This paper aims to contribute to the existing literature on normative cognition by providing a lineage explanation of human social norm psychology. This approach builds upon theories of goal-directed behavioral control in the reinforcement learning and control literature, arguing that this form of control defines an important class of intentional normative mental states that are instrumental in nature. I defend the view that great ape capacities for instrumental reasoning and our capacity (or family of capacities) for shared intentionality coadapted (...) to each other and argue that the evolution of this capacity has allowed the representation of social norms and the emergence of our capacity for normative guidance. (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)

Mapping the paths that stem and progenitor cells take en route to differentiate and elucidating the underlying molecular controls are key goals in developmental and stem cell biology. However, with population level analyses it is difficult − if not impossible − to define the transition states and lineage trajectory branch points within complex developmental lineages. Single‐cell RNA‐sequencing analysis can discriminate heterogeneity in a population of cells and even identify rare or transient intermediates. In this review, we propose that using (...) these data, one can infer the lineage trajectories of individual stem cells and identify putative branch points. Clonal lineage tracing of stem cells allows one to define the outcome of differentiation. Integrating these single cell‐based approaches provides a robust strategy for establishing and testing models of how an individual stem cell changes through time to differentiate and self‐renew. (shrink)

Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution of life. I introduce the “mixture” account of population lineages (...) that escapes these assumptions by dissolving the Modern Synthesis’s sharp line separating reproduction and development and characterizing reproductive integration in population lineages by the ephemerality of isolated subgroups rather than random mating. The mixture account provides a single criterion for reproductive integration that accommodates both sexual and asexual reproduction, unifying their treatment under Kevin de Queiroz’s generalized lineage concept of species. The account also provides a new basis for empirically assessing the effect of random mating as an idealization on the empirical adequacy of population genetic models. (shrink)

Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of “open lineages” to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with “closed lineages,” in which most of the changes are caused (...) by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed. (shrink)

China has undergone a rapid process of modernization since 1949. The modernization process has accelerated with the development of the market economy and rural-to-urban migration after the 1980s. Nevertheless, Chinese regions still exhibit substantial differences in terms of individualist/collectivist cultural orientations. The rice theory and the climato-economic theory have attempted to explain this variation by analyzing provincial-level data. Based on a quantitative analysis of more granular, county-level variables spanning from the early 1990s until 2010, we offer an alternative account of (...) this cultural variety based on lineage development in different Chinese regions. Using the ArcGIS geographic information system, we first present the regional distribution of individualism/collectivism indicators at the county level through descriptive statistics and spatial analysis. We also run a regression model to analyze county-level data on individualism/collectivism that includes three periods. Our multi-level analysis shows that lineage development is a critical variable that explains more regional variation of culture in China when compared to other variables. While rice farming, the key variable of the rice theory, is a significant variable, its explanatory power is less than the lineage variable. Finally, our analysis shows that the climato-economic theory fails to explain the regional variation of culture. (shrink)

The fundamental dialectic of Science as a Process is the interaction between two narrative levels. At one level, the book is a historical narrative of one aspect of one ongoing problem in systematics. At the second level, Hull presents a theoretical model of the scientific process which draws heavily on invoked similarities between biological and scientific change. I first situate the model as one alternative among several which loosely fit under the umbrella of 'evolutionary epistemologies.' Second, I explore (...) one of the implications of Hull's model, namely, that insofar as scientific theories are [parts of] "conceptual lineages," they are "conceptual individuals.". (shrink)

Biologists are nearing the creation of the first fully synthetic eukaryotic genome. Does this mean that we still soon be able to create genomes that are parts of an existing genetic lineage? If so, it might be possible to bring back extinct species. But do genomes that are synthetically assembled, no matter how similar they are to native genomes, really belong to the genetic lineage on which they were modelled? This article will argue that they are situated within (...) the same genetic lineage. To see why requires closely examining whether material overlap between parents and offspring is a necessary feature of biological reproduction. The processes used to create synthetic genomes shows that these processes are a form of scaffolded reproduction because they use external machinery and take ownership of the material parts used to create synthetic genomes. Closely examining these processes also reveals, surprisingly, that ‘synthetic reproduction’ can take place between entities that don’t participate in the same biological lineages. 1Introduction2The Argument for Lineage-less Genomes3Synthetic Eukaryotic Chromosomes and Material Overlap4Biological Reproduction, Material, and Information5Synthetic Reproductive Processes and Their Implications. (shrink)

