Phenotypic Evolution explicitly recognizes organisms as complex genetic-epigenetic systems developing in response to changing internal and external environments. As a key to a better understanding of how phenotypes evolve, the authors have developed a framework that centers on the concept of the Developmental Reaction Norm. This encompasses their views: (1) that organisms are better considered as integrated units than as disconnected parts (allometry and phenotypic integration); (2) that an understanding of ontogeny is vital for evaluating evolution of adult forms (ontogenetic (...) trajectories, epigenetics, and constraints); and (3) that environmental heterogeneity is ubiquitous and must be acknowledged for its pervasive role in phenotypic expression. (shrink)

Phenotypic plasticity integrates the insights of ecological genetics, developmental biology, and evolutionary theory. Plasticity research asks foundational questions about how living organisms are capable of variation in their genetic makeup and in their responses to environmental factors. For instance, how do novel adaptive phenotypes originate? How do organisms detect and respond to stressful environments? What is the balance between genetic or natural constraints (such as gravity) and natural selection? The author begins by defining phenotypic plasticity and detailing its history, including (...) important experiments and methods of statistical and graphical analysis. He then provides extended examples of the molecular basis of plasticity, the plasticity of development, the ecology of plastic responses, and the role of costs and constraints in the evolution of plasticity. A brief epilogue looks at how plasticity studies shed light on the nature/nurture debate in the popular media. (shrink)

Some claim that digital phenotyping will revolutionize understanding of human psychology and experience and significantly promote human wellbeing. This paper investigates the nature of digital phenotyping in relation to its alleged promise. Unlike most of the literature to date on philosophy and digital phenotyping, which has focused on its ethical aspects, this paper focuses on its epistemic and methodological aspects. The paper advances a tetra-taxonomy involving four scenario types in which knowledge may be acquired from human “digitypes” by digital phenotyping. (...) These scenarios comprise two causal relations and a correlative and constitutive relation that can exist between information generated by digital systems/devices on the one hand and psychological or behavioral phenomena on the other. The paper describes several modes of inference involved in deriving knowledge within these scenarios. After this epistemic mapping, the paper analyzes the possible knowledge potential and limitations of digital phenotyping. It finds that digital phenotyping holds promise of delivering insight into conditions and states as well producing potentially new psychological categories. It also argues that care must be taken that digital phenotyping does not make unwarranted conclusions and is aware of potentially distorting effects in digital sensing and measurement. If digital phenotyping is to truly revolutionize knowledge of human life, it must deliver on a range of fronts, including making accurate forecasts and diagnoses of states and behaviors, providing causal explanations of these phenomena, and revealing important constituents of human conditions, psychology, and experience. (shrink)

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only (...) sharpened the need for a different conceptual treat- ment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable soft- ware. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem. (shrink)

Phenotype, whether conventional or extended, is defined as a reflectionof an underlying genotype. Adaptation and the natural selection thatfollows from it depends upon a progressively harmonious fit betweenphenotype and environment. There is in Richard Dawkins' notion ofthe extended phenotype a paradox that seems to undercut conventionalviews of adaptation, natural selection and adaptation. In a nutshell, ifthe phenotype includes an organism's environment, how then can theorganism adapt to itself? The paradox is resolvable through aphysiological, as opposed to a (...) genetic, theory of natural selection andadaptation. (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)

An exploration of the nexus between ecology, evolutionary biology and molecular biology, via the concept of phenotypic plasticity.

Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic (...) plasticity, macroevolutionary studies of integration, and statistical and conceptual issues in the study of the evolution of complex phenotypes. I then conclude with a brief discussion of what I see as the major future directions of research on phenotypic integration and how they relate to our more general quest for the understanding of phenotypic evolution within the neo-Darwinian framework. I suggest that studying integration provides a particularly stimulating and truly interdisciplinary convergence of researchers from fields as disparate as molecular genetics, developmental biology, evolutionary ecology, palaeontology and even philosophy of science. (shrink)

A new voice in the nature-nurture debate can be heard at the interface between evolution and development. Phenotypic integration is a major growth area in research.

