Ensaio final
Are we really tree-thinking when classyifing organisms?
Leandro J.C.L. Moraes
The title question is a seemingly irresolute conflict that reverberates in the application of systems intended to classify the diversity of organisms (e.g., Queiroz & Gauthier, 1990). To understand this issue and its impacts, we need to overview its historical roots and development. Therefore, in this essay I briefly summarize this conflict and present some perspectives, inviting the reader to further deeper investigate this issue.
Systematize the reality is an intrinsic characteristic of human reasoning (Rapini, 2004). By doing this, we aim to summarize the observable complexity to better understand it and improve our communication (Manktelow, 2010). It is not by chance that biological disciplines that aim to systematize and name the organisms (Systematics and Taxonomy) have deep and interconnected historical roots (Mayr, 1982).
In fact, we know about the use of a classification system for organisms since at least the fourth century BC (Balme, 1970, Manktelow, 2010). At that time, the Greek philosopher Aristotle roughly classified organisms according to their major morphological affinities (dividing plants or animals, the second vertebrate or not) (Balme, 1970). It is clear now that this system is an extreme oversimplification of our reality, but some of Aristotelian conclusions are still part of our current knowledge (Balme, 1970).
Following a stasis period, Systematics and Taxonomy reached relevant new steps only after about 1.500 years (e.g., Cesalpino, 1583). This progress was the result of advances in our analytical capacities, allowing obtaining new and more refined data to support organism comparisons (Manktelow, 2010). Over time, there was a natural increase in the classification of organisms, but in largely independent and non-standardized manners (Manktelow, 2010). Therefore, these multiple approaches failed to fulfill one of the most fundamental principles of a classification system: improving our communication.
The Swedish naturalist Carl von Linné elegantly resolved the growing chaos with the publication of a new standardized classification system in 1758. In summary, Linnaean system groups organisms into hierarchical nomenclatural categories according to their affinities (i.e., a rank-based nomenclature) (Linnaeus, 1758) (Figure 1). One of the main advantages of the Linnaean system at the time was its broad potential for the standardized classification of different organisms (Manktelow, 2010).
Interestingly, this 263-year proposal is still the landmark that supports the current praxis of Systematics and Taxonomy (Queiroz & Gauthier, 1990). By having crossed so many generations, changes in its application would be natural considering the knowledge advances. The fact that some basic aspects of these disciplines remain linked to such a historical idea worryingly indicates that they do not fully incorporate relevant paradigm shifts in modern Biology (Queiroz, 1994). However, what were the main drivers for such a historical stasis?
One of the most obvious is the consequent formulation of particularly inflexible rulebooks to govern the nomenclature based on the Linnean system. There are some independent rank-based nomenclatural codes, which regulates classification systems for different types of organisms (Knapp et al., 2004). For example, the “Botanical Code” regulate proposals for algae, fungi, and plants (ICN) (Knapp et al., 2011), whereas the “Zoological Code” regulate proposals for animals (ICZN, 1999).
Despite using the theoretical architecture of the Linnaean system as a framework, different codes are slightly divergent in its regulations (Hawksworth, 2011). Furthermore, several groups of microorganisms particularly ignored in Linnaean times are also consequently neglected in those codes (Lahr et al., 2012). Such gaps cause numerous conflicts, such as some organisms with classification systems not properly regulated by code principles, or others that had their affinities revised and are currently governed by more than one code (Patterson & Larsen, 1992).
However, the major issue regarding these codes is that they are anchored in a theoretical basis from before the proposition of the Theory of Evolution (de Queiroz & Gauthier, 1990). Only about a century after the proposal of the Linnaean system, Charles Darwin and Alfred Wallace establish the foundations of evolutionary theory (Darwin & Wallace, 1858), which is now the unifying principle of modern Biology. Systematics and Taxonomy naturally promptly assimilate the major suggestions of the Darwin-Wallace’s theory into their theoretical frameworks, such as that organism descend from common ancestors (with modifications) (Darwin & Wallace, 1858). However, a more tight assimilation will only occur years later.
The german entomologist Willi Hennig was responsible for such a tighter assimilation (Hennig, 1966). He reached this by strongly supporting classification systems in schematic diagrams representing the evolutionary relationships of species (phylogenetic trees) (Hennig, 1966). The advent of the Phylogenetic Systematics is of such relevance that the correct interpretation of phylogenetic trees and assimilation of their results (“tree-thinking”; O’Hara, 1997) are currently paramount in virtually all biological disciplines (O’Hara, 1997).
Even as this knowledge advanced, nomenclatural codes remained fixed in Linnaean ideas and under a certain sacrosanct status (Queiroz & Gauthier, 1990). This certainly made it impracticable to fully incorporate the tree-thinking into Systematics and Taxonomy (Queiroz & Gauthier, 1990). In summary, it seems that these disciplines indeed incorporate the analyses of phylogenetic trees into theoretical interpretation of their results, but tree-thinking was not the main anchor in the practice of classify and name organisms (a historical relict of the independence of Linnean system from such a concept) (Queiroz & Gauthier, 1990). To clarify this conflict, I present an illustrative example of how the abrupt and arbitrary hierarquical categories of the Linnean system does not fully match a fluid and continuous evolutionary proccess (Figure 2).
