This article reads the uptake of facial-matching algorithms by fertility clinics in Spain through the lens of ‘the fertility fix’: a software fix to the social reconfiguration of kinship and a fixed capital investment made by competing fertility companies and firms. ‘The fertility fix’ is proposed as a critical, ethical lens through which to situate algorithmic facial-matching in assisted reproduction in the context of the racial politics of the face and phenotype and the spatial politics of market (...) expansion. While an ‘infertility crisis’ is often mentioned when explaining the growth of the assisted reproductive technologies (ARTs) industry, the use of donated reproductive cells is tied up in societal, ecological and economic shifts. Combining Software Studies analysis with Marxist Feminist and trans*feminist perspectives on shifting re/production dynamics, the article details the role of computational technologies in promoting certain ideas and beliefs about family and fixing certain territories of capital flow. (shrink)

This article reads the uptake of facial-matching algorithms by fertility clinics in Spain through the lens of ‘the fertility fix’: a software fix to the social reconfiguration of kinship and a fixed capital investment made by competing fertility companies and firms. ‘The fertility fix’ is proposed as a critical, ethical lens through which to situate algorithmic facial-matching in assisted reproduction in the context of the racial politics of the face and phenotype and the spatial politics of market (...) expansion. While an ‘infertility crisis’ is often mentioned when explaining the growth of the assisted reproductive technologies (ARTs) industry, the use of donated reproductive cells is tied up in societal, ecological and economic shifts. Combining Software Studies analysis with Marxist Feminist and trans*feminist perspectives on shifting re/production dynamics, the article details the role of computational technologies in promoting certain ideas and beliefs about family and fixing certain territories of capital flow. (shrink)

Conventional forensic DNA analysis involves a matching principle, which compares DNA profiles from evidential samples to those from reference samples of known origin. In casework, however, the accessibility to a reference sample is not guaranteed which limits the use of DNA as an investigative tool. This has led to the development of phenotype prediction, which uses SNP analysis to estimate the physical appearance of the sample donor. Physical traits, such as eye, hair and skin colour, have been associated (...) with certain alleles within specific genes involved in the melanogenesis pathways. These genetic markers are also associated with ancestry and their trait prediction ability has mainly been assessed in European and North American populations. This has prompted research investigating the discriminatory power of these markers in other populations, especially those exhibiting admixture. South Africa is well known for its diversity, and the viability of these particular SNPs still needs to be assessed within this population. South African law currently restricts the use of DNA for molecular phenotyping, and there are also numerous ethical and social considerations, all of which are discussed. (shrink)

Assisted reproduction using donor gametes is a procedure that allows those who are unable to produce their own gametes to achieve gestational parenthood. Where conception is achieved using donor sperm, the child lacks a genetic link to the intended father. Where it is achieved using a donor egg, the child lacks a genetic link to the intended mother. To address this lack of genetic kinship, some fertility clinics engage in the practice of matching the ethnicity of the gamete donor (...) to that of the recipient parent. The intended result is for the child to have the phenotypic characteristics of the recipient parents. This paper examines the philosophical and ethical problems raised by the policy of ethnic matching in gamete donation. I consider arguments for the provision of ethnic matching based on maximising physical resemblance and fostering ethnic identity development. I then consider an argument against ethnic matching based on the charge of racialism. I conclude that while the practice of ethnic matching in gamete donation could promote positive ethnic identity development in donor-conceived children from historically subjugated ethnic minorities, it also risks endorsing the problematic societal attitudes and assumptions regarding ethnicity that enabled such subjugation in the first place. (shrink)

Human homogamy may be caused in part by individuals’ preference for phenotypic similarities. Two types of preference can result in homogamy: individuals may prefer someone who is similar to themselves (self-referent phenotype matching) or to their parents (a sexual-imprinting-like mechanism). In order to examine these possibilities, we compare faces of couples and their family members in two ways. First, “perceived” similarity between a pair of faces is quantified as similarity ratings given to the pair. Second, “physical” similarity between (...) two groups of faces is evaluated on the basis of correlations in principal component scores generated from facial measurements. Our results demonstrate a tendency to homogamy in facial characteristics and suggest that the tendency is due primarily to self-referent phenotype matching. Nevertheless, the presence of a sexual-imprinting-like effect is also partially indicated: whether individuals are involved in facial homogamy may be affected by their relationship with their parents during childhood. (shrink)

Westermarck’s Hypothesis is widely accepted by evolutionary scientists as the best explanation for human incest avoidance. However, its explanatory shortcomings have been largely ignored and it has never been pitted against alternative biological hypotheses. Although WH may account for incest avoidance between co-reared kin, it cannot explain other forms of incest avoidance, and cannot account for the differential incidence of sibling-sibling, mother-son, father-daughter and other forms of incest. WH also faces problems adequately addressing phenomena within its explanatory domain. Neither of (...) the studies generally considered to corroborate WH provides a genuine test of it, and the results of experiments thought to confirm WH are vitiated by methodological problems. The present article considers two alternatives to WH: the shared mother hypothesis and the maternal phenotype-matching hypothesis . SMH states that human infants imprint on their mother, and then treat as kin those individuals toward whom their mother behaves in akin-like or mate-like manner. MPMH states that humans unconsciously use the maternal phenotype as a visual template for estimating coefficients of relatedness, and that these estimates regulate altruistic and mating behavior. Both SMH and MPMH are able to account for the kibbutz and simpua marriage data, and entail additional epidemiological and experimental predictions. SMH and MPMH have greater explanatory power than WH. (shrink)

It has long been thought that gene expression is tightly regulated in multicellular eukaryotes, so that expression profiles match functional profiles. This conception emerged from the assumption that gene activity is synonymous with gene function. This paradigm was first challenged by comparative protein electrophoresis studies showing extensive differences in expression patterns among related species. The paradigm is now being challenged by evolutionary transcriptomics using microarray technologies. Most gene expression profiles display features that lack any obvious functional significance. The so‐called “ectopic” (...) expression refers to the expression of genes at times and locations where the target gene is not known to have a function. However, ectopic expression might be associated with genuine function even if this function is not essential or has yet to be ascertained. Alternatively, ectopic expression might come about as a superfluous by‐product of regulatory systems, which would call for a revision of prevailing ideas about the specificity of gene regulation. We herein review available evidence for ectopic expression and the hypotheses proposed for its origin and evolution. We propose that ectopic expression must be regarded as part of an integrated phenotypic whole. It seems likely that ectopic expression represents a leak in the evolution of regulatory systems, but one that is endowed with considerable evolutionary possibilities. BioEssays 27:592–601, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

��This paper investigates how an evolutionary al- gorithm with an indirect encoding exploits the property of phenotypic regularity, an important design principle found in natural organisms and engineered designs. We present the first comprehensive study showing that such phenotypic regularity enables an indirect encoding to outperform direct encoding con- trols as problem regularity increases. Such an ability to produce regular solutions that can exploit the regularity of problems is an important prerequisite if evolutionary algorithms are to scale to high-dimensional real-world (...) problems, which typically contain many regularities, both known and unrecognized. The indirect encoding in this case study is HyperNEAT, which evolves artificial neural networks (ANNs) in a manner inspired by concepts from biological development. We demonstrate that, in contrast to two direct encoding controls, HyperNEAT produces both regular behaviors and regular ANNs, which enables HyperNEAT to significantly outperform the direct encodings as regularity increases in three problem domains. We also show that the types of regularities HyperNEAT produces can be biased, allowing domain knowledge and preferences to be injected into the search. Finally, we examine the downside of a bias toward regularity. Even when a solution is mainly regular, some irregularity may be needed to perfect its functionality. This insight is illustrated by a new algorithm called HybrID that hybridizes indirect and direct encodings, which matched HyperNEAT’s performance on regular problems yet outperformed it on problems with some irregularity. HybrID’s ability to improve upon the performance of HyperNEAT raises the question of whether indirect encodings may ultimately excel not as stand-alone algorithms, but by being hybridized with a further process of refinement, wherein the indirect encoding produces patterns that exploit problem regu-. (shrink)

The conditions animals experience during the early developmental stages of their lives can have critical ongoing effects on their future health, welfare, and proper development. In this paper we draw on evolutionary theory to improve our understanding of the processes of developmental programming, particularly Predictive Adaptive Responses (PAR) that serve to match offspring phenotype with predicted future environmental conditions. When these predictions fail, a mismatch occurs between offspring phenotype and the environment, which can have long-lasting health and welfare (...) effects. Examples include metabolic diseases resulting from maternal nutrition and behavioral changes from maternal stress. An understanding of these processes and their evolutionary origins will help in identifying and providing appropriate developmental conditions to optimize offspring welfare. This serves as an example of the benefits of using evolutionary thinking within veterinary science and we suggest that in the same way that evolutionary medicine has helped our understanding of human health, the implementation of evolutionary veterinary science (EvoVetSci) could be a useful way forward for research in animal health and welfare. (shrink)

This paper begins by calling attention to a puzzling feature of our deep past: an apparent mis-match between morphological evolution in our lineage, including the expansion of our brain and neocortex, and changes in material culture. Three ideas might explain this mis-match. The apparent mis-match is an illusion: change in material culture is indeed driven by biological evolution, but of a kind difficult to identify in the fossil record; the mismatch is caused by the fact that material culture is sensitive (...) to the social and demographic environment, not just the native cognitive capacities of individual agents. Innovation and its uptake is more reliable in larger social worlds. The mis-match is made possible by adaptive phenotypic plasticity; in particular, cognitive plasticity. Just as material culture evolves through cumulative cultural learning, so too do cognitive skills, including ones which make innovations in, and the transmission of, material culture more efficient. This paper is targeted on the second of these ideas, and distinguishes three different versions of the view that increases in social scale support increases in the complexity of material culture. Those are: cultural selection is more efficient in larger social worlds; larger social worlds support more specialisation, which in turn supports a more complex material culture; cultural learning is more efficient in larger social worlds. The paper argues that the first two of these pathways are probably more important than the third in explaining otherwise puzzling features of the archaeological and ethnographic record. (shrink)

We here develop a concept of an individualized niche in analogy to Hutchison’s population-level concept of the ecological niche. We consider the individualized niche as the range of environmental conditions under which a particular individual has an expected lifetime reproductive success of ≥ 1. Our concept has primarily an ecological function, as it refers to the match of an individual phenotype to its contemporary environment while we discuss evolutionary fitness as an evaluative parameter of this fit. We address four (...) specific challenges that occur when scaling the niche down from populations to individuals. In particular, we discuss the consequences of uniqueness of individuals in a population and the corresponding lack of statistical replication, the dynamic nature of individualized niches and how they can be studied either as time-slice niches, as prospective niches or as trajectory-based niches, the dimensionality of the individualized niche, that is greater than the population niche due to the additional dimensions of intra-specific niche space, how the boundaries of individualized niche space can be defined by expected lifetime reproductive success and how expected reproductive success can be inferred by marginalizing fitness functions across phenotypes or environments. We frame our discussion in the context of recent interest in the causes and consequences of individual differences in animal behavior. (shrink)

Contrary to widely held assumptions, an evolutionary metaethics need not be non-cognitivist. I define evolutionary metaethics as the claim that certain phenotypic traits expressing certain genes are both necessary and sufficient for explanation of all other phenotypic traits we consider morally significant. A review of the influential cognitivist Immanuel Kants metaethics shows that much of his ethical theory is independent of the anti-naturalist metaphysics of transcendental idealism which itself is incompatible with evolutionary metaethics. By matching those independent aspects to (...) an evolutionary metaethics a cognitivist Kantian evolutionary metaethical theory is a possibility for researchers to consider. (shrink)

Parental effects are a major source of phenotypic plasticity and may influence offspring phenotype in concert with environmental demands. Studies of “environmental epigenetics” suggest that (1) DNA methylation states are variable and that both demethylation and remethylation occur in post‐mitotic cells, and (2) that remodeling of DNA methylation can occur in response to environmentally driven intracellular signaling pathways. Studies of mother‐offspring interactions in rodents suggest that parental signals influence the DNA methylation, leading to stable changes in gene expression. If (...) parental effects do indeed enhance the “match” between prevailing environmental demands and offspring phenotype, then the potential for variation in environmental conditions over time would suggest a mechanism that requires active maintenance across generations through parental signaling. We suggest that parental regulation of DNA methylation states is thus an ideal candidate mechanism for parental effects on phenotypic variation. (shrink)

Classification of the boys in 48 families of three or more brothers according to their Moray House Test (VIQ) scores awarded at age 11±1[fraction one-half] years in 1947–75 confirms the postulated existence of a total of nine male phenotypes for this X-linked trait in the score range <70 to 140 points. The phenotypic means lie close to the sequence 69(8)133. Recombination is shown to occur. An additive effect of three alleles at each of two X-chromosome loci is the most likely (...) simple scheme. An iterative approach matching the observed mixtures of proposed genotypes in the families with probabilities for variable levels of homozygosity, non-crossover/crossover heterozygosity, and maternal meiotic recombination yields a best goodness of fit where this last is 20%. (shrink)

A recently published study(1) has identified a set of candidate genes for human diseases based on findings from Drosophila. Each human expressed sequence tag (EST) in a large database was compared with all known Drosophila genes. After eliminating matches between genes of already known function, the remaining sequences were mapped in the human genome. In each region, the phenotypes of all known human diseases were compared with the phenotypes of known Drosophila mutations in order to identify candidate genes for the (...) human diseases. Are the correspondences real or coincidental? (shrink)

This article explores the processes through which Australian recipients select unknown donors for use in assisted reproductive technologies and speculates on how those processes may affect the future life of the donor-conceived person. I will suggest that trust is an integral part of the exchange between donors, recipients, and gamete agencies in donor conception and heavily informs concepts of relatedness, race, ethnicity, kinship, class, and visibility. The decision to be transparent about a child’s genetic parentage affects recipient parents’ choices of (...) donor, about who is allowed to “know” children’s genetic backgrounds, and how important it is to be able to “pass” as an unassisted conception. In this way, recipients must trust the process, institutions, and individuals involved in their treatment, as well as place trust in the future they imagine for their child. The current market for donor gametes reproduces normative conceptions of the nuclear family, kinship, and relatedness by facilitating “matching” donors to recipients by phenotype and cultural affinities. Recipient parents who choose not to prioritize “matching,” and actively disclose the process of children’s conceptions, may embark on a project of queering heteronormative family structures and place great trust in both their own children and changing social attitudes to reduce stigma and generate acceptance for non-traditional families. (shrink)

The traditional divide between nature and culture restricts to the latter the use of information. Biosemiotics claims instead that the divide between nature and culture is a mere subdivision within the living world but that semiosis is the specific feature which distinguishes the living from the inanimate. The present paper is intended to reformulate this basic tenet in information-theoretic terms, to support it using information-theoretic arguments, and to show that its consequences match reality. It first proposes a ‘receiver-oriented’ interpretation of (...) semiosis. This interpretation implies that the means for recording, storing and processing information exclusively reside in the living world (extended so as to include the artefacts it produces). Then it may be argued that the main difference between the inanimate world and the living one lies in the fact that the very existence of the latter relies on information, which on the contrary is not relevant to the former. Thus, besides matter and energy, information is an entity irreducible to them which must be taken into account in any attempt for describing and understanding life. Information can interact with the real world only provided it is borne by some physical support: it must be ‘physically inscribed’. Contrary to matter and energy, information can be shared, not necessarily exchanged, so a same information can be borne by a number of distinct supports. Any living thing possesses means for recording, storing and processing information which are necessary for keeping it alive and securing its progeny. In particular, its genome contains hereditary information, can be replicated, and instructs the construction and maintenance of a phenotype. The simultaneous existence of a phenotype and of a genome, where the latter bears the symbolic description of the former, is mandatory for enabling the self-reproduction of an organism. Bearing and using information then endows a living thing with the ability to decrease the physical entropy, hence to act as Maxwell’s demon. Not only its own life is maintained against physical entropy, but its self-reproduction multiplies clones of the demon. Taking information as the entity which differentiates the living from the inanimate also supports Rovelli’s ‘relational’ interpretation of quantum physics. Experimental apparatuses then appear as information-theoretic channels from the inanimate world to a living observer. Besides having its own perspective (as stated by Rovelli), each of these channels has its own horizon because its capacity is necessarily finite. As another consequence, we may assert that the physicists’ quest of a ‘theory of everything’ is doomed to failure since, for lack of considering information as a relevant entity, physicists deny the living world, hence themselves. (shrink)