In addition to considerable debate in the recent evolutionary literature about the limits of the Modern Synthesis of the 1930s and 1940s, there has also been theoretical and empirical interest in a variety of new and not so new concepts such as phenotypic plasticity, genetic assimilation and phenotypic accommodation. Here we consider examples of the arguments and counter- arguments that have shaped this discussion. We suggest that much of the controversy hinges on several misunderstandings, including unwarranted fears of a general (...) attempt at overthrowing the Modern Synthesis paradigm, and some fundamental conceptual confusion about the proper roles of phenotypic plasticity and natural selection within evolutionary theory. (shrink)

This chapter contains section titled: Introduction: What is Phenotypic Plasticity? Developmental Conversion and Developmental Sensitivity: Two Forms of Phenotypic Plasticity Environmental Heterogeneity, Cues, and Plasticity Phenotypic Plasticity and Developmental Buffering The Future of Phenotypic Plasticity Research Acknowledgments References Further Reading.

The great majority of phenotypic characteristics are complex traits, complicating the identification of the genes underlying their expression. However, both methodological and theoretical progress in genome‐wide association studies have resulted in a much better understanding of the underlying genetics of many phenotypic traits, including externally visible characteristics (EVCs) such as eye and hair color. Consequently, it has become possible to predict EVCs from human samples lacking phenotypic information. Predicting EVCs from genetic evidence is clearly appealing for forensic applications involving the (...) personal identification of human remains. Now, a recent paper has reported the genetic determination of eye and hair color in samples up to 800 years old. The ability to predict EVCs from ancient human remains opens up promising perspectives for ancient DNA research, as this could allow studies to directly address archaeological and evolutionary questions related to the temporal and geographical origins of the genetic variants underlying phenotypes. (shrink)

Hyperplasia and hypertrophy are elements of phenotypic plasticity adjusting organ size and function. Because they are costly, we assume that they are beneficial. In this review, the authors discuss examples of tissue and organ systems that respond with plastic changes to osmotic stress to raise awareness that we do not always have sufficient experimental evidence to conclude that such processes provide fitness advantages. Changes in hydranth architecture in the hydroid Cordylophora caspia or variations in size in the anal papillae of (...) insect larvae upon changes in medium salinity may be adaptive or not. The restructuring of salt glands in ducklings upon salt‐loading is an example of phenotypic plasticity which indeed seems beneficial. As the genomes of model species are recently sequenced and the animals are easy to rear, these species are suitable study objects to investigate the biological significance of phenotypic plasticity and to study potential epigenetic and other mechanisms underlying phenotypic changes. (shrink)

Mathematical modeling can ground communication and reciprocal enrichment among fields of knowledge whose domains are very different. We propose a new mathematical model applicable in biology, specified into ecology and evolutionary biology, and in cultural transmission studies, considered as a branch of economics. Main inspiration for the model are some biological concepts we call “eco-phenotypic” such as development, plasticity, reaction norm, phenotypic heritability, epigenetics, and niche construction. “Physiology” is a core concept we introduce and translate differently in the biological and (...) cultural domains. The model is ecological in that it aims at describing and studying organisms and populations that perform living, intended as a thermodynamic, matter-energy process concerning resources gathering, usage, and depletion in a spatiotemporal context with given characteristics, as well as with multiplication and space occupation. The model also supports evolution, intended as a dynamics including cumulative change in the features of unique organisms that are connected into breeding populations. The model is then applicable to the economics of cultural transmission in which individuals form their attitudes and patterns of behavior under a complex system of influences derived from their “cultural parents”, other members of the society, and the environment. On the side of biology, an innovative goal is to integrate in a single model all the eco-phenotypic concepts as well as both evolution and ecology. On the side of cultural transmission, eco-phenotypic modeling seems more appropriate in capturing some aspects of cultural systems which are modeled away in the earlier framework based on Mendelian population genetics. (shrink)

