Home: Scrying: For the love of species VIII: Sorting out the little guys

For the love of species VIII: Sorting out the little guys

March 22, 2006

Now, back to this speciation problem. So far, I’ve hinted that microorganisms can be a problem when it comes to deciding what is related and what isn’t. Now, I’ll get into the meaty details of that problem.

Previously, I roughly defined a species as a group of genetically distinct individuals, isolated in some manner by others of their kind. I realize now, however, that this will not always work. A certain pathogenic strain of Escherichia coli, for instance, contains a significantly larger genome than other E. coli. The pathogenic version of E. coliShould these separate strains, because of my definition, be considered different species? I don’t believe so. The two strains are similar to each other, but distinctly different from other members of the same genus, such as the lesser-known E. blattae (found in cockroaches in London.) Classification at the species level is necessary, (although often arbitrary,) but difficult at the microbial level. In these cases, it can be helpful to give separate definitions of “species” for different groups, such as protists, prokaryotes, and viruses.

Protists all over the place: this tree shows some of the many branches of the tree of life where protists might belong

Species of Protists

Protists present a challenge for classification not because of subtle differences in DNA, but because of the broad diversity of types. Most types of protists ought to be considered parts of other kingdoms, such as the green algae that gave rise to plants, but some, like the motile fungus-like slime mold, seem to belong in multiple kingdoms. Some reproduce asexually, others sexually, and still others do both. Protists should be classified into the existing kingdoms, regardless of, or perhaps accommodating, exceptions. For instance, proper placement on the tree of life may require phase-domains and phase-kingdoms, to accommodate those organisms which seem to fall in-between. This sort of reclassification may result in changes down to the level of species.

So, how should we classify the individual species of protists? An amoeba, a type of protist, called Chaos. The name alone makes this organism worthy of inclusion on Chaotic Utopia. Unfortunately, my camera made the image look far yellower than it should be.Determining species by morphology, such as the presence or type of cell wall, works in some cases, while isolating others by reproductive mechanisms works in others—as long as they reproduce sexually. In any case, differences in protists arise as mutations in the DNA are shared or passed on through generations, unless they render the affected organism unfit to survive or reproduce. In other words, protists, like all living things, evolve by means of natural selection. Usually, species of protists should be able to be classified by significant shared differences in the genetic code. For the time being, this does not allow us to place all protists on the tree of life. However, someday, as we understand more about DNA, we should eventually straighten it out; at least until we find something less classifiable.

Species of Bacteria and Archaebacteria

Since bacteria can evolve rapidly, producing thousands of potentially different offspring in a manner of hours, genetic descent is nearly useless when it comes to classification. While the sequence of amino acids can be useful in placing bacteria onto the tree of life, it is inadequate for basic identification and classification. Instead, several qualities of bacteria (or of their cousins, archaebacteria,) including morphology and function, should be used in tandem with genetic information.

When separating species of bacteria by morphology, factors to consider include the shape of the cell, the presence of certain structures, or the amount of peptidoglycan in a cell wall. Shapes come in several varieties, most generally the cocci (or little balls), bacilli (or rods) and spirillia (spirals.) Shape can further be determined by the way the organisms clump together, as in chains or clusters. Identifiable structures include cilia or flagella, the presence of a capsule, or the ability to form spores. The amount of peptidoglycan in a cell wall can be determined through a Gram-stain test, and can identify one organism as distinct from another.

The function of bacteria can be used for even further classification. Microbiologists can compare by the product(s) consumed by a bacterium, whether it be light, chemicals, or other organisms. The chemicals a bacterium produces as a byproduct of metabolism can also be of aid. Essentially, when it comes to bacteria, there are many ways of separating and classifying separate species. While comparing the differences in DNA sequences is still probably the best way to go, bacteria should be viewed pragmatically. That is, if it seems distinct enough for some reason, it probably is a distinct species, or at least a distinct strain.

Species of Viruses

If bacteria and protists seem like difficult things to place on the tree of life, what do we do with viruses, not even considered by some to be alive? Personally, even though viruses lack their own cells, I feel they should be considered alive, simply because they evolve. The concept of “aliveness” can quickly become the subject of a philosophical debate here, as others consider planetary systems and the universe itself to be evolving, but that is not the issue at hand. Viruses should be considered to be living, simply because it is useful to do so. It is too difficult to say that the adapting flu virus keeping you sweating on your deathbed is NOT alive. Since it is practical to consider a virus alive, it is also practical to consider that viruses evolve and speciate.

A virus, an obligate intracellular parasite, is essentially nothing more than a chunk of genetic code in a protein bag. We can classify a virus both by the shape of the bag and the function and resulting effects of the virus. These aspects tend to be interrelated; no single aspect can be considered for identification of a viral species. The shape of the bag, just like a woman’s purse, tends to fit the function of the contents—simply to infiltrate a certain host and use everything available to continue the reproductive process.

For instance, a bacteriophage is shaped in such a way that it can cling on to an organism of a similar size, and dump the contents of the bag to attack. The bag contains only what it needs, instructions for the victim. (Likewise, an evening purse only has to be large enough to hold a lipstick or a can of mace; choose your weapon, either carries a deadly message.) Conversely, if the function of the virus is more complex, the variety of proteins within it is likely to be more complex. (Similarly, a baby bag has to be large enough to cover ever filthy or embarrassing contingency imaginable.)

Viruses have probably been alongside cellular life since the beginning, evolving and adapting by means of natural selection. They tend to be specific in the types of organisms they attack, so perhaps should be classified in the tree of life alongside the affected groups of organisms. This is essentially how we have come to classify mitochondria. Rather than remaining simple purple sulfur bacteria, mitochondria are found in every branch of the eukaryotic limb on the tree of life. Viruses ought to be considered in the same way; detailed by genetic form, content, and as a result function.

A Final Note

None of these definitions have been very conclusive. I’ve done that on purpose… defining speciation in the past has been a vague and tricky topic. As we learn more about our bacterial origins, we have a chance to really sort things out more definitively. I’ve still yet to apply my philosophical theories (see “What’s with the doodles?“) to the speciation problem—at least on paper or online. I’ll probably take a month long break from this topic, and then present my thoughts in a final post. Thanks to all of you who have stuck around all this time, without any specific answers.

Notes: Tree of Life via Early Earth and the Origin of Life at the Ohio State University, E. coli image via a microbiology project page by Joan Slonczewski at Kenyon College.