Taxonomy - The classification of living things
Here we shall not go into taxonomy in depth, but simply state what is needed to put the pages in this
BioTech section into context.

It is important to classify living creatures, first and foremost to assist in identification. If a biologist in Europe
is studying the onion fly, a type of insect, they need to know whether or not they are studying the same
insect that a Canadian may call the onion fly. This is the first point -  English names are colloquial, for
example the bluebell in England is not the same flower as what the Scottish commonly call the bluebell and
the Spanish have a variety which is similar but distinctly different. To overcome these problems, scientists
give every species or type of living thing a special name, which usually takes the form of a Latin binomen
('binomen' means 'double name') for example,
Quercus robur is the English oak and Homo sapiens (lit.
'wise man') is the human species.

Note that the binomen is always written in italics (or alternatively underlined) to distinguish it from the
English name and also that the first name (the genus name) is capitalised whilst the second name (the
species name) is not. The second name is never given without the first name, though the first name can be
given by itself to refer to the whole genus or if the species is not certain.

The genus represents a larger class,
Quercus is the genus which includes all oak trees, such as Quercus
robur
(the English oak) and Quercus virginiana (the Florida live oak) which are two different species of oak
tree. A species is defined as that group of organisms of a given type that are capable of breeding with one
another - pollen from
Quercus robur will (usually) only fertilise female organs of Quercus robur trees, and
not those of
Quercus virginiana, and likewise Quercus virginiana breeds with its own species. There are
exceptions to this, especially in plants, when occasionally two species will interbreed to give a hybrid, which
is essentially a new species (this is one mechanism whereby evolution produces new species).

What makes
Quercus virginiana and Quercus robur both oak trees? Well, these trees have certain
characteristics in common - both produce fruit of the acorn type and both have similar bark and are similar
sizes, but there are differences -
Quercus virginiana has branches that arch gracefully toward the ground,
which made them ideal for building ship hulls, whilst
Quercus robur has branches that tend to twist and
bend in serpentine fashion. This is useful - if you know that a tree is called
Quercus ilex then you might
suspect that it too will produce acorns, and indeed it does, but if you guessed its leaves would like those of
Quercus robur, then you would be in error, its leaves are more like those of the holly (Ilex genus) in that
they are leathery and the tree is evergreen. If I told you that all oak trees produce acorns, then you know
what type of fruit
Quercus rubra (the red oak) produces and could well guess its shape and general
appearance. Also if you find a species you are not familiar with but see that it has acorns, then you know it
belongs to the genus
Quercus. Thus, classification helps us to identify things and also teaches us a lot
about the nature of those things.

If our European and our Canadian both study
Delia antiqua (the onion fly) then we know they are working
on the same insect. This is very important! Take the beetle
Aleochara bilineata and the beetle Aleochara
bipustulata
- both belong to the same genus and are almost indistinguishable by eye, but a very close
examination reveals which is which - the Latin names avoid confusion between the two.

Other than genus we have some larger classifications, in fact in descending order the classification
categories are: Kingdom, phylum, class, order, family, genus and species. For example, human beings
belong to the following categories:

Kingdom: Animalia (animals)
Phylum: Chordata (chordates)
Class: Mammalia (the mammals)
Order: Primates
Family: Hominidae
Genus:
Homo
Species: sapiens

(The Chordata are animals with stiffening rods in their spines, includes the vertebrates which have
backbones).

Note that the larger categories can be given both a Latin name, e.g. Mammalia, and an English equivalent,
mammals, in which case the Latin version is capitalised, but not the English version and neither is italicised
or underlined (Latin words are generally italicised in English, however, italicising
Mammalia makes it look
like a genus name, so we tend not to italicise it!)

Here is one more example - the English Oak:

 Kingdom: Plantae (plants)
 Phylum: Angiospermaphyta (angiosperms or flowering plants)
 Class: Magnoliopsida (Dicotyledoneae)
 Order: Fagales
 Family: Fagaceae (beach family)
 Genus:
Quercus
 Species: robur

The full breakdown like this is rarely given, except in classification keys, but its is helpful to know that oak
trees (
Quercus genus) are in the same family as beech trees (Fagus genus) because this tells me that the
two have some similarities, though I would not expect beech trees to produce acorns, and indeed they
don't. Families are usually named after a representative genus, such as the beech trees in this case, but
not all members of the family belong to this genus!

