Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

Folk Botanical Life-Forms: Their Universality and Growth

Folk botanical life-form terms are added to languages in a highly regular manner. The first life-form to be lexically encoded is always "tree"and the second, a small herbaceous plant class (GRERB). The addition of "bush," "vine," and "grass" follows with "vine" always preceding "grass." An explanation of this encoding sequence is proposed which refers to certain general principles of naming-behavior recently outlined by Witkowski and Brown (1977). In addition, size of folk botanical life-form vocabularies is positively correlated with both societal complexity and botanical species diversity. An explanation of these associations is presented . [cognitive anthropology, ethnobotany, folk classification, language universale, language change]     

Folk Zoological Life-Forms: Their Universality and Growth

Folk zoological life-form terms, like folk botanical life-form terms (Brown 1977a), are added to languages in a highly regular manner. Life-forms of the triad FISH, BIRD, and SNAKE are lexically encoded first, although in no particular order, followed by WUG (e.g., American English hug) and then MAMMAL. Four general principles of naming-behavior underlie these regularities: (1) criteria clustering; (2) conjunctivity (including binary opposition); (3) dimension salience; and (4) marking. In addition, size of folk zoological life-form vocabularies is positively correlated with societal complexity. This is caused by the decay of folk biological taxonomies as societies become more complex. [cognitive anthropology, ethnobiology, folk classification, language universals, language change]     

Causes,kinds and forms

Realist philosophies of science posit a dialectical relation between theoretical, explanatory knowledge and practical, including taxonomic knowledge. This paper examines the dialectic between the theory of descent and empirical, Linnaean taxonomy which is based on a logic of traditional classes. It considers the arguments of David Hull to the effect that many of the practical problems of empirical classification can be resolved by means of an ontology based upon the theory of descent in which species taxa are regarded as individuals rather than as classes or natural kinds.Contra Hull, it is argued that this view is, at best, only partially consistent with taxonomic practice and that it cannot sustain experimental practice which presupposes that species taxa be regarded as natural kinds. An outline is given of a possible alternative dialectic between a field theory of morphogenesis and a rational systematics involving a logic of relations.     

Folk knowledge of invertebrates in Central Europe - folk taxonomy,nomenclature, medicinal and other uses,folklore, and nature conservation

Background

There is scarce information about European folk knowledge of wild invertebrate fauna. We have documented such folk knowledge in three regions, in Romania, Slovakia and Croatia. We provide a list of folk taxa, and discuss folk biological classification and nomenclature, salient features, uses, related proverbs and sayings, and conservation.

Methods

We collected data among Hungarian-speaking people practising small-scale, traditional agriculture. We studied “all” invertebrate species (species groups) potentially occurring in the vicinity of the settlements. We used photos, held semi-structured interviews, and conducted picture sorting.

Results

We documented 208 invertebrate folk taxa. Many species were known which have, to our knowledge, no economic significance. 36 % of the species were known to at least half of the informants. Knowledge reliability was high, although informants were sometimes prone to exaggeration. 93 % of folk taxa had their own individual names, and 90 % of the taxa were embedded in the folk taxonomy.Twenty four species were of direct use to humans (4 medicinal, 5 consumed, 11 as bait, 2 as playthings). Completely new was the discovery that the honey stomachs of black-coloured carpenter bees (Xylocopa violacea, X. valga) were consumed. 30 taxa were associated with a proverb or used for weather forecasting, or predicting harvests. Conscious ideas about conserving invertebrates only occurred with a few taxa, but informants would generally refrain from harming firebugs (Pyrrhocoris apterus), field crickets (Gryllus campestris) and most butterflies. We did not find any mythical creatures among invertebrate folk taxa. Almost every invertebrate species was regarded as basically harmful. Where possible, they were destroyed or at least regarded as worth eradicating. However, we could find no evidence to suggest any invertebrate species had suffered population loss as a result of conscious destruction. Sometimes knowledge pertaining to the taxa could have more general relevance, and be regarded as folk wisdom concerning the functioning of nature as a whole.

Conclusions

The high number of known invertebrate folk taxa suggests that it would be worth conducting further investigations in other areas of Europe.

     

Some notes on relation between taxon and character in taxonomy (regarding the paper of A.A. Stekol'nikov "A problem of truth...", Zhurnal Obshchei Biologii. 2003.V.64. No 4. P.367-368)

Under brief consideration is the problem of primary or secondary status of the judgments about taxa relative to the judgments about characters in the biological classifications. The following formal definition of taxonomic system (classification) TS is provided: TS = BT[T, C(t), R(t), R(c), R(tc)], where BT is a biological theory constituting content-wise background of the system, T is a set of taxa, C(t) is a set of taxonomic characters, R(t) is a set of relationships among taxa (similarity, kinship, etc.), R(c) is a set of relationships among characters (homology, etc.), and R(tc) is a set of correspondences among taxa and characters. The latter correspondences may be complete or incomplete. At ontological level, there two basical traditions exist in biological systematics regarding R(tc) according to which the biological diversity is patterned either as a set of groups of organisms (taxa) or as a set of their properties (characters). In the first case, taxon is "primary" relative to character (in cladistics); in its opposite, character is "primary" relative to taxon (in scholasticism, classical typology, classical phylogenetics). At epistemological level, incompleteness of the taxon-character correspondence makes classificatory procedure iterative and taxonomic diagnoses context-dependent. The interative nature of classificatory procedure makes the "primary" or "secondary" status of both taxa and characters relative and alternating. This makes it necessary to introduces a kind of uncertainty relation in biological systematics which means impossibility of simultaneous definition of both extensional and intentional parameters of the taxonomic system at each step of classificatory iterations.     

Indifferent Philosophy versus Almighty Authority: On consistency,consensus and unitary taxonomy

The ability of the taxonomic community to heed Charles Godfray's wake‐up call to create ‘unitary’ taxonomic systems and make them available on the internet is hampered by real difficulties over achieving taxonomic consistency, and a cultural reluctance amongst systematists to embrace consensus. This paper explores these issues by examining the taxonomic history of an African milkweed butterfly, Amauris damocles sensu lato. Recent differences of opinion over the classification of this insect relate to fundamental differences in the theory and practice of systematics, from creationism through authoritarianism to cladistics, differences of a kind that will forever bedevil the distributed taxonomic system. If practical unitary schemes are to emerge, then the taxonomic community will need to adopt new ways of managing and recording taxonomic change, and develop a more responsible attitude towards the needs of others who are dependent of the primary products of systematics ‐names, and the classification schemes they symbolize.     

The Nature of Folk-Botanical Life Forms

Original work by Brent Berlin, Eugene Hunn, Cecil Brown, and other ethnoscientists has produced significant findings pertaining to claims of universality for folk-biological ranks, in general, and folk-botanical life forms, in particular. These findings implicitly call into question conventional wisdom in the history of biology, which tends to consider life forms as the outworn vestiges of scholastic tradition or as merely socially practical ways of carving up the living world. Unfortunately, however, ethnobiologists continue to rely on faulty analytical schema for assessing the nature of life forms which philosophers and historians of biology have developed in their ignorance of the popular conceptual foundations of folk taxonomy. The error is compounded by the adoption into ethnosystematics of the most empiricistically reductionist, and logically confused, interpretation of such schema that derives from the neo-Adansonian, or pheneticist, school of modern system-atics. This interpretation confounds (1) meaning and reference, (2) the semantics of cognitively distinct object domains, and (3) the conceptual differences between common sense and science. These points are challenged, and it is concluded that life forms, though anthropocentrically biased, are no more "artificial" or "special-purpose" than higher-order scientific taxa. Finally, the problem of so-called "unaffiliated" and "ambiguous" generics is addressed and a new analysis offered.     

Two issues in archaeological phylogenetics: taxon construction and outgroup selection

Cladistics is widely used in biology and paleobiology to construct phylogenetic hypotheses, but rarely has it been applied outside those disciplines. There is, however, no reason to suppose that cladistics is not applicable to anything that evolves by cladogenesis and produces a nested hierarchy of taxa. This includes cultural phenomena such as languages and tools recovered from archaeological contexts. Two methodological issues assume primacy in attempts to extend cladistics to archaeological materials: the construction of analytical taxa and the selection of appropriate outgroups. In biology the species is the primary taxonomic unit used, irrespective of the debates that have arisen in phylogenetic theory over the nature of species. Also in biology the phylogenetic history of a group of taxa usually is well enough known that an appropriate taxon can be selected as an outgroup. No analytical unit parallel to the species exists in archaeology, and thus taxa have to be constructed specifically for phylogenetic analysis. One method of constructing taxa is paradigmatic classification, which defines classes (taxa) on the basis of co-occurring, unweighted character states. Once classes have been created, a form of occurrence seriation-an archaeological method based on the theory of cultural transmission and heritability-offers an objective basis for selecting an outgroup.     

Reflections on the classification of yeasts for different end-users in biotechnology,ecology, and medicine

The approach to yeast identification has significantly changed in just a few decades due to the rapid increase in basic biological knowledge, increased interest in the practical applications and biodiversity of this important microbial group, and enormous technological advances. While some conventional methods can still be validly applied, many molecular techniques have been developed that allow for strain classification on all taxonomic levels. A critical evaluation of the actual scope of each identification procedure will in the end determine the most appropriate use of the many protocols now available. Nonetheless, the oldest tool of microbiology, the microscope, is still a fundamental accessory for studies involving yeast biology, biodiversity and taxonomy.     

A problem of truth in biological systematics

A possibility to put a question of truth of knowledge in biological systematics is studied. It is shown that the problem of truth in reference to systematics is wider than a question of classified information reliability. Prerequisites needed for logically accurate formulation of a definition and criteria of truth are considered. It is shown that such prerequisites are present in taxonomic practice, namely in a process of diagnosis compiling. Philosophical analysis of this work has been carried out. Interpretation of an essence of systematics as classification is connected with use of classical concept of truth (which defines truth as correspondence between knowledge and object) in its undeveloped form. Carried analysis allows supposing that a theory of systematics based on diagnostics rather than on classification would be more prospective. Use of imperfect concept of truth can be seen also in notions that system of taxa must reflect its evolutionary history. Development and modernization of Aristotle's orientation to discovery of the object form can become an alternative to such opinions. An aspiration to achieve the truth is the main motive of systematic work. An influence of this aspiration on a selection of purposes of taxonomic work and theoretical comprehension of its bases is shown. Such features of modern biological systematics as its accessibility for new results, criticism in respect of external morphological characters, and interest in intraspecific variability are connected with this aspiration. This motive comes into contradiction with a tendency to withdraw the problem of truth as such, which takes place in some brunches of theoretic systematics.     

中生代银杏类植物系统发育、分类和演化趋向

长期以来银杏类植物化石分类都依据营养叶形态为基础。由于叶形态的多型性和异源性,导致分类和系统发育解释的紊乱。根据对保存完好的繁殖器官(胚珠器官)系统发育分析结果所作的银杏目分类表明中生代除了银杏和银杏科以外,至少还存在着3．5个已灭绝的科级单元。此方案把已知其繁殖器官的成员和仅仅根据营养器官建立起来的分类位置不明的属严格地区分开来,并注明各科的限定性特征和已知成员的地质地理分布。银杏目植物自古生代起源,至早中生代以后朝着不同的方向辐射,呈现出丰富的多样性并经历了错综复杂的演化过程,其总的演化趋向是退缩：叶片扁化、蹊化和融合;胚珠器官简化,胚珠增大、数目减少,珠柄趋于消失。     

TACO: Taxonomic prediction of unknown OTUs through OTU co-abundance networks

Background: A main goal of metagenomics is taxonomic characterization of microbial communities. Although sequence comparison has been the main method for the taxonomic classification, there is not a clear agreement on similarity calculation and similarity thresholds, especially at higher taxonomic levels such as phylum and class. Thus taxonomic classification of novel metagenomic sequences without close homologs in the biological databases poses a challenge. Methods: In this study, we propose to use the co-abundant associations between taxa/operational taxonomic units (OTU) across complex and diverse communities to assist taxonomic classification. We developed a Markov Random Field model to predict taxa of unknown microorganisms using co-abundant associations. Results: Although such associations are intrinsically functional associations, we demonstrate that they are strongly correlated with taxonomic associations and can be combined with sequence comparison methods to predict taxonomic origins of unknown microorganisms at phylum and class levels. Conclusions: With the ever-increasing accumulation of sequence data from microbial communities, we now take the first step to explore these associations for taxonomic identification beyond sequence similarity. Availability and Implementation: Source codes of TACO are freely available at the following URL: https://github.com/baharvand/OTU-Taxonomy-Identification implemented in C++, supported on Linux and MS Windows.     

Covert Categories and Folk Taxonomies

Much of the recent work in ethnoscience has been concerned with the nature of folk taxonomies, an often stated definition of which requires that all folk taxa be monolexemically labeled. This paper offers evidence that unlabeled categories may also be of crucial taxonomic significance, and we feel that it is inappropriate to treat such categories apart from the named taxonomic entities of the system. More importantly, evidence presented indicates that by recognizing unnamed taxa one may gain an understanding of the structure of a particular semantic domain that is actually obscured if one focuses solely on lexically labeled units.     

