Becoming Aware of the Method

The scientific style of cognitive activity is characterized primarily by rationality, i.e., by its subordination to a certain explicitly construed formalized method. Its natural-philosophical background is initially shaped by presuming that a true method leads to true knowledge; positivists will later add to this that a properly organized method makes the results of research subject-free and testable. This does not mean certain technical algorithms: rather, the Method (Aristotle’s Organon) is meant as a rigorous logical argumentation scheme common to all branches of knowledge about Nature.

This rational scheme lays the foundation for proto-science in Antiquity; it will be refined by scholastics in the Middle Ages, from which contemporary science will begin to grow with its unified understanding of both research tasks and techniques [Gaydenko 1980; Lindberg 2007].

An original rational idea of the Method (Organon) is loaded with a profound natural philosophy, which makes it very productive. Its key inspiration is that the main goal of cognition is the understanding of what Nature itself is and what makes it what it is; from this naturally follows the question about what the Method of comprehension of Nature should be. An answer to this complex question seems to be quite obvious to antique thinkers; it is substantiated as follows [Akhutin 1988]. Nature is uniformly and rationally (“reasonably”) organized in its bases. Therefore, a uniformly and rationally organized Method of exploring Nature must correspond to Nature itself: this means that, for the Method to lead to comprehending Nature, its logic must correspond to the logic (dialectics) of Nature. This metaphysical unity of Nature and Method allows one to expect that, through a properly organized and applied true Method, the true “nature of things” is certainly uncovered; it is formalized by the contemporary principle of onto-epistemic correspondence (see Section 3.2.1).

The key constituent of the Method thus understood is a qualitative categorization of all that is known about Nature, with a general classifying algorithm being thought of as its most adequate implementation. Its main task is to distinguish natural (true, existing in Nature) and artificial (false, “invented” by man) groups of objects employing true (logically consistent) judgments about them. Its rationality presumes that these judgments are inferred based on a syllogistic scheme construed as a set of uniformly fixed rules of logic. On this basis, a classification version of the “methodical” cognitive program is formed. It is first developed by antique thinkers followed by neo-Platonists and scholastics; in the 16th century it will be embodied in the fundamental ideas of the natural classification and the natural method leading to it.

The conceptual history of proto-science as an initial form of a rationally organized cognitive activity covers a long period from Antiquity to the Renaissance. Its principal advancement is in developing the “methodical” cognitive program as an onto-epistemic foundation of the entire cognitive activity, including the essentialist vision of Nature and deductive scheme of its description. At the same time, a “collectionist” program also develops as a continuation of the folk systematic tradition, but in a more advanced version of the systematization of plants and animals of the entire Oecumene. These two advancements mean the gradual maturation of proto-systematics associated with the development of some important ideas and general methods of classification activity.

Early Antiquity is customary to consider as the beginning of the development of the Method in its general understanding, outlined above. Two great philosophers of the 4th century bc, Plato and Aristotle, a teacher and his disciple, are most influential in this respect. They are antipodes in most of their natural-philosophical views, and nevertheless their ideas, somehow combined in the later works of neo-Platonists and scholasticists, will enter conjointly the body of theoretical knowledge of the early scientific systematics.

Plato’s natural philosophy is based on a conception of eidos (éíÓoo, idea, plural eide) as permanent and eternal supra-material basic units of the Universe (Cosmos). A totality of eide arises as a result of the successive emanation of the One as a creative principle and driving force of all that exists: the One gives rise to the most general eide; they emanate lower-order eide, until the latter are embodied in concrete material things. In some contexts, Plato mentions eidos as a form or model or template (twioç), based on which concrete material things are made: this is how the notion of “type” first appears in descriptions of the world of ideas and things [Hammen 1981]. Cosmos thus understood is ordered by a descending cascade of causal relations among eide of different levels of generality (steps of emanation): more general phenomena cause more particular ones. According to this, the Method must reproduce the sequence of this emanation and causation: it begins with the identification of most general categories and divides them sequentially into more particular ones to reach the lowest levels of the Universe. This is the general natural-philosophical background for what will be subsequently denoted as a deductive (from general to particular) argumentation scheme.