Many natural and technological systems are complex, with organizational structures that exhibit characteristic patterns but defy concise description. One effective approach to analyzing such systems is in terms of repeated topological motifs. Here, we extend the motif concept to characterize the dynamic behavior of complex systems by introducing developmental motifs, which capture patterns of system growth. As a proof of concept, we use developmental motifs to analyze the developmental cell lineage of the nematode Caenorhabditis elegans, revealing a new perspective (...) on its complex structure. We use a family of computational models to explore how biases arising from the dynamics of the developmental gene network, as well as spatial and temporal constraints acting on development, contribute to this complex organization. © 2010 Wiley Periodicals, Inc. Complexity 16: 48‐57, 2011. (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)

The ability to convert human somatic cells into induced pluripotent stem cells (iPSCs) is allowing the production of custom‐tailored cells for drug discovery and for the study of disease phenotypes at the cellular and molecular level. IPSCs have been derived from patients suffering from a large variety of disorders with different severities. In many cases, disease related phenotypes have been observed in iPSCs or their lineage‐specific progeny. Several proof of concept studies have demonstrated that these phenotypes can be reversed (...) in vitro using approved drugs. However, several challenges must be overcome to take full advantage of this technology. Here, we highlight recent advances in the field and discuss the main challenges associated with this technology as it applies to disease modelling. (shrink)

The fundamental dialectic of Science as a Process is the interaction between two narrative levels. At one level, the book is a historical narrative of one aspect of one ongoing problem in systematics - the dispute between cladists and more traditional evolutionary taxonomists and amongst the cladists themselves on the correct method of classifying species. This narrative is replete with details of the process whereby scientists promote and publish their ideas. It is an informative and somewhat ‘racy’ account of the (...) rough and tumble battleground of ideas which puts the lie to the mythical ideal of the scientist as disinterested pursuer of the Truth. At the second level, Hull presents a theoretical model of the scientific process - a model which draws heavily on invoked similarities between biological and scientific change. The narrative serves as the evidence for the model. The model, in turn, helps shape the historical narrative. (shrink)

Morin has written a rich and valuable book. Its main aim is to isolate the factors involved in maintaining behavioural lineages over time, and to understand how these factors might interact. In doing so, it takes issue with the abstract and idealised models and arguments of dual-inheritance theorists, which are alleged in this account to rely on an overly simplistic notion of imitative learning. Morin’s book is full of ethnographic, anthropological, and psychological research, and there is much to commend in (...) it. However, Morin’s arguments against the dual-inheritance theorists are less convincing when put under scrutiny, and his positive picture which includes appeals to ostensive communication, intrinsic appeal and cultural attraction has some difficulties. I argue that when we contrast dual-inheritance theorists and Morin, we find that there may be fewer differences and greater commonalities than Morin’s book might suggest. (shrink)

Development of gene transfer systems provides a key tool for understanding gene function. Exciting and often unexpected consequences from embryo manipulations are yielding insights into molecular mechanisms underlying development under normal and pathogenic states, and are providing animal models for diseases. Contributing to this progress is the elegant work on c‐fos(1), where Wagner and coworkers identify this proto‐oncogene as a primary factor which directs cell differentiation along the osteoclast/macrophage lineages, and thus regulates bone remodeling. Their studies support a link between (...) skeletogenesis, marrow formation and hematopoiesis, and may help to delineate mechanisms underlying the oncogenic transformation of skeletal and hematopoietic cells. (shrink)

Chelicerates (scorpions, horseshoe crabs, spiders, mites and ticks) are the second largest group of arthropods and are of immense importance for fundamental and applied science. They occupy a basal phylogenetic position within the phylum Arthropoda, and are of crucial significance for understanding the evolution of various arthropod lineages. Chelicerates are vectors of human diseases, such as ticks, and major agricultural pests, such as spider mites, thus this group is also of importance for both medicine and agriculture. The developmental genetics of (...) chelicerates is poorly understood and a challenge for the future progress for many aspects of chelicerate biology is the development of a model organism for this group. Toward this end, we are developing a chelicerate genetic model: the two‐spotted spider mite Tetranychus urticae. T. urticae has the smallest genome of any arthropod determined so far (75 Mbp, 60% of the size of the Drosophila genome), undergoes rapid development and is easy to maintain in the laboratory. These features make T. urticae a promising reference organism for the economically important, poorly studied and species‐rich chelicerate lineage. BioEssays 29:489–496, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