A novel “phylogenetic nomenclature” emerge as a possible solution in this conflicting context (Queiroz & Gauthier, 1990). The International Code of Phylogenetic Nomenclature (abbreviated as PhyloCode) represents the basis of this novel proposal for organism classification (Queiroz & Cantino, 2020). Despite its recent publication in hard copy, its theoretical foundations were developed decades ago (Queiroz & Gauthier, 1990, 1992, 1994). The main difference in this system is the abolition of Linnean hierarchical categories above the species level in favor of just two units: species and clades (i.e., group of organisms descending of a common ancestor) (Queiroz & Cantino, 2020).
Based on the fact that species and clades are the basic units of phylogenetic trees, those diagrams can effectively shape the result in this classification system (Queiroz & Cantino, 2020). Therefore, in essence, phylogenetic nomenclature would represent an effective incorporation of tree-thinking into the practice of Systematics and Taxonomy (Queiroz & Cantino, 2020). In the example of Figure 2, the application of this code would exempt the abrupt relative categorization that currently group organisms with different evolutionary depths.
It is difficult to trace the future of this conflict in theoretical and practical basis of Systematics and Taxonomy. Nevertheless, one thing seems certain: historical stasis on already refuted ideas are scientifically undesirable. In this sense, the best method for classifying organisms seems to be the one anchored as firmly as possible in tree thinking, and the proposal of the phylogenetic nomenclature seems promising (Queiroz & Cantino, 2020). However, as a relatively recent idea, it is difficult to estimate whether it actually represents the proposed unifying concept (Nixon et al., 2003). Furthermore, it also needs continuous adjustments to become fully functional and cause minor impacts if applied (Nixon et al., 2003). PhyloCode's most important current contributions are perhaps the broad dissemination of the need for change, and the planting of its seeds.
At this point I imagine the reader expected me to completely favor a theoretical framework, or to indicate a more certain future for this conceptual conflict. Nevertheless, I imagine the ideas presented here are naturally systematizing in your reasoning, therefore, I kindly leave this final mission to you.
References
Balme, D.M. 1970. Aristotle and the Beginnings of Zoology. Journal of the Society for the Bibliography of Natural History, 5, 272–285.
Cesalpino, A. 1583. De plantis libri XVI. Florence, Italy: Giorgio Marescottu.
Darwin, C., Wallace, A. R. 1858. On the tendency of species to form varieties; and the perpetuation of varieties and species by natural selection. Journal of the Proceedings of the Linnean Society, Zoology, 3, 53–62.
de Queiroz, K. 1994. Replacement of an essentialistic perspective on taxonomic definitions as exemplified by the definition of “Mammalia.” Systematic Biology, 43, 497–510.
de Queiroz, K., Cantino, P.D. 2020. International Code of Phylogenetic Nomenclature (PhyloCode). CRC Press, Boca Raton, FL.
de Queiroz, K., Gauthier J. 1990. Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Systematics Zoology, 39, 307–322.
de Queiroz, K., Gauthier J. 1992. Phylogenetic taxonomy. Annual Review of Ecology, Evolution, and Systematics, 23: 449–480.
de Queiroz, K., Gauthier J. 1994. Toward a phylogenetic system of biological nomenclature. Trends in Ecology and Evolution, 9: 27–31.
Hawksworth, D.L. 2011. Introducing the draft BioCode (2011). Taxon, 60, 199–200.
International Commission on Zoological Nomenclature. 1999. International code of zoological nomenclature. London: International Trust for Zoological Nomenclature.
Knapp, S., Lamas, G., Lughadha, E.N., Novarino, G. 2004. Stability or stasis in the names of organisms: the evolving codes of nomenclature. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences, 359, 611–622.
Knapp, S., McNeill, J., Turland, N.J. 2011. Fungal nomenclature. Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne what does e-publication mean for you? Mycotaxon, 117, 509–515.
Lahr, D.J.G., Lara, E., Mithcell, E.A.D. 2012. Time to regulate microbial eukaryote nomenclature. Biological Journal of the Linnean Society, 107, 469–476.
Manktelow, M. 2010 History of Taxonomy. Lecture from Dept. of Systematic Biology, Uppsala University. Available at atbi.eu/summerschool/files/summerschool/Manktelow_Syllabus.pdf.
Mayr, E. 1982 The Growth of Biological Thought. Belknap P. of Harvard U.P, Cambridge (Mass.).
Nixon, K.C., Carpenter, J.M. & Stevenson, D.W. 2003. The PhyloCode Is Fatally Flawed, and the "Linnaean" System Can Easily Be Fixed. The Botanical Review, 69, 111–120.
