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)

How to use a model organism to study phenotypic integration and constraints on evolution.

Psychiatry has witnessed a new wave of approaches to clinical phenotyping and the study of psychopathology, including the National Institute of Mental Health’s Research Domain Criteria, clinical staging, network approaches, the Hierarchical Taxonomy of Psychopathology, and the general psychopathology factor, as well as a revival of interest in phenomenological psychopathology. The question naturally emerges as to what the relationship between these new approaches is – are they mutually exclusive, competing approaches, or can they be integrated in some way and used (...) to enrich each other? In this opinion piece, we propose a possible integration between clinical staging and phenomenological psychopathology. Domains identified in phenomenological psychopathology, such as selfhood, embodiment, affectivity, etc., can be overlaid on clinical stages in order to enrich and deepen the phenotypes captured in clinical staging (‘high resolution’ clinical phenotypes). This approach may be useful both ideographically and nomothetically, in that it could complement diagnosis, enrich clinical formulation, and inform treatment of individual patients, as well as help guide aetiological, prediction, and treatment research. The overlaying of phenomenological domains on clinical stages may require that these domains are reformulated in dimensional rather than categorial terms. This integrative project requires assessment tools, some of which are already available, that are sensitive and thorough enough to pick up on the range of relevant psychopathology. The proposed approach offers opportunities for mutual enrichment: clinical staging may be enriched by introducing greater depth to phenotypes; phenomenological psychopathology may be enriched by introducing stages of severity and disorder progression to phenomenological analysis. (shrink)

Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can investigate concerning (...) any object or phenomenon: material (what something is made of), formal (what distinguishes that particular object from others), efficient (how was the object made) and final (why was the object made). The example is provided by ongoing research on different aspects of flowering time in the model system Arabidop- sis, a small weed belonging to the mustard family. I show that understanding how flowering time is controlled is an epistemologically different sort of question from why and how it evolved, and that the two research agendas can be pursued largely independently of each other. Toward the end, I propose that the real goal of integrative biology is to understand the boundary layers between levels of biologi- cal analysis, something to which modern philosophy of science can contribute significantly. (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)

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)

D. C. Matthew argues that although integration offers blacks social and economic benefits, it also creates the conditions for phenotypic devaluation that leads to harm against black self-worth and servile behavior. Therefore, he advises against integration because the resulting self-worth harms outweigh the benefits of integration. I argue that Matthew’s cost-benefit calculation against integration lacks the requisite evidence, and amounts to a luxury belief that will result in more harm. Moreover, his interpretation of behavior — (...) which he construes as being indicative of a lack of self-worth — is unfounded. Further, his cost-benefit calculation results in socially reactionary sexual policing and ideological purity tests. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also (...) provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell (...) biology. We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

I argue that an explicit distinction between cognitive characters and cognitive phenotypes is needed for empirical progress in the cognitive sciences and their integration with evolution-guided sciences. I elaborate what ontological commitment to characters involves and how such a commitment would clarify ongoing debates about the relations between human and nonhuman cognition and the extent of cognitive abilities across biological species. I use theoretical proposals in episodic memory, language, and sociocultural bases of cognition to illustrate how cognitive characters are (...) being introduced in scientific practice. (shrink)

