Frequent evolutionary birth and death events have created a large quantity of biologically important, lineage‐specific DNA within mammalian genomes. The birth and death of DNA sequences is so frequent that the total number of these insertions and deletions in the human population remains unknown, although there are differences between these groups, e.g. transposable elements contribute predominantly to sequence insertion. Functional turnover – where the activity of a locus is specific to one lineage, but the underlying DNA (...) remains conserved – can also drive birth and death. However, this does not appear to be a major driver of divergent transcriptional regulation. Both sequence and functional turnover have contributed to the birth and death of thousands of functional promoters in the human and mouse genomes. These findings reveal the pervasive nature of evolutionary birth and death and suggest that lineage‐specific regions may play an important but previously underappreciated role in human biology and disease. (shrink)

The hematopoietic system consists of more than ten differentiated cell types, all of which are derived from a single type of hematopoietic stem cell. The accessibility and interest of this system have made it a model for understanding normal and abnormal differentiation of mammalian cells. Newer techniques have generated a mass of data that requires integrative approaches for analysis and interpretation. The traditional view of the differentiation program holds that a small number of regulators are involved in each stage of (...) cell specification. However, this may not be the case. Recent analyses have shown that almost all substantial subsets of genes, including the set of broadly expressed transcription factors, are expressed in patterns that are unique for each lineage. Further, much of this difference between lineages can be captured in two‐dimensional graphs. Understanding the biologic significance, mechanisms and constraints underlying these differences is a challenge for experimentalists and computational biologists alike. BioEssays 26:1276–1287, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” (...) but it is unable per se to choose among them: the emergence of a specific phenotype is enabled by physical constraints that drive the system toward a preferred solution. These findings may help in understanding how cells and tissues behave in both development and cancer. In microgravity, cells undergo spontaneous and reversible transitions between different phenotypes. In the absence of physical constraints, living systems could yield bi-stable decisions. On the contrary, physical ‘boundaries’ constrain cells to acquire only a specific configuration by selecting and shaping different gene expression patterns provided by the intrinsic genetic stochasticity. (shrink)

Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, proposing (...) the lineage view of stem cells as an ontological framework for conceptualizing organismal development. This account is grounded on experimental practices of stem cell research, with emphasis on new techniques for generating biological organization in vitro. On the lineage view, a stem cell is the starting point of a cell lineage with a specific organismal source, time-interval of existence, and ‘tree topology’ of branch-points linking the stem to developmental termini. The concept of ‘enkapsis’ accommodates the cell-organism relation within the lineage view; this hierarchical notion is further explicated by considering the methods and results of stem cell experiments. Results of this examination include a (partial) characterization of stem cells’ developmental versatility, and the context-dependence of developmental processes involving stem cells. (shrink)

Co-creating knowledge takes a new approach to human phenotypic morality as a biologically based, human lineage specific trait. Authors from very different backgrounds first review research on the nature and origins of morality using the social brain network, and studies of individuals who cannot “know good” or think morally because of brain dysfunction. They find these models helpful but insufficient, and turn to paleoanthropology, cognitive science, and neuroscience to understand human moral capacity and its origins long ago, in (...) the genus Homo. An unusual narrative capturing “morality in action” takes the reader back 900,000 years, and then the authors analyze the essential features of moral thinking and behavior as expressed by early and later species on our lineage. In what has primarily been the province of philosophers to date, the authors’ morality model is presented for further scientific testing. (shrink)

Biological boundaries are important because of what they reveal about the evolution of a lineage, the relationship between organisms of different lineages, the structure and function of particular subsystems of the organism, the interconnection between an organism and its environment, and a myriad of other important issues related to individuality, development, and evolution. Since there is no single unifying theory for all biological sciences, there are various possible theoretical characterizations of what counts as a biological boundary. Theoretical specificity is (...) crucial for the full characterization of a boundary; to this end, it is useful to begin with general properties and then to compare these to those properties specific to a particular biological boundary. This dual heuristic approach—top-down and bottom-up—can then be repeated to increase the robustness of the boundary characterization. In what follows, I explore both the general structural and functional aspects of biological boundaries and those specific to a biological subsystem, which itself is critical to boundary formation, maintenance, and evolution—the vertebrate immune system. It is a remarkable and sobering regularity of nature that organisms remain whole because their parts are constantly being built up and broken down, and this is no less true of their boundaries. The vertebrate immune system is at the center of this process of biological boundary maintenance and breakdown. (shrink)

Previous work has suggested that many stem cells can be found in microanatomic niches, where adjacent somatic cells of the niche control the differentiation and proliferation states of their resident stem cells. Recently published work examining intestinal stem cells (ISCs) in the adult Drosophila midgut suggests a new paradigm where some stem cells actively control the cell fate decisions of their daughters. Here, we review recent literature(1) demonstrating that, in the absence of a detectable stem cell niche, multipotent Drosophila ISCs (...) modulate the Notch signaling pathway in their adjacent daughter cells in order to specify the differentiated lineages of their descendants. These observations made in Drosophila are challenging and advancing our understanding of stem cell biology. BioEssays 30:107–109, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

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 not only requires observation and experimentation, but also dynamical modeling. We propose six criteria of process homology, combining recognized indicators with novel ones derived from dynamical systems modeling. 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 programs, such as process structuralism and developmental approaches to morphological homology. (shrink)