Patterson, D.J., Larsen, J. 1992. A perspective on protistan nomenclature. Journal of Eukaryotic Microbiology, 39, 125–131.
Rapini, A. 2004. Modernizando a taxonomia. Biota Neotropica, 4, 1–4.
Dia 1. Definição do tema e outline geral
Tree-thinking when naming organisms: a scientific stasis?
1. Princípios das nomeações de espécies. O que é taxonomia.
2. Taxonomia Lineana - códigos de nomenclatura.
3. Evolução do tree-thinking e a estase na prática da taxonomia.
4. Phylocode. Explicação do conceito e diagramas ilustrativos.
5. Exemplos?
6. Fechamento - futuro do método.
Dia 2. Ajuste do tema.
herança histórica na nomeação
amparar em arvore é desejável
métodos regulamentados - códigos
Conflito entre métodos tradicionais de nomenclatura que não se conversam - direção de tree-thinking
manter o foco - ancorado na realidade
Tree-thinking é incompatível com o anterior
basear em código é problema
Myxomicetos regido por dois sistemas
paradigmas incompatíveis
Tema novo: The conflicts of effective tree-thinking when classifying organisms
Historical stasis versus tree-thinking when classifying organisms
The rise of tree-thinking when classifying organisms
1. Brevíssimo histórico sobre a classificação de organismos.
A theoretical conflict of difficult resolution reverberates nowadays in classification systems of diversity of organisms on Earth (REF). However, to understand its formation, we need to overview the origins and evolution of associated knowledge. It is well known that systematize and classify the reality is an intrinsic characteristic of human reasoning (REF). By doing this, we aim to improve our communication and summarize the observable complexity to better understand it (REF). It is not by chance that biological disciplines aiming to classify and name the organisms (Systematics and Taxonomy, respectively) have deep and interconnected historical roots (REF).
In fact, we know about the use of a classification system for organisms since at least the fourth century BC. At that time, the Greek philosopher Aristotle roughly classified organisms according to their major morphological affinities (dividing plants or animals, the second vertebrate or not) (REF). It is clear now that this system is an extreme oversimplification of our reality, but some of Aristotelian major subdivisions are still part of our current knowledge (REF). Following a stasis period, Systematics and Taxonomy only reached new steps around XXXX (REF). This progress was the result of advances in our analytical capabilities, allowing obtaining new and more refined data to support organism comparisons (REF).
Over time, there is a natural increase in the classification of organisms, but in independent and non-standardized ways. Therefore, these approaches did not fulfill one of the most fundamental principles of a classification system: improve our communication. The Swedish botanist Carolus Linaeus elegantly resolved the growing chaos in Systematics and Taxonomy with the publication of a new standardized classification system in 1753. In summary, Linnaean system groups organisms into inclusive hierarchical nomenclatural categories according to their affinities (i.e., a rank-based nomenclature). One of the main advantages of the Linnaean system at that time is its capacity of being widely applied across the classification proposals of different organisms. Interestingly, this historical proposal represents the theoretical architecture that we still practice today in these disciplines.
2. Definição dos códigos de nomenclatura.
3. Exemplos de organismos com posicionamentos problemáticos entre códigos.
3. Evolução do tree-thinking e a estase nos códigos de nomenclatura - exemplo da filogenia de cobras?.
4. Phylocode. Explicação do conceito e diagramas ilustrativos.
6. Fechamento. Futuro do método.
Auto-avaliação
Considero que a disciplina cumpriu totalmente as minhas expectativas inicias, que eram principalmente: o reaquecimento de ideias em meu pensamento; aprendizado de pilares básicos que desconhecia em ferramentas que já utilizo; e desconstrução de ideias consolidadas em minha mente. Além disso, certamente utilizarei o referencial teórico transmitido em textos e aulas como banco de dados para consultas futuras. Consegui manter um bom ritmo de dedicação às atividades, apesar de demandas paralelas que surgiram no decorrer da disciplina, e termino o curso com a sensação que aprendi imensamente tanto com o professor quanto com os colegas. Nesse sentido ressalto que, apesar de em certo momento da disciplina o professor ter nos incitado a treinarmos a docência, acredito que o modo como ele planejou, desconstruiu, conduziu, pensou e flexibilizou a disciplina foi o maior ensinamento sobre docência que ele poderia nos transmitir. Com relação especial às tarefas de avaliação, considero que ajudaram muito para que eu notasse meus vícios históricos na escrita (ainda não me livrei de todos, certamente), e a interação de ideias nos grupos foi extremamente benéfica. Considero que das atividades que cabiam a mim, somente não consegui manter leituras mais profundas dos textos indicados, especialmente nas últimas semanas da disciplina. Portanto, levando tudo isso em consideração, considero uma nota de 0.9 condizente com o meu desempenho.