The field of the philosophy of biology is flourishing in its aim to evaluate and rethink the view inherited from the previous century ---the Modern Synthesis. Different research areas and theories have come to the fore in the last decades in order to account for different biological phenomena that, in the first instance, fall beyond the explanatory scope of the Modern Synthesis. This thesis is anchored and motivated by this revolt in the philosophy of biology. -/- The central target in (...) this context is the possibility of naturalizing teleology, a classical nightmare for the history of biology itself. This requires, principally, understanding the causes of teleological explanations without assuming an unfashioned backward causation of sorts. As the riddles of teleological explanations are about their temporal dimension, I analyze different temporal scales of biological processes: evolutionary, developmental, and physiological. -/- The first one is the one defended in the context of the Modern Synthesis. As expected, one of the aims of this thesis is to evaluate the adequacy of an evolutionary account of teleological explanation. The scrutiny is negative. Evolutionary explanations in the context of the Modern Synthesis lack the necessary causal roots to naturalize teleology. Concerning the physiological scale, a long tradition pushed up by Kant and the organicist movement in the 20th century allows us to better understand how teleological explanations can be naturalized in physiological process. The key notions in this temporal scale are self-organization and the recursive, looped character of physiological process. While the physiological scale may be suitably accounted by contemporaries views, such as Autonomous Systems Theory, different central teleological phenomena remain unexplained from a purely physiological perspective. In particular, different issues concerning the (adaptive) construction of organism ---such as plasticity, robustness, variation, novelty, inheritance--- deserve an ontogenetic analysis. -/- The principal aim of this thesis is to provide a theory of teleological development that falls beyond the Modern Synthesis' framework and is prompted by different insights from the history of biology. I call it Agential Teleosemantics. It rests on two central pillars. First, that developmental processes, beyond any gene-centered stance, can be understood in informational terms; i.e. developmental processes are about the interaction of developmental resources conveying biological information. The second ingredient is agentivity, namely the idea that development is regulated by an agentive system according to the adaptiveness of the phenotypic outcomes produced. The role of agency in Agential Teleosemantic is equivalent to the role of genes in the Modern Synthesis: it is responsible for explaining the order and the adaptive complexity in the living realm. -/- The second target of this thesis regards the possibility of naturalizing intentional explanations in cognitive science. The central project involved in such an aim is known as teleosemantics. Classical teleosemantics however is etiological: it explains the teleofunctions of representational systems in terms of evolutionary processes. The different disputes in the contemporary philosophy of biology provide two insights to analyze teleosemantics in cognitive science. First, the challenges against the Modern Synthesis must be extended to the evolutionary approach of etiological teleosemantics. Second, as Agential Teleosemantics suggests an alternative source for teleofunctions ---ontogeny, I offer an attempt to integrate Agential Teleosemantics into cognitive science in order to provide an alternative teleosemantic project to understand intentional explanations in cognitive science. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (...) (CIDO). As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated (...) the development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...) the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

How micro- and macroevolutionary evolutionary processes produce phenotypic change is without question one of the most intriguing and perplexing issues facing evolutionary biologists. We believe that roadblocks to progress lie A) in the underestimation of the role of the environment, and in particular, that of the interaction of genotypes with environmental factors, and B) in the continuing lack of incorporation of development into the evolutionary synthesis. We propose the integration of genetic, environmental and developmental perspectives on the evolution (...) of the phenotype in the form of the concept of the developmental reaction norm (DRN) The DRN represents the set of multivariate ontogenies that can be produced by a single genotype when it is exposed to environmental variation. It encompasses: 1) the processes that alter the phenotype throughout the ontogenetic trajectory, 2) the recognition that different aspects of the phenotype are (and must be) correlated and 3) the ability of a genotype to produce phenotypes in different environments. This perspective necessitates the explicit study of character expression during development, the evaluation of associations between pairs or groups of characters (e.g., multivariate allometries), and the exploration of reaction norms and phenotypic plasticity. We explicitly extend the concept of the DRN to encompass adjustments made in response to changes in the internal environment as well. Thus, ‘typical’ developmental sequences (e.g., cell fate determination) and plastic responses are simply manifestations of different scales of ‘environmental’ effects along a continuum. We present: (1) a brief conceptual review of three fundamental aspects of the generation and evolution of phenotypes: the changes in the trajectories describing growth and differentiation (ontogeny), the multivariate relationships among characters (allometry), and the effect of the environment (plasticity); (2) a discussion of how these components are merged in the concept of the developmental reaction norm; and (3) a reaction norm perspective of major determinants of phenotypes: epigenesis, selection and constraint. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Biological evolution and technological innovation, while differing in many respects, also share common features. In particular, implementation of a new technology in the market is analogous to the spreading of a new genetic trait in a population. Technological innovation may occur either through the accumulation of quantitative changes, as in the development of the ocean clipper, or it may be initiated by a new combination of features or subsystems, as in the case of steamships. Other examples of the latter type (...) are electric networks that combine the generation, distribution, and use of electricity, and containerized transportation that combines standardized containers, logistics, and ships. Biological evolution proceeds, phenotypically, in many small steps, but at the genetic level novel features may arise not only through the accumulation of many small, common mutational changes, but also when distinct, relatively rare genetic changes are followed by many further mutations. In particular, capabilities of biologically modern man may have been initiated, perhaps some 150 000 years ago, by one or few accidental but distinct combinations of modules and subroutines of gene regulation which are involved in the generation of the neural network in the cerebral cortex. It is even conceivable that it was one primary genetic event that initiated the evolution of biologically modern man, introducing some novel but subtle feature of connectivity into the cerebral cortex which allowed for meta-levels of abstraction and upgraded modes of information processing. This may have set the stage for the evolution of integrated but diverse higher capabilities such as structured language, symbolic thought, strategic thought, and cognition based empathy. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for (...) the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

I am broadly sympathetic to Dale Matthew’s analysis concerning phenotypic devaluation and disadvantage. However, in what follows, I restrict my remarks to a few areas where I think he either lacks empirical precision, or overstates his case.