Evolutionary systems biology (ESB) aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations of (...) specific traits. Next, these tensions are further clarified by considering a recent case from another field focused on developmental dynamics: stem cell biology. In the stem cell case, incompatible explanatory aims block integration. Experimental approaches aim at mechanistic explanation while dynamical system models offer explanation in terms of general principles. We then discuss an ESB case in which integration succeeds: search for general attractors using a dynamical systems framework synergizes with the experimental search for detailed mechanisms. Contrasts between the positive and negative cases suggest general lessons for achieving an integrated understanding of developmental and evolutionary dynamics. The key integrative move is to acknowledge two complementary aims, both relevant to explanation: identifying the space of possible dynamic states and trajectories, and mechanistic understanding of causal interactions underlying a specific phenomenon of interest. These two aims can support one another in a joint project characterizing dynamic aspects of evolving lineages. This more inclusive project can lead to insights that cannot be reached by either approach in isolation. (shrink)

The largest proportion of microRNAs in humans (ca. 40–50%) originated in the phylogenetic grouping defined as primates. The dynamic evolution of this family of non‐coding RNA is further demonstrated by the presence of microRNA unique to the human species. Investigations into the role of microRNA in cancer have until recently mainly focused on the more ancient members of this RNA family that are widely conserved in the animal kingdom. As I describe in this review the evolutionary young lineage and (...) species‐specific microRNA could be important contributors to cancers, especially in particular organs in primates compared to more distantly‐related research models. Elucidating the biological significance of primate and human‐specific microRNA in cancer could have important implications for cancer research and the use of non‐primate animal models. (shrink)

The formal framework of Kauffman (1991) depicts the constraints of self-organization on the evolution of complex systems and the relation of self-organization to selection. We discuss his treatment of 'generic constraints' as sources of order (section 2) and the relation between adaptation and organization (section 3). We then raise a number of issues, including the role of adaptation in explaining order (section 4) and the limitations of formal approaches in explaining the distinctively biological (section 5). The principal question we pose (...) is the relation of generic constraints on evolution to more specific local constraints, imposed, for example, by the characteristic materials out of which organisms are constructed, the accidental features characteristic of the Bauplan of a lineage, and the local vicissitudes of adaptation. We offer no answer to this large question. (shrink)

Despite ever‐increasing accumulation of genomic data, the fundamental question of how individual genes are switched on during development, lineage‐specification and differentiation is not fully answered. It is widely accepted that this involves the interaction between at least three fundamental regulatory elements: enhancers, promoters and insulators. Enhancers contain transcription factor binding sites which are bound by transcription factors (TFs) and co‐factors expressed during cell fate decisions and maintain imposed patterns of activation, at least in part, via their epigenetic modification. This (...) information is transferred from enhancers to their cognate promoters often by coming into close physical proximity to form a ‘transcriptional hub’ containing a high concentration of TFs and co‐factors. The mechanisms underlying these stages of transcriptional activation are not fully explained. This review focuses on how enhancers and promoters are activated during differentiation and how multiple enhancers work together to regulate gene expression. We illustrate the currently understood principles of how mammalian enhancers work and how they may be perturbed in enhanceropathies using expression of the α‐globin gene cluster during erythropoiesis, as a model. (shrink)

Two welcome extensions of evolutionary thinking have come to prominence over the last thirty years: the so-called ’extended evolutionary synthesis’ (EES) and debate about biological kinds and individuals. These two agendas have, however, remained orthogonal to one another. The EES has mostly restricted itself to widening the explanations of adaptation offered by the preceding ’modern evolutionary synthesis’ by including additional mechanisms of inheritance and variation; while discussion of biological kinds has turned toward philosophical questions of essential vs. contingent properties of (...) life forms and realist vs. epistemological approaches to categorization and classification. Here we attempt to broaden the explanatory scope of evolutionary theory by linking these two agendas. We expand on the mechanistic orientation of the EES, using new understandings of networked systems of components in order to engage the distinct intellectual challenge of the origination of “historical kinds”. With this phrase we designate a subset of natural kinds that acquires, through evolutionary processes, a quasi-independent lineage-history. Such kinds emerge in both biology and culture, and we enlarge the limited number of historical kinds that have thus far been recognized in evolutionary biology in a series of paradigmatic exemplars, from genes and cell types to rituals and music. For each exemplar we discern specific mechanisms by which it arose and persists; comparing these, we suggest a general unity in the ways in which diverse historical kinds originate. (shrink)

