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G-protein-coupled receptors (GPCRs) are considered therapeutically important due to their involvement in a variety of processes governing several cellular functions, and their tractability as drug targets. A large percentage of drugs on the market, and in development stages, target the super family of the GPCRs. The enormous interest in GPCR drug design is, however, limited by the scarcity of structural information. The only GPCR for which a three dimensional (3D) structure is reported is bovine rhodopsin and it belongs to class A of the GPCR family. As a result, there has been considerable interest in alternative techniques, for example, homology modeling of GPCRs, in order to derive useful three dimensional models of other proteins for use in structure-based drug design. However, homology modeling of GPCRs is not straightforward, and encounters several problems, owing to the availability of a single structural template, as well as the low degree of sequence homology between the template and target sequences. There are several key issues which need to be considered during every stage of GPCR homology modeling, in order to derive reasonable 3D models. Homology modeling of GPCRs has been utilized increasingly in the past few years and has been successful, not only in furthering the understanding of ligand-protein interactions, but also in the identification of new and potent ligands. Thus, with the lessons learned from past experiences and new developments, homology modeling in case of GPCRs can be harnessed for developing more reliable three dimensional models. This, in turn, will provide better tools to use in structure-based drug design leading to the identification of novel and potent GPCR ligands for several therapeutic indications.

Although flourishing, I argue that evo-devo is not yet a mature scientific discipline. Its philosophical foundation exhibits an internal inconsistency that results from a metaphysical confusion. In modern evolutionary biology, species and other taxa are most commonly considered as individuals. I accept this thesis to be the best available foundation for modern evolutionary biology. However, evo-devo is characterized by a remarkable degree of typological thinking, which instead treats taxa as classes. This metaphysical incompatibility causes much distorted thinking. In this paper, I will discuss the logical implications of accepting the individuality thesis for evo-devo. First, I will illustrate the degree to which typological thinking pervades evo-devo. This ranges from the relatively innocent use of typologically tainted language to the more serious misuse of differences between taxa as evidence against homology and monophyly, and the logically flawed concept of partial homology. Second, I will illustrate how, in a context of typological thinking, evo-devo's harmless preoccupation with distant ancestors has become transformed into a pernicious problem afflicting the choice of model organisms. I will expose the logical flaws underlying the common assumption that model organisms can be expected to represent the clades they are a part of in an unambiguous way. I will expose the logical flaws underlying the general assumption that basal taxa are the best available stand-ins for ancestors and that they best represent the clade of which they are a part, while also allowing for optimal extrapolation of results.

This paper investigates Willi Hennig's approach to homology in terms of character transformation series. Hennig adopted the botanist Walter Zimmermann's empirico-critical approach to systematics, which Zimmermann defended against "typological systematics" as expounded by the botanist B. H. Danser. In developing his concepts of (sym)plesiomorphy and (syn)apomorphy, Hennig built on J. H. Woodger's formal approach to homology in terms of symbolic logic and set theory. Woodger's formalization of the relation of homology, and Hennig's use of it, are discussed in the light of modem approaches to developmental biology.

Studies of the biology of music (as of language) are highly interdisciplinary and demand the integration of diverse strands of evidence. In this paper, I present a comparative perspective on the biology and evolution of music, stressing the value of comparisons both with human language, and with those animal communication systems traditionally termed "song". A comparison of the "design features" of music with those of language reveals substantial overlap, along with some important differences. Most of these differences appear to stem from semantic, rather than structural, factors, suggesting a shared formal core of music and language. I next review various animal communication systems that appear related to human music, either by analogy (bird and whale "song") or potential homology (great ape bimanual drumming). A crucial comparative distinction is between learned, complex signals (like language, music and birdsong) and unlearned signals (like laughter, ape calls, or bird calls). While human vocalizations clearly build upon an acoustic and emotional foundation shared with other primates and mammals, vocal learning has evolved independently in our species since our divergence with chimpanzees. The convergent evolution of vocal learning in other species offers a powerful window into psychological and neural constraints influencing the evolution of complex signaling systems (including both song and speech), while ape drumming presents a fascinating potential homology with human instrumental music. I next discuss the archeological data relevant to music evolution, concluding on the basis of prehistoric bone flutes that instrumental music is at least 40,000 years old, and perhaps much older. I end with a brief review of adaptive functions proposed for music, concluding that no one selective force (e.g., sexual selection) is adequate to explaining all aspects of human music. I suggest that questions about the past function of music are unlikely to be answered definitively and are thus a poor choice as a research focus for biomusicology. In contrast, a comparative approach to music promises rich dividends for our future understanding of the biology and evolution of music.