In recent years philosophers have attempted to clarify the units of selection controversy in evolutionary biology by offering conceptual analyses of the term 'unit of selection'. A common feature of many of these analyses is an emphasis on the claim that units of selection are entities exhibiting heritable variation in fitness. In this paper I argue that the demand that units of selection be characterized in terms of heritability is unnecessary, as well as undesirable, on historical, theoretical, and philosophical grounds. (...) I propose a positive account of the proper referent of the term 'unit of selection', distinguishing between the processes of evolution and phenotypic selection. The main result of this analysis is greater clarity about the conceptual structure of evolutionary theory. (shrink)

The ‘phenotypic gambit,’ the assumption that we can ignore genetics and look at the fitness of phenotypes to determine the expected evolutionary dynamics of a population, is often used in evolutionary game theory. However, as this paper will show, an overlooked genotype to phenotype map can qualitatively affect evolution in ways the phenotypic approach cannot predict or explain. This gives us reason to believe that, even in the long-term, correspondences between phenotypic predictions and dynamical outcomes are not robust for (...) all plausible assumptions regarding the underlying genetics of traits. This paper shows important ways in which the phenotypic gambit can fail and how to proceed with evolutionary game theoretic modeling when it does. (shrink)

The paper describes the context and the origin of a particular debate that concerns the evolution of phenotypic plasticity. In 1965, British biologist A. D. Bradshaw proposed a widely cited model intended to explain the evolution of norms of reaction, based on his studies of plant populations. Bradshaw’s model went beyond the notion of the “adaptive norm of reaction” discussed before him by Dobzhansky and Schmalhausen by suggesting that “plasticity” the ability of a phenotype to be modified by the (...) environment should be genetically determined. To prove Bradshaw’s hypothesis, it became necessary for some authors to identify the pressures exerted by natural selection on phenotypic plasticity in particular traits, and thus to model its evolution. In this paper, I contrast two different views, based on quantitative genetic models, proposed in the mid-1980s: Russell Lande and Sara Via’s conception of phenotypic plasticity, which assumes that the evolution of plasticity is linked to the evolution of the plastic trait itself, and Samuel Scheiner and Richard Lyman’s view, which assumes that the evolution of plasticity is independent from the evolution of the trait. I show how the origin of this specific debate, and different assumptions about the evolution of phenotypic plasticity, depended on Bradshaw’s definition of plasticity and the context of quantitative genetics. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Phenotype/Genotype Distinction and the Disappearance of the BodyGabriel GuddingThe discipline of genetics has long been a rhetorical and heuristic locus for social and political issues. As such, the science has influenced culture through the avenues of law, medicine, warfare, social work, and even, since 1972 in California, the education of kindergarten students. It has affected how we view the body, morality, romance, biography, and agency—not to mention (...) procreation and death.In many ways the delamination of genotype from phenotype was the first cut, so to speak, in this new cosmetics of life. The distinction between structure and expression arose from an interdisciplinary struggle for authority in the biological sciences at the turn of the century. This preceptual split in the organism between structure and expression came over time to fundamentally alter the percepts of the body, in terms of how the body is juridically, medicinally, and otherwise, generally perceived and understood. More importantly and interestingly, this delamination within the organism between its genotype and phenotype eventually led to a sense of the body’s fragility and its eventual “disappearance” as a seat of agency, morality, and identity; and in turn these three groundings of modernity have been redistributed to the gene, the genotype, and the genome. In one sense, then, this paper traces not so much the birth of a new view of the body (the genetic) but the drama of its disappearance, in which the body melts to a silhouette and is replaced by the genotype and its expression, the phenotype.In 1911 Wilhelm Johannsen of the University of Copenhagen published “The Genotype Conception of Heredity,” 1 which introduced to geneticists the ideas of “phenotype” and “genotype.” Johannsen coined these terms in objection to what he considered to be an erroneous conception of heredity, [End Page 525] which he called the “transmission view”: the idea that “personal qualities” (such as honesty or good looks) could themselves be or otherwise influence “the true heritable elements or traits” passed on from one generation to another. He called this transmission view “apparent heredity” and claimed that this idea relied upon an economic-juridical model of the transmission of property—and thereby provided no disciplined or profound understanding of true heredity. He asserted that in factthe transmission-conception of heredity represents exactly the reverse of the real facts, just as the famous Stahlian theory of “phlogiston” was an expression diametrically opposite to the chemical reality. The personal qualities of any individual organism do not at all cause the qualities of its offspring; but the qualities of both ancestor and descendent are in quite the same manner determined by the nature of the “sexual substances”—i.e., the gametes—from which they have developed. Personal qualities are then the reactions of the gametes joining to form a zygote; but the nature of the gametes is not determined by the personal qualities of the parents or ancestors in question. This is the modern view of heredity. 2This was indeed a profoundly new view of heredity: Johannsen quite boldly and deliberately intended his genotype-phenotype distinction to stand as a watershed between the old science of heredity—exemplified by Mendel, Galton, Weismann, and others—and the new science of genetics. He said, “The science of genetics is in a transition period, becoming an exact science just as the chemistry in the times of Lavoisier, who made the balance an indispensable implementation in chemical research.” 3 And he was right: genetics was indeed in a transition period, primarily due to the theoretically accommodating qualities of this new distinction. The science of genetics became radically simplified: the confusion which arose from the attempts to correlate characteristics to their corresponding units of hereditarian influence diminished. Viewing personal qualities and characteristics, in all their variation, as expressions of underlying structures instead of mutual correlates to them drastically simplified the theoretical and experimental aspects of heredity.Not only did this distinction revolutionize the science of heredity, it helped insinuate the new science of genetics into a position of autonomy and authority with respect to the other life sciences. Historians of science, such as Jan Sapp, have suggested that the genotype-phenotype distinction played a... (shrink)