There have been rumblings for some time to the effect that the neo-darwinian synthesis of the early twentieth century is incomplete and due for a major revision. In the past decade, several authors have written books to articu- late this feeling and to begin the move towards a second synthesis. David Rollo, in his book Phenotypes (Kluwer, 1994), was among the first to attempt to bring the focus back to the problems posed by phenotypic evolution. In Phenotypic Evolution (...) (Sinauer, 1998), Carl Schlichting and I framed the debate in terms of the integration of development, environ- ment and genetics by articulating the concept of “developmental reaction norms”. (shrink)

No two individuals with the autism diagnosis are ever the same—yet many practitioners and parents can recognize signs of ASD very rapidly with the naked eye. What, then, is this phenotype of autism that shows itself across such distinct clinical presentations and heterogeneous developments? The “signs” seem notoriously slippery and resistant to the behavioral threshold categories that make up current assessment tools. Part of the problem is that cognitive and behavioral “abilities” typically are theorized as high-level disembodied and modular functions—that (...) are assessed discretely (impaired, normal, enhanced) to define a spectral syndrome. Even as biology reminds us that organic developing bodies are not made up of independent switches, we remain often seduced by the simplicity of mechanistic and cognitive models. Developmental disorders such as autism have accordingly been theorized as due to different modular dysfunctions—typically of cortical origin, i.e., failures of “theory of mind” (Baron-Cohen et al., 1985), of the “mirror neuron system” (Ramachandran and Oberman, 2006), of “weak central coherence” (Happe and Frith, 2006) or of the balance of “empathizing” and “systemizing” (Baron-Cohen, 2009), just to list a few. -/- The broad array of autonomic (Ming et al., 2005; Cheshire, 2012) and sensorimotor (Damasio and Maurer, 1978; Maurer and Damasio, 1982; Donnellan and Leary, 1995; Leary and Hill, 1996; Donnellan and Leary, 2012; Donnellan et al., 2012) differences experienced and reported by people with autism have by such theories typically been sidelined as “co-morbidities,” possibly sharing genetic causes, but rendered as incidental and decisively behaviorally irrelevant symptoms—surely disconnected from cognition. But what if the development of cortically based mental processes and autonomous control relies on the complexities and proper function of the peripheral nervous systems? Through such an “embodied” lens the heterogeneous symptoms of autism invites new interpretations. We propose here that many behavioral-level findings can be re-defined as downstream effects of how developing nervous systems attempt to cope and adapt to the challenges of having various noisy, unpredictable, and unreliable peripheral inputs. (shrink)

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)

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

Background: One of the all-time questions in evolutionary biology regards the evolution of organismal shapes, and in particular why certain forms appear repeatedly in the history of life, others only seldom and still others not at all. Recent research in this field has deployed the conceptual framework of constraints and natural selection as measured by quantitative genetic methods. Scope: In this paper I argue that quantitative genetics can by necessity only provide us with useful statistical sum- maries that may lead (...) researchers to formulate testable causal hypotheses, but that any inferential attempt beyond this is unreasonable. Instead, I suggest that thinking in terms of coordinates in phenotypic spaces, and approaching the problem using a variety of empirical methods (seeking a consilience of evidence), is more likely to lead to solid inferences regarding the causal basis of the historical patterns that make up most of the data available on phenotypic evolution. (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)

Different cognitive functions recruit a number of different, often overlapping, areas of the brain. Theories in cognitive and computational neuroscience are beginning to take this kind of functional integration into account. The contributions to this special issue consider what functional integration tells us about various aspects of the mind such as perception, language, volition, agency, and reward. Here, I consider how and why functional integration may matter for the mind; I discuss a general theoretical framework, based on (...) generative models, that may unify many of the debates surrounding functional integration and the mind; and I briefly introduce each of the contributions. (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)

In this paper, an account of theoretical integration in cognitive (neuro)science from the mechanistic perspective is defended. It is argued that mechanistic patterns of integration can be better understood in terms of constraints on representations of mechanisms, not just on the space of possible mechanisms, as previous accounts of integration had it. This way, integration can be analyzed in more detail with the help of constraintsatisfaction account of coherence between scientific representations. In particular, the account has (...) resources to talk of idealizations and research heuristics employed by researchers to combine separate results and theoretical frameworks. The account is subsequently applied to an example of successful integration in the research on hippocampus and memory, and to a failure of integration in the research on mirror neurons as purportedly explanatory of sexual orientation. (shrink)