Applying a theory of homology to rhetorical pedagogy, this article suggests that Plato's and Augustine's discursive methods—dialectic and hermeneutics/homiletics respectively—function as unlocking devices via their formal structures. Dialectics unlock the discourses produced in/about the sensory world to reveal a higher level of material reality; hermeneutics/homiletics unlock Biblical ambiguities to produce a truer level of insight. Unlocking discourses, thus, give access to knowledge that would otherwise lie beyond reach for the untrained. The attention to form permits a different perspective on interpretation and pedagogy than more traditional approaches because it emphasizes audience's cognitive and “erotic” response to form and style.

I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are ‘abnormality inclusive’—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations of selected function to abstract away from variation and pathology to form a canonical description of a class of biological systems.

This paper applies “interest,” as a dominant eighteenth-century model of human nature, to Richardson's Clarissa; it proceeds to explore the construction of a new ethics of sexual relationship in the novel by focusing on the homology between usury and libertinism as two kinds of speculation judged immoral due to absence of risk. Clarissa's economic language reveals her to be an astute exegete of her culture's politics and enables her to redress the sexual imbalance of risk; Lovelace, by contrast, troubles the assumptions of the “interest” paradigm by subscribing to an aristocratic economy of expenditure that is at odds with the economic prudence of the bourgeoisie.

We use modular invariant theory to establish a complete set of relations of the mod $p$ homology of $\{QS^k\}_{k\geq0}$, for $p$ odd, as a ring object in the category of coalgebras (also known as a coalgebraic ring or a Hopf ring). We also describe the action of the mod $p$ Dyer-Lashof algebra as well as the mod $p$ Steenrod algebra on the coalgebraic ring., 26 pages; To appear in Proceedings of the London Mathematical Society

In this paper, I briefly review some comparative data that provide an empirical basis for research on the evolution of music making in humans. First, a brief comparison of music and language leads to discussion of design features of music, suggesting a deep connection between the biology of music and language. I then selectively review data on animal "music." Examining sound production in animals, we find examples of repeated convergent evolution or analogy (the evolution of vocal learning of complex songs in birds, whales, and seals). A fascinating but overlooked potential homology to instrumental music is provided by manual percussion in African apes. Such comparative behavioral data, combined with neuroscientific and developmental data, provide an important starting point for any hypothesis about how or why human music evolved. Regarding these functional and phylogenetic questions, I discuss some previously proposed functions of music, including Pinker's "cheesecake" hypothesis; Darwin's and others' sexual selection model; Dunbar's group "grooming" hypothesis; and Trehub's caregiving model. I conclude that only the last hypothesis receives strong support from currently available data. I end with a brief synopsis of Darwin's model of a songlike musical "protolanguage," concluding that Darwin's model is consistent with much of the available evidence concerning the evolution of both music and language. There is a rich future for empirical investigations of the evolution of music, both in investigations of individual differences among humans, and in interspecific investigations of musical abilities in other animals, especially those of our ape cousins, about which we know little.

Three-item data are a new way of looking at homology. Past views on homology are contrasted, and some historical details of the development of the concept are given. Application of three-item data is given for some simple examples, with a detailed series of problems outlined in the appendix (from a privately, informally published pamphlet entitled “Nullius in Verba,” by G. Nelson).

The homology concept has had a long and varied history, starting out as a geometrical term in ancient Greece. Here we describe briefly how a typological use of homology to designate organs and body parts in the same position anatomically in different organisms was changed by Darwin’s theory of evolution into a phylogenetic concept. We try to indicate the diversity of opinions on how to define and test for homology that has prevailed historically, before the important books by Hennig (1950. Grundzuge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin) and Remane (1952. Die Grundlagen des Naturlichen Systems, der Vergleichenden Anatomie und der Phylogenetik. Geest & Portig, Leipzig) brought more rigor into both the debate on homology and into the usage of the term homology among systematists. Homology as a theme has recurred repeatedly throughout the history of the “Phylogenetisches Symposium” and we give a very brief overview of the different aspects of homology that have been discussed at specific symposia over the last 48 years. We also honour the fact that the 2004 symposium was held in Jena by pointing to the roles played by biologists active in Jena, such as Ernst Haeckel and Carl Gegenbaur, in starting the development towards a homology concept concordant with an evolutionary world view. As historians of biology, we emphasize the importance of major treatises on homology and its history that may be little read by systematists active today, and have sometimes also received less attention by historians of biology than they deserve. Prominent among these are the works of Dietrich Starck, who also happened to be both a student, and later a benefactor, of systematics at Jena University.

