God doesn’t like labels

The big tree of life based on ribosomal RNA

Nature’s complexity goes beyond human imagination. The discovery and exploitation of biodiversity has undoubtedly helped us to reach a certain level of understanding of the natural world. Even though all essential ecological processes of the biosphere are determined and regulated by microorganism activity, for most people, nature is reduced to big vertebrates, some colourful insects and some remarkable natural areas. The planet’s surface has changed in response to life activity. Likewise, life has changed in response to Earth evolution. Microorganisms have played a crucial role in evolution, even though this has only been recently acknowledged. All great metabolic innovations (cell compound synthesis and degradation) as well as some structural ones (like cytoskeletons or programmed cell death) happened before animals, plants or fungi emerged.

Ever since Aristotle’s time, living organisms had been divided into two big «kingdoms»: animals and plants. This tradition can be seen in Ramon Llull’s work — a Majorcan author— in the Middle Ages. In Arbor scientiae Llull describes all living creatures, and those that lack feelings are included in its second book, Arbor uegetalis. In Arbor sensualis—third book in the series— the living creatures described have feelings — animals. Given the ambiguity of some unicellular organisms discovered during the 19th century, Ernst Haeckel (1834-1919) proposed in 1886 a tree of life that included a third «kingdom», Protista, which included all organisms that are halfway between plants and animals, protozoa, unicellular algae, etc. Within this «kingdom» we could find bacteria, which were named Monera. In 1977, as a result of the publication of Carl Woese’s studies (1928) on the 16S rRNA nucleotide system, prokaryotes were divided into two groups— Eubacteria and Ar­chaebacteria. In the 1990’s, Woese proposed the reclassification of the eukaryote and the prokaryote groups (eubacteria and archaebacteria) in three different groups— Eukarya, Bacteria and Archaea.

«Living organisms don’t come with a label telling us their name and group, just as we see them in museums. We can never be sure that the discovery of a new organism is going to force us to change the label»

Classification, nomenclature, identification, systematics, taxonomy, phylogenetics, are different words often used by biologists very vaguely. Classification is a very broad term which be used beyond biology. It is the arrangement of objects (organisms in biology’s case), according to specific criteria. These criteria can be arbitrary, but they seek to be useful for the purposes of the classification. There is a gradation in classification, systematics, taxonomy and phylogenetics. As we have already seen, classification can be arbitrary, but in biology criteria have to try to find evolutionary relationships between organisms. An accurate classification can be named systematics. Systematics following a group’s evolutionary history wants to be named taxonomy. Very frequently, however, even specialised books tend to confuse these terms. Taxonomy (taxon in Greek means “ordering”) obstudies how organisms are related by common ancestors and how these groups gradually separate, like branches in a tree. Phylogenetics (phylon in Greek means “tribe” o “race”) is the determination of organism evolutionary history, which can be done today using the powerful tools of genomics, which enable us to describe exact nucleotide sequences in heritable material. 

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Organisms in the tree
1. LUCA (Last Universal Common Ancestor)
2. Deinococcus radiodurans (ancient bacterial group)
3. Borrelia burgdorferi (Spirochaete)
4. Clostridium botulinum
(Gram-postive bacterium)
5. Escherichia coli
6. Mitochondrion
7. Gloeocapsa aeruginosa (Cyanobacteria)
8. Chloroplast
9. Chloroflexus aurantiacus
10. Pyrococcus furiosus
11. Methanosarcina barkeri
12. Haloquadratum walsbyi
13. Giardia lamblia
14. Trypanosoma cruzi
15. Amoeba proteus
16. Lingulodinium polyedrum (dinoflagellate).
17. Paramecium bursaria.
18. Viscum album (plants).
19. Amanita muscaria (fungi).
20. Parus major (animals).

If we knew all genetic sequences in every organism, both living organisms and fossil organisms, it would not be difficult to establish accurate phylogenetic relationships, and taxonomy’s main role would be creating increasingly larger groups that would be tracing the history of life back to its origins —around 3.800 million years ago, when the planet was still very young. But we don’t know all sequences, particularly from fossils, nor sequences are always clear, since genetic material is promiscuous and many genes pass from organism to organism even though they are not related by descent. This is known as horizontal gene transmission. Living organisms (past and present) don’t come with a label telling us their name and group, just as we see them in museums. We can never be sure that the discovery of a new organism (past or present) is going to force us to change the label. Nature (God) produces different organisms, not taxons. Scientists arrange and order them. Limits between taxonomic groups are not always clear-cut and can change with subsequent studies. In Thomas Mann’s The Magic Mountain we find the following quote: «Order and simplification are the steps to follow to get to master a subject, the real enemy is the unknown». When we are able to order the systematics and taxonomy we have available, we will be able to order the initial chaos in the entangled bank, as Darwin used to say, and grasp how marvellous and colourful the tapestry woven by nature and evolution in the biosphere is.

© Mètode 2011 - 70. Online only. When wildfires burn - Summer 2011

Illustrator, Barcelona.

Member of the Institute of Catalan Studies and Academic Director of the Barcelona Knowledge Hub of the Academia Europaea.

Dept. of Microbiology and Parasitology. University of Barcelona.