This article offers a general definition of self-knowledge that embraces all forms and levels of self-knowledge in animals and humans. It is hypothesized that various levels of self-knowledge constitute an ordinal scale such that each species in a lineage displays the forms of self-knowledge found in related species as well as new forms it and its sister species may have evolved. Likewise, it is hypothesized that these various forms of levels of self-knowledge develop in the sequence in which they (...) evolved. Finally, a general hypothesis for the functional significance of self-knowledge is proposed along with subhypotheses regarding the adaptive significance of various levels of self-knowledge in mammals including human and nonhuman primates. The general hypothesis is that self-knowledge serves as a standard for assessing the qualities of conspecifics compared to those of the self. Such assessment is crucial to deciding among alternative reproductive and subsistence strategies. The qualities that are assessed, which vary across taxa, range from the size and strength of the self to its mathematical or musical abilities. This so-called assessment model of self-knowledge is based on evolutionary biological models for social selection and the role of assessment in animal communication. (shrink)

Knowledge of eukaryotic life cycles and associated genome dynamics stems largely from research on animals, plants, and a small number of “model” (i.e., easily cultivable) lineages. This skewed sampling results in an underappreciation of the variability among the many microeukaryotic lineages, which represent the bulk of eukaryotic biodiversity. The range of complex nuclear transformations that exists within lineages of microbial eukaryotes challenges the textbook understanding of genome and nuclear cycles. Here, we look in‐depth at Foraminifera, an ancient (∼600 million‐year‐old) (...) lineage widely studied as proxies in paleoceanography and environmental biomonitoring. We demonstrate that Foraminifera challenge the “rules” of life cycles developed largely from studies of plants and animals. To this end, we synthesize data on foraminiferal life cycles, focusing on extensive endoreplication within individuals (i.e., single cells), the unusual nuclear process calledZerfall, and the separation of germline and somatic function into distinct nuclei (i.e., heterokaryosis). These processes highlight complexities within lineages and expand our understanding of the dynamics of eukaryotic genomes. (shrink)

Monogenesis of language is widely accepted, but the conventional argument seems to be mistaken; a simple probabilistic model shows that polygenesis is likely. Other prehistoric inventions are discussed, as are problems in tracing linguistic lineages. Language is a system of representations; within such a system, words can evoke complex and systematic responses. Along with its social functions, language is important to humans as a mental instrument. Indeed, the invention of language,that is the accumulation of symbols to represent emotions, objects, (...) and acts may be the most important event in human evolution, because so many developments follow from it. For example, Edward Sapir speculated that some embryonic form of language must have been available to early man to help him fashion tools from stone (Sapir,1921). Sophisticated biface stone tools date to early Homo erectus some 1.5 million years ago, suggesting a similar age for language. This paper considers whether the invention of language occurred at only one pre-historic site or at several sites. In other words, did language emerge by monogenesis or polygenesis? Early thinkers believed in monogenesis, against a background of divine creation. Perhaps the best known account is the biblical story of Adam giving names to plants and animals in the Garden of Eden. Similar legends are found among many peoples. Modern linguists too assume monogenesis, but on probabilistic grounds (see, for instance, Southworth and Daswani, 1974, p.314). The argument seems to be that the invention of language is an extremely unlikely event, because symbolization involves abstraction and requires synchronized insight by several individuals; therefore, the probability of occurrence at more than one site must be vanishingly small. We have found no explicit quantitative treatment of this question in the literature, but the underlying logic has to be the multiplication of probabilities. If p is small at one site,then p.p for two sites is smaller still, and so on. This reasoning is false, as we show here. The fallacy lies in the focus on two particular sites rather than consideration of all pairs of sites. (shrink)

Markov models of evolution describe changes in the probability distribution of the trait values a population might exhibit. In consequence, they also describe how entropy and conditional entropy values evolve, and how the mutual information that characterizes the relation between an earlier and a later moment in a lineage’s history depends on how much time separates them. These models therefore provide an interesting perspective on questions that usually are considered in the foundations of physics—when and why does entropy increase (...) and at what rates do changes in entropy take place? They also throw light on an important epistemological question: are there limits on what your observations of the present can tell you about the evolutionary past? (shrink)

Why do humans menstruate while most mammals do not? Here, we present our answer to this long‐debated question, arguing that (i) menstruation occurs as a mechanistic consequence of hormone‐induced differentiation of the endometrium (referred to as spontaneous decidualization, or SD); (ii) SD evolved because of maternal–fetal conflict; and (iii) SD evolved by genetic assimilation of the decidualization reaction, which is induced by the fetus in non‐menstruating species. The idea that menstruation occurs as a consequence of SD has been proposed in (...) the past, but here we present a novel hypothesis on how SD evolved. We argue that decidualization became genetically stabilized in menstruating lineages, allowing females to prepare for pregnancy without any signal from the fetus. We present three models for the evolution of SD by genetic assimilation, based on recent advances in our understanding of the mechanisms of endometrial differentiation and implantation. Testing these models will ultimately shed light on the evolutionary significance of menstruation, as well as on the etiology of human reproductive disorders like endometriosis and recurrent pregnancy loss. (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)