For example, keeping in mind the subject of our book, an idea of “animality” first arises at some stage of emanation of the One, giving rise to an idea of “four-footedness”; the latter emanates an idea of “horseness,” and the latter is embodied in concrete horses. Therefore, to understand what a horse is and what its place is in the Universe, it is to be comprehended what is “horseness” and what is its position in the hierarchy of eide, from “animality” through “four-footedness,” etc., downward. From this general ontological scheme of the hierarchy of Cosmos, an epistemic classification algorithm is inferred to describe its structure [Makovelsky 2004]. This algorithm allows the recognition of certain classes of objects that are manifestations of particular eide of certain levels of generality. Of prime importance is that, according to the underlying natural philosophy, these classes, i.e., universalia (“animals in general,” “quadrupeds in general,” “horses in general”) are no less real than observed individual horses, i.e. naturalia. In modern natural science, eidically given universals correspond, with some reservations, to natural kinds (in the sense of [Quine 1996]), and in systematics they are represented by taxa of different ranks.

Aristotle’s natural philosophy is fundamentally different. It is based on an idea of ousia (ovoict, plural ousiai): like Plato’s eidos, it is unchanging and eternal, but unlike the latter, it is embodied in the things (primary ousia) and in their natural grouping (secondary ousia), and does not lay outside and above them. Primary ousiai are the “bricks” of the Universe; they are hidden in the things and determine their “whatnesses”; the latter make the material (observable) things what they are in the Universe [Gotthelf 2012]. One of the interpretations of the “whatness” is the “soul” of a thing in its Aristotelian understanding [French 1994; Tipton 2014]. Variations on his “theme of the soul” will form the basis for understanding and searching for organismic “whatnesses” in scholastic systematics.

One detail should be noted in the later interpretations of Aristotelian natural philosophy, which is significant for understanding the origins of the classification method of early systematics. In scholastics, an original concept of ousia

will be denoted by its Latin equivalent essentia, which corresponds to secondary ousia, i.e., "horses in general,” "horsesness.” Later, as the scholastic understanding of the essence develops, an important difference between Plato’s eidos and Aristotelian secondary ousia will disappear; they will be referred to uniformly as essence [Balme 1962, 1987a; Winsor 2003; Berti 2016]. Be that as it may, such an interpretation will predetermine the focus of earlier systematicians on the search for essences; their comprehension will be thought of as a necessary condition for comprehending the true “nature of things.”

According to Aristotle, Nature is organized hierarchically, but in an order directly opposite to Plato’s Cosmos: it is arranged by an ascending cascade of causal relations, in which more particular ousiai are the causes of more general ones. According to this, primary ousiai give rise to secondary, tertiary, etc. higher-order ousiai, so all of Nature represents a hierarchy of ousiai of different orders [Gaydenko 1980; Sokolov 2001; Tipton 2014]. Turning back to the above “horse” example, this means that there is a primary ousia of concrete horses, based on which a secondary ousia of “horseness” arises, then an ousia of “four-footedness,” etc. To this scheme of the Universe corresponds such a Method that is aimed at identifying, first, the primary ousiai and, following the ascending cascade, allows an understanding of the ousiai of higher orders. Although Aristotle himself prefers deductive argumentation, for w'hich all his categories are designed [Pellegrin 1982; Falcon 1997], his ideas concerning ascending causalities of ousiai will later lay the foundations of the inductive (from particular to general) argumentation scheme.

It is important to keep in mind that Aristotle understands ousia functionally and teleologically, i.e., as a goal, a purpose of existence of a certain part of an animal or plant: for him, these parts exist for the sake of a work for which they are designed by their respective ousiai [Aristotle 2001]. Such a functional understanding of ousiai and how they are embodied in certain parts, organs, etc. of particular organisms will become one of the foundations of the natural method of scholastic systematics and some later taxonomic theories, up to the modern ones (such as biomorphics; see Section 5.5).

In all of Aristotle’s natural philosophy, the principles of perfection and plentitude are very important [Lovejoy 1936; Balme 1987; French 1994; Gotthelf 2012]. They are manifested jointly in an idea of the Ladder of Perfection, in w'hich each ousia occupies a certain “place,” they all relate to each other in a consistent and strict degree of affinity, and there is no “gap” between them. According to the ascending cascade of causal relations among ousiai, the orderliness of the Ladder is also ascending. To comprehend how the Ladder is ordered and hence how' all of Nature is organized, it is necessary to understand how specific ousiai relate to each other within the global Ladder; this yields a comprehension of natural interrelations between animals and plants embodying the respective ousiai. In the Middle Ages, this general idea will turn into an idea of the Great Chain of Being, or the Ladder of Nature (Scala Naturae) [Lovejoy 1936]; in natural science of the 17th—18th centuries, it will give birth to a conception of the Natural Order, which has a significant impact on the ideas of early post-scholastic systematics.

One may wonder what all this ancient natural philosophy has in common with modern systematics, in which the dominant idea is the construction of phylogenetic schemes based on calculating similarity by molecules. Oddly enough, it actually does have a very direct link. Indeed, why do some taxonomists believe that it is necessary to develop phylogenetic classifications, while others think of typological ones? Obviously, because the former are committed to evolutionary and the latter to typological natural philosophies. And how do phylogeneticists know that by building tree-like schemes, they actually get a certain representation of the real process of phylogenesis? Obviously, because their algorithms for tree inference reproduce in a way certain important aspects of the real processes of phylogenesis; this is how some modern methods of phylogenetic reconstructions are justified (see Section 5.7.1). Otherwise, what makes a phylogeneticist believe that a phylogenetic tree really reflects the phylogeny and is not just accidentally related to it? And if this is not hidden following the ancient natural philosophy with its natural-philosophical unity of Nature and Method, then what is it?

In the writings of Aristotle, the categories that are fundamental for the entire classification method of cognitive activity are developed in detail: genus (yevoo), species (siSoo), common (ouvaycoyij), and difference (Staipeotq) [Grene 1974; Pellegrin 1982, 1987; Wilkins 2009]. Thanks to their subsequent developments by neo-Platonism and scholastics, they will firmly enter the generic-species scheme for describing the world of living beings—and with it, the method of systematics.

When reconstructing the conceptual history of systematics, it is necessary to take into account that the meanings of categories of genus and species in Aristotle’s writings are very polysemous and context-dependent. On the one hand, in his work “On the Parts of Animals,” these categories relate basically to the essential properties of the objects [Lennox 1980], that is, they are partonomic, not taxonomic. According to this, for example, “species” is not the species in its current biological understanding as a specific group of organisms, but rather a particular quality (essence) of organisms of the respective natural group. Accordingly, the primary exploratory task is to identify the essences of organisms (a partonomic issue), while the delineation of their groups endowed with a common essence (a taxonomic issue) is secondary to it. So, it is more a method of definition rather than a method of classification, though it works well in both cases [Falcon 1997]. In such an understanding, the Aristotelian method will form the basis of the generic-species scheme of scholastics, and then it will be incorporated in the natural method of typological systematics. On the other hand, the same two categories correspond to the groups of organisms of different levels of generalities, just as in contemporary taxonomic classifications. As a result, it is important to realize that Aristotle, in his “Categories,” separates terminologically two understandings of such groups: he uses the terms ysvoo and si6oo to designate them as the “formal” classification units, while the terms opoyeveio and opocptXeio designate them as the “natural” units [Wilkins 2009]. For him, the latter units are not a result of logical division, but rather real groups, each with its own secondary ousia and with its own “genesis” or “phylesis” (ysvsio, cprZeio) [Grene 1974; Pratt

1984; French 1994]. It is curious enough that, because of the scholastic legacy, contemporary taxonomists will denote the respective units uniformly as “genera” and “species” regardless of their naturalness, while Aristotle’s notions of “homogenes” and “homophyles” will be forgotten.

In both interpretations, Aristotelian genera and species, even in their “taxonomic” connotation, do not have fixed ranks and precise biological meaning. For example, in his “On The Parts of Animals,” Aristotle recognizes the “genus” of animals with blood, divides it into “species” of viviparous and oviparous beasts, and recognizes among the latter the “lower species” of crocodiles and snakes [Aristotle 2001]. At the same time, he designates the “genera” of oviparous and viviparous reptiles in his “The History of Animals” [Aristotle 1910]. Thus, Aristotle can hardly be considered a forerunner of something like the contemporary biologically sound concept of species, which role he is often assigned in many textbooks on the history of biology and systematics.

Aristotle’s position regarding the classification procedure is also highly ambiguous; in contrast to widespread opinion, the logical principle of single basis of division does not look as strict to him as it will be later developed by scholastics [Falcon 1997]. In his works on natural history, he emphasizes that the main task is distinguishing between natural groups (genera), rather than formally separating them by dichotomous division by a single feature; and since genera are defined by several essential features, it is more correct to divide them according to several characters [Aristotle 2001]. So, from the contemporary (presentist) viewpoint, Aristotle’s method at this point looks more natural than that of scholastic systematics of the 16th century.

