botanist and physician born in the early 18th century, Carl Linnaeus's contribution to the field of taxonomy is so profound that he is often recognized as the father of modern taxonomy. Throughout his scientific career, he had published several influential pieces such as the Imperium Naturae, Species Plantarum for plants, and the Systema Naturae for animals which will later serve as the foundation for modern biological nomenclature. Although the first edition of Systema Naturae was published in 1735, the 10th edition published in 1758 is often regarded as being the most influential because Linnaeus started naming animals in two words (specifically binomial nomenclature). After Linnaeus' death in 1778, the 13th (also the last) edition of Systema Naturae was published by Johann Friedrich Gmelin somewhere between 1788 and 1793.
Linnaeus’s hierarchical classification separates organisms into three major groups, namely the Animal kingdom (Regnum Animale), the Vegetable kingdom (Regnum Vegetabile), and the Mineral kingdom (Regnum Lapideum). These kingdoms are further divided into classes, orders, genera, and species.
Throughout several editions of his Systema Naturae, Linnaeus proposed 6 classes under the animal kingdom, 5 of which are still used today after more than 250 years. Although the mineral kingdom is now defunct, Linnaeus's Animal & Vegetable (Plant) kingdoms survived.
You are learning a naming system in biology that is at least 250 years old. How cool is that?
Attributing to hard works from individual scientists as well as the collaborative efforts of various researchers from across different time period, more kingdoms were subsequently introduced. Some notable mentions include the Protista kingdom that was brought to the light by German biologist Ernst Haeckel, the Monera kingdom created by American biologist Herbert Faulkner Copeland, and the Fungi kingdom introduced by American plant ecologist Robert Harding Whittaker who also compiled all existing kingdoms at the time to create the five-kingdom scheme.
In 1977, with the aid of RNA molecular analysis, American microbiologist Carl Richard Woese revised the Monera kingdom and came out with two distinct kingdoms – Eubacteria and Archaebacteria. Due to the profound differences between eubacteria, archaebacteria and eukarya, Woese created the three-domain system that we now know today. Cavalier-Smith later revised the Protista kingdom and came up with the Protozoa and Chromista kingdom. While many major kingdoms have survived and remained relatively unchanged to this day, several taxonomic groups have undergone rigorous revision as the sciences to detect organism relatedness evolve and improve with time.
1.3 Binomial Nomenclature
Binomial nomenclature is a two-word naming convention that scientists used to name living thing. Although binomial nomenclature was first proposed and used inconsistently by Gaspard Bauhin in 1623, the idea of using binomial nomenclature as a standardized naming convention was initiated by Carl Linnaeus in his 10th edition of Systema Naturae. To this day, this naming convention is upheld and governed by several organizations, such as the International Code of Zoological Nomenclature (ICZN) and the International Code of Nomenclature for algae, fungi, and plants (ICNafp) to serve as a unanimous guideline for species naming.
The binomial nomenclature provides each organism with a genus name and a specific epithet (both written in Latin). See the right diagram for an illustration of the scientific names for modern human and several early human species.
Consider a world where naming convention isn't standardized. That was exactly the period before Linnaeus published some of his influential pieces. Before the Species Plantarum was published in 1753 and the 10th edition of Systema Naturae was published in 1758, long, descriptive polynomial Latin names were given to both plants and animals. There are simply too many ways an organism can be called! "Well, how about a standardized generic name for some animals then?" - you ask. Take a closer look at the following animals. Using as few words as possible (in English), try to think of a generic name that can be used to describe all three of them.
>I will give you a few minutes. Continue reading when you are ready.
Madagascar Day Gecko Yemen or Veiled Chameleon Chinese Water Dragon
Phelsuma madagascariensis Chamaeleo calyptratus Physignathus cocincinus
Most people would go with"green lizard". However, this generic name isn't too helpful either consider it can literally point towards tens of thousands of lizard-like organisms that also happen to be green. Given the constraints caused by language barrier, cultural influences, and personal interpretation when practicing science in different parts of the world, a consensus in scientific or Latin name will certainly help worldwide scientists to communicate better.
1.3.1 Rules in Binomial Nomenclature
The general rule is that each specific epithet corresponds to one unique species that exists within the same genus. However, the specific epithet alone does NOT represent the species name of such organism. More explanations are listed below:
The species name MUST always be expressed in its full, binomen state (genus name plus a specific epithet).
A genus name (e.g., Homo) and a species name (Homo sapiens) should always be italicized OR underlined.
The first letter of a genus name MUST always be capitalized; all letters in a specific epithet should be in lower case.
Unlike the specific epithet, a genus name represents a specific group thus can be used independent of an epithet.
Higher taxonomic levels (e.g., kingdom or division, phylum, class, order, family) should be capitalized but should not be italicized.
Abbreviation of the genus name with just its initial is acceptable when referring to species of the same genus multiple times.
Extinct species still uses the same naming convention with no exception. However, the symbol "†" is usually present to indicate extinction.
In both biological sciences and linguistics, the species name is always singular. (Homo sapiens is...) ✓ (Homo sapiens are...) ✗ (Homines sapientes are...) Unconventional (Three Homo sapiens specimens are...) ✓
Have fun naming living thing!
 Linnaeus, C. (1735). Systemae Naturae, sive regna tria naturae, systematics proposita per classes, ordines, genera & species.
 https://archive.org/details/generellemorphol01haec/page/n9 (Haeckel, 1866)
 https://www.jstor.org/stable/2808554?seq=1#page_scan_tab_contents (Copeland, 1938)
 http://www.ib.usp.br/inter/0410113/downloads/Whittaker_1969.pdf (Whittaker, 1969)
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC432104/ (Woese & Fox, 1977)
https://www.researchgate.net/publication/22732598_An_ancient_divergence_among_the_bacteria (Woese et al., 1977)
 https://www.ncbi.nlm.nih.gov/pubmed/2112744 (Woese et al., 1990)
 https://mmbr.asm.org/content/mmbr/57/4/953.full.pdf (Cavalier-Smith, 1993)
 https://www.ncbi.nlm.nih.gov/pubmed/9809012 (Cavalier-Smith, 1998)
 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418965/#pone.0119248.ref019 (Ruggiero et al., 2015)