This begs the most important question - how do we decide whether or not beech trees, pine trees, rose
bushes and dandelions belong to the same family as oak trees? Well, first we can look at obvious
characteristics - beech trees are about the same height and girth as oak trees, both also shed their leaves
in winter - they are deciduous and both are broad-leaved trees. Pine trees are evergreen and have
narrow, needle-like leaves. Rose bushes have broad leaves and are woody plants, whereas the dandelion
is not even a tree, but it is a flowering plant and so a member of the angiosperms. Pine trees do not
produce flowers, so belong to a different phylum (the Coniferales, or conifers). By this scheme the
dandelion is more similar to an oak tree than is a pine tree! Nevertheless, the fact that pine trees produce
cones instead of flowers is actually a more useful distinguishing feature than its size and woodiness. In
prehistoric times, dwarf species of elephant existed that were a little bigger than a swan, so size is not so
reliable as a defining characteristic!

This kind of scheme, based upon observable characteristics is essential to the field biologist or naturalist
who wishes to identify the creature they are looking at. It also tells us something about genetic and
evolutionary relationships - as it happens cone-bearing plants appeared long before flowering plants, so
an oak tree is indeed a closer relative of the dandelion that it is of the pine tree! However, looks can be
deceiving - sometimes organisms that appear similar are distant relatives and organisms that look different
are close relatives. Their is a species of willow tree that is a small flat shrub-like plant, but it shares a
common ancestry - changing a few genes can dramatically alter a creature's appearance! Conversely, a
bat may be warm-blooded and have wings, but as a mammal it is more closely related to
Homo sapiens
than it is to a pigeon!

For this reason, biologists have devised classification schemes that are based on genetic similarities
rather than appearances. These schemes are useful to help us tell how closely related two organisms are.
For example, if I wanted to know how closely related a yew tree was to a giant sequoia, then I could look at
their genetic similarity.

Controversy!

Here lies a problem caused by taxonomists - they constantly restructure the 'official' classification scheme
to reflect evolutionary relationships - great for helping us understand biology, but not so great to our
naturalists who is unlikely to fingerprint the DNA of every creature they find!

For this reason most biologists ignore the official scheme and use whichever one fits their purposes. The
good news is, that most of the confusion is in the class, order and family categories, which usually concern
field biologists the least. However, some organisms have old binomens that are no longer in use - if you
study
Delia antiqua, then you need to know its earlier names if you want to access the older literature!

Here we shall largely ignore these details. For now, let us concentrate on the Kingdoms. Taxonomists even
disagree on the number of kingdoms (!) but we shall use the following Six-Kingdom Classification:
bacteria link
Kingdom 1: The bacteria (prokaryotes or monera):

Characteristics: Cellular (comprised of one or more cells); DNA is (with very few exceptions)
not enclosed in a nuclear membrane but is free in the cytoplasm; cells are usually small (about
2 micrometres long) and many of these creatures alternate between single-celled stages and
multicellular slime colony stages, most form simple multicellular arrangements such as
filaments, sheets and balls but do not contain differentiated tissues or organs. The cells
usually have rigid walls. Feed by releasing enzymes into their surroundings (or by expressing
enzymes on their surface) to break down organic matter (either living in teh case of parasitic
bacteria) or dead remains or produce their own food by photosynthesis (see plants below).
Kingdom 2: The protoctistans:

Characteristics: Cellular and eukaryotic (lit. have a 'true nucleus' with a double membrane
enclosing the DNA) - the cells may or may not have rigid walls. These organisms are
proto-fungi, proto-animals and proto-plants, that is they are ancient and less complex forms of
these creatures. For example, the amoeba, shown below, is single-celled but resembles an
animal cell and some amoebae form relatively simple multicellular organisms (see cellular slime
moulds). Seaweeds are ancient aquatic plant-like creatures. Water moulds resemble fungi in
many respects. Hence these creatures may be single-celled or multicellular and represent a
huge diversity of natural 'experiments' in body type. Some of the multicellular types are
filamentous, some are sheets, cubes or balls of cells and some form leafy bodies (seaweeds).
In fact anything which does not fit into the other kingdoms is placed here. Some are
photosynthetic, like plants, others feed on decomposing remains, like fungi, and others are
predators and grazers, like animals.

