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The homology group of a tiling introduced by M. Reid is studied for certain topological tilings. As in the planar case, for finite square grids on topological surfaces, the method of homology groups, namely the non-triviality of some specific element in the group allows a "coloring proof" of impossibility of a tiling. Several results about the non-existence of polyomino tilings on certain square-tiled surfaces are proved in the paper.

Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their evolutionary relationships to other proteins. However, phylogenetics analyses can be challenging: they are computationally expensive and must be performed carefully in order to avoid systematic errors and artifacts. PANTHER (http://pantherdb.org) is a publicly available, user-focused knowledgebase that stores the results of an extensive phylogenetic reconstruction pipeline that includes computational and manual processes and quality control steps. First, fully reconciled phylogenetic trees (including ancestral protein sequences) are reconstructed for a set of "reference" protein sequences obtained from fully sequenced genomes of organisms across the tree of life. Second, the resulting phylogenetic trees are manually reviewed and annotated with function evolution events: inferred gains and losses of protein function along branches of the phylogenetic tree. Here, we describe in detail the current contents of PANTHER, how those contents are generated, and how they can be used in a variety of applications. The PANTHER knowledgebase can be downloaded or accessed via an extensive API. In addition, PANTHER provides software tools to facilitate the application of the knowledgebase to common protein sequence analysis tasks: exploring an annotated genome by gene function; performing "enrichment analysis" of lists of genes; annotating a single sequence or large batch of sequences by homology; and assessing the likelihood that a genetic variant at a particular site in a protein will have deleterious effects. This article is protected by copyright. All rights reserved.

Two knots are homology concordant if they are smoothly concordant in a homology cobordism. The group $\hat{\mathcal{C}}_{\mathbb{Z}}$ (resp. $\mathcal{C}_{\mathbb{Z}}$) was previously defined as the set of knots in homology spheres that bounds homology balls (resp. in $S^3$), modulo homology concordance. We prove $\hat{\mathcal{C}}_{\mathbb{Z}} / \mathcal{C}_{\mathbb{Z}}$ contains a $\mathbb{Z}^{\infty}$ subgroup. We construct our family of examples by applying the filtered mapping cone formula to $L$--space knots, and prove linear independence with the help of the connected knot complex., Comment: 27 pages, 11 figures. Minor revisions. This is the version to appear in the Journal of Topology

Symposium on Geometry Processing 2021, SGP, online, 12 Jul 2021 - 14 Jul 2021; Computer graphics forum 40(5), 193-203 (2021). doi:10.1111/cgf.14367 special issue: "Symposium on Geometry Processing 2021 : Hosted online July 12 – 14, 2021 / K. Crane and J. Digne (Guest Editors)", Published by Wiley-Blackwell, Oxford

The furcula is a distinctive element of the pectoral skeleton in birds, which strengthens the shoulder region to withstand the rigor of flight. Although its origin among theropod dinosaurs is now well-supported, the homology of the furcula relative to the elements of the tetrapod pectoral girdle (i.e., interclavicle vs clavicles) remains controversial. Here, we report the identification of the furcula in the birdlike theropod Halszkaraptor escuilliei. The bone is unique among furculae in non-avian dinosaurs in bearing a visceral articular facet in the hypocleideal end firmly joined to and overlapped by the sternal plates, a topographical pattern that supports the primary homology of the furcula with the interclavicle. The transformation of the interclavicle into the furcula in early theropods is correlated to the loss of the clavicles, and reinforced the interconnection between the contralateral scapulocoracoids, while relaxing the bridge between the scapulocoracoids with the sternum. The function of the forelimbs in theropod ancestors shifted from being a component of the locomotory quadrupedal module to an independent module specialized to grasping. The later evolution of novel locomotory modules among maniraptoran theropods, involving the forelimbs, drove the re-acquisition of a tighter connection between the scapulocoracoids and the interclavicle with the sternal complex.

The study of male genital appendages is often necessary to identify a species and to characterise the higher systematics ranks for the Cercopidae, a large family of Hemiptera. Therefore, many authors have used them in their work but without any clear consensus on the terms used for each part constituting the male terminalia. A standardised terminology is important for the quality of a taxonomic description but even more essential when we want to compare species and establish a primary homology between states of character and their use in the frame of phylogenetic analysis. The use of a consensus terminology should ensure that we are all observing, speaking and describing the same genital appendage and comparing homologous characters. In order to propose a consensus terminology, we have reviewed all the major works on the anatomy of terminalia for the family since the first description using those characters in 1922. We proposed the use of consensual terms, listed with their definitions. In addition we studied a diversified panel of male specimens, chosen in order to represent as many Cercopidae tribes as possible. We categorised five different groups of Cercopidae according to their male terminalia structures. This opens the reflection on the evolutionary patterns for these structures.

Are higher status cultural tastes in the modern United States better described as being inclusive and broad or exclusive and narrow? We construct an original dataset in response to conflicting answers to this question. We fill a major gap in the literature on cultural tastes by simultaneously considering taste for both musical genres and artists within genres. By examining the compositional balance of respondents’ taste portfolios, we reconcile seemingly incommensurate theoretical frameworks of class homology and omnivorousness. The results indicate that an omnivorous disposition to music is a relatively middle-status position in the social structure. In contrast, positions characterized by higher levels of cultural capital map onto exclusive and narrower tastes for consecrated culture.

The Principle of Homology Continuity (PHC) based covering learning method is an effective method to solve the pattern recognition problem. However, PHC and the existence of optimal coverage are not mathematical proven. To address this issue, we firstly give the mathematical description and theoretical proof of PHC. On this basis, the theoretical definition of optimal coverage is introduced. Optimal coverage can determine the internal connections among samples as prior knowledge and use covering neurons to learn prior knowledge. Finally, we propose a kind of covering neuron model, and the effectiveness of which is demonstrated through extensive experiments conducted on the CIFAR-10, LFW, and YTF datasets.

This essay traces the features of a symbolic construct which seldom garners much attention among scholars of biblical and Second Temple texts, including the Dead Sea Scrolls, namely, the likening of earth and womb. It contends that understanding this symbolism brings clarity to several texts whose interpretation is disputed and illuminates important aspects of sectarian thought, including a perspective on human sexuality which has escaped some current scholarship. The representation of the sexed body in the Thanksgiving Psalms (or “Hodayot”) receives extended attention. These psalms, it is shown, have been influenced by the negative rhetorical application of the phrase “born of woman” as found in the book of Job and by a tradition reflected in Jubilees and 4Q265 which employs the creation of Adam and Eve as a paradigm for the purification of new mothers (as described in Lev 12). The argument will show how a homology of earth and womb lies behind or can be derived from each of these traditions and how it comes to shape a profoundly negative, if highly contextualized, view of sexuality in the Psalms of Thanksgiving.

Snakes-a subset of lizards-have traditionally been divided into two major groups based on feeding mechanics: "macrostomy," involving the ingestion of proportionally large prey items; and "microstomy," the lack of this ability. "Microstomy"-considered present in scolecophidian and early-diverging alethinophidian snakes-is generally viewed as a symplesiomorphy shared with non-snake lizards. However, this perspective of "microstomy" as plesiomorphic and morphologically homogenous fails to recognize the complexity of this condition and its evolution across "microstomatan" squamates. To challenge this problematic paradigm, we formalize a new framework for conceptualizing and testing the homology of overall character complexes, or "morphotypes," which underlies our re-assessment of "microstomy." Using micro-computed tomography (micro-CT) scans, we analyze the morphology of the jaws and suspensorium across purported "microstomatan" squamates (scolecophidians, early-diverging alethinophidians, and non-snake lizards) and demonstrate that key components of the jaw complex are not homologous at the level of primary character state identity across these taxa. Therefore, rather than treating "microstomy" as a uniform condition, we instead propose that non-snake lizards, early-diverging alethinophidians, anomalepidids, leptotyphlopids, and typhlopoids each exhibit a unique and nonhomologous jaw morphotype: "minimal-kinesis microstomy," "snout-shifting," "axle-brace maxillary raking," "mandibular raking," and "single-axle maxillary raking," respectively. The lack of synapomorphy among scolecophidians is inconsistent with the notion of scolecophidians representing an ancestral snake condition, and instead reflects a hypothesis of the independent evolution of fossoriality, miniaturization, and "microstomy" in each scolecophidian lineage. We ultimately emphasize that a rigorous approach to comparative anatomy is necessary in constructing evolutionary hypotheses that accurately reflect biological reality.