Selection operates at many levels. Some of the most obvious cases are organismic, such as changes in coloration under the influence of predation (cf. Kettlewell 1973; also Endler 1986). It also operates at other levels. Meiotic drive involves selection for a gene, independently of its effect on the organism. At a higher level, there may also be selection for patterns of colony growth in social insects, again under the influence of predation (cf. Wilson 1971). The appropriate level of selection is (...) a matter of the causal patterns exhibited, or the target of selection. It can also be understood as a question of the appropriate level at which to seek explanatory laws.Robert Brandon (1982, 1990) first clearly distinguished the question of the level of selection from debates over the units of selection. In doing so, he argued that the phenotype is commonly the target of selection, whatever the unit of selection might be. (shrink)

Selection operates at many levels. Robert Brandon has distinguished the question of the level of selection from the unit of selection, arguing that the phenotype is commonly the target of selection, whatever the unit of selection might be. He uses "screening off" as a criterion for distinguishing the level of selection. Cave animals show a common morphological pattern which includes hypertrophy of some structures and reduction or loss of others. In a study of a cave dwelling crustacean, Gammarus minus, (...) we find evidence for selection for both increased antennal size and reduction of eyes. The genetic structure of the population does not support the view that the phenotype screens off the genotype in explaining the differences in fitness. Nonetheless, the results do indicate that the level of selection is at least at the level of the phenotype in both cases. (shrink)