Many of the most virulent and problematic eukaryotic pathogens have evolved from photosynthetic ancestors, such as apicomplexans, which are responsible for a wide range of diseases including malaria and toxoplasmosis. The primary barrier to understanding the early stages of evolution of these parasites has been the difficulty in finding parasites with closely related free‐living lineages with which to make comparisons. Parasites found throughout the florideophyte red algal lineage, however, provide a unique and powerful model to investigate the genetic (...) origins of a parasitic lifestyle. This is because they share a recent common ancestor with an extant free‐living red algal species and parasitism has independently arisen over 100 times within this group. Here, we synthesize the relevant hypotheses with respect to how these parasites have proliferated. We also place red algal research in the context of recent developments in understanding the genome evolution of other eukaryotic photosynthesizers turned parasites. (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)

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)

In lieu of an abstract, here is a brief excerpt of the content:Foundations For Flow:A Philosophical Model For Studio InstructionKrista RiggsThe need for a new approach to studio instruction becomes evident when the current state of the profession and the effects of typical teaching methods are considered. In a profession with relatively little demand for a large supply of candidates for professional employment, realistically very few undergraduate music performance majors will achieve success as either orchestral players or as soloists. (...) Extreme competitiveness and the political hierarchy common in a typical music studio setting can squelch creativity and hinder a student's possibility to attain optimal experience in performance. Such an environment can pose a threat to a student's self-image and motivation, possibly becoming detrimental to the success of the student in any chosen occupation, whether ultimately within music or outside the profession.1As Roland Persson notes, studio teachers are generally hired primarily for their performance accomplishments and place in the historic lineage of their instrument's pedagogy without much regard for previous training in educational theories.2 With a lack of training in instructional methods or developmental theories, college music teachers tend to conduct lessons in the manner in which they were taught. Thus, little attention may be paid to individual differences or developmental issues.3 Studio instruction has also traditionally been approached [End Page 175] in a maestro-like, authoritarian manner with one-directional commands given as law from master teacher to seemingly subordinate students. Such a manner of teaching may contradict the tendency of creative individuals to show more deviant traits of critical and independent thought, possibly hindering the student's potential for artistic growth.4Many music students tend to gain much of their concept of self-worth based on how they perceive their musical ability to be assessed by their studio instructor.5 A dependency for approval can lead to the pursuit of unachievable perfection that can be detrimental to the emotional development and self-confidence of the student.6 A common focus on a final product in instruction rather than on the creative process of personal and artistic growth can also contribute to the detrimental setting of unrealistic goals and resulting lack of self-esteem in the student. Evaluation of artistically, intellectually, and emotionally developing students against an unattainable perceived aesthetic ideal or in comparison to other students of differing strengths and levels of development can hinder motivation while increasing anxiety, extreme competition, and negative emotional response in the learning experience.7 In a more personalized curriculum that centers on individual strengths and weaknesses through a mentoring approach, each student may be guided to develop the intellectual, emotional, physical, and spiritual faculties leading to optimal experience. From creative flow and the peak experiences of self-actualization comes intrinsic motivation for students to pursue creativity as a way of life, with further motivation to find moments for artistic expression and personal satisfaction in all aspects of their being.8A new model concerned with the development of the "whole" student as an individual can serve as a philosophical supplement to studio instructors who may not have received much training in developmental issues, educational theories, or related facets of the psychology of learning and performance. Although each aspect of the model can be considered separately, the potential of guiding a student toward the attainment of optimal experience is increased when all aspects are considered according to strengths and weaknesses present in the individual student. Incorporating the theories and ideas in studio instruction may help enhance a student's artistic and personal development while also strengthening a healthy mentoring relationship between teacher and student. While the model presents aspects of psychology alongside developmental and educational theories, the focus remains as a philosophical synthesis of diverse ideas into a unified system with flow at the center. Rather than aiming to deconstruct or refute opposing theories, the model synthesizes supporting ideas. As Estelle Jorgensen notes, the purpose of a synthesis-oriented or "synoptic" model is not so much to argue or refute contrasting views as it is to build upon the supporting theories and ideas of other writers. The "body of thought" serves an explanatory purpose [End Page 176] of the "clarification of terms and exposition... (shrink)