Examples:
amoeba (shown below) and other 'proto-animals' or 'protozoans', water moulds,
cellular slime moulds, plasmodial slime moulds and algae.
Tree link
Kingdom 4: The Plants:

Characteristics: Cellular and eukaryotic. Complex multicellular bodies. Produce their own food
and building materials using light energy and inorganic mineral nutrients by photosynthesis.
Generally consist of roots, one or more stems and branches bearing leaves, though one or more
of these body subdivisions may be absent (e.g. liverworts are flat leafy planst with rhizoids
instead of roots and no obvious stem). Their cells are enclosed in rigid walls containing cellulose.
Produce spore-bearing reproductive structures, such as sori (ferns), cones (conifers) and fruit
(flowering plants).

Examples: liverwort (e.g.
Marchantia), moss, fern, horsetail, yew tree, daffodil, tulip and oak tree
(shown below).
Kingdom 3: Fungi:

Characteristics: Eukaryotic, comprised of elongated threadlike 'cells' enclosed in rigid walls and
forming a network of threads called the mycelium. The mycelium may produce large sporing
bodies, such as toadstools. Obtain their food from other organisms either parasitically or by
feeding on dead and decaying remains. Afew (the lichens) are composite organisms - consisting
of a fungus body and resident photosynthetic bacteria or algae that provide the fungal host with
food produced by photosynthesis..

Examples: bread mould, mildew, mushrooms, toadstools, bracket fungi, puffballs and jelly fungi.
Jellyfish link
Kingdom 5: The Animals:

Characteristics: Eukaryotic with complex multicellular bodies. Animal cells have no rigid walls
enclosing them. Feed in a variety of ways - either by eating other animals as predators, eating
plants as grazers (herbivores) or as parasites or by consuming dead or decaying matter. None
have their own ability to photosynthesis, but some do contain resident bacteria or algae that can
photosynthesise on their behalf. Most animals have complex nervous systems and animals
typically exhibit dramatic movements and responses

Examples: sponge,
jellyfish (shown below), starfish, worms, fish, frogs, birds, reptiles and
mammals including humans.
Kingdom 6: The Viruses:

Characteristics: Non-cellular protein capsules with or without a lipid membrane and containing
genetic material (DNA or RNA). Energy parasites - viruses are unable to generate their own
energy and so cannot build their own bodies, instead they infect and take control of cells
belonging to other creatures and turn them into 'virus factories' (they are cell pirates) disrupting
the cell's normal function. Each species infects a fairly narrow range of host cells, often a specific
cell type in a specific species, for example Hepatitis B infects liver cells in humans.

Example: Bacteriophage T4 (infects certain bacteria) and shown below, hepatitis B (causes liver
disease in humans), HIV (human immunodecifiency virus, attacks certain immune cells in
humans) and TMV (tobacco mosaic virus, attacks tobacco plant cells).
Controversy!

The official stance is not to count viruses as living creatures since they do not produce their own
energy or process their own raw materials, however, in my opinion such a stance is absurd. No
definition of 'living thing' can easily separate viruses from all other living creatures, indeed every living
thing is dependent on one or more other living things. Thus, although a virus may not constitute an
'organism' as it has few connected parts, it does do what is most crucially required of life - it ensures
the survival of its own genetic information. Life is a system that ensures the survival of chemical
information that is able to replicate and change its message - note the information must have a
'meaningful' message in the sense that the message must assist its own survival by containing useful
information (for example telling a cell how to grow and reproduce, or a virus how to gain entry and
take command of its host cell in order to replicate). It is this 'genetic information' that is key to life as
we know it. It has been argued that viruses are not living things because they depend upon other
living things to replicate - well, so does almost every other 'living thing' that I can think of - the unit of
life is not really the organism but is rather the ecosystem. We tend to define life in anthropocentric
and egocentric terms - as being that which is like ourselves, however, our own individuality is
somewhat illusory and our definition of (a self-sustainable) 'individual' is purely artificial. According to
my (hopefully more natural) definition of life as a system of replicating genetic information, viruses are
just as much alive as we are! (This has no implication on consciousness - again many lay-people tend
to think of living things as conscious things, but again this is anthropocentric and not necessarily the
case).
Controversy!

The bacteria consist of two main groups - the eubacteria (lit. 'true bacteria') and the
archaebacteria. Genetically, eubacteria appear to be more closely related to human beings
than they are to archaebacteria, even though the two bacterial types look very similar down a
microscope! For this reason, many biologists divide life into two primary groups - the
archaebacteria and everything else (accept viruses). However, in sticking to the earlier
meaning of 'bacteria' and in keeping with our field observational approach we continue to
classify both eubacteria and archaebacteria as bacteria, both are certainly prokaryotes, so
use this term if preferred.