Autism Spectrum Disorder (ASD) is extremely heterogeneous clinically and genetically. There is a pressing need for a better understanding of the heterogeneity of ASD based on scientifically rigorous approaches centered on systematic evaluation of the clinical and research utility of both phenotype and genotype markers. This paper presents a holistic PheWAS-inspired method to identify meaningful associations between ASD phenotypes and genotypes. We generate two types of phenotype-phenotype (p-p) graphs: a direct graph that utilizes only phenotype data, (...) and an indirect graph that incorporates genotype as well as phenotype data. We introduce a novel methodology for fusing the direct and indirect p-p networks in which the genotype data is incorporated into the phenotype data in varying degrees. The hypothesis is that the heterogeneity of ASD can be distinguished by clustering the p-p graph. The obtained graphs are clustered using network-oriented clustering techniques, and results are evaluated. The most promising clusterings are subsequently analyzed for biological and domain-based relevance. Clusters obtained delineated different aspects of ASD, including differentiating ASD-specific symptoms, cognitive, adaptive, language and communication functions, and behavioral problems. Some of the important genes associated with the clusters have previous known associations to ASD. We found that clusters based on integrated genetic and phenotype data were more effective at identifying relevant genes than clusters constructed from phenotype information alone. These genes included five with suggestive evidence of ASD association and one known to be a strong candidate. (shrink)

The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where (...) additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development. (shrink)

The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space. Most conveniently, a Euclidean vector space is used, representing phenotypic properties by real-valued variables. Computational work on the biophysical genotype-phenotype model of RNA folding, however, suggests a rather different picture. If phenotypes are organized according to genetic accessibility, the resulting space lacks a metric and can be formalized only in terms of a relatively (...) unfamiliar structure. Patterns of phenotypic evolution—such as punctuation, irreversibility, and modularity—result naturally from the properties of the genotype-phenotype map, which, given the genetic accessibility structure, define accessibility in the phenotype space. The classical framework, however, addresses these patterns exclusively in terms of natural selection on suitably constructed fitness landscapes. Recent work has extended the explanatory level for phenotypic evolution from fitness considerations alone to include the topological structure of phenotype space as induced by the genotype-phenotype map. Lewontin’s notion of “quasi-independence” of characters can also be formalized in topological terms: it corresponds to the assumption that a region of the phenotype space is represented by a product space of orthogonal factors. In this picture, each character corresponds to a factor of a region of the phenotype space. We consider any region of the phenotype space that has a given factorization as a “type”, i.e., as a set of phenotypes that share the same set of phenotypic characters. Thus, a theory of character identity can be developed that is based on the correspondence of local factors in different regions of the phenotype space. (shrink)

Proponents of precision medicine envision that digital phenotyping can enable more individualized strategies to manage current and future health conditions. We problematize the interpretation of digital phenotypes as straightforward representations of individuals through examples of what we call data inheritance. Rather than being a digital copy of a presumed original, digital phenotypes are shaped by larger data collectives that precede and continuously change how the individual is represented. We contend that looking beyond the individual is crucial for understanding the factors (...) that can ‘bend’ digital mirrors in specific directions. Since algorithms used for digital profiling are based on historical data, their predictions often inherit and increase the values and perspectives of past data practices. Moreover, the data legacies we leave behind today may return as so-called ‘data phantoms’ that conflict with the interests of the individual and contest who and what the ‘original’ is. (shrink)

I identify six types of phenotypic plasticity and categorize them with respect to their cognitive status. I look at differences and relations between some of these types of plasticity and then analyze how phenotypic outcomes are transmitted across generations. I engage with the relevant literature on developmental scaffolding and entrenchment in cultural evolution. I argue that that the typology I present here can be beneficial for such a debate and therefore instructive to better comprehend the evolution and development of human (...) cognition. (shrink)

Against the neo-Darwinian assumption that genetic factors are the principal source of variation upon which natural selection operates, a phenotype-first hypothesis strikes us as revolutionary because development would seem to constitute an independent source of variability. Richard Watson and his co-authors have argued that developmental memory constitutes one such variety of phenotypic variability. While this version of the phenotype-first hypothesis is especially well-suited for the late metazoan context, where animals have a sufficient history of selection from which to (...) draw, appeals to developmental memory seem less plausible in the evolutionary context of the early metazoans. I provide an interpretation of Stuart Newman’s account of deep metazoan phylogenesis that suggests that spandrels are, in addition to developmental memory, an important reservoir of phenotypic variability. I conclude by arguing that Gerd Müller’s “side-effect hypothesis” is an illuminating generalization of the proposed non-Watsonian version of the phenotype-first hypothesis. (shrink)