The recognition of correspondences has long been a fundamental activity among systematists. Advocates of Naturphilosophie, such as Lorenz Oken, drew far-fetched analogies between taxonomic groups and all sorts of other things, including the Persons of the Trinity. They treated change through time either as analogous to an ontogeny or as the product of divinely instituted laws of nature. Darwin changed things by making the taxonomic units strictly historical, implying that they are not classes but rather individuals in a broad metaphysical sense. That means that taxa are concrete, particular things, or wholes made up of parts which are themselves individuals, and that there are no laws of nature for them. Homology is a relationship of correspondence between parts of organisms that are also parts of populations and lineages. It is not a relationship of similarity, and unlike similarity it is transitive. Analogy is a relationship of correspondence between parts of organisms that are members of classes, and is not necessarily due to function. Taxa, like other individuals, can change indefinitely, and the only thing that they must share is a common ancestor. They do not share an essence, Platonic Idea or Bauplan, although "conservative characters" may be widespread in them. Iterative homology likewise is a relationship of correspondence, but the nature of that correspondence remains unclear. The difficulties of the homology concept can be overcome by treating phylogenetics and comparative biology in general as historical narrative.

Scholars have been interested in the extent to which organizational phenomena generalize across levels of analysis for quite some time. However, theoretical frameworks for developing homologous multilevel theories (i.e., theories involving parallel relationships between parallel constructs at different levels of analysis) have yet to be developed, and current analytical tools for testing such theories and models are limited and inflexible. In this article, the authors first propose a typology of multilevel theories of homology that considers different stages of theory development and different levels of similarity in relationships across levels. Building on cross-validation principles, the authors then delineate and demonstrate a comprehensive and flexible statistical procedure for testing different multilevel theories of homology. Finally, the authors discuss implications for theory, research, and practice, as well as potential caveats of the new statistical tests.

This paper synthesizes research on linguistic practice and critically examines the legacy of Pierre Bourdieu from the perspective of linguistic anthropology. Bourdieu wrote widely about language and linguistics, but his most far reaching engagement with the topic is in his use of linguistic reasoning to elaborate broader sociological concepts including habitus, field, standardization, legitimacy, censorship, and symbolic power. The paper examines and relates habitus and field in detail, tracing the former to the work of Erwin Panofsky and the latter to structuralist discourse semantics. The principles of relative autonomy, boundedness, homology, and embedding apply to fields and their linkage to habitus. Authority, censorship, and euphemism are traced to the field, and symbolic power is related to misrecognition. And last, this chapter relates recent work in linguistic anthropology to practice and indicates lines for future research.

By reading the implied perception posited by Fergusson, and amplified by Collins and Price, the notions of cooks and architects' reciprocal influences, and the crossing over of dishes' and buildings' sources in an all signifying system, from table settings to site settings, becomes a way to identify a possible cosmospoiesis. Culinary and architectural works are not simply products of a single mentality, but of a mentality connecting buildings and dishes within the structure of the sensual homology existing between building and cooking. Any dish or building is constructed through a tectonic mosaic by which any dish or building results from the assimilation and transformation of other buildings and dishes. As creators of images architects and cooks can relate to their future buildings and dishes through a long series of intertextual, intermediary and intersensorial steps, a discipline that begins in the mastery of the reuse of leftovers.

This article examines the contemporary phenomenon of raves. Although explicit religious references abound in rave culture and also in scholarly interpretations of raves, these references are generally analogous and avoid direct mention of "religion" proper. In this article, we apply the theory of displacement of religious experience and the sacred to draw out the structural and phenomenological religious homology of raves and set the study of this youth phenomenon and the subculture which surrounds it firmly within the field of religious studies. We also propose avenues for further investigation. The article begins with a brief history and definition of "rave." Then it turns to the symbolic and religious references found in raves as well as the meanings both participants and commentators attribute to this phenomenon. Third, it presents and discusses the ritual structure of rave, using the theory of the mechanism and dynamics of the transgression-fuelled festal ritual ( la fête), as defined by Georges Bataille. Its purpose is to contribute to an understanding of how contemporary religious economy develops, particularly a religious economy that concerns a now largely secularized youth.

This paper examines how professional service firms have used a combination of clan and bureaucratic control techniques to manage change over a 100-year period. Both sets of controls have been present throughout, but the mix between the two has altered to reflect changes in the broader institutional environment. These shifts create new contradictions that eventually undermine their very success. However, in the midst of these changes and shifts, the basic institutional features of homology, trust and reputational capital have continued to structure these professional arenas.

An ideographic concept of character is indispensable to phylogenetic inference. Hennig proposed that characters be conceptualized as ‘‘transformation series’’, a proposal that is firmly grounded in evolutionary theory and consistent with the method of inferring transformation events as evidence of phylogenetic propinquity. Nevertheless, that concept is usually overlooked or rejected in favor of others based on similarity. Here we explicate Hennig’s definition of character as an ideographic concept in the science of phylogenetic systematics. As transformation series, characters are historical individuals akin to species and clades. As such, the related concept of homology refers to a historical identity relation and is not equivalent to or synonymous with synapomorphy. The distinction between primary and secondary homology is dismissed on the grounds that it conflates the concept of homology with the discovery operations used to detect instances of that concept. Although concern for character dependence is generally valid, it is often misplaced, focusing on functional or developmental correlation (both of which are irrelevant in phylogenetic systematics but may be valid in other fields) instead of the historical ⁄ transformational independence relevant to phylogenetic inference. As an ideographic science concerned with concrete objects and events (i.e. individuals), intensionally and extensionally defined properties are inconsistent with the individuation of characters for phylogenetic analysis, the utility of properties being limited to communicating results and facilitating future rounds of testing. � The Willi Hennig Society 2004.

This paper presents a simple typology of different forms of engagement with the Internet by families with children with various forms of chronic illness. The analysis is informed by ongoing debates about the nature, distribution and efficacy of reflexivity in contemporary social life, especially as it relates to the changing nature of information and knowledge. Drawing upon qualitative interviews with sixty-nine parents and sixteen children, the paper offers a nuanced account of the manner in which laypeople are engaging with e- health. It is an account that argues that any reading of the 'digital divide' that is based upon a simple homology between socio-structural location, reflexivity and differential ability to gain material purchase from information in the 'information age' is misjudged.

Marianne Doury: Classification of arguments on ordinary discourses. The representations ordinary speakers have about argumentative procedures is necessary to the scientific analysis of argumentation itself. Actually, this ordinary knowledge of argumentation is of great influence on the strategies speakers use in specific contexts. In particular, their perception of the social legitimacy and value of an argument is crucial for their choices when criticising the antagonist discourse. The question arises of the homology of scientific and non-scientific categorisations of arguments and of their respective use in argumentative interactions., Doury Marianne. La classification des arguments dans les discours ordinaires. In: Langages, 38ᵉ année, n°154, 2004. Représentations métalinguistiques ordinaires et discours, sous la direction de Jean-Claude Beacco. pp. 59-73.

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals.

Vedic philosophers developed a doctrine of homological relations based on a principle of ‘resemblance’ in order to make meaningful the mediation of the microcosmic and macrocosmic realms through ritual practice. This general approach to signification is shown to inhere in a variety of other contexts, specifically in the structure of ritual manuals and in the use of metalinguistic devices in Sanskrit grammar, demonstrating the multiple ways that culturally specific means of construing signs and signification can regiment various orders of social life and knowledge production.

Focusing on the epistemological homology between the construction of archaeological knowledge, archaeological evidence and the nature of archaeological representation, I examine the visual archive produced by Sir Mortimer Wheeler in India between 1944-48, to analyze the ideological ramification of the archaeological project. The discursive nature of Wheeler’s representations was deeply embedded in the disciplinarian ideologies of the colonial project, the scientific project and the military project. This article analyzes Wheeler’s methodical attempt at conflating the three projects by disciplining archaeology as a scientific practice in a colonial space. I argue that this was articulated by appropriating the ideas of ‘epistemic marker’ and ‘ethnic marker’ as visual tropes to transform the visual representations produced in a colonial context into a scientific discourse, aimed at transforming the discipline.

Based on the discourse of sport hunters, “hate criminals, “ and stranger rapists, this essay argues that a common interpretive framework rhetorically informs all three activities. The four features of the homology identified are: (a) the rhetor symbolically constructs and physically initiates an adversarial relationship with non‐consenting victims/prey class members, (b) victims/prey class members are selected opportunistically and constructed impersonally as relatively interchangeable class representatives, (c) rhetors distance and impersonalize victims/prey, without objectifying them or diminishing their presumed potency or the status accompanying conquering them, and (d) rhetors express a desire to physically assert—and take pleasure in exhibiting—dominance and superior hierarchical status. An important finding is that the violent actors studied symbolically construe their victims/prey as “Others,” sensate and worth dominating, not merely as valueless objects, and experience themselves in relationship ...

Theoretical models have assumed that efficacy beliefs operate similarly (i.e., are homologous) across levels of analysis (e.g., Lindsley, Brass, & Thomas, 1995), yet limited empirical support exists to confirm this supposition. This research empirically tested a multilevel model to determine if individual-level and team-level relations involving experience, achievement motivation, efficacy beliefs, and performance are in fact homologous across levels. Members of action teams in both lab and field settings completed measures assessing individual differences and efficacy beliefs. Subsequent ratings of individual performance and objective team performance were obtained following multiple performance episodes. Results revealed both similarities and dissimilarities between individual-level and team-level antecedents and consequences of efficacy beliefs, suggesting the assumption of homology in models of efficacy beliefs should be revisited. Contributions and implications to efficacy research and other multilev...

Homology is a natural kind term and a precise account of what homology is has to come out of theories about the role of homologues in evolution and development. Definitions of homology are discussed with respect to the question as to whether they are able to give a non-circular account of the correspondence or sameness referred to by homology. It is argued that standard accounts tie homology to operational criteria or specific research projects, but are not yet able to oer a concept of homology that does not presuppose a version of homology or a comparable notion of sameness. This is the case for phylogenetic definitions that trace structures back to the common ancestor as well as for developmental approaches such as Wagner's biological homology concept. In contrast, molecular homology is able to oer a definition of homology in genes and proteins that explicates homology by reference to more basic notions. Molecular correspondence originates by means of specific features of causal processes. It is speculated that further understanding of morphogenesis might enable biologists to give a theoretically deeper definition of homology along similar lines: an account which makes reference to the concrete mechanisms that operate in organisms.

La metaphore est envisagee ici au niveau linguistique mais aussi en tant que figure presentant une grande diversite d’expressions dans plusieurs systemes semiotiques. Dans cette perspective, ce n’est pas seulement une analogie, mais encore une homologie qui est impliquee dans la plupart des metaphores spatiales. Contrairement a l’approche courante qui tient cette figure pour un phenomene deviant, l’accent est mis sur son role irremplacable pour conceptualiser et dire des choses qui ne pourraient etre conceptualisees ni dites sans elles.

In this paper, I address the question of what an evolutionary account of intentional states should look like. I suggest that many accounts rest on the (usually implicit) assumption that, so far as intentionality is concerned, differences between animal species should be understood solely in terms of comparative sophistication. I argue that this assumption is misguided. Such accounts ignore an important biological distinction between functional and anatomical characterisations and seek to explain comparative differences that are symptomatic of functional divergence by appealing solely to a cognitive analogue of anatomical complexity. This results in accounts that are fundamentally incomplete or beside the point.

Morphology, the oldest discipline in the biosciences, is currently experiencing a renaissance in the field of comparative phenomics. However, morphological/phenotypic research still suffers on various levels from a lack of standards. This shortcoming, first highlighted as the "linguistic problem of morphology", concerns the usage of terminology and also the need for formalization of morphological descriptions themselves, something of paramount importance not only to the field of morphology but also when it comes to the use of phenotypic data in systematics and evolutionary biology. We therefore argue, that for morphological descriptions, the basis of all systematic and evolutionary interpretations, ontologies need to be utilized which are based exclusively on structural qualities/properties and which in no case include statements about homology and/or function. Statements about homology and function constitute interpretations on a different or higher level. Based on these "anatomy ontologies", further ontological dimensions (e.g., referring to functional properties or homology) may be exerted for a broad use in evolutionary phenomics. To this end we present the first organ-based ontology for the most species-rich animal group, the Arthropoda. Our Ontology of Arthropod Circulatory Systems (OArCS) contains a comprehensive collection of 383 terms (i.e., labels) tied to 296 concepts (i.e., definitions) collected from the literature on phenotypic aspects of circulatory organ features in arthropods. All of the concepts used in OArCS are based exclusively on structural features, and in the context of the ontology are independent of homology and functional assumptions. We cannot rule out that in some cases, terms are used which in traditional usage and previous accounts might have implied homology and/or function (e.g. heart, sternal artery). Concepts are composed of descriptive elements that are used to classify observed instances into the organizational framework of the ontology. That is, descriptions in ontologies are only descriptions of individuals if they are necessary/and or sufficient representations of attributes (independently) observed and recorded for an individual. In addition, we here present for the first time an entirely new approach to formalizing phenotypic research, a semantic model for the description of a complex organ system in a highly disparate taxon, the arthropods. We demonstrate this with a formalized morphological description of the hemolymph vascular system in one specimen of the European garden spider Araneus diadematus. Our description targets five categories of descriptive statement: "position", "spatial relationships", "shape", "constituents", and "connections", as the corresponding formalizations constitute exemplary patterns useful not only when talking about the circulatory system, but also in descriptions in general. The downstream applications of computer-parsable morphological descriptions are widespread, with their core utility being the fact that they make it possible to compare collective description sets in computational time, that is, very quickly. Among other things, this facilitates the identification of phenotypic plasticity and variation when single individuals are compared, the identification of those traits which correlate between and within taxa, and the identification of links between morphological traits and genetic (using GO, Gene Ontology) or environmental (using ENVO, Environmental Ontology) factors. [Arthropoda; concept; function; hemolymph vascular system; homology; terminology.].

Szucsich, N.U., Wirkner C.S. and Pass G. 2011. Deconstructing morphology: reply to Scholtz (2010). —Acta Zoologica (Stockholm) 00: 1–3 Abstract Whenever concepts are taken over into new fields scientists have to take care that these concepts do not become unsubstantial due to ambiguities regarding their applicability. Here we argue why it makes sense to define the homology-concept in a way, so it is applicable for phylogenetic purposes. If used to define the relation among structures of organisms assigned to the same character state of a phylogenetic character, homology has to represent an equivalence relation, with the properties of transitivity and symmetry. This is exactly the reason why correspondence, not similarity should be used to define homology, since the latter is not transitive. Homology then also cannot be used to define the relation among character states of the same phylogenetic character, since this relation necessarily is asymmetric.

Many programs have been designed to view the 3D structures of protein molecules in 2D. However, three types of linked information haven't been previously defined in a systematic way that highlights the interface design challenge. Specifically, a scientist must have sequence, structure, and homology information in working memory to manipulate and understand a protein structure or related protein structures. Categorizing information types enables the application of classical interaction principles to the design of an intuitive interface for both expert and novice users. In a comparative user evaluation, their Molli system enhances the exploratory process of manipulating proteins of varying complexity by preserving the underlying data's linkages and relations.

The subdisciplines within computational biology, especially those of bioinformatics, are relatively new, the word “bioinformatics” not being coined until the early to mid-1970s by Hesper and Hogeweg, 2011. With roots in computer science, information theory, biochemistry, and biology, it was and is a natural nexus of the four disciplines. However, before it could really take off, two essential factors had to become a reality, that of readily and freely available sequence and 3D structural databases and the development of powerful and relatively inexpensive computing power. Both of these are now very much a reality, having followed and/or exceeded the 18 month doubling exponential growth rate of Moore’s law (e.g., Moore, 1965; Wetterstrand, 2012; and see GenBank growth statistics at ftp://ftp.ncbi.nih.gov/ genbank/gbrel.txt) since their development. Within this entire field, one of the most important developments has been the ability for researchers to gain biological understanding of molecules and organismal systems based solely on sequence data. So, given the nucleotide or amino acid sequence of a biological molecule, what can be known about that molecule? Searching for small relevant patterns in sequences that may reflect some function allows for the inference of biologically relevant information. These can be cataloged motifs ascribed to catalytic activities; restriction enzyme or protease cut sites; regional physical attributes, such as secondary structure predictions, hydrophobicities; or even a sequence’s overall content and composition, as is used in some of the gene finding techniques. However, what about comparisons with other sequences? Can one molecule tell another’s story? Yes, naturally it can; inference through homology is a fundamental principle to all the biological sciences. A tremendous amount of knowledge can be gained by comparing one sequence against others. When a sequence is found to fall into a preexisting 30

Although they intervened on a culture of financialization in two very different ways, both Speculation and scrypt explore the intersection of money with the history of media, imperialism, colonialism, and computation. If capitalism is a kind of computer, a difference engine propagating vectors of exchange, these projects attempted to reprogram its operations. Apart from exploring the homology between money, language, computation, and philosophies of abstraction, Speculation and scrypt engage in collaborative practices that interrupt forms of classroom pedagogy based around the concept of the neoliberal individual (and neoliberal university). When money is pursued not for profit, but play, and when money is transformed from a medium of exchange to a medium for artistic practice, these two moneygames make invisible hands visible.

This is the accepted manuscript of a book chapter published by Oxford University Press. Reproduced by permission of Oxford University Press.

1. Homology and the inference of systematic relationships: some historical and philosophical perspectives, Andrew Brower 2. A survey for primary homology assessment: different botanists perceive and define characters in different ways Julie Hawkins 3. Experiments in coding multi-state characters Peter Forey and Iain Kitching 4. On characters and character states: do overlapping and non overlapping variation, morphology and molecules all yield data of the same value? Peter Stevens 5. Heuristic reconstruction of hypothetical-ancestral DNA sequences: sequence alignment versus direct optimisation Ward Wheeler 6. 'Cryptic' characters in monocotyledons: Homology and coding Paula Rudall 7. Process morphology from a cladistic perspective Peter Weston 8. Homology, coding and three taxon statement analysis Robert Scotland 9. Characters, homology and three-item analysis David Williams and Darrell Siebert Forey, The National History Museum, UK, Julie Hawkins, The University of Reading, UK, an Kitching, The Natural History Museum, UK, Toby Pennington, Royal Botanic Gardens, UK, Paula Rudall, Royal Botanic Gardens, UK, Robert Scotland, University of Oxford, UK, Peter Stevens, University of Missouri-St Louis, USA, Darrell Siebert, The Natural History Museum, UK, Peter Weston, Royal Botanic Gardens, UK, Ward Wheeler, American Museum of Natural History, USA, David Williams, The Natural History Museum, UK.

This chapter, contains various applications and developments of the techniques of mod 2 (co)homology. Most of them are somewhat original

Misconceptions arising from efforts to translate panbiogeography into terms used in other biogeographic and evolutionary theories are discussed with respect to Cox’s (1998, Journal of Biogeography, 25, 813–828) critique of panbiogeography. Croizat’s rejection of ‘Darwinian dispersal’ applies only to efforts to utilize this concept as a general explanation for biogeographic patterns. The conceptual difference between distribution and panbiogeographic dispersal maps is illustrated to show that Croizat did not synonymize distribution and dispersal. Croizat’s position on continental drift and plate tectonics does not support Cox’s (1998) claim that Croizat ‘for a long time’ refused to accept the theory of plate tectonics. The methodological relationship between panbiogeographic analysis and geology suggests an independence of methodology that prevents geological theory from falsifying panbiogeographic predictions. Panbiogeographic predictions for the eastern Pacific are shown to be in agreement with current historical geological models. Claims by Cox (1998) that the panbiogeographic method is variable and questionable are evaluated with respect to the biogeographic homology of primitive frogs, ratite birds, and southern beeches to demonstrate the consistent application of minimal distance, main massing, phylogenetic affinity and baseline criteria. Panbiogeographic classification concepts are contrasted with the Darwinian system (supported by Cox) utilizing a concept of unitary geographical area based on the language of Roman military rule. Inconsistent positions expressed in recent critiques of panbiogeography may indicate an underlying and implicit acceptance of the empirical and theoretical progress generated by panbiogeography within modern biogeography. ‘The formation of groups has an invigorating effect in all spheres of human striving, perhaps mostly due to the struggle between the convictions and aims represented by the different groups’ (Einstein, 1938. Collier’s, 26 November).

Here is a book certain to cause controversy as the author himself admits. Jonathan Wells, trained in both religious studies and molecular biology, addresses the status of evolutionary theory from ‘scientific’ and ‘philosophical’ viewpoints. He is a harsh critic of Darwinism as presented in many standard American textbooks, which he grades very poorly. Most of the book is devoted to picking holes in the explanations advanced to support favourite icons of evolution such as the origin of life, vertebrate homology, Haeckel’s embryos, Archaeopteryx , peppered moths, Darwin’s finches, fruit flies, horse and hominid evolution. His final …

The notion of exterior space consists of a topological space together with a certain nonempty family of open subsets that is thought of as a ‘system of open neighborhoods at infinity’. An exterior map is a continuous map which is ‘continuous at infinity’. A strongly locally finite CW-complex X, whose skeletons are provided with the family of the complements of compact subsets, can be considered as an exterior space X. Associated with a compact metric space we also consider the open fundamental complex OFC(X) introduced by Lefschetz.In this paper we use sequences of cycles converging to infinity to introduce ‘ordinary’ sequential homology and cohomology theories in the category of exterior spaces. One of the interesting differences with respect to the ordinary theories of topological spaces is that the role of a point is played by the exterior space N of natural numbers with the discrete topology and the cofinite externology.For a strongly locally finite CW-complex X, we see that the singular homology of X is isomorphic to H•seq(X;⊕0∞Z), the locally finite homology is isomorphic to H•seq(X;∏0∞Z) and the end homology is isomorphic to H•seq(X;∏0∞Z/⊕0∞Z). For cohomology one has that the compact support cohomology is isomorphic to H•seq(X;⊕0∞Z), the singular cohomology is isomorphic to H•seq(X;∏0∞Z) and the end cohomology is isomorphic to H•seq(X;∏0∞Z/⊕0∞Z).With respect to the Lefschetz fundamental complex, one has that the Čech homology of a compact metric space can be found as a subgroup of H•seq(OFC(X);R), the Steenrod homology is isomorphic to H•+1seq(OFC(X);∏0∞Z/⊕0∞Z) and the Čech cohomology of X is isomorphic to H•seq(OFC(X);∏0∞Z/⊕0∞Z).Finally, one also has a Poincaré isomorphism Hqseq(M)≅Hn−qseq(M), where M is a triangulable, second countable, orientable, n-manifold. We remark that in both sides of the isomorphism we are using sequential theories.

Este artigo se baseia no argumento de Philippe Descola de que há uma homologia entre a maneira como as pessoas tratam a natureza e a maneira como se tratam entre si. Ele contrasta os povos jívaro e tukano - o primeiro organizando a relação em termos de predação, o último em termos de reciprocidade. É introduzido um terceiro elemento na comparação: a região das Guianas, onde se encontraria, segundo a hipótese aqui formulada, um certo grau de autocontenção do grupo social e de isolamento diante da natureza. Isto de fato é verdade, mas é também possível identificar, dependendo dos dados e do contexto, relações predatórias e recíprocas com a natureza ou o exterior. É então sugerido que este seja não apenas o caso das Guianas, mas da Amazônia de um modo geral.This paper is based on Descola's argument that there is an homology between the way in which people treat nature and the way in which they treat each other. He contrasts the Jivaroan peoples with the Tukanoans; the former organizing the relationship in terms of predation, the latter reciprocity. A third contrast in the form of the Guiana region is introduced and it is hypothesized that a degree of self-containment, an isolation from nature, will be found there. In fact it is, but it also possible to identify, depending on data and context, predatory and reciprocal relationships with nature or the outside. It is suggested that this is likely to be generally the case.