Experiments with cell lines have unveiled the implication of the Rho/Rac family of GTPases in cytoskeletal organization, mitogenesis, and cell migration. However, there have not been adequate animal models to investigate the role of these proteins in more physiological settings. This scenario has changed recently in the case of the T‐cell lineage after the generation of animal models for Rho/Rac family members, their regulators, and effectors. These studies have revealed the implication of these GTPases on multiple regulatory layers of (...) T‐cells, including the coordination of cytoskeletal change, activation of kinase cascades, stimulation of calcium fluxes, and the induction of gene expression. These pathways affect the transition of different T‐cell maturation stages, the positive/negative selection of thymocytes, T‐cell responses to antigens, and the homeostasis of peripheral T‐lymphocytes. Moreover, these animals have revealed interesting cross‐talks between Rho/Rac pathways and other signal transduction routes that participate in lymphocyte responses. BioEssays 24:602–612, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Embryonic stem cells are derived from the preimplantation embryo and can differentiate into virtually any other cell type, which is governed by lineage specific transcriptions factors binding to cis regulatory elements to mediate changes in gene expression. The reliance on transcriptional regulation to maintain pluripotency makes ESCs a valuable model to study the role of distal CREs such as enhancers in modulating gene expression to affect cell fate decisions. This review will highlight recent advance on transcriptional enhancers, focusing (...) on studies performed in ESCs. In addition, we argue that the Nanog locus, which encodes for an ESC-critical TF, is particularly informative because it contains multiple co-regulated genes and enhancers in close proximity to one another. The unique landscape at Nanog permits the study of ongoing questions including whether multiple enhancers function additively versus synergistically, determinants of gene specificity, and cell-to-cell variability in gene expression. Nanog encodes a transcription factor required to maintain ESC pluripotency. The Nanog locus is an ideal model to study enhancers because it contains multiple highly potent super-enhancers within a small region. Nanog and three super-enhancers are in close physical proximity but only two SEs are required for Nanog expression. (shrink)

The Hawaiian Drosophila have been a model system for evolutionary, ecological, and ethological studies since the inception of the Hawaiian Drosophila Project in the 1960s. Here we review the past and present research on this incredible lineage and provide a prospectus for future directions on genomics and microbial interactions. While the number of publications on this group has waxed and waned over the years, we assert that recent systematic, biogeographic, and ecological studies have reinvigorated Hawaiian Drosophila as an (...) evolutionary model system. The characteristics that distinguish good model clades from good model organisms (e.g., Drosophila melanogaster) are somewhat different so we first define what constitutes a good evolutionary model. We argue that the Hawaiian Drosophila possess many desired aspects of a good evolutionary model, describe how this group of geographically isolated flies have been used in the past, and propose some exciting avenues for future evolutionary research on this diverse, dynamic clade of Drosophila. (shrink)

Pregnancy has been traditionally defined as the period during which developing embryos are incubated in the body after egg–sperm union. Despite strong similarities between viviparity in mammals and other vertebrate groups, researchers have historically been reluctant to use the term pregnancy for non‐mammals in recognition of the highly developed form of viviparity in eutherians. Syngnathid fishes (seahorses and pipefishes) have a unique reproductive system, where the male incubates developing embryos in a specialized brooding structure in which they are aerated, osmoregulated, (...) protected and likely provisioned during their development. Recent insights into physiological, morphological and genetic changes associated with syngnathid reproduction provide compelling evidence that male incubation in these species is a highly specialized form of reproduction akin to other forms of viviparity. Here, we review these recent advances, highlighting similarities and differences between seahorse and mammalian pregnancy. Understanding the changes associated with the parallel evolution of male pregnancy in the two major syngnathid lineages will help to identify key innovations that facilitated the development of this unique form of reproduction and, through comparison with other forms of live bearing, may allow the identification of a common set of characteristics shared by all viviparous organisms. BioEssays 29:884–896, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

David Hull’s book (1988) provides an evolutionary account of the development of science which pays attention to both the social and conceptual aspects of that process. Unlike most philosophers who only invoke Darwinian metaphors in a casual way, Hull takes the analogy between the biological evolution of species and the growth of scientific knowledge quite seriously and by providing abstract definitions of terms such as replicator, interactor and lineage, he makes it possible for us to see clearly the structural (...) similarities between the two historical processes.Other symposiasts will comment on how tight that analogy really is. I must remark in passing that I have never understood the intense interest which evolutionary epistemologists take in this comparison. Surely our major job is to understand how science works, perhaps by using evolutionary theory as a fallible heuristic, but nothing seems to hinge on the extent of the formal analogy. (shrink)