Predicting the phenotype of an organism from its genotype is a central question in genetics. Most importantly, we would like to find out if the perturbation of a single gene may be the cause of a disease. However, our current ability to predict the phenotypic effects of perturbations of individual genes is limited. Network models of genes are one tool for tackling this problem. In a recent study, (Lee et al.) it has been shown that network models covering the (...) majority of genes of an organism can be used for accurately predicting phenotypic effects of gene perturbations in multicellular organisms. BioEssays 30:707–710, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Developmental plasticity as the nexus between genetics and ecology.

The narrative of the digital phenotype as a transformative vector in healthcare is nearly identical to the concept of “data drivenness” in other fields such as law enforcement. We examine the role of a prescription drug monitoring program in California—a computerized law enforcement surveillance program enabled by a landmark Supreme Court case that upheld “broad police powers”—in the interprofessional conflict between physicians and law enforcement over the jurisdiction of drug use. We bring together interview passages, clinical artifacts, and academic (...) and gray literature to investigate the power relations between police, physicians, and patients to show that prescribing data appear to the physician as evidence of problematic patient behavior by the patients, and to law enforcement as evidence of physician misconduct. In turn, physicians have adopted a disciplinary approach to patients, using quasi-legalistic documents to litigate patient behavior. We conclude that police powers have been used to pave data infrastructure through a contested jurisdiction, and law enforcement have used that infrastructure to enroll physicians into the work of disciplining patients. (shrink)

In this paper, we examine the practice and promises of digital phenotyping. We build on work on the ‘data self’ to focus on a medical domain in which the value and nature of knowledge and relations with data have been played out with particular persistence, that of Alzheimer's disease research. Drawing on research with researchers and developers, we consider the intersection of hopes and concerns related to both digital tools and Alzheimer's disease using the metaphor of the ‘data shadow’. We (...) suggest that as a tool for engaging with the nature of the data self, the shadow is usefully able to capture both the dynamic and distorted nature of data representations, and the unease and concern associated with encounters between individuals or groups and data about them. We then consider what the data shadow ‘is’ in relation to ageing data subjects, and the nature of the representation of the individual's cognitive state and dementia risk that is produced by digital tools. Second, we consider what the data shadow ‘does’, through researchers and practitioners’ discussions of digital phenotyping practices in the dementia field as alternately empowering, enabling and threatening. (shrink)

Evolutionary biology is paying increasing attention to the mechanisms that enable phenotypic plasticity, evolvability, and extra‐genetic inheritance. Yet, there is a concern that these phenomena remain insufficiently integrated within evolutionary theory. Understanding their evolutionary implications would require focusing on phenotypes and their variation, but this does not always fit well with the prevalent genetic representation of evolution that screens off developmental mechanisms. Here, we instead use development as a starting point, and represent it in a way that allows genetic, environmental (...) and epigenetic sources of phenotypic variation to be independent. We show why this representation helps to understand the evolutionary consequences of both genetic and non‐genetic phenotype determinants, and discuss how this approach can instigate future areas of empirical and theoretical research. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

The concept of the digital phenotype has been used to refer to digital data prognostic or diagnostic of disease conditions. Medical conditions may be inferred from the time pattern in an insomniac’s tweets, the Facebook posts of a depressed individual, or the web searches of a hypochondriac. This paper conceptualizes digital data as an extended phenotype of humans, that is as digital information produced by humans and affecting human behavior and culture. It argues that there are ethical obligations (...) to persons affected by generalizable knowledge of a digital phenotype, not only those who are personally identifiable or involved in data generation. This claim is illustrated by considering the health-related digital phenotypes of precision medicine and digital epidemiology. (shrink)

