Towards a Natural System of Organisms

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Proposal for the domains Archaea, Bacteria, and Eucarya


Prior classification of organisms fundamentally relied on classical phenotypes, complex morphologies, and detailed fossil records. However; with advancements made in molecular biology during the 20th century, Woese et. al proposed a new organismal classification at the highest level termed “domains”. The three proposed domains that encompass all biological life are Archaea, Bacteria, and Eucarya.

By dividing biological life on their molecular characterization, organisms are classified on grounds that reveal more about their evolutionary relationships. In this effort, the authors believe that the domain classification provide an organic characterization of organisms at the highest levels, establish a proper division between plants and animals, eukaryotes and prokaryotes as well as Archaea and Bacteria, and foster an understanding of the diverse ancient microbial lineages [1].

*Highlights show the key messages


The traditional organism classification system was iteratively but separately developed by Haeckel, Copeland, and Whittaker. Their work formed the classification of life into five kingdoms; Animalia, Plantae, Fungi, Protista, and Monera [2–4]. In spite of their efforts, there was still not a proper understanding of organism classification, even at a cellular level once the prokaryote and eukaryote division was established by Chatton [5].

In addition, the traditional system only contained “20% of the total evolutionary time span”. Flaws of the traditional classification system have been acknowledged by microbiologists for over a century and the former division of life into eukaryotes and prokaryotes was misunderstood [6]. During the 1950s, the field of molecular biology was advancing quickly. Unfortunately, the discipline at that time was applied to only a few model systems. Once molecular characterization was applied in organismal classification, profound differences were identified among three major classes of organisms which the authors name domains of life.


The proposed domain taxon was formed on the basis of molecular evidence from biological life. A major misconception the traditional classification system unrealized was cytological and phylogenetic. To address these misconceptions, an understanding of the deepest level of organismal development, or organismal molecular makeup, was explored as a classification tool. Three major groupings within the taxon domain are proposed; Archaea, Bacteria, and Eucarya.

One example of separating organisms by domain using molecular sequencing is through identifying differences in organisms’ ribosomal RNA (rRNA). Since rRNA has been extensively studied, distinct differences of their makeup, such as rRNA structural features on different positions of the molecule, enabled the separation of organisms into three domains. Specifically, whereas eubacteria all have nearly the same subunit pattern in their RNA polymerases, eukaryotes uniquely have three separate RNA polymerase functions [6].

While establishing the need for a new taxon, the authors considered the importance of maintaining present names that were established in the traditional classification system, suggest basic characteristics for each group, and demonstrate no relatability between eubacteria and archaebacteria in spite of their common names.

To address that there is no relationship between eubacteria and archaebacteria, the authors suggest not using the common “bacteria” name for Archaebacteria since it can be misleading that the Archaea and Bacteria are more closely related. With regard to subdividing each of the major three domains into kingdoms, the article only specifies the kingdoms of the Archaea since it only contains two kingdoms whereas the other two domains contain numerous kingdoms. The two kingdoms within the Archaea domain proposed are Euryarchaeota, which comprise of methanogens and their relatives, and Crenarchaeota, which comprise of the ancestral Archaea phenotype [7].

In conclusion, the authors proposed taxon will enable natural classification at the highest levels, provide classification of microorganisms, recognize that plants and animals are not evolutionarily privileged, and establish independence and diversity between Archaea and Bacteria along with other ancient microbial organisms.


During the time this article was published, the authors rightfully acknowledged a need to modify the traditional organism classification system using molecular characterization. As a commentary article in the journal of Proceedings of the National Academy of Sciences of the United States of America, personal opinions are expressed without original research. Therefore, the grounds of their proposal greatly rely on research done by others and critiquing misconceptions the authors believe were produced from a conventional system. The article goes in great depth of the historical development and flaws of the five kingdom taxonomy as well as the eukaryote-prokaryote division.

However; not enough examples are shown about how molecular biology can be used to fix the flawed systems. The article only refers to one example of its application by examining rRNA and thereafter, continues to explain flaws that are already acknowledged. For instance, as opposed to mentioning an example of how the fossil record incorrectly identifies ancestral origins of life, the article could have replaced the paragraph with another specific example as to how molecular sequencing objectively classifies organisms. The first paragraphs of the article, after the abstract, explicitly convey that the old system is flawed who “at best cover 20% of the total evolutionary timespan”. Therefore, supplemental examples would be unnecessary to revisit. Another fault of the commentary article is its organization.

The present structure of the paper does not logically flow from the prior. For example, in the subheading “Need for Restructuring Systematics”, paragraphs one and two lead the reader into a need to change the old system, ending in “The system we develop will be one that is completely restructured at the highest levels”. As opposed to explaining the change specifically needed, the next paragraph goes into the history of the traditional classification systems development. In this instance, I would recommend providing the history first before explaining its flaws and a need to change the system.


Archaea and Bacteria have been commonly confused as related organisms because of their common names archaebacteria and eubacteria. One fundamental difference between Archaea and Bacteria is that they belong in two separate domains. One basis by which they belong in separate domains is that Archaea and Bacteria have different RNA polymerase subunit patterns. In addition, when viewing the proposed phylogenetic tree of the domains, the Archaea are more related to Eucarya than Bacteria in part because of their rRNA patterns. The authors also foresee the Archaea to only have two sub kingdoms whereas the Bacteria will contain numerous.

From the conventional dichotomous classification of eukaryotes and prokaryotes, there also existed similarities and differences among the classifications. From the proposal, one similarity between the classes is the basis by which they were characterized and more specifically, “the eukaryote-prokaryote concept is fundamentally cytological and by inference phylogenetic”. However; what made the prior classification of eukaryotes and prokaryotes different is based on either a presence or lack thereof complex properties. What is now understood is that prokaryotes lack a nucleus, complex endomembrane system and cytoskeleton whereas eukaryotes contain these characteristics [9].

*Highlights guide reader to explicit answer


  1. C. R. Woese, O. Kandler, and M. L. Wheelis, ‘Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.,’ Proc. Natl. Acad. Sci. 87, 4576–4579 (1990).
  2. E. Haeckel, ‘Generelle Morphologie der Organismen: Allgemein Grunndzuge der Organischen Formen-Wissenschaft, Mechanisch Bergrundet durch die von Charles Darwin Reformite Descendenz-Theorie,’ Georg. Reimer, Berlin 2, (1866).
  3. C. H.F, ‘No Title,’ Q. Rev. Biol. 13, 383–420 (1938).
  4. W. R.H, ‘No Title,’ Q. Rev. Biol. 13, 210–226 (1959).
  5. E. Chatton, Titres et Travaux Scientifiques (1906-1937) de Edouard Chatton (Sète, E. Sottano, 1938).
  6. Cohn F, ‘No Title,’ Beitr. Biol. Pfl. 1, (1875).
  7. G. Puhler, H. Leffers, F. Gropp, P. Palm, H. P. Klenk, F. Lottspeich, R. A. Garrett, and W. Zillig, ‘Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome.,’ Proc. Natl. Acad. Sci. 86, 4569–4573 (1989).
  8. C. Woese, ‘Bacterial evolution background,’ Microbiology 51, 221–271 (1987).
  9. T. Vellai, G. Vida, and P. R. S. L. B, ‘The origin of eukaryotes : the difference between prokaryotic and eukaryotic cells The origin of eukaryotes : the difference between prokaryotic and eukaryotic cells,’ 1571–1577 (1999).
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Towards a Natural System of Organisms. (2022, Jul 27). Retrieved from https://samploon.com/towards-a-natural-system-of-organisms/

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