The closest followers of Aristotle develop the emerging natural history mainly within the framework of the “collectionist” program. Of these, his direct disciple Theophrastus is to be mentioned for his famous complete botanical encyclopedia, “Enquiry into Plants.” It contains a clear understanding that Nature acts following its own design, and not in order to be useful to humans. Accordingly, Theophrastus classifies plants based on the totality of their features (in their essential understanding), which together provide an integral and clear appearance of the entire plant [Theophrastus 1916]. This natural “basis of division” will be forgotten by herbalists and scholars of the 14th—18th centuries and will later be recalled by theoreticians of natural systematics by the end of the 18th century. Following his main idea, Theophrastus divides all plants into four “main species,” which are trees, shrubs, perennial shrubs, and grasses. This division is quite consistent with the main life forms of plants already distinguished by folk systematics; it will be substantiated by A. von Humboldt at the beginning of the 19th century as one of the important (in long-term assessment) developments of natural systematics [Humboldt 1806]. One peculiarity of Theophrastus’ understanding of “species” arising from Aristotelian metaphysics is noteworthy: he believes it is possible for plants to shift from one “species” to another if they are modified after their living conditions change. This is because the “matter” becomes clothed in different “forms,” i.e., it becomes different “species” under different circumstances [Zirkle 1959]. A similar idea of transmutation of organisms from one species to another will be rather common in Medieval natural philosophy [Amundson 2005]; something similar can be found in the 19th century in Edward Cope’s classification theory [Cope 1887].

Neo-Platonism is the next important stage in the formation of the Method, which will form the basis of future systematics. Late Antique neo-Platonist philosophers are engaged in developing and detailing ideas of Plato and Aristotle, bringing them to a state of the “method” in its narrow sense, i.e., as a specific algorithm. They borrow deductive method and fundamental classification categories from their early antique predecessors [Makovelsky 2004]. The neo-Platonists’ lengthy comments on the works of Aristotle become the main link between his teachings and early (scholastic) systematics [Sorabji 1990; Wilkins 2009; Richards 2016]. One of the central figures here is Porphyry, best known for his “Introduction to Aristotle’s Categories,” which summarizes Aristotle’s method; another key person is Boethius, with his “Commentaries on Porphyry” [Boethius 1906].

The main contribution of neo-Platonism to the foundations of early systematics is a detailed elaboration of the deductive generic-species scheme as a specific classification algorithm based on a sequential division of logical “genera” into logical “species” of different levels of generality. The basis of this scheme is a universal Aristotle’s formula of the definition of any notion (except for the most general) by indicating its “generic common and species particular” (per genus proximum et differentiam specificam) [Pellegrin 1982]. This formula makes the logical notions of “genus” and “species” fundamental for any deductive argumentation schemes, with the latter’s famous illustration being a classification tree-like graphical scheme, the so-called “tree of Porphyry.” This scheme will become the basic method of scholastic systematics, so its key notions will become basic elements of the taxonomic thesaurus, and the “tree of Porphyry” will appear in most of the works of the 16th—18th centuries.

For neo-Platonists, who are mostly concerned about the logical consistency of the genus-species scheme, the notions of genus and species lose their Aristotelian multifaceted content. They appear to be reduced to logical predicates (judgments) as elements of the classification scheme, so their “natural” understanding as primarily the elements of Nature appears almost washed out [Wilkins 2009; Richards 2016]. Their logical interpretation will then be strengthened by scholastics and from them will pass into scholastic systematics. Accordingly, the future anti-scholastic revolution will be largely associated with the rejection of the logical interpretation of these notions in favor of the biological one.

And nevertheless, neo-Platonic natural philosophy obliges its adherents to discuss seriously the problem of the ontological status of genera and species. In this regard, one of the most important questions becomes as follows: when using the genericspecies scheme and distinguishing “genera” and “species,” do we mean something real and existing in Nature outside of us and beside us, or are they only conditional and therefore arbitrary categories, behind which there is no natural background? In particular, neo-Platonists and after them scholasticists worry about species, which is expressed by Boethius’ aphorism “if we do not know what species is, nothing would secure us from delusion” (translated after [Boethius 1906: 1.04.10]). In this respect, the contemporary discussants of the species problem are all “Boethians.”

Medieval scholasticism covers a very long period of the development of European cognitive culture: it follows the neo-Platonic phase of Antiquity and lasts more than a thousand years. It will be usually mentioned in manuals on the history of natural science as a “dark era”—in the sense that it generates a minimum of new knowledge about material things because of being engaged basically in the issues of their supra-material causes. The reason is that the transformation of Christianity into an official state religion, actively defending its right to own an ultimate truth, makes the Bible, as the “Book of Revelation,” the main source of the latter. So it is the Bible that appears at the center of the attention of intellectuals of this time, while Nature as such is supplanted into the background; by analogy with the “Book of Revelation” it is now interpreted as just a “Book of Nature.” According to this metaphor, introduced by one of the Church Fathers, ex-neo-Platonist Aurelius Augustine, the human does not investigate Nature; instead, he “reads” the “Book of Nature” and delves into its text guided by the meanings that the “Book of Revelation” carries [Gaydenko 1980; Lyubarsky 2015]. This view of Nature gives rise to a specific semiotic cognitive model; on its basis, at the turn of the 16th—17th centuries, Galileo Galilei, one of the founders of European science, will formulate his aphorism “The Book of Nature is written in the language of mathematics,” which will become a kind of symbol of all contemporary mathematized natural science. Its notable manifestation in systematics of the 19th century will become the following aphorism: “Species are the letters whereby the Book of Nature must be read” [McOuat 1996: 473].