While niche construction theory locates animal artefacts in their constructors’ environment, hence treating them as capable of exerting selective pressure on both the constructors and their descendants, the extended phenotype concept assimilates artefacts with their constructors’ genes. Analogous contrasts apply in the case of endoparasite and brood parasite genes influencing host behaviour. The explanatory power of these competing approaches are assessed by re-examining the core chapters of Richard Dawkins’ _The Extended Phenotype_. Because animal artefacts have multiple evolutionary consequences for (...) their constructors, the extra-body effects of a gene seemingly include feedback effects on multiple other genes, a result which is more consistent with niche construction theory than with selfish gene theory. In the case of endoparasite genes influencing host behaviour, Dawkins’ argument leaves out what appears to be the key explanatory component, namely the role of the host’s own bodily systems in making it possible for such genes to exist. For action at a distance, it is unclear whether the key genes have extended effects because they sit in the body of the manipulating organism, or alternatively do not have such effects because they sit in the body of its victim. It is argued that niche construction theory offers a superior explanation in all three cases, regardless of whether the extended phenotype concept is interpreted in selfish gene or selfish organism terms. (shrink)

A phenome occurs through the many pathways of the complex net of interaction between the phenome and its environment; therefore researching and understanding how it arises requires investigation into many possible causes that are in constant interaction with each other. The most comprehensive investigations in biology are the ones in which many biologists from different sub-areas—evolutionary biology, developmental biology, molecular biology, physiology, genetics, epigenetics, ecology—have collaborated. Still, biologists do not always need to collaborate or look for the most comprehensive explanations. (...) A more standard investigation in biology occurs within a single subarea, and uses well-defined experiments with very specific conditions. This paper is about causation and related explanation in plant phenome research and its relevance to Aristotle’s Theory of Four Causes. I argue that there are causes which resemble Aristotle’s formal, material, and efficient causes in phenotype explanation and occurrence; but causes which resemble Aristotle’s final causes occur in phenotype explanation only, not in the occurrence. (shrink)

The distinction between phenotype and genotype is fundamental to the understanding of heredity and development of organisms. The genotype of an organism is the class to which that organism belongs as determined by the description of the actual physical material made up of DNA that was passed to the organism by its parents at the organism's conception. For sexually reproducing organisms that physical material consists of the DNA contributed to the fertilized egg by the sperm and egg of its (...) two parents. For asexually reproducing organisms, for example bacteria, the inherited material is a direct copy of the DNA of its parent. The phenotype of an organism is the class to which that organism belongs as determined by the description of the physical and behavioral characteristics of the organism, for example its size and shape, its metabolic activities and its pattern of movement. (shrink)

The integration of digital phenotyping in psychiatry promises unprecedented insights into mental health, particularly in college settings where mental well-being is a growing concern. The COVID-19...

Editor's suggested further reading in BioEssays: Evolution in response to climate change: In pursuit of the missing evidence AbstractHow will fish that evolved at constant sub‐zero temperatures cope with global warming? Notothenioids as a case study Abstract.

We attempt to improve the understanding of the notion of agene being `for a phenotypic trait or traits. Considering theimplicit functional ascription of one thing being `for another,we submit a more restrictive version of `gene for talk.Accordingly, genes are only to be thought of as being forphenotypic traits when good evidence is available that thepresence or prevalence of the gene in a population is the resultof natural selection on that particular trait, and that theassociation between that trait and the gene (...) in question isdemonstrably causal. It is therefore necessary to gatherstatistical, biochemical, historical, as well as ecologicalinformation before properly claiming that a gene is for aphenotypic trait. Instead of hampering practical use of the `genefor talk, our approach aims at stimulating much needed researchinto the functional ecology and comparative evolutionary biologyof gene action. (shrink)