American biologists in the late nineteenth century pioneered the descriptive-comparative study of all cell divisions from zygote to gastrulation -- the cell lineage. Data from cell lineages were crucial to evolutionary and developmental questions of the day. One of the main questions was the ultimate causation of developmental patterns -- historical or mechanical. E. B. Wilson's groundbreaking lineage work on the polychaete worm Nereis in 1892 set the stage for (1) an attack on Haeckel's phylogenetic-historical notion of recapitulation (...) and (2) support for mechanistic explanations of cleavage patterns. As more lineage work -- especially Lillie's work on "Unio" and Conklin's on "Crepidula" -- became available in the mid-late 1890s, mechanism was tempered with more evolutionary, homology-based views. However, as I show by focusing on three major issues -- homology, body plans and life history -- these views were primarily based on the precocious segregation and prospective significance -- what the cell became not what it was. Even on issues like adaptation, most lineagists argued teleologically from the adult backward. Most cell lineage workers, by 1900, were to varying degrees mechanist/experimentalist and recapitulationist simultaneously. The exception was E. G. Conklin, whose views were more akin to a Darwinian evolutionist than either mechanist or recapitulationist. Lineage work eventually declined and by 1907 published accounts of new lineages had basically stopped. I argue that established workers and younger researchers stopped wanting to take on cell lineage projects because the general patterns were the same for all the spiralians while the specifics showed too much variation. It was hard to theoretically encompass or analyze the minutiae of variation in a recapitulationist or mechanist framework. The only established worker who continued to do comparative lineage studies was E. G. Conklin, perhaps because the variation could best be accommodated by Darwinian evolution. (shrink)

An important mechanism for the evolution of phenotypic complexity, diversity and innovation, and the origin of novel gene functions is the duplication of genes and entire genomes. Recent phylogenomic studies suggest that, during the evolution of vertebrates, the entire genome was duplicated in two rounds (2R) of duplication. Later, ∼350 mya, in the stem lineage of ray‐finned (actinopterygian) fishes, but not in that of the land vertebrates, a third genome duplication occurred—the fish‐specific genome duplication (FSGD or 3R), leading, (...) at least initially, to up to eight copies of the ancestral deuterostome genome. Therefore, the sarcopterygian (lobe‐finned fishes and tetrapods) genome possessed originally only half as many genes compared to the derived fishes, just like the most‐basal and species‐poor lineages of extant fishes that diverged from the fish stem lineage before the 3R duplication. Most duplicated genes were secondarily lost, yet some evolved new functions. The genomic complexity of the teleosts might be the reason for their evolutionary success and astounding biological diversity. BioEssays 27:937–945, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Sponges branch basally in the metazoan phylogenetic tree and are believed to be composed of four distinct lineages with still uncertain relationships. Indeed, some molecular studies propose that Homoscleromorpha may be a fourth Sponge lineage, distinct from Demospongiae in which they were traditionally classified. They harbour many features that distinguish them from other sponges and are more evocative of those of the eumetazoans. They are notably the only sponges to possess a basement membrane with collagen IV and specialized cell‐junctions, (...) thus possessing true epithelia. Among Homoscleromorphs, we have chosen Oscarella lobularis as a model species. This common and easily accessible sponge is characterized by relatively simple histology and cell composition, absence of skeleton, and strongly pronounced epithelial structure. In this review, we explore the specific features that make O. lobularis a promising homoscleromorph sponge model for evolutionary and developmental researches. (shrink)

Evolutionary developmental biology (evo-devo) is often vindicated by theoreticians of the field as a mechanistic science that brings a mechanistic perspective into evolutionary biology. Usually, it is also portrayed as stressing the causal role that development plays in the evolutionary process. However, mechanistic studies in evo-devo typically refer to lineage-specific transformations and lack the generality that evolutionary explanations usually aim for. After reviewing the prospects and limits of a mechanistic view of evo-devo and their studies of (...) homology and novelty, in this chapter I propose a way to combine the mechanistic view of evo-devo with the population-level inclination of more classical approaches to evolution. Such a proposal provides a philosophical framework for understanding the causal role of development in evolution both as mechanistic and as generalizable, population-level. (shrink)

The recent genome sequencing of a non‐vertebrate deuterostome, the ascidian tunicate Ciona intestinalis, makes a substantial contribution to the fields of evolutionary and developmental biology.1 Tunicates have some of the smallest bilaterian genomes, embryos with relatively few cells, fixed lineages and early determination of cell fates. Initial analyses of the C. intestinalis genome indicate that it has been evolving rapidly. Comparisons with other bilaterians show that C. intestinalis has lost a number of genes, and that many genes linked together (...) in most other bilaterians have become uncoupled. In addition, a number of independent, lineage‐specific gene duplications have been detected. These new results, although interesting in themselves, will take on a deeper significance once the genomes of additional invertebrate deuterostomes (e.g. echinoderms, hemichordates and amphioxus) have been sequenced. With such a broadened database, comparative genomics can begin to ask pointed questions about the relationship between the evolution of genomes and the evolution of body plans. BioEssays 25:529–532, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Recent sequencing of the metazoan Oikopleura dioica genome has provided important insights, which challenges the current understanding of eukaryotic genome evolution. Many genomic features of O. dioica show deviation from the commonly observed trends in other eukaryotic genomes. For instance, O. dioica has a rapidly evolving, highly compact genome with a divergent intron‐exon organization. Additionally, O. dioica lacks the minor spliceosome and key DNA repair pathway genes. Even with a compact genome, O. dioica contains tandem repeats, comparable to other eukaryotes, (...) and shows lineage‐specific expansion of certain protein domains. Here, we review its genomic features in the context of current knowledge, discuss implications for contemporary biology and identify areas for further research. Analysis of the O. dioica genome suggests that non‐adaptive forces such as elevated mutation rates might influence the evolution of genome architecture. The knowledge of unique genomic features and splicing mechanisms in O. dioica may be exploited for synthetic biology applications, such as generation of orthogonal splicing systems. (shrink)

Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...) of genetic causes consists in. In this paper, I show that the set of biomolecules that are normally considered to be information-bearers (DNA, mRNA) can be shown to be the most specific causes of protein primary structure, provided that causal specificity is measured over a relevant space of biological possibilities, disregarding physical as well as logically possible states of the causal variables. (shrink)

Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, if (...) at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification. (shrink)

Based on historical data pertaining to the Krummhörn population (eighteenth and nineteenth centuries, Germany), we compared reproductive histories of mothers according to whether the maternal grandmother (MGM) or the paternal grandmother (PGM) or neither of them was resident in the parents’ parish at the time of the mother’s first birth. In contrast to effects of PGMs, we discovered conditional differences in the MGM’s effects between landless people and wealthier, commercial farmers. Our data indicate that the presence of the MGM only (...) lowers the woman’s age at marriage (AAM) and her age at the birth of her first child (AFB) in the case of landless families. However, among commercial farmers, who can generally be characterized by a lower AAM and AFB, we found opposite tendencies for the MGM’s effect leading to a relatively small delay in AAM and AFB. Moreover, we also analyzed differences in the completed fertility (i.e., children ever born: CEB). Results indicate that landless families in general do have fewer CEB compared with commercial farmers except for those families in which the MGM has been present. Emphasizing that the adaptiveness of investment decisions should depend on the interaction of genetic, lineage-specific (intrinsic) and ecologically imposed (extrinsic) constraints, we conclude that kin strategies consequently address different fitness components under different conditions. (shrink)

Palaeontology developed as a field dependent upon comparison. Not only did reconstructing the fragmentary records of fossil organisms and placing them within taxonomic systems and evolutionary lineages require detailed anatomical comparisons with living and fossil animals, but the field also required thinking in terms of behavioural, biological and ecological analogies with modern organisms to understand how prehistoric animals lived and behaved. Yet palaeontological material often worked against making easy linkages, bringing a sense of mystery and doubt. This paper will look (...) at an animal whose study exemplified these problems: the Chalicothere. Increasingly recognized as a specific type from finds across North America and Eurasia from the early nineteenth century onwards, these prehistoric mammals showed short back legs terminating in pawed feet, long front limbs ending in sharp claws, a long flexible neck, and herbivorous grinding teeth. The Chalicothere became a significant organism within palaeontological studies, as the unexpected mix of characters made it a textbook example against the Cuvierian notion of “correlation of parts,” while explaining how the animal moved, fed and behaved became puzzling. However, rather than prevent comparisons, these actually led to comparative analogies becoming flexible and varied, with different forms of comparison being made with varying methods and degrees of confidence, and with the anatomy, movement and behaviour of giraffes, bears, horses, anteaters, primates and other organisms all serving at various points as potential models for different aspects of the animal. This paper will examine some of the attempts to reconstruct and define the Chalicotheres across a long timescale, using this to show how multiple comparisons and analogies could be deployed in a reconstructive and evolutionary science like palaeontology, and illustrate some of the limits and tensions in comparative methods, as they were used to reconstruct organisms which were thought to be incomparable to any modern animal. (shrink)

The establishment of distinct cellular identities was pivotal during the evolution of Metazoa, enabling the emergence of an array of specialized tissues with different functions. In most animals including vertebrates, cell specialization occurs in response to a combination of intrinsic (e.g., cellular ontogeny) and extrinsic (e.g., local environment) factors that drive the acquisition of unique characteristics at the single‐cell level. The first functional organ system to form in vertebrates is the cardiovascular system, which is lined by a network of endothelial (...) cells whose organ‐specific characteristics have long been recognized. Recent genetic analyses at the single‐cell level have revealed that heterogeneity exists not only at the organ level but also between neighboring endothelial cells. Thus, how endothelial heterogeneity is established has become a key question in vascular biology. Drawing upon evidence from multiple organ systems, here we will discuss the role that lineage history may play in establishing endothelial heterogeneity. (shrink)

Priming of lineage‐specific genes in pluripotent embryonic stem cells facilitates rapid and coordinated activation of transcriptional programmes during differentiation. There is growing evidence that pluripotency factors play key roles in priming tissue‐specific genes and in the earliest stages of lineage commitment. As differentiation progresses, pluripotency factors are replaced at some primed genes by related lineage‐specific factors that bind to the same sequences and maintain epigenetic priming until the gene is activated. Polycomb and trithorax group (...) proteins bind many genes in pluripotent cells generating bivalent domains that contain both active and repressive histone modifications. The properties of polycomb proteins suggest that they act as gatekeepers, helping to maintain silencing in pluripotent stem cells while establishing a chromatin environment that is permissive for priming by sequence‐specific factors. The overall effect of factor‐mediated priming is to initiate the input of information required for cell differentiation before the first lineage choices have been made. (shrink)

This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of (...) other evolutionary conceptions of the unit of heredity, such as the replicator, the reproducer, and the Darwinian individual. We argue that these conceptions are based on the requirement of lineage formation, which we argue to be unnecessary for the existence of evolutionary heredity. In the second part, we introduce the reconstitutor, which we base on the concept of Stability of Traits, and illustrate how it covers cases of hereditary phenomena not covered by the previous accounts. Secondly, we illustrate how the reconstitutor could serve as a platform to rethink ecological inheritance and other forms of inheritance that have been recently introduced under the song/singer model of evolution. (shrink)