The idea that justified modal belief can be accounted for in terms of empirically justified, non-modal belief is enjoying increasing popularity in the epistemology of modality. One alleged reason to prefer modal empiricism over more traditional, rationalist modal epistemologies is that empiricism avoids the problem with the integration challenge that arise for rationalism, assuming that we want to be realists about modal metaphysics. In this paper, I argue that given two very reasonable constraints on what it means to meet (...) the integration challenge for modality, empiricism is currently at best on a par with, but potentially worse off than, rationalist alternatives, with respect to the integration challenge. (shrink)

I defend an empirically-oriented approach to the analysis and remediation of social injustice. My springboard for this argument is a debate—principally represented here between Tommie Shelby and Elizabeth Anderson, but with much deeper historical roots and many flowering branches—about whether racial-justice advocacy should prioritize integration (bringing different groups together) or community development (building wealth and political power within the black community). Although I incline toward something closer to Shelby’s “egalitarian pluralist” approach over Anderson’s single-minded emphasis on integration, many (...) of Shelby’s criticisms of integrationism are misguided, and his handling of the empirical literature is profoundly unbalanced. In fact, while both Shelby and Anderson defend the importance of social science to their projects, I’ll argue that each takes a decidedly unempirical approach, which ultimately obscures the full extent of our ignorance about what we can and ought to do going forward. A more authentically empirical tack would be more epistemically humble, more holistic, and less organized around what I’ll call prematurely formulated “Grand Unified Theories of Social Change.” I defend a more “diversified experimentalist” approach, which rigorously tests an array of smaller-scale interventions before trying to replicate and scale up the most promising results. (shrink)

In the past decade, policy-makers in science have been concerned with harmonizing research integrity standards across Europe. These standards are encapsulated in the European Code of Conduct for Research Integrity. Yet, almost every European country today has its own national-level code of conduct for research integrity. In this study we document in detail how national-level codes diverge on almost all aspects concerning research integrity – except for what constitutes egregious misconduct. Besides allowing for potentially unfair responses to joint misconduct by (...) international collaborations, we argue that the divergences raise questions about the envisaged self-regulatory function of the codes of conduct. (shrink)

Developmental plasticity as the nexus between genetics and ecology.

Integrated Information Theory (IIT) identifies consciousness with having a maximum amount of integrated information. But a thing’s having the maximum amount of anything cannot be intrinsic to it, for that depends on how that thing compares to certain other things. IIT’s consciousness, then, is not intrinsic. A mereological argument elaborates this consequence: IIT implies that one physical system can be conscious while a physical duplicate of it is not conscious. Thus, by a common and reasonable conception of intrinsicality, IIT’s consciousness (...) is not intrinsic. It is then argued that to avoid the implication that consciousness is not intrinsic, IIT must abandon its Exclusion Postulate, which prohibits overlapping conscious systems. Indeed, theories of consciousness that attribute consciousness to physical systems, should embrace the view that some conscious systems overlap. A discussion of the admittedly counterintuitive nature of this solution, along with some medical and neuroscientific realities that would seem to support it, is included. (shrink)

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, (...) and describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

Digital phenotyping will potentially enable earlier detection and prediction of mental illness by monitoring human interaction with and through digital devices. Notwithstanding its promises, it is certain that a person’s digital phenotype will at times be at odds with their first-person testimony of their psychological states. In this paper, we argue that there are features of digital phenotyping in the context of psychiatry which have the potential to exacerbate the tendency to dismiss patients’ testimony and treatment preferences, which can be (...) instances of epistemic injustice. We first explain what epistemic injustice is, and why it is argued to be an extensive problem in health and disability settings. We then explain why epistemic injustice is more likely to apply with even greater force in psychiatric contexts, and especially where digital phenotyping may be involved. Finally, we offer some tentative suggestions of how epistemic injustice can be minimised in digital psychiatry. (shrink)

Integral human development is a human-centered development perspective that originated from Catholic social teaching. The perspective holds that authentic development is development that makes every person “more human.” Although it is seldom named in the literature, integral human development has had considerable influence on notions of authentic development, and in turn, development ethics. In this short chapter, I provide a brief explanation of the origins and implications of the conceptual foundations of integral human development both within and beyond the Catholic (...) Church. I argue that integral human development offers a truly radical participatory approach to human development. I briefly raise and respond to some concerns about agency, civic liberty, and integral human development’s connection to the Catholic Church. I conclude with a short explanation of integral human development in practice. (shrink)