Historical biogeography is going through an extraordinary revolution concerning its foundations, basic concepts, methods, and relationships to other disciplines of comparative biology. There are external and internal forces that are shaping the present of historical biogeography. The external forces are: global tectonics as the dominant paradigm in geosciences, cladistics as the basic language of comparative biology and the biologist’s perception of biogeography. The internal forces are: the proliferation of competing articulations, recourse to philosophy and the debate over fundamentals. The importance of the geographical dimension of life’s diversity to any understanding of the history of life on earth is emphasized. Three different kinds of processes that modify the geographical spatial arrangement of the organisms are identified: extinction, dispersal and vicariance. Reconstructing past biogeographic events can be done from three different perspectives: (1) the distribution of individual groups (taxon biogeography) (2) areas of endemism (area biogeography), and (3) biotas (spatial homology). There are at least nine basic historical biogeographic approaches: centre of origin and dispersal, panbiogeography, phylogenetic biogeography, cladistic biogeography, phylogeography, parsimony analysis of endemicity, event-based methods, ancestral areas, and experimental biogeography. These nine approaches contain at least 30 techniques (23 of them have been proposed in the last 14 years). The whole practice and philosophy of biogeography depend upon the development of a coherent and comprehensive conceptual framework for handling the distribution of organisms and events in space.

What is a species? Darwin, with Sir John Herschel, called it the ‘mystery of mysteries’. John Wilkins traces the history of this question from Plato and Aristotle via Locke and Darwin to Mayr, Hennig, and into contemporary debates about species concepts. Before he begins, Wilkins justifies the writing of a history of ideas, something that he notes is out of fashion with professional historians. Indeed, it may be difficult to accept Wilkins’s comparison of the topology of Porphyry’s tree with a contemporary cladogram (29 & 205), the idea that Pierre Belon (1517–1564) was occupied with the study of homology (54), that Darwin came close to being a cladist (153; Wilkins concedes the anachronism here implied in a

gist, Willi Hennig (1950), and became widely known to Englishspeakers in 1965 and 1966 under the name ’phylogenetic sys- Up to this point, groups have been described in Hennig’s termstematics.’ Hennig wanted a method for implementing Darwin’s of common ancestry. But groups are not discovered in this way.concepts of ancestors and descendants. Hennig explained his In practice, they are discovered through analysis of characterideas within an evolutionary framework; he wrote about spe- distributions. So we must turn to characters to look again atcies, speciation, and the transformation of morphology through the definition of groups. We can separate characters on theirthe process of evolution. In this introductory chapter, we will ability to describe groups. Those characters that allow us tobegin with Hennig’s explanations, but then move slowly to- specify monophyletic groups are synapomorphies. Monophy-ward a modern cladistic view, which dispenses with the need letic groups are discovered by finding synapomorphies. A veryto rely on any particular theory of evolution for the analysis important conceptual leap came when homology was equatedof systematic problems. with synapomorphy. (Patterson, 1982)Howtheyaccomplishthatmove turnsouttobedistinc

T. A. Vaughan, J. M. Ryan, N. J. Czaplewski. 2000. Mammalogy. 4th ed. Saunders College Publishing, Fort Worth, Texas, 565 pp. ISBN 0-03-025034-X, price (hardcover), $86.50. This edition of a popular mammalogy textbook is attractive, the scientific illustrations are magnificent, and the print is readable with important words set in boldface type. Web sites listed at the end of each chapter suggest additional information. A mammalogy textbook is a treatise on one hand and a learning device for a student on the other. Years ago, this reviewer's class was mostly graduate students in vertebrate zoology, some had courses in paleontology, and all had comparative anatomy. In my teaching (63 semesters with 2–3 classes each), students were mostly undergraduates. I love this book, but for many students today it extends well beyond their available time and earlier coursework. Even for less-advanced mammalogy classes, certainly to be considered important, instructors will find this comprehensive work helpful. In “Classification,” within the Introduction (Chapter 1), one appreciates the quote from George Gaylord Simpson (1945) about putting all things into formal arrangement. Simpson continued further that modern taxonomy includes other sciences, and that studies on phylogeny will extend mammalian taxonomy a couple of centuries. To him, and to us, taxonomy (or what our authors call “systematics”) becomes mammalogy. This text introduces students to powerful, modern phyletics. The authors introduce early in the book terms as synapomorphies and outgroups, all part of the powerful, modern way of making phylogenetic dendrograms. This is painful initiation for field-oriented students of general biology and wildlife management. However, terms such as phylogeny, homology, and analogy ought to be introduced. Analogy and homology are not confined to interspecific comparisons (e.g., serial homology is the basis of the dental formula). The text has a drawback in hardly emphasizing the Linnaean system, and not naming Carolus Linnaeus as the starting point of our taxonomy. Nomenclature is never defined; such a technological text should mention its basic rules: priority, synonymy, …

There are many problems relating to defining the terminology used to describe various biological relationships and getting agreement on which definitions are best. Here, I examine 15 terminological problems, all of which are current, and all of which relate to the usage of homology and its associated terms. I suggest a set of definitions that are intended to be totally consistent among themselves and also as consistent as possible with most current usage.