The most interesting biological molecules are long polymers. In analogy with human alphabetic languages, they can be called texts and analysed, as to the primary structure, as sequences of letters or of words . It is considered that the study of words, in a linguistic approach, may contribute positively to the understanding of molecular interactions . The molecular and human languages and dialects are contrasted. The molecular one is peculiarly distinct from the human, for instance, by its use of a (...) tridimensional morphology, temporal dynamics, absence of spacings and punctuation, and overlapping messages. A mathematical method is presented, for discovering words in texts. The word AAA was studied in the evolution of the 5S ribosomal RNA. It was shown that this word is more frequent in less complex organisms and less frequent in the more complex ones, in the fungi, plants, and vertebrates lineages. In the two latter ones, the degree of genie variability was also reduced. To the contrary, a moderate degree of usage of this word persisted in the whole invertebrates lineage, where a high degree of genie variability was maintained. In mitochondria, plastids and mycoplasmas, the frequency of the word AAA was increased, consistently with their need for interactions with a wider range of variation. These behaviors indicate that the monotonous AAA word allows for ambiguity in interactions. With the evolution of organic complexity and of greater molecular specificity, ambiguous words were progressively avoided.As moléculas biológicas mais interessantes são longos polímeros. Em analogia com a linguagem humana alfabética, estes podem ser chamados de textos, e analisados, quanto à estrutura primária, como sequência de letras ou de palavras . Considera-se que o estudo das palavras, em abordagem de tipo lingüístico, possa contribuir para o entendimento das interações moleculares. As linguagens e dialetos, moleculares e humanos, são contrastados. A linguagem molecular se distingue peculiarmente da humana, por exemplo, por utilizar forma tridimensional, dinâmica temporal, ausência de espaçamento e pontuação, e sobreposição de significados. Apresenta-se um método matemático para descoberta, de palavras em textos. A palavra AAA foi estudada na evolução do RNA ribossômico 5S. Observou-se que esta palavra é mais freqüente em organismos menos complexos e menos freqüente nos mais complexos, das linhagens de fungos, plantas e vertebrados. Nas duas últimas, reduziu-se também o grau de variabilidade gênica. Pelo contrário, grau moderado de freqüência da palavra persistiu em toda a linhagem dos invertebrados, com manutenção paralela de alto nível de variabilidade gênica. Nas mitocôndrias, plastídeos e micoplasmas, a freqüência da palavra AAA foi aumentada, de acordo com sua necessidade de interações com maior amplitude de variação. Esses comportamentos indicam que a palavra monótona AAA permite ambigüidade de interações. Com a evolução da complexidade orgânica e da maior especificidade molecular, as palavras ambíguas foram progressivamente evitadas. (shrink)

The standard picture of evolution, is externalist: a causal arrow runs from environment to organism, and that arrow explains why organisms are as they are (Godfrey-Smith 1996). Natural selection allows a lineage to accommodate itself to the specifics of its environment. As the interior of Australia became hotter and drier, phenotypes changed in many lineages of plants and animals, so that those organisms came to suit the new conditions under which they lived. Odling-Smee, Laland and Feldman, building on the (...) work of Richard Lewontin, have shown that while sometimes appropriate, this is an inadequate conception of the relationship between organisms and the environments in which they live. Over time organisms alter their environment as well as being altered by their environments (Lewontin 1982; Lewontin 1983; Lewontin 1985). For example, animals modulate the effects of their physical and biological environment by building shelters: the beaver’s dam and lodge system, and termite mounds are two famous cases of animal structures, but they are few of many. There are many thousands of animals which make nests, burrows and other shelters. Likewise, animals make tools that give them access to resources from which they would otherwise be excluded: thus the Galapagos woodpecker finch uses a cactus needle to extract insects from crevasses in bark — insects that they would otherwise be unable to catch (Tebbich, Taborsky et al. 2001). Tool making is not as common as shelter-making, but it is common. For example many animals make traps: there are many species of pit-making antlions. Thus in part organisms make the world in which they live. They partially construct their own niches. Odling-Smee, Laland and Feldman argue that this has five major and under-appreciated consequences for biological theory. (shrink)

Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as “partial” homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following a (...) long scientific tradition, we advocate a strategy of “theoretical articulation” that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages. (shrink)

Theoretical accounts of development exhibit several internal tensions and face multiple challenges. They span from the problem of the identification of the temporal boundaries of development (beginning and end) to the characterization of the distinctive type of change involved compared to other biological processes. They include questions such as the role to ascribe to the environment or what types of biological systems can undergo development and whether they should include colonies or even ecosystems. In this chapter we discuss these conceptual (...) issues, and we argue that adopting an organizational approach may help solve or clarify them. -/- While development is usually identified with the achievement of an adult form with the capability to reproduce and therefore maintain a lineage, adopting the organizational approach may provide a different strategy, which focuses also on the maintenance of the current organization of the organism. By doing so an organizational approach favors a switch in perspective which consists in analyzing how organisms maintain their viability at each moment of development rather than considering them as going through intermediate stages of a process directed toward a specific goal state. This developmental dimension of biological organization has yet to be given a general and detailed analysis within the organizational theoretical perspective, apart from some preliminary attempts. How a biological organization is maintained through a series of radical organizational changes and what these changes are issues that still require clarification. In this chapter we offer the beginnings of such an analysis of developmental transitions, understood as changes in functionality brought forth by regulatory mechanisms in the context of the continued maintenance of organizational viability at every step. (shrink)