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)

Consequentialism is enticing, and yet it also seems overly demanding. As a result, many non-consequentialists try to explain why we aren’t required to maximize the good. One explanation is the Integrity Explanation: we aren’t required to maximize the good because morality must make room for us to pursue the projects we value most deeply. Some people hope that the Integrity Explanation will not just explain why consequentialism is false, but simultaneously vindicate the common-sense permission to generally refrain from promoting the (...) good of other people and instead spend our time on non-harmful actions of our choice. I argue that this hope is unrealistic, because if any version of the Integrity Explanation is correct, morality won’t contain broad permissions to refrain from promoting the good of others and do as we choose. Instead the basic structure of morality must be fundamentally different from what we usually take it to be. Our common-sense moral theories say that we take on responsibilities to others only in certain specific situations, but may otherwise engage in non-harmful actions of our choice. But if the Integrity Explanation is correct, then we are entitled to pursue our own interests to at least some extent, but unless we do, we come under obligations to maximize the good of others. (shrink)

Integral development as the most assertive path of sustainable development models is presented as a new paradigm in the social teaching of the church. It is a question of identifying the theoretical foundations that precede the encyclical Laudato Si’ (ls) from philosophy and theology: the harmony of quaternity, the mystique of creation, the science-faith dialogue and the theology of the small and the poor. At the same time it tries to recover and remember the reflections and teachings that are already (...) in the tradition of the church on the “common house”. It proposes a renewed theological attitude and joint ethical action of all humanity, believers and non-believers. (shrink)

This integral investigation explored phenomenological and neurophysiologic, individual and collective dimensions of Christian Trinitarian meditation experiences in a volunteer, convenience sample of 10 practicing Christians, 6 men and 4 women, with a mean age of 48 years and an age range from 21 to 85 years. Participants meditated for a minimum period of 15 minutes, during which neurophysiologic data in the form of electroencephalographic (EEG), electromyographic (EMG), blood volume pulse (BVP) and respiratory activity were recorded. A phenomenological analysis indicated that (...) the meditation process generally involved a movement from body to mind to spirit as evident in reports of an increasingly relaxed, contented and focused state of consciousness characterised by Christian Trinitarian imagery, wonder, surrender, peace, bliss, openness and formlessness. The neuropsychological findings indicated significant increases, from baseline to meditation recordings, in the alpha and beta range, accompanied by increasing mean trends in the theta and gamma range, and decreasing mean trends in the delta range, EMG, BVP and respiration. Integrative findings indicated the practical theological value of small doses of Christian Trinity meditation to enhance spiritual life for those forms of waking, thinking, conscious behaviour needed in everyday world involvement and healing. Findings were discussed in relation to further integrative investigations and interventions with practical theological implications. (shrink)

Integrity not only is a central concept within virtue ethics and a subject of considerable debate among philosophers regarding its nature and relation to other virtues, but also is important for our understanding of what it means to possess a constituted and coherent self. Much of the literature on integrity is focused on relationships among moral principles and virtues, while less attention is paid to any relationship that integrity might have to practical agency or personal identity. In maintaining this focus, (...) philosophers fail to appreciate the special relation integrity has to the constitution of a coherent self. Central to integrity are considerations about self-identity and agency because it is through ongoing and deliberate activities that reflect the type of person with which she wishes to identify that a person constitutes self-identity and agency in a coherent manner. Once the relationship between integrity and a coherent self is properly understood, it becomes clear that the moral content of integrity is relatively thin and that the approbation usually associated with a person of integrity stems not from judgments about convictions or principles, but from the relationship between actions and commitments. (shrink)

The Integrated Information Theory is a leading scientific theory of consciousness, which implies a kind of panpsychism. In this paper, I consider whether IIT is compatible with a particular kind of panpsychism, known as Russellian panpsychism, which purports to avoid the main problems of both physicalism and dualism. I will first show that if IIT were compatible with Russellian panpsychism, it would contribute to solving Russellian panpsychism’s combination problem, which threatens to show that the view does not avoid the main (...) problems of physicalism and dualism after all. I then show that the theories are not compatible as they currently stand, in view of what I call the coarse-graining problem. After I explain the coarse-graining problem, I will offer two possible solutions, each involving a small modification of IIT. Given either of these modifications, IIT and Russellian panpsychism may be fully compatