Classification of Living Things

by David Goldstein

(Seattle, Washington, USA)


The system of classifying or naming living things may seem very "scientific". But in fact, the system involves much human judgment and there is dispute and uncertainty about it. It is a system in constant flux as new information is discovered.


 

When a beginning microscopist looks through a microscope at an organism, the first question asked is "what is the name of that thing?" It is in the nature of man to want to organize, classify and name anything that we study and a complicated system has been developed to try to match the extraordinary complexity of nature. We want to know how living things are related to each other and to things that once lived but are now extinct. However, any system we devise is manmade and will always in some sense be arbitrary. No matter how many levels of classification we have or how many divisions within each level are assigned, there will always be those who argue for different or fewer or greater divisions.

The current system owes it genesis to the father of modern classification or "taxonomy", a Swede named Carl von Linné (1707-1778). He is better known by the Latinized name he adopted, Carolus Linnaeus. Linnaeus introduced the hierarchy from broadest to most specific which today with some amendment consists of a "kingdom", "phylum" or "division", "class", "order", "family", "genus", and "species".

From Aristotle's time until at least the mid-twentieth century, there were two kingdoms of life recognizedPlants and Animals (or Plantae and Animalia in Latin). However, starting in the late nineteenth century, this number began to be questioned with regard to the simpler life forms which were often not easily classified into one of the two kingdoms. A current approach now argued for is for five kingdomsProkarya or Bacteria, Animalia, Plantae, Fungi and Protoctista.

The Kingdom Prokarya or Bacteria are distinguished from the life forms in all other kingdoms in that they do not have a membrane bound nucleus containing the genetic material of the cell. They are called "prokaryotes". The genetic material is simply found in strands ("plasmids") within the cell's cytoplasm. Note that what was previously called blue green algae are now classified as cyanobacteria because they are prokaryotes. Since they are so different from all other life, under the five kingdom system, Bacteria also comprise the Superkingdom Prokarya.

The cells of life forms in the other four kingdoms are classified as "eukaryotes" and have a nucleus in which the genetic material is organized on "chromosomes" within a cellular nucleus. These four kingdoms comprise the Superkingdom Eukarya. Besides the presence or absence of a nucleus, there are other major differences between prokaryotes and eukaryotes. For example, Bacteria are all over the map in whether they utilize oxygen or another gas such as nitrogen or methane. Some cannot even tolerate oxygenfor these "anaerobic" Bacteria, oxygen is a poison. Almost all eukaryotes are aerobesthey need oxygen to live. That some Bacteria require an oxygen-free environment harkens back to the earth's earliest times and suggest their ancient origin.

The Kingdom Animalia is comprised of multi-celled organisms which develop from an embryo resulting from the fertilization of an egg by a much smaller sperm. However, even among the vertebrate animals, there is an exception to sexual reproduction that makes the definition slightly less than a 100% accurate. A species of lizard of the genus Cnemidophorus reproduces by parthenogenesisno males or sperm required. Yet I think everyone would accept that this lizard is an animal (this lizard being one exception that proves the rulethere are other a few other parthenogenetic animals). Animals also share the characteristic that most must ingest or eat other living or decayed organic matter as food to live (or live as parasites or symbionts off of the nutrients provided by other living things) (although this trait is also shared with some of the members of the Kingdom Protoctista).

The Kingdom Plantae is composed of multi-celled organisms that grow from embryos that are usually the result of sexual fusion of a male and female cell. Again there are exceptions although somewhere in every plant's past, there were sexual forbears. Most plants (but again not all) plants engage in photosynthesisthat complicated and almost miraculous process whereby the energy of sunlight is used by the plant to produce carbohydrates and gaseous O2from H2O and CO2. As a result, plants are the great producers of life. Plants generally have a rigid cell wall composed of cellulose. They are non-motile (the entire organism does not move about under its own energy) but some produce motile cells.




The Kingdom Fungi is comprised of non-motile cells that have cell walls made of chitin (the same hard stuff that the outer bodies of insects are made of) and not cellulose. Therefore, some argue that fungi are more closely related to animals than plants. Fungi develop from spores without any embryonic stage. They digest other living things outside their bodies by releasing enzymes and then absorbing the product.








Kingdom Protoctista is the catch-all kingdom for everything that does not fit into the other four. It is comprised of many microscope organisms that are of great interest to this group (as well as some macroscopic organisms). These include protozoa (or protista under the more modern name) and algae but also such diverse organisms as slime molds and slime nets. Although we often think of this group from its microscopic members, it is also comprised of some large organisms such as giant kelps that can grow as much as 10 meters (over 30 feet).

The five kingdom model is not universally accepted. Some argue for three (with the bacteria divided among two and all eukaryotes in one), two (prokaryotes in one and eukaryotes in the other) or even one. Some go in the other direction and argue that the inhabitants of the Kingdom Protoctista are simply too diverse for one kingdom and should be divided into separate kingdoms.

Any of the divisions and assignments below the kingdom level are also the subject of constant debate and change. The most specific level of the classification system is the species. Linnaeus devised a naming system for species that is still in use today. The genus is named first and is capitalized followed by the species which is not. Both the genus and species are often italicized. When organisms are referred to in Micscape articles, it is often by their genus. For example, Amoeba and Paramecium are each an example of a genus. Examples of species under each of these genera (plural for genus) are Amoeba proteus and Paramecium caudatum respectively.

How do you decide how to classify organisms into each of the narrowing categories? The classic method used was through visual (and later microscopic) identification of the form of the organism. At the higher or more general levels of classification, such distinctions are easier to make (but not always easy). They become increasingly more difficult as you become more specific. For example, how do you decide an individual organism is a member of one species and not another? The classic definition of a "species" is related organisms that share common characteristics and are capable of interbreeding. This works fine for "higher" (from our homocentric viewpoint) life forms such as Homo sapiens, the species to which you and I belong (or at least I do). We look significantly different than chimpanzees and cannot mate with them to produce offspring despite being closely related.

The problem is that this definition breaks down or is more difficult to implement in the "lower" life forms which microscopists are particularly interested in, depending on what one means by "interbreeding". For example, all different types of bacteria, although they do not reproduce sexually, are notoriously "promiscuous" about exchanging genetic material between species (such as how to become resistant to antibiotics). Further, different species (and even genera) of microorganisms look confusingly similar.

More modern tools have come into play. One way is to not only go by appearance but the life cycles, habitat, and chemical processes of organisms. For example, we would have little to go on if we only used the form of bacteria. They come in a relatively few forms. In 1884, Hans Christian Gram developed the staining technique which bears his name and is an early example of using a chemical means of differentiating bacteria. Gram noticed that some bacteria stained purple (called gram positive) and some pink (gram negative) using his method. This differentiation has proven to be much more than a merely interesting artifact of Gram's staining process but an indicator of fundamental micro-structural differences between gram positive and negative bacteria. Electron microscopy has confirmed that gram negative bacteria have a double cell wall which gram positive bacteria do not. Biochemical research has also determined that there is a significant difference in the molecules which make up the cell wall. How the bacteria reacts to its environment and to drugs can be significantly affected by these variances. Further, there are still some unanswered questions about the biological differences between gram positive and negative bacteria.

Perhaps the most modern and significant means of differentiating organisms and finding interrelationships today is through the incredible increase in our knowledge of genetics. It is now possible to sequence and compare the genes in different organisms and this has led to wholesale reclassifications in the last couple of decades of organisms which are now found to be unrelated even though similar in appearance. It has also lead to striking conclusions advanced by many that the more complex cells of higher organisms with membrane bound organelles are the ancestors of simple bacteria developing symbiotic relationships with each other and some eventually giving up their individual identity over time. Perhaps the most interesting example is the close genetic relationship between chloroplasts in plants and cyanobacteria which are capable of a form of photosynthesis. The genetic material in the chloroplasts shows a close affinity with that of cyanobacteria but not with that in the plant cell's nucleus. It seems likely, therefore that one of the most important aspects of plants, their ability to conduct photosynthesis was derived by importing and later adopting cyanobacteria.

The one trouble with these modern methods of classification is that they are generally not available to help in classifying extinct species.

Whenever, new knowledge is developed, there will always be realignments in the classification system and disputes will arise. When looking at protoctista, it sometimes takes an expert to identify what you are looking at (and they can be wrong too). It is also very possible that you are seeing a species or even genus that has never been identified before (I have seen estimates that for every known species of protoctista, there may be 6 to 25 unidentified specieswho knows). Therefore, when you read the name of an organism, or someone identifies it for you (or even if you identify it yourself), take the name given with a grain of salt.


 

Acknowledgments

Large parts of this article were based on the books of Prof. Lynn Margulis and particularly the Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, 3rd Edition, Lynn Margulis, Karlene V. Schwartz / Hardcover / Pub. Price: $39.95, published January 1998 by W. H. Freeman & Co. More information about this book and the methodology reflected in it can be found at the publisher's Web site. To go there, click on W. H. Freeman. (Editor's note: also see Micscape Book Review May 1998).

I would like to thank Dr. Dennis Kunkel for permission to use three of his breathtaking images. Please click on his name to go to his Web page and see more of his outstanding photography through the microscope. I would also like to thank Bill Amos, Dave Walker and my wife, Sally-Jo for taking the time to read a draft of this article and providing me with some helpful comments.


 

Copyright 1998 David Goldstein Please click on my name to send me an e-mail. I would appreciate any comments or thoughts you have.

 

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