This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely (...) accepted that there is an ‘incremental constraint’ on evolutionary change, in an important class of cases it is difficult to see how to satisfy this constraint. I show that lineage explanations answer important questions about evolutionary change, but do so by demonstrating differences between individuals rather than invoking population processes, such as natural selection.1. Introduction2. Turning a ‘Scale’ into a ‘Plume’3. Lineage Explanations in Biology3.1. The evolution of eyes3.2. The evolution of feathers4. The Two Dimensions of a Lineage Explanation4.1. The production dimension4.2. The continuity dimension4.3. The dual role of the parts5. Constraining the Explanations6. Operational and Generative Lineages7. Explaining Change Without Populations8. Conclusion. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop (...) a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Development of an animal embryo involves the coordination of cell divisions, a variety of inductive interactions and extensive cellular rearrangements. One of the biggest challenges in developmental biology is to explain the relationships between these processes and the mechanisms that regulate them. Teleost embryos provide an ideal subject for the study of these issues. Their optical lucidity combined with modern techniques for the marking and observation of individual living cells allow high resolution investigations of specific morphogenetic movements and (...) the construction of detailed fate maps. In this review we describe the patterns of cell divisions, cellular movements and other morphogenetic events during zebrafish early development and discuss how these events relate to the formation of restricted lineages. (shrink)

Competence is an active state that defines the way in which cells respond to an inductive signal. A challenge of developmental biology is to explain not just the nature of the signalling molecules that promote cell specification or differentiation, but also how cells acquire competence to respond to these signals and what that reflects in molecular terms. A recent paper by Carmena et al.(1) has revealed how several signalling mechanisms are used sequentially and in specific combinations to specify (...) two mesodermal lineages in Drosophila. BioEssays 21:455–458, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal specificity of certain biological (...) processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes. (shrink)

Biology arises from the crowded molecular environment of the cell, rendering it a challenge to understand biological pathways based on the reductionist, low‐concentration in vitro conditions generally employed for mechanistic studies. Recent evidence suggests that low‐affinity interactions between cellular biopolymers abound, with still poorly defined effects on the complex interaction networks that lead to the emergent properties and plasticity of life. Mass‐action considerations are used here to underscore that the sheer number of weak interactions expected from the complex mixture (...) of cellular components significantly shapes biological pathway specificity. In particular, on‐pathway—i.e., “functional”—become those interactions thermodynamically and kinetically stable enough to survive the incessant onslaught of the many off‐pathway (“nonfunctional”) interactions. Consequently, to better understand the molecular biology of the cell a further paradigm shift is needed toward mechanistic experimental and computational approaches that probe intracellular diversity and complexity more directly. Also see the video abstract here https://youtu.be/T19X_zYaBzg. (shrink)

It is widely agreed that humans have specific abilities for cooperation and culture that evolved since their split with their last common ancestor with chimpanzees. Many uncertainties remain, however, about the exact moment in the human lineage when these abilities evolved. This article argues that cooperation and culture did not evolve in one step in the human lineage and that the capacity to stick to long-term and risky cooperative arrangements evolved before properly modern culture. I present evidence (...) that Homo heidelbergensis became increasingly able to secure contributions form others in two demanding Paleolithic public good games (PPGGs): cooperative feeding and cooperative breeding. I argue that the temptation to defect is high in these PPGGs and that the evolution of human cooperation in Homo heidelberngensis is best explained by the emergence of modern-like abilities for inhibitory control and goal maintenance. These executive functions are localized in the prefrontal cortex and allow humans to stick to social norms in the face of competing motivations. This scenario is consistent with data on brain evolution that indicate that the largest growth of the prefrontal cortex in human evolution occurred in Homo heidelbergensis and was followed by relative stasis in this part of the brain. One implication of this argument is that subsequent behavioral innovations, including the evolution of symbolism, art, and properly cumulative culture in modern Homo sapiens , are unlikely to be related to a reorganization of the prefrontal cortex, despite frequent claims to the contrary in the literature on the evolution of human culture and cognition. (shrink)

A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a ‘living fossil’ that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra-specific molecular diversity does not imply low (...) mutation rate, (ii) studies not showing low substitution rates in coelacanth are often neglected, (iii) the morphological stability of coelacanths is not supported by paleontological evidence. We recall that intra-species levels of molecular diversity, inter-species genome divergence rates and morphological divergence rates are under different constraints and they are not necessarily correlated. Finally, we emphasise that concepts such as ‘living fossil’, ‘basal lineage’, or ‘primitive extant species’ do not make sense from a tree-thinking perspective.Editor's suggested further reading in BioEssays Tree thinking for all biology: the problem with reading phylogenies as ladders of progress Abstract. (shrink)

This article begins with arguments evident at the time of writing about the 5th revision of the Diagnostic and Statistical Manual of the American Psychiatric Association. The historical lineages of those arguments are international and not limited to the USA. The concern with psychiatric diagnosis both internationally and in the USA came to the fore at the end of the Second World War with the construction of the American Psychiatric Association’s Diagnostic and Statistical Manual and the World Health Organization’s classification (...) of ‘Diseases, Injuries and Causes of Death’. However, the linkage between categories of morbidity, assumptions about natural biological categories and treatment specificity with ‘magic bullets’ emerged in the middle of the 19th century in physical medicine. This article explores the legitimacy of current psychiatric diagnoses in the light of that international, not national, history of medical knowledge. In conclusion it explores judgements about current cultural imperialism and an older picture of Eurocentrism, which is now being refracted in more recent globalizing knowledge-claims about mental disorder. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Ideas 61.2 (2000) 285-304 [Access article in PDF] Vacher de Lapouge and the Rise of Nazi Science Jennifer Michael Hecht * In the literature on the history of the Shoah the existence of a tradition of explicit anti-morality has been generally ignored. 1 This article argues that the materialist anthropology of the late nineteenth and early twentieth centuries waged a direct attack on morality, (...) which was described as inherently linked to religion. Strict materialism also denied any human access to the eternal except through biological lineage, linking the past, present, and future. This concern with procreation, which culminated in a desire to change the racial content of the world, led anthropology to aim its attack on morality on restrictive sexual mores and the injunction not to kill. Still, anti-morality was not conjured up in order to further eugenics; it was an independent idea and an explicit response to the loss of God. The anthropologist who best illustrates this scientific anti-morality is Georges Vacher de Lapouge, the French inventor of "anthroposociology." The present article explicates Lapouge's anti-morality and establishes a connection between his racial theories and those of a coterie of German colleagues. Most notable among these German colleagues was Hans Günther, whose vision had a role in shaping Nazi racial policy, in particular the Nazi interest in head measurements. Scholars investigating the origins of German racism have discovered French influence but have focused on Gobineau and his almost anti-scientific literary racism. This article argues that Lapouge and his scientific racism were also important.The relative significance of ideology in the "Final Solution" is the subject of some debate. This article seeks not to enter that debate but rather to reevaluate the nature of the ideology. It seems clear that whatever may have been the relative importance of ideas to, for instance, mundane careerism and conformity, the [End Page 285] ideas did play a role. 2 Within that context it will be demonstrated that Lapouge's anthroposociology helped to legitimate racialist utopianism. The scientific status of anthroposociology was deliberately engaged as propaganda for the regime, even after the specifics of its injunctions were no longer of much interest to the programmers of genocide.Whatever made people enact and accept genocide as daily routine, the idea of it came from somewhere, and somehow "the moral sensitivities" of the people were dulled. 3 Increasingly, historians stress that along with older forms of anti-Semitism, new scientific doctrines had a direct effect on events. There are a number of studies on the role of science in National Socialist doctrine, but they tend to be more about the role of doctors and the medical model of society than they are about anthropology. 4 Those that do deal with anthropology tend to mention Lapouge as an interesting forerunner but consistently fail to recognize his direct influence on Nazi doctrine. 5Lapouge's contribution to racism was a quantitative, well-written race theory that was replete with the language and tools of science. It was particularly appealing because it described a collection of human groups which sounded too scientific and clinical to be political. The value-laden descriptions of these clinical types (based on head shape) were easily transferred to known "racial" or social groups--with the simple claim that this or that group tended to have this or that head shape. Lapougian race theory was convincing because it was alien and yet confirmed familiar suspicions. It was thus highly instrumental in vitalizing dormant or mild prejudice. These ideas (and the endless columns of measurements and descriptions of head shapes) have grown so foreign to present day beliefs that they have become somewhat invisible to our eyes. Because of this, historians have not fully appreciated one of the important factors contributing to the "respectability" and credibility of a genocidal doctrine.In studying people who were guilty of unparalleled cruelty, historians expected to find moral agony and found instead a bureaucratic, mechanistic, banality. [End Page 286] In considering scientific racism, on the other hand, historians... (shrink)

The ascidian embryo has long provided a model system for ‘mosaic’ development. This article reviews recent advances in the study of ascidian developmental biology. These include: (a) the re‐analysis of cell lineages in ascidian embryos with the ascertainment of developmental fates of every blastomere of a 110‐cell embryo; (b) the development of several tissue‐specific monoclonal antibodies; (c) the investigation and description of cell cycle requirements for differentiation; it has been found that neither cytokinesis nor nuclear division is required (...) for differentiation, but that several rounds of DNA replication are essential for the expression of certain tissue‐specific genes; and (d) the demonstration by new descriptive and experimental studies of the presence of cytoplasmic factors or determinants responsible for specification of embryonic cell features; myoplasm which is thought to contain muscle determinants has been isolated, and immunological attempts to elucidate the molecular nature of the factors have begun. (shrink)

In the past decade many studies have demonstrated the existence of a mirror mechanism that matches the sensory representation of a biological stimulus with its somatomotor and visceromotor representation. This mechanism, likely phylogenetically very old, explains several types of mirroring behaviours, at different levels of complexity. The presence in primates of dedicated neuroanatomical pathways for specific sensorimotor integrations processes implies, at least in the primate lineage, a hard-wired mirror mechanism for social cognitive functions.