It has long been recognized that cancer onset and progression represent a type of reversion to an ancestral quasi‐unicellular phenotype. This general concept has been refined into the atavistic model of cancer that attempts to provide a quantitative analysis and testable predictions based on genomic data. Over the past decade, support for the multicellular‐to‐unicellular reversion predicted by the atavism model has come from phylostratigraphy. Here, we propose that cancer onset and progression involve more than a one‐off multicellular‐to‐unicellular reversion, (...) and are better described as a series of reversionary transitions. We make new predictions based on the chronology of the unicellular‐eukaryote‐to‐multicellular‐eukaryote transition. We also make new predictions based on three other evolutionary transitions that occurred in our lineage: eukaryogenesis, oxidative phosphorylation and the transition to adaptive immunity. We propose several modifications to current phylostratigraphy to improve age resolution to test these predictions. Also see the video abstract here: https://youtu.be/3unEu5JYJrQ. (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)

Cancer stem cells (CSC) represent malignant cell subsets in hierarchically organized tumors, which are selectively capable of tumor initiation and self‐renewal and give rise to bulk populations of non‐tumorigenic cancer cell progeny through differentiation. Robust evidence for the existence of prospectively identifiable CSC among cancer bulk populations has been generated using marker‐specific genetic lineage tracking of molecularly defined cancer subpopulations in competitive tumor development models. Moreover, novel mechanisms and relationships have been discovered that link CSC to cancer therapeutic resistance (...) and clinical tumor progression. Importantly, proof‐of‐principle for the potential therapeutic utility of the CSC concept has recently been provided by demonstrating that selective killing of CSC through a prospective molecular marker can inhibit tumor growth. Herein, we review these novel and translationally relevant research developments and discuss potential strategies for CSC‐targeted therapy in the context of resistance mechanisms and molecular pathways preferentially operative in CSC. (shrink)

We describe a recent approach for distinguishing between stochastic and deterministic sources of variability, focusing on the mammalian cell cycle. Variability between cells is often attributed to stochastic noise, although it may be generated by deterministic components. Interestingly, lineage information can be used to distinguish between variability and determinism. Analysis of correlations within a lineage of the mammalian cell cycle duration revealed its deterministic nature. Here, we discuss the sources of such variability and the possibility that the underlying (...) deterministic process is due to the circadian clock. Finally, we discuss the “kicked cell cycle” model and its implication on the study of the cell cycle in healthy and cancerous tissues. (shrink)

Is the brain really a computer? In particular, is our intelligence a computational achievement: is it because our brains are computers that we get on in the world as well as we do? In this paper I will evaluate an ambitious new argument to the contrary, developed in Landgrebe and Smith (2021a, 2022). Landgrebe and Smith begin with the fact that many dynamical systems in the world are difficult or impossible to model accurately (inter alia, because it is intractable (...) to find exact solutions to the differential equations that describe them—meaning we have to approximate—but at the same time they are such that small differences in starting conditions lead to big differences in final conditions, thwarting accurate approximation). Yet we manage to survive and thrive in a world full of such systems. Landgrebe and Smith argue from these premises that it is not because our brains are computers that we get on as well as we do: instead it is because of the various ways that we dynamically couple with such systems, these couplings themselves impossible to model well enough to emulate in silico. Landgrebe and Smith thus defend a dynamical systems model in the lineage of Gibson (1979), Van Gelder (1995), and Thompson (2007), though their focus is on decisively refuting the computationalist alternatives rather than developing the positive account. Here I will defend the claim that human intelligence is genuinely computational (and that whole brain emulation and others forms of AGI may be possible) against this argument. (shrink)

My aim in this chapter is to use Marina Sbisà’s idea of interactional negotiation to consider what it is for conversing agents to follow illocutionary conventions or, as John L. Austin would put it, what it is for an illocutionary act to be done as conforming to a convention. The chapter is organized into two parts. In the first one, I use the Austinian notions of uptake and response as well as the Lewisian concept of accommodation to discuss a few (...) examples of force negotiation and develop a model of its underlying mechanisms. In the second part, I suggest that interactional negotiation plays a key role in the functioning of all language conventions—phatic, rhetic, illocutionary, etc.—construed along the Millikanian lines, i.e., as families or lineages of linguistic precedents. My contention is that the ideas I propose in this chapter are compatible with Sbisà’s theory of speech acts and can be regarded as its possible extension. (shrink)

Evolution is a continuous trial and error process in which most lineages go extinct without leaving fossil remains. Many of these lineages would be closely related and occasionally hybridized with lineages that gave rise to extant species. Hence, it is likely that one can find genetic signatures of these ancient introgression events in present‐day genomes, so‐called ghost introgression. The increasing availability of high‐quality genome assemblies for non‐model organisms and the development of more sophisticated methods for detecting introgression will undoubtedly (...) reveal more cases of ghost introgression, indicating that the Tree of Life is even more reticulated than assumed. The presence of ghost introgression has important consequences for the study of numerous evolutionary processes, including adaptation, speciation, and macroevolutionary patterns. In addition, detailed studies of introgressed regions could provide insights into the morphology of the extinct lineage, providing an unexpected link between genomics and the fossil record. Hence, new methods that take into account ghost introgression will need to be developed. (shrink)

David Hull's (1988c) model of science as a selection process suffers from a two-fold inability: (a) to ascertain when a lineage of theories has been established; i.e., when theories are descendants of older theories or are novelties, and what counts as a distinct lineage; and (b) to specify what the scientific analogue is of genotype and phenotype. This paper seeks to clarify these issues and to propose an abstract model of theories analogous to particulate genetic structure, (...) in order to reconstruct relationships of descent and identity. (shrink)

That holobionts are units of selection squares poorly with the observation that microbes are often recruited from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what (...) is of interest in holobiont thinking, we propose casting metabolic and developmental interaction patterns, rather than the taxa responsible for them, as units of selection. Such units need not directly reproduce or form parent-offspring lineages: their prior existence has created the conditions under which taxa with the genes necessary to carry out their steps have evolved in large numbers. These taxa or genes will reconstruct the original interaction patterns when favorable conditions occur. Interaction patterns will vary in ways that affect the likelihood of and circumstances under which such reconstruction occurs. Thus, they vary in fitness, and evolution by natural selection will occur at this level. It is on the persistence, reconstruction, and spread of such interaction patterns that students of holobiosis should concentrate, we suggest. This model also addresses other multi-species collectively beneficial interactions, such as biofilms or biogeochemical cycles maintaining all life. (shrink)

Is there anything that members of each binary category of gender have in common? Even many non-essentialists find the lack of unity within a gender worrying as it undermines the basis for a common political agenda for women. One promising proposal for achieving unity is by means of a shared historical lineage of cultural reproduction with past binary models of gender. I demonstrate how such an account is likely to take on board different binary and also non-binary systems of (...) gender. This implies that all individuals construed as members of the category, “women” are in fact not members of the same historical kind after all! I then consider different possible means of modifying the account but conclude negatively: the problem runs deeper than has been appreciated thus far. (shrink)

Biologists often study living systems in light of their having evolved, of their being the products of various processes of heredity, adaptation, ancestry, and so on. In their investigations, then, biologists think comparatively: they situate lineages into models of those evolutionary processes, comparing their targets with ancestral relatives and with analogous evolutionary outcomes. This element characterizes this mode of investigation - 'comparative thinking' - and puts it to work in understanding why biological science takes the shape it does. Importantly, comparative (...) thinking is local: what we can do with knowledge of a lineage is limited by the evolutionary processes into which it fits. In light of this analysis, the Element examines the experimental study of animal cognition, and macroevolutionary investigation of the 'shape of life', demonstrating the importance of comparative thinking in understanding both the power and limitations of biological knowledge. (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)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational science, (...) they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

Autocatalytic networks have been used to model the emergence of self‐organizing structure capable of sustaining life and undergoing biological evolution. Here, we model the emergence of cognitive structure capable of undergoing cultural evolution. Mental representations (MRs) of knowledge and experiences play the role of catalytic molecules, and interactions among them (e.g., the forging of new associations) play the role of reactions and result in representational redescription. The approach tags MRs with their source, that is, whether they were acquired (...) through social learning, individual learning (of pre‐existing information), or creative thought (resulting in the generation of new information). This makes it possible to model how cognitive structure emerges and to trace lineages of cumulative culture step by step. We develop a formal representation of the cultural transition from Oldowan to Acheulean tool technology using Reflexively Autocatalytic and Food set generated (RAF) networks. Unlike more primitive Oldowan stone tools, the Acheulean hand axe required not only the capacity to envision and bring into being something that did not yet exist, but hierarchically structured thought and action, and the generation of new MRs: the concepts EDGING, THINNING, SHAPING, and a meta‐concept, HAND AXE. We show how this constituted a key transition toward the emergence of semantic networks that were self‐organizing, self‐sustaining, and autocatalytic, and we discuss how such networks replicated through social interaction. The model provides a promising approach to unraveling one of the greatest anthropological mysteries: that of why development of the Acheulean hand axe was followed by over a million years of cultural stasis. (shrink)