Definitions in phylogenetic taxonomy: critique and rationale

A general rationale for the formulation and placement of taxonomic definitions in phylogenetic taxonomy is proposed, and commonly used terms such as "crown taxon" or "node-based definition" are more precisely defined. In the formulation of phylogenetic definitions, nested reference taxa stabilize taxonomic content. A definitional configuration termed a node-stem triplet also stabilizes the relationship between the trio of taxa at a branchpoint, in the face of local change in phylogenetic relationships or addition/deletion of taxa. Crown-total taxonomies use survivorship as a criterion for placement of node-stem triplets within a taxonomic hierarchy. Diversity, morphology, and tradition also constitute heuristic criteria for placement of node-stem triplets.     

A botanical critique of cladism

Clade versus grade is an old question in taxonomy, going back as far as Darwin himself. Taxonomists have long believed that both must be taken into account in the formation of a general-purpose system. Recently clade has been elevated to a position of total dominance by a group of taxonomists who take their inspiration from Willi Hennig. Mayr has dubbed this approach cladism, and its exponents cladists. Cladistic theory is being vigorously developed and propounded by Hennig’s disputatious disciples, and much of the present-day theory would scarcely be recognized by the founder. I here address myself to what I consider the core features of present-day cladism. The essential distinctive feature of cladism, and its fatal flaw, is that a group is considered to be monophyletic, and thus taxonomically acceptable, only if it includesall the descendants from the most recent common ancestor. The traditional taxonomic view has been that a group can still be considered monophyletic (and thus taxonomically acceptable) after some of its more divergent branches have been trimmed off. This simple and seemingly innocuous difference has profound consequences to the taxonomic system. In Hennigian classification, organisms are ranked entirely on the basis of recency of common descent, that is, on the basis of the sequence of dichotomies in the inferred phylogeny. Theamount of divergence scarcely enters into the picture. This procedure represents an effort to capture taxonomy for a narrowly limited special purpose, at the expense of the important and necessary function of providing a general-purpose system that can be used by all who are concerned with similarities and differences among organisms. The first corollary of the Hennigian concept of phylogenetic taxonomy is that no existing taxon can be ancestral to any other existing taxon. The descendant must be included in the same taxon as its ancestor. At the level of species this is palpably false. The ancestral species often continues to exist for an indefinite time after giving rise to one or more descendants. At the higher taxonomic levels adherence to the principle often requires excessive lumping or excessive splitting to avoid paraphyletic groups (i.e., groups that do not include all of their own descendants), and it forbids the taxonomic recognition of many conceptually useful groups. Neither the prokaryotes nor the dicotyledons form a cladistically acceptable taxon, since both are paraphyletic. The prokaryotes are putatively ancestral to the eukaryotes, and the dicotyledons are putatively ancestral to the monocotyledons. Many other traditional and readily recognizable taxa would have to be abandoned, without being replaced by conceptually useful groups. Fossils present a special problem, because the whole concept of cladistic classification depends on the absence of taxa at the branch points of the cladogram. Presumably all of these branch points were at some time in the past represented by actual taxa, which under cladistic theory can neither be assigned to one of their descendants nor treated as paraphyletic taxa. The difficulty is mitigated somewhat by the gaps in the known fossil record. Once it is admitted that paraphyletic as well as holophyletic groups are taxonomically acceptable, there is much value in cladistic methodology. Formal outgroup comparison for the establisment of polarity, and the emphasis on synapomorphies in the construction of a cladogram can both be usefully incorporated into taxonomic theory and practice. These require no revolution in taxonomic thought. There are unresolved problems, however, in how to gather and manipulate the data, and how to interpret the cladogram produced by computers. In any complex group, the computer may produce several or many cladograms of equal or nearly equal parsimony. This is particularly true in angiosperms, among which the extensive evolutionary parallelism casts doubt on the importance of parsimony and may lead to the production of hundreds of such cladograms for a single group. Despite the claims of objectivity and repeatability in cladistic taxonomy, the necessity for some subjective decisions remains. The Wagner groundplan-divergence method has most of the advantages of formal cladism without the most important disadvantages. Wagner accepts paraphyletic taxa in principle, and he casts a wider net for data bearing on the polarity of characters. In complex groups consisting of many taxa, however, both methods retain a strong subjective component in the computer manipulation and in the degree of reliance on absolute parsimony.     

A cryptic taxon of Galápagos tortoise in conservation peril

As once boldly stated, 'bad taxonomy can kill', highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.