The notion that anthracotheres had hippo-like body proportions, locomotion and lifestyles has been in the literature for so long, and has been repeated so many times, that it has taken on the aura of unquestionable truth. However, right from the beginning of studies into hippo-anthracothere relationships over a century and a half ago, observations were made that revealed the existence of fundamental differences in dental, cranial and postcranial anatomy in the two groups. The aim of this paper is to review the possible role of anthracotheres in the evolution of hippopotamids. It is concluded that they played no part in it, whereas palaeochoerids could well represent the ghost lineage that has evaded scientists for more than a century.

Osteoporosis is a systemic chronic metabolic bone disease, mainly in the elderly and postmenopausal women. At present, most of the clinical treatment is western medicine, but the curative effect is not very significant. In the treatment of osteoporosis, traditional Chinese medicine (TCM) is mainly based on the overall concept of TCM. This article briefly analyzes osteoporosis from the theory of “liver and kidney homology,” discusses the research on osteoporosis in TCM, and hopes to provide reference for the clinical treatment and research of osteoporosis.

Teeth are frequently used in phylogeny in order to better characterize the evolution of extinct mammal species. While most studies have focused on the adult dentition, the consideration of characters from the deciduous dentition could also contribute to reinforce phylogenetic assumptions or disentangle phylogenetic issues. We chose to investigate the characters of the deciduous dentition in cetartiodactyl taxa in relation to the disputed relationships within hippopotamoids, especially the position of Hippopotamidae. We describe the deciduous dentition of 51 species, among a dataset of 70 cetartiodactyls. We noticed that second and third deciduous premolars have a much lower degree of molarization, and are more suitable for coding than fourth deciduous premolars. Thirty-nine resulting characters were thus added to a previously published matrix, and parsimony and maximum-likelihood analyses were performed. Both analyses provided a better resolved topology for most taxa than without these characters, and with better support for most nodes in the parsimony analysis. Moreover, this analysis provides additional characters supporting the hypothesis of an emergence of hippopotamids within bothriodontine anthracotheres from the Palaeogene of Africa. The promising use of characters from the deciduous dentition in phylogeny should allow discussion of the underlying ontogenetic mechanisms at the origin of dental homology.

This paper intends to illustrate the close similarities between Salwa Bakr's short story Thirty-One Beautiful Green Trees (1986) and Han Kang's novel The Vegetarian (2007) through the lens of the ecofeminism theory as a comparative study that has not been attempted so far. Ecofeminism is a theory that mainly linked the oppression of women and nature. Both of them are exploited under the patriarchal culture of the Egyptian and the South Korean societies as it will be depicted in the present paper. Bakr's Thirty-One Beautiful Green Trees tackles social ecofeminism that portrays the colonization of women's identity and body as well as nature. While Kang's The Vegetarian handles vegetarian ecofeminism that rejects the idea of dealing harshly with women and animals as objects that have no rights. Both of these works explore the spiritual side that the protagonists adhere to and their psychological suffering.

Language change and biological evolution are sufficiently similar that biologists and linguists often face similar challenges in reconstructing paths of historical change connecting different species or languages. Tracing evolutionary change over time requires us to consider how shared features have been modified in different lineages since they shared a common ancestor, and this means we have to be able to establish meaningful comparability between traits. In some cases, we may wish to understand how the same ancestral trait has been modified in each lineage in response to different pressures. But in other cases, we may wish to ask whether particular traits often arise in response to certain circumstances. Biologists must therefore consider different reasons for similarities between species, and choose to compare those traits that are relevant to the story they want to tell. To reconstruct histories of change, we need to compare homologous traits (those similar due to shared ancestry). But comparing analogous traits (independently derived but similar traits) highlights how separate evolutionary lineages can find similar solutions to common problems. I will illustrate the importance of comparability in constructing evolutionary explanations using one of the more obscure yet fascinating examples of Charles Darwin’s scientific researches, his multi-volume taxonomic treatise on barnacles. Darwin faced the challenge of how to explain the evolutionary trajectory of unique and highly modified traits that appear to have no equivalents in related taxa. He did this by tracing the development of unique traits within growing individuals, looking for variation in these strange adaptations between individuals, and comparing them across species that varied in their degree of modification from their ancestor. Using meticulous observations to establish comparability, even in such an incomparable animal as the barnacle, he could reconstruct plausible evolutionary explanations for even the most bizarrely modified traits, such as the presence of parasitic males and the invention of the cement that sticks barnacles to rocks, boats and whales. Nowadays, scientists increasingly rely on DNA evidence to trace evolutionary paths, which brings both advantages and challenges in establishing comparability. Even if you, like most people, are not particularly interested in barnacles, Darwin’s underappreciated taxonomic work is a surprisingly good place to go to if you want to think about the issue of comparability and why it matters to understanding evolution.

In this article, I compare WANG Bi’s 王弼 rendition of Dao 道 as the nameless, unfathomable root of language and the totality of beings, with Derrida’s analysis of the term khōra. Both cases include a text that presents itself as a commentary on another text, namely the Laozi 老子 for Wang Bi and Plato’s Timaeus for Derrida, whose matter is declared as elusive and ungraspable. I analyze the analogies between these two attempts to convey the unsayable, as well as the philosophical differences in highlighting the “ipseity,” or the “otherness,” of what resides beyond the edge of discourse. On the basis of my analysis, I claim that decisive parallelisms can be found in the homology between text and theme, in the linguistic strategies and common metaphors, whereas the main difference lies in the metaphysical background. Whereas the Dao presumes a harmonious ability for self-ordering, khōra is centered on the concept of absolute otherness, whose unsayability is that of an entity that is constantly removing itself from any determination and which properly consists in dispossessing itself.

In his account of epistēmē, the highest level of understanding attainable in philosophical inquiry, Aristotle articulates standards for the ideal explanations that confer this level of understanding. I argue that Aristotle's key standard for epistēmē is of central importance for the biological homology concept. The explanatory shortcoming that results from violating this standard has been vaguely articulated in recent literature on homology; Aristotle's account offers a more neutral and precise formulation of the shortcoming and its antidote. Further, the risk for this shortcoming has heightened with recent accounts of homology grounded in genetics, increasing the contemporary relevance of Aristotelian epistēmē.

O presente trabalho visa comparar a forma composicional da canção, “Perisséia” de Tom Zé à de Macunaíma: o herói sem nenhum caráter, de Mário de Andrade. Conforme espera-se demonstrar, a canção do músico baiano estabelece uma homologia criativa com os princípios formais do livro do escritor modernista.

Sociologists often imagine society as spaces, yet how social spaces are related remains ambiguous in most theories. In developing his field theory, Bourdieu used extensively the concept of homology to describe the structural similarities across fields, but he had not taken seriously the spaces between fields or how fields are related to each other. Adopting the Simmelian approach of formal sociology, this article outlines six basic social forms by which social spaces are related. It argues that relations between social spaces can be understood along two dimensions: heterogeneity and social distance. In terms of heterogeneity, social spaces can be kindred, symbiotic or oppositional. In terms of social distance, they can be linked, nested or overlapping. These social forms of interspatial relations are constituted by the boundary work of a variety of actors, including guardians, brokers and space travellers. The article provides a general vocabulary for thinking about how social spaces are related and how they interact across boundaries.

Despite the rapid development of computational technologies and methods and the increasing number of publications related to the geomorphometric analysis of terrain, no summaries in this branch of geomorphology were created in the last decade. In the “Russian-language” articles and books in geomorphometry this problem is especially relevant. Sometimes, geomorphometry has become regarded as a semi-marginal discipline which has no real importance for studying of landforms. The list of the main drags for thegeomorphometric analysis development is given in the article: geomorphological convergence and homology, not-interpretability of complex statistical models, slight representativeness of common metrics for automatictracing of geomorphological boundaries, and so on. The possible solutions of these problems on the way to the morpho-chrono-genetic mapping of landforms are scheduled. A short review is provided of clustering, classification, computer vision and pattern recognition, development and using of unusual geomorphometric variables. The article encourages geomorphologists to intensify their efforts (and to lead the researches if possible) in these four thematic directions to prevent the proceeding separation of traditional geomorphology and geomorphometry.

The aim of this article is to develop and supplement arguments in support of Leszek Kolakowski’s thesis concerning the ideological and practical continuity of Marx’s philosophy and the 20th-century political attempts to implement it (‘institutionalism of Marxism’). The forms of the indicated homology have been divided into three categories: unjustified prophecies (historicism), propagation of violence and scientific misconduct. The article also explores numerous 19th-century exante sources that show the dangerous consequences of the Marxist philosophy of history long before they were confirmed by the revolutionary experiences of the 20th century. The final part describes the consequences of the conceptual ferment related to the attempts to separate Marx’s theory (in particular by giving up its systemic lectures) and modern totalitarian experiments with communism which are still present in political discourse and preserved in the dominant forms of collective memory.

The order of states in a transformation series describes an internested set of synapomorphies. States adjacent to each other in the transformation series thus share a degree of homology not found in the other states. Whether the level of homology is relatively apomorphic is determined by rooting the order with outgroup comparison. The analysis of state order is a homology problem and is solved with a two-step process using similarity and congruence with other characters as criteria. Other methods that have been proposed (e.g. transformation series analysis, non-additive analysis, morphocline analysis, ontogenetic analysis) fail to apply both similarity and congruence, and thus cannot be used independently for determining character state order.

Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.

When parsimony ancestral character reconstruction is ambiguous, it is often resolved in favour of the more complex character state. Hence, secondary loss (secondary ‘‘absence’’) of a complex feature is favoured over parallel gains of that feature as this preserves the stronger hypothesis of homology. We believe that such asymmetry in character state complexity is important information for understanding character evolution in general. However, we here point out an inappropriate link that is commonly made between this approach and the accelerated transformation (ACCTRAN) algorithm. In ACCTRAN, changes are assigned along branches of a phylogenetic tree as close to the root as possible. This has been taken to imply that ACCTRAN will minimize hypotheses of parallel origins of complex traits and thus that ACCTRAN is philosophically better justified than the alternatives, such as delayed transformation (DELTRAN), where changes are assigned along branches as close to the tips as possible. We provide simple examples to show that such views are mistaken and that neither ACCTRAN nor DELTRAN consistently minimize parallel gain of complex traits. We therefore do not see theoretical grounds for favouring the popular ACCTRAN algorithm. � The Willi Hennig Society 2008.

The present article discusses the need for standardization in morphology in order to increase comparability and communicability of morphological data. We analyse why only morphological descriptions and not character matrices represent morphological data and why morphological terminology must be free of homology assumptions. We discuss why images only support and substantiate data but are not data themselves. By comparing morphological traits and DNA sequence data we reveal fundamental conceptual shortcomings of the former that result from their high average degree of individuality. We argue that the delimitation of morphological units, of datum units, and of evidence units must be distinguished, each of which involves its own specific problems. We conclude that morphology suffers from the linguistic problem of morphology that results from the lack of (i) a commonly accepted standardized morphological terminology, (ii) a commonly accepted standardized and formalized method of description, and (iii) a rationale for the delimitation of morphological traits. Although this is not problematic for standardizing metadata, it hinders standardizing morphological data. We provide the foundation for a solution to the linguistic problem of morphology, which is based on a morphological structure concept. We argue that this structure concept can be represented with knowledge representation languages such as the resource description framework (RDF) and that it can be applied for morphological descriptions. We conclude with a discussion of how online databases can improve morphological data documentation and how a controlled and formalized morphological vocabulary, i.e. a morphological RDF ontology, if it is based on a structure concept, can provide a possible solution to the linguistic problem of morphology. © The Willi Hennig Society 2009.

Contrasting definitions of organs based either on function or on strictly morphological criteria are the legacy of a tradition starting with Aristotle. This floating characterization of organs in terms of both form and function extends also to organ systems. The first section of this review outlines the notions of organ and body part as defined, explicitly or implicitly, in representative works of nineteenth century’s comparative morphology. The lack of a clear distinction between the two notions led to problems in Owen’s approach to the comparative method (definition of homolog vs. nature of the vertebrate archetype) and to a paradoxical formulation, by Anton Dohrn, of the principle of functional change. Starting from the second half of the twentieth century, with the extensive use of morphological data in phylogenetic analyses, both terms – organ and body part – have been often set aside, to leave room for a comparison between variously characterized attributes (character states) of the taxa to be compared. Throughout the last two centuries, there have been also efforts to characterize organs or body parts in terms of the underlying developmental dynamics, both in the context of classical descriptive embryology and according to models suggested by developmental genetics. Functionally defined organ are occasionally co-extensive with morphologically defined body parts, nevertheless a clear distinction between the former and the latter is a necessary prerequisite to a study of their evolution: this issue is discussed here on the example of the evolution of hermaphroditism and gonad structure and function.

The contribution of Etienne Geoffroy Saint-Hilaire (1772–1844) to evolutionary biology is reviewed in commemoration of his 250th birthday. Geoffroy's views on saltational changes during embryogenesis of animals characterize him as a predecessor of the epigenetic concept of evolution, which is now developing in the frames of the extended evolutionary synthesis or evo-devo. While Lamarck distinguished between the two modes of evolution, one within the same level of organization and the other characterized by the transition to a more complex organization, Geoffroy Saint-Hilaire attempted to explain the second mode by the changes in embryogenesis triggered by environmental influences. In this regard, he placed the phenomenon of complexification in the centre of the evolutionary context. Geoffroy Saint-Hilaire can be considered also as an early predecessor of the cell theory. His ideas about the unique plan of structure for animal species and of the fundamental connections that establish the homology of anatomical parts represent an important contribution to the evolutionary concept.

With the nexus of super computing and the biotech revolution, it seems an era of predictive biology through systems biology may be at hand. Modern omics capabilities enable examination of the state of biological system in exquisite detail. The genome, transcriptome, proteome, and metabolome may all be largely knowable, at least for some model systems, providing a basis for modeling and simulation of molecular mechanisms, or pathways, that could capture a biological system's emergent properties. However, there are significant challenges remaining that impede the realization of this vision, perhaps the most significant being the missing functional annotation of genes and gene products. For even the most well-studied organisms as much as a third of called genes for a given genome are not annotated and more than half may be tenuous. Homology inferred from sequence similarity is the basis for much of genome annotation. Homology inferred from structural similarity could be a powerful complement to sequence-based annotation methods. Structural biology or structural informatics can be used to assign molecular function and may have increasing utility with the rapid growth of gene sequence databases and emerging methods for structure determination, like structure prediction based on coevolution. Here we describe tools and provide example cases using structural similarity at the level of quaternary structure, domain content, domain topology, and small 3D motifs to infer homology and posit function. Ultimately annotation by similarity, be it 3D structure homology or more classically primary sequence homology, must be founded by accurate annotation of one ortholog in the group-understanding every function encoded by a genome remains a major challenge to life science.

Recent advances in science and engineering have facilitated the development of artificial intelligence voice assistants. While this is true from a technical aspect, smart speakers and voice assistants did not develop in isolation from the rest of human society. The devices may be new, but the practices and patterns in their development and use are not. Using Lévi-Strauss’s structural anthropology, I map homologous practices of smart speaker interaction onto historical conceptions of supernatural magic use. This structural comparison suggests that practices and patterns that were essential to magic use have re-emerged in smart speaker utilization in similar forms. Some of these practices are noteworthy for their homology alone. However, other homologous behaviors revive patterns of inequity that, in Western magical traditions, had privileged the traditionally educated man. The goal of this paper is to elucidate the ghost in the machine: the prejudiced social practices of supernatural magic that were asserted to be eradicated yet which are now, nevertheless, newly instantiated within our most cutting-edge devices.

We develop a multilevel framework that proposes the main and interactive effects of person-group (PG) fit in values and abilities on creativity at the individual and group levels. Our analysis of field data collected from 738 members comprising 108 work teams provides empirical support for our multilevel model of PG fit. Specifically, ability fit and collective ability fit exhibit consistent positive effects on individual and team creativity, respectively (i.e., multilevel homology). By contrast, at the individual level, value fit suppresses the positive effect of ability fit on individual creativity, while at the group level, collective value fit accentuates the positive effect of collective ability fit on team creativity (i.e., multilevel discontinuity). This study highlights the significance of multilevel interactive perspective on person-environment fit.