Understanding the role mechanistic constraints play in shaping evolution can relieve the tension between the generally accepted intuition that there are no strict laws in biology and empirical findings showing that evolutionary processes are biased toward preferred outcomes. Mechanistic constraints explain why some evolutionary outcomes are more probable than others and allow for predictions in specific lineages. At the same time, mechanistic constraints are neither necessary nor universal in the way laws are traditionally characterized: they remain contingent on (...) the past evolution of the biological mechanisms underpinning them and only constrain the future evolution of the organisms possessing them. (shrink)

The nature and status of cultural evolution and its connection with biological evolution are controversial in part because of Richard Dawkin’s suggestion that the scientific study of culture should include “memetics,” an analog of genetics in which genes are replaced by “memes”—the hypothetical units of cultural evolution. Memetics takes different forms; I focus on its minimal form, which claims merely that natural selection shapes to some extent the evolution of some aspects of culture. Advocates and critics of memetics disagree about (...) the scientific status of memetics, but they agree that memetics must face the following fundamental problems. Problem 1: Cultural evolution differs too much from biological evolution. Problem 2: Culture is too complex. Problem 3: Memes are too difficult to identify and track. Problem 4: Memetics produces only trivial results. This paper examines these problems in the context of a minimal memetic analysis in one specific context: patented inventions. Technology is a special subset of culture, and patented inventions are a special subset of technology—not least because there is a detailed written record of every patent. I describe four recent empirical results on technological innovation derived from memetic analysis of the patent record. Result 1: Inkjet printing, PCR, and stents are key drivers of technological innovation. Result 2: Patent genealogies are tangled and incestuous. Result 3: Door-opening innovations drive the evolution of technology. Result 4: The evolving content of the drivers of innovation confirms the importance of inkjet printing, PCR, and stents, among other inventions. These results show that minimal memetics can provide a novel and illuminating analysis the evolution of patented technology. Furthermore, this memetic analysis can answer all of the main problems with memetics. Problem 1 can be dismissed because culture and biology can be quite disanalogous, provided that natural selection still operates in both. Problem 2 is a mirage, because memetic analysis of the patented inventions is consistent with the full richness and complexity of the evolution of technology. Problem 3 is easy to solve, because the patent record makes it trivial to identify and track patents and their key traits through lineages. Problem 4 can be fully answered only after memetic analysis becomes widespread, but the results reviewed here shows that minimal memetics does yield scientific results that are nontrivial and interesting. (shrink)

Advances in genetics and genomics have raised new questions in trout restoration and management, specifically about species identity and purity, which fish to value, and where these fish belong. This paper examines how this molecular turn in fisheries management is influencing wild and native trout policy in Colorado. Examples from two small Colorado watersheds, Bear Creek and Sand Creek, illustrate how framing trout as genetic bodies can guide managers to care for or kill trout populations in the interest of rectifying (...) decades of genetic disruption caused by human activity. While trout management has typically relied on human intervention, the turn to genetic science is prompting new classifications of lineage and taxa, altering long-standing conservation priorities, and reorienting the manipulation of biological processes such as reproduction and dispersal. As a result, other social and ecological factors may be pushed to the margins of management decisions. These changes warrant greater conversation about the consequences of molecular analyses and the values embedded in trout science and conservation more broadly. (shrink)

Competence is an active state that defines the way in which cells respond to an inductive signal. A challenge of developmental biology is to explain not just the nature of the signalling molecules that promote cell specification or differentiation, but also how cells acquire competence to respond to these signals and what that reflects in molecular terms. A recent paper by Carmena et al.(1) has revealed how several signalling mechanisms are used sequentially and in specific combinations to specify (...) two mesodermal lineages in Drosophila. BioEssays 21:455–458, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

The process by which the genetically identical cell lineages of a multicellular organism acquire the propensity to express distinct arrays of gene products is among the most significant and fascinating questions in modern biology. Not surprisingly, this complex process requires control at several levels, each level providing a condition that is necessary but not sufficient for transcription to occur. Evidence suggests that one level of control concerns a region of DNA much larger than the transcription unit itself – the (...) chromatin domain. This domain must be in a specific chromatin conformation in order to permit transcription; other control mechanisms may be required to bring about overt transcription. A hypothesis concerning the nature of chromatin domains and the relationship between early replication and transcription potential is presented. (shrink)

The repertoire of acceptor glycoproteins for concanavalin A expressed by a cultured tumour cell reflects the normal developmental lineage from which it was derived, as well as the degree of maturation along that lineage. Antibodies to this particular set of glycoproteins show a considerable specificity towards normal differentiation antigens which are often preferentially associated with the less mature intermediates of the corresponding pathway. In addition, comparisons between ‘immature’ and ‘mature’ tumour cells can be used to identify glycoproteins associated (...) with specific differentiated functions such as secretion. Thus tumour cell glycoproteins provide useful probes for analysis of the molecular biology of development and differentiation. (shrink)

The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less‐characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant. Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and (...) cell biological evidence and propose testable models of how red algal cells might perform processes including cell motility, cytokinesis, intracellular transport, and secretion, given their reduced cytoskeletons. In addition to enhancing understanding of red algae and lineages that evolved from red algal endosymbioses (e.g., apicomplexan parasites), these ideas may also provide insight into cytoskeletal processes in animal cells. (shrink)