Heterogeneity within MDD has hampered identification of biological markers (e.g., intermediate phenotypes, IPs) that might increase risk for the disorder or reflect closer links to the genes underlying the disease process. The newer characterizations of dimensions of MDD within Research Domain Criteria (RDoC) domains may align well with the goal of defining IPs. We compare a sample of 25 individuals with MDD compared to 29 age and education matched controls in multimodal assessment. The multimodal RDoC assessment included the primary IP (...) biomarker, positron emission tomography (PET) with a selective radiotracer for 5-HT1A ([11C]WAY-100635), as well as event-related functional MRI with a Go/No-go task targeting the Cognitive Control network, neuropsychological assessment of affective perception, negative memory bias and Cognitive Control domains. There was also an exploratory genetic analysis with the serotonin transporter (5-HTTLPR) and monamine oxidase A (MAO-A) genes. In regression analyses, lower 5-HT1A binding potential (BP) in the MDD group was related to diminished engagement of the Cognitive Control network, slowed resolution of interfering cognitive stimuli, one element of Cognitive Control. In contrast, higher/normative levels of 5-HT1A BP in MDD (only) was related to a substantial memory bias toward negative information, but intact resolution of interfering cognitive stimuli and greater engagement of Cognitive Control circuitry. The serotonin transporter risk allele was associated with lower 1a BP and the corresponding imaging and cognitive IPs in MDD. Lowered 5HT 1a BP was present in half of the MDD group relative to the control group. Lowered 5HT 1a BP may represent a subtype including decreased engagement of Cognitive Control network and impaired resolution of interfering cognitive stimuli. Future investigations might link lowered 1a BP to neurobiological pathways and markers, as well as probing subtype-specific treatment targets. (shrink)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)

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)

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)

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)

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)

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)

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.

(2013). Matching bias in syllogistic reasoning: Evidence for a dual-process account from response times and confidence ratings. Thinking & Reasoning: Vol. 19, No. 1, pp. 54-77. doi: 10.1080/13546783.2012.735622.

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)

A variety of theoretical frameworks predict the resemblance of behaviors between two people engaged in communication, in the form of coordination, mimicry, or alignment. However, little is known about the time course of the behavior matching, even though there is evidence that dyads synchronize oscillatory motions (e.g., postural sway). This study examined the temporal structure of nonoscillatory actions—language, facial, and gestural behaviors—produced during a route communication task. The focus was the temporal relationship between matching behaviors in the interlocutors (...) (e.g., facial behavior in one interlocutor vs. the same facial behavior in the other interlocutor). Cross-recurrence analysis revealed that within each category tested (language, facial, gestural), interlocutors synchronized matching behaviors, at temporal lags short enough to provide imitation of one interlocutor by the other, from one conversational turn to the next. Both social and cognitive variables predicted the degree of temporal organization. These findings suggest that the temporal structure of matching behaviors provides low-level and low-cost resources for human interaction. (shrink)

The phenomenon known as matching bias consists of a tendency to see cases as relevant in logical reasoning tasks when the lexical content of a case matches that of a propositional rule, normally a conditional, which applies to that case. Matching is demonstrated by use of the negations paradigm that is by using conditionals in which the presence and absence of negative components is systematically varied. The phenomenon was first published in 1972 and the present paper reviews the (...) history of research and theorising on the problem in the subsequent 25 years. Theories of matching bias considered include those based on several broad frameworks including the heuristic-analytic theory, the mental models theory, the theory of optimal data selection, and relevance theory as well as the specific processing-negations account. The ability of these theories to account for a range of phenomena is considered, including the effects of linguistic form, realistic content, and explicit negation on the matching bias effect. Of particular importance are recent findings showing that the bias is observable on a wider range of linguistic forms than has generally been thought, and that it is almost entirely dependent on the use of implicit negation in the logical cases to which rules are applied. The reasons for the general suppression of matching when realistic content is used are, however, unclear and a need for further research is identified here. It is concluded that matching bias is a highly robust effect which is closely connected with the problem of understanding implicit negation. Most of the theories in the literature are unable to account for at least some of the major phenomena discovered in research on the bias. The accounts that fare best are those that posit local effects of negation, including the heuristic-analytic and processing negations theories. (shrink)

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)

When charitable matching occurs, both the person initially offering the matching donation and the person taking up the offer may well feel they have done something better than if they had donated on their own without matching. They may well feel they deserve some credit for the matched donation as well as their own. Can they both be right? Natural assumptions about charitable matching lead to puzzles that are challenging to resolve in a satisfactory way.

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

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)

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 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)

ABSTRACT Match-fixing is a major ethical issue in sports. Although research interest in match-fixing has increased in recent years, we remain largely in the dark regarding how both betting- and non-betting-related match-fixing relate to the moral decision-making of those involved. Drawing on Rest’s theory of morality and on the perceptions of a large sample of participants in Flemish sports, this study indicates that most match-fixing incidents are non-betting-related, while moral motivation and associated challenges clearly differ according to the type of (...) match-fixing. Therefore, each type of match-fixing requires different preventive measures. (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)

Many conserved eukaryotic traits, including apoptosis, two sexes, speciation and ageing, can be causally linked to a bioenergetic requirement for mitochondrial genes. Mitochondrial genes encode proteins involved in cell respiration, which interact closely with proteins encoded by nuclear genes. Functional respiration requires the coadaptation of mitochondrial and nuclear genes, despite divergent tempi and modes of evolution. Free‐radical signals emerge directly from the biophysics of mosaic respiratory chains encoded by two genomes prone to mismatch, with apoptosis being the default penalty for (...) compromised respiration. Selection for genomic matching is facilitated by two sexes, and optimizes fitness, adaptability and fertility in youth. Mismatches cause infertility, low fitness, hybrid breakdown, and potentially speciation. The dynamics of selection for mitonuclear function optimize fitness over generations, but the same selective processes also operate within generations, driving ageing and age‐related diseases. This coherent view of eukaryotic energetics offers striking insights into infertility and age‐related diseases. (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)

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 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 The Selfish Gene, Richard Dawkins crystallized the gene's eye view of evolution developed by W.D. Hamilton and others. The book provoked widespread and heated debate. Written in part as a response, The Extended Phenotype gave a deeper clarification of the central concept of the gene as the unit of selection; but it did much more besides. In it, Dawkins extended the gene's eye view to argue that the genes that sit within an organism have an influence that reaches (...) out beyond the visible traits in that body - the phenotype - to the wider environment, which can include other individuals. So, for instance, the genes of the beaver drive it to gather twigs to produce the substantial physical structure of a dam; and the genes of the cuckoo chick produce effects that manipulate the behaviour of the host bird, making it nurture the intruder as one of its own. This notion of the extended phenotype has proved to be highly influential in the way we understand evolution and the natural world. It represents a key scientific contribution to evolutionary biology, and it continues to play an important role in research in the life sciences. The Extended Phenotype is a conceptually deep book that forms important reading for biologists and students. But Dawkins' clear exposition is accessible to all who are prepared to put in a little effort. Oxford Landmark Science books are 'must-read' classics of modern science writing which have crystallized big ideas, and shaped the way we think. (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)

Partial matching theory, which maintains that some memory representations of target items in immediate memory are overwritten by others, can predict both a “theoretical” and an “actual” maximum memory span provided no chunking takes place during presentation. The latter is around 4 ± 2 items, the exact number being determined by the degree of similarity between the memory representations of two immediately successive target items.