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Jawless fishes were the first vertebrates to evolve. It is thus important to investigate them to determine whether consciousness was acquired in the common ancestor of all vertebrates. Most jawless fish lineages are extinct, and cyclostomes (lampreys and hagfish) are the sole survivors. Here, I review the empirical knowledge on the neurobiology of cyclostomes with special reference to recently proposed “markers” of primary, minimal consciousness. The adult lamprey appears to meet the neuroanatomical criteria but there is a practical limitation to behavioral examination of its learning ability. In addition, the consciousness-related neuroarchitecture of larvae and its reconstruction during metamorphosis remain largely uninvestigated. Even less is known of hagfish neurobiology. The hagfish forebrain forms the central prosencephalic complex, and the homology of its components to the brain regions of other vertebrates needs to be confirmed using modern techniques. Nevertheless, as behavioral responses to olfactory stimuli in aquariums have been reported, it is easier to investigate the learning ability of the hagfish than that of the lamprey. Based on these facts, I finally discuss the potential future directions of empirical studies for examining the existence of consciousness in jawless fishes.

The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.

Molecular timescales estimate that early animal lineages diverged tens of millions of years before their earliest unequivocal fossil evidence. The Ediacaran macrobiota (~574–538 million years ago) are largely eschewed from this debate, primarily due to their extreme phylogenetic uncertainty, but they remain germane. We characterize the development of Charnia masoni and establish the phylogenetic affinity of rangeomorphs, among the oldest and most enigmatic components of the Ediacaran macrobiota. We provide the first direct evidence for the internal interconnected nature of rangeomorphs, and show Charnia was constructed of repeated branches that derived successively from pre-existing branches. We find homology and rationalise morphogenesis between disparate rangeomorph taxa, before producing a new phylogenetic analysis, resolving Charnia as a stem-eumetazoan and expanding the anatomical disparity of that group to include a long-extinct bodyplan. These data bring competing records of early animal evolution into closer agreement, reformulating our understanding of the evolutionary emergence of animal bodyplans.

In this work, we automatically distinguish between different clones of the same bacteria species (Klebsiella pneumoniae) based only on microscopic images. It is a challenging task, previously seemed unreachable due to the high clones' similarity. For this purpose, we apply a multi-step algorithm with attention-based deep multiple instance learning, which returns parts of the image crucial to the prediction. Except for obtaining high accuracy, we introduce extensive explainability based on persistence homology, increasing the understandability and trust in the model. Our work opens a plethora of research pathways towards cheaper and faster epidemiological management.

My aim in this paper is twofold. First, I provide an analysis of the notion of cognitive homology. In contrast with the well-known concept of structural (or morphological) homology in biology—defined as the same structure in different animals regardless of form and function—the notion of cognitive homology captures the idea that the basic cognitive contribution of a given homologous brain structure tends to remain stable over long evolutionary time scales. Second, I argue that this notion provides a powerful conceptual tool for the study of cognition. Since a cognitive homology will often consist of an evolutionarily conserved relationship between a homologous brain structure and its basic cognitive contribution, such structure–function mappings can be conceived as basic building blocks of human cognition.

Reconstructing ancestral species is a challenging endeavour: fossils are often scarce or enigmatic, and inferring ancestral characters based on novel molecular approaches (e.g. comparative genomics or developmental genetics) has long been controversial. A key philosophical challenge pertinent at present is the lack of a theoretical framework capable of evaluating inferences of homology made through integration of multiple kinds of evidence (e.g. molecular, developmental, or morphological). Here, I present just such a framework. I start with a brief history and critical assessment of attempts at inferring morphological homology through developmental genetics. I then bring attention to a recent model of homology, namely Character Identity Mechanisms (DiFrisco et al. 2020), intended partly to elucidate the relationships between morphological characters, developmental genetics, and homology. I utilise and build on this model to construct the evaluative framework mentioned above, which judges the epistemic value of evidence of each kind in each particular case based on three proposed criteria: effectiveness, admissibility, and informativity, as well as providing a generalised guideline on how it can be scientifically operationalised. I then point out the evolution of the eumetazoan body plan as a case in point where the application of this framework can yield satisfactory results, both empirically and conceptually. I will conclude with a discussion on some potential implications for more general philosophy of biology and philosophy of science, especially surrounding evidential integration, models and explanation, and reductionism.