Since Darwin, the idea of psychological continuity between humans and other animals has dominated theory and research in investigating the minds of other species. Indeed, the field of comparative psychology was founded on two assumptions. First, it was assumed that introspection could provide humans with reliable knowledge about the causal connection between specific mental states and specific behaviors. Second, it was assumed that in those cases in which other species exhibited behaviors similar to our own, similar psychological causes were at (...) work. In this paper. we show how this argument by analogy is flowed with respect to the case of second-order mental states. As a test case, we focus on the question of how other species conceive of visual attention, and in particular whether chimpanzees interpret seeing as a mentalistic event involving internal states of perception, attention, and belief. We conclude that chimpanzees do not reason about seeing in this manner, and indeed, there is considerable reason to suppose that they do not harbor representations of mental states in general. We propose a reinterpretation model in which the majority of the rich social behaviors that humans and other primates share in common emerged long before the human lineage evolved the psychological means of interpreting those behaviors in mentalistic terms. Although humans, chimpanzees, and most other species may be said to possess mental states, humans alone may have evolved a cognitive specialization for reasoning about such states. (shrink)

One of the major developments in cancer research in recent years has been the construction of models that treat cancer as a cellular population subject to natural selection. We expand on this idea, drawing upon multilevel selection theory. Cancer is best understood in our view from a multilevel perspective, as both a by-product of selection at other levels of organization, and as subject to selection at several levels of organization. Cancer is a by-product in two senses. First, cancer cells co-opt (...) signaling pathways that are otherwise adaptive at the organismic level. Second, cancer is also a by-product of features distinctive to the metazoan lineage: cellular plasticity and modularity. Applying the multilevel perspective in this way permits one to explain transitions in complexity and individuality in cancer progression. Our argument is a reply to Germain’s scepticism towards the explanatory relevance of natural selection for cancer. The extent to which cancer fulfills the conditions for being a paradigmatic Darwinian population depends on the scale of analysis, and the details of the purported selective scenario. Taking a multilevel perspective clarifies some of the complexities surrounding how to best understand the relevance of evolutionary thinking in cancer progression. (shrink)

Maximum Parsimony (MP) and Maximum Likelihood (ML) are two methods for evaluating which phlogenetic tree is best supported by data on the characteristics of leaf objects (which may be species, populations, or individual organisms). MP has been criticized for assuming that evolution proceeds parsimoniously -- that if a lineage begins in state i and ends in state j, the way it got from i to j is by the smallest number of changes. MP has been criticized for needing to (...) assume some model or other of the evolutionary process even though biologists often do not know what that process really is. This paper critically evaluates both criticisms. (shrink)

Behavioural flexibility is often treated as the gold standard of evidence for more sophisticated or complex forms of animal cognition, such as planning, metacognition and mindreading. However, the evidential link between behavioural flexibility and complex cognition has not been explicitly or systematically defended. Such a defence is particularly pressing because observed flexible behaviours can frequently be explained by putatively simpler cognitive mechanisms. This leaves complex cognition hypotheses open to ‘deflationary’ challenges that are accorded greater evidential weight precisely because they offer (...) putatively simpler explanations of equal explanatory power. This paper challenges the blanket preference for simpler explanations, and shows that once this preference is dispensed with, and the full spectrum of evidence—including evolutionary, ecological and phylogenetic data—is accorded its proper weight, an argument in support of the prevailing assumption that behavioural flexibility can serve as evidence for complex cognitive mechanisms may begin to take shape. An adaptive model of cognitive-behavioural evolution is proposed, according to which the existence of convergent trait–environment clusters in phylogenetically disparate lineages may serve as evidence for the same trait–environment clusters in other lineages. This, in turn, could permit inferences of cognitive complexity in cases of experimental underdetermination, thereby placing the common view that behavioural flexibility can serve as evidence for complex cognition on firmer grounds. (shrink)

An idea is not a replicator because it does not consist of coded self-assembly instructions. It may retain structure as it passes from one individual to another, but does not replicate it. The cultural replicator is not an idea but an associatively-structured network of them that together form an internal model of the world, or worldview. A worldview is a primitive, uncoded replicator, like the autocatalytic sets of polymers widely believed to be the earliest form of life. Primitive replicators (...) generate self-similar structure, but because the process happens in a piecemeal manner, through bottom-up interactions rather than a top-down code, they replicate with low fidelity, and acquired characteristics are inherited. Just as polymers catalyze reactions that generate other polymers, the retrieval of an item from memory can in turn trigger other items, thus cross-linking memories, ideas, and concepts into an integrated conceptual structure. Worldviews evolve idea by idea, largely through social exchange. An idea participates in the evolution of culture by revealing certain aspects of the worldview that generated it, thereby affecting the worldviews of those exposed to it. If an idea influences seemingly unrelated fields this does not mean that separate cultural lineages are contaminating one another, because it is worldviews, not ideas, that are the basic unit of cultural evolution. (shrink)