All this leads to a loss of interest in the “collectionist” program (gathering facts about phenomena), but gives rise to a powerful intellectual work within the framework of the “methodical” program (substantiating judgments about phenomena). Due to this, Medieval scholasticism plays a very important role in the formation of the analytical cognitive model of modern science. The basic problems it tries to solve, among most closely related to the subject of this book, were originally defined by neo-Platonists: (a) do genera and species exist in reality (objectively) or only in thought (subjectively)? (b) if they really exist, are they material or insubstantial? (c) if they are immaterial, do they exist outside of things or in the things themselves? These questions relate to the most fundamental issues of ontology and epistemology, in which contexts the whole of natural science, including systematics, will be developing [Gaydenko 1980; Gaydenko and Smirnov 1989]. These categories are realism, nominalism, conceptualism, and rationalism; they are briefly considered in the theoretical part of this book (see Section 3.3.3).

For the formation of natural-philosophical foundations of early systematics, an idea of the levels of the hierarchical structure of natural and super natural worlds, developed by scholastics, is of great importance. In the teachings of Aurelius Augustine and Anselm of Canterbury, the Platonic eide and the Aristotelian “genera” and “species,” embodied in the biblical context, become hierarchically arranged Divine prototypes of the material world contained in the Divine plan of creation [Amundson 1998; Sokolov 2001]. Supplemented with Anselm’s concept of the principal essence (essentia principalis) [Holopainen 1996], it will become an important part of the substantiation of the natural method of scholastic systematics.

The generic-species classification scheme, a key for rationalization of the future systematic, after its reworking by scholastics, acquires the following principal features. It is construed as a sequential deductive division of notions by which “genera” of different levels of generality are distinguished, with “species” being designated at its final step. It begins with the highest “genus” (genus summum), proceeds with recognition of intermediate “genera” (genera intermedia); the last of the latter (genus proximum) is divided into “species” (species ínfima). At each step, this division follows the principle of dichotomy, according to which all “genera” are divided strictly into two “genera” of the next lower rank (and eventually into two “species”). All these “genera” are primarily logical, their levels of generality are not fixed, so this scheme yields rankless generic classification. Sequential division is carried out on a certain basis of division (fundamentum divisionis). To the extent that “genera” and “species” should reflect certain natural phenomena, the basis of division is to be shaped by an essential character (essentia), while non-essential characters (accidentiae) should not be taken into account. The logical consistency of the entire generic-species scheme is ensured by the principle of single basis of division: it prohibits the use of different characters in the given scheme if they yield different divisions, since (according to the principle of the excluded third) only one of its possible outcomes (hierarchies of “genera”) can be true. Accordingly, of prime importance is the selection of a “true” essential character at the very first step of division and, once selected, it should determine the entire sequence of division steps. With such an embodiment of the generic-species divisive algorithm, a hierarchy of essences of different levels is first revealed (partonomic division), and then, on this basis, classes of objects endowed with these essences are distinguished (taxonomic division). Thus, in modern terms, this scholastic scheme presumes rather strict taxoncharacter correspondence, in which “character precedes taxon”; it will be accepted in scholastic systematics, typology, and biomorphics [Pavlinov 2018] (see Section 6.2).

Concluding this briefest review, once again the very significant contribution of general principles of onto-epistemology developed by scholasticism to the emergence of early systematics should be emphasized. Adoption of the generic-species scheme of division of notions (“genera”) endows natural history with the classification cognitive program which will define the principal way of comprehending Nature as its classifying [Stafleu 1971; Rozova 1986; Wilkins and Ebach 2014]. Considered from this program, the general trend in the conceptual history of systematics over the next several centuries will be shaped by a combination of two different vectors [Pavlinov 2018]. One is set by an adaptation of systematics to scholastic rationality, whereas the other is set by an adaptation of this rationality to the complexity of plant and animal diversity. At first, biological systematics will be developing following the formal classification principles (early scholastic systematics), and later by overcoming them (late scholastic and nearly all post-scholastic systematics).

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