Viruses are abundant, diverse and ancestral biological entities. Their diversity is high, both in terms of the number of different protein families encountered and in the sequence heterogeneity of each protein family. The recent increase in sequenced viral genomes constitutes a great opportunity to gain new insights into this diversity and consequently urges the development of annotation resources to help functional and comparative analysis. Here, we introduce PHROG (Prokaryotic Virus Remote Homologous Groups), a library of viral protein families generated using a new clustering approach based on remote homology detection by HMM profile-profile comparisons. Considering 17 473 reference (pro)viruses of prokaryotes, 868 340 of the total 938 864 proteins were grouped into 38 880 clusters that proved to be a 2-fold deeper clustering than using a classical strategy based on BLAST-like similarity searches, and yet to remain homogeneous. Manual inspection of similarities to various reference sequence databases led to the annotation of 5108 clusters (containing 50.6 % of the total protein dataset) with 705 different annotation terms, included in 9 functional categories, specifically designed for viruses. Hopefully, PHROG will be a useful tool to better annotate future prokaryotic viral sequences thus helping the scientific community to better understand the evolution and ecology of these entities.

Comparative biology builds up systematic knowledge of the diversity of life, across evolutionary lineages and levels of organization, starting with evidence from a sparse sample of model organisms. In developmental biology, a key obstacle to the growth of comparative approaches is that the concept of homology is not very well defined for levels of organization that are intermediate between individual genes and morphological characters. In this paper, we investigate what it means for ontogenetic processes to be homologous, focusing specifically on the examples of insect segmentation and vertebrate somitogenesis. These processes can be homologous without homology of the underlying genes or gene networks, since the latter can diverge over evolutionary time, while the dynamics of the process remain the same. Ontogenetic processes like these therefore constitute a dissociable level and distinctive unit of comparison requiring their own specific criteria of homology. In addition, such processes are typically complex and nonlinear, such that their rigorous description and comparison requires not only observation and experimentation, but also dynamical modelling. We propose six criteria of process homology, combining recognized indicators (sameness of parts, morphological outcome and topological position) with novel ones derived from dynamical systems modelling (sameness of dynamical properties, dynamical complexity and evidence for transitional forms). We show how these criteria apply to animal segmentation and other ontogenetic processes. We conclude by situating our proposed dynamical framework for homology of process in relation to similar research programmes, such as process structuralism and developmental approaches to morphological homology. ispartof: Interface Focus vol:11 issue:3 pages:1-18 ispartof: location:England status: published

The increasingly widespread availability of genomic data has created a growing need for fast, sensitive and scalable comparative analysis methods. A key aspect of comparative genomic analysis is the study of synteny, co-localized gene clusters shared among genomes due to descent from common ancestors. Synteny can provide unique insight into the origin, function, and evolution of genome architectures, but methods to identify syntenic patterns in genomic datasets are often inflexible and slow, and use diverse definitions of what counts as likely synteny. Moreover, the reliable identification of putatively syntenic regions (i.e., whether they are truly indicative of homology) with different lengths and signal to noise ratios can be difficult to quantify. Here, we present Mology, a fast, flexible, alignment-free, nonparametric method to detect regions of syntenic elements among genomes or other datasets. The core algorithm operates on consecutive, rank-ordered elements, which could be genes, operons, motifs, sequence fragments, or any other orderable element. It is agnostic to the physical distance between distinct elements and also to directionality and order within syntenic regions, although such considerations can be addressed post hoc. We describe the underlying statistical theory behind our analysis method, and employ a Monte Carlo approach to estimate the false positive rate and positive predictive values for putative syntenic regions. We also evaluate how varying amounts of noise affect recovery of true syntenic regions among Saccharomycetaceae yeast genomes with up to ~100 million years of divergence. We discuss different strategies for recursive application of our method on syntenic regions with sparser signal than considered here, as well as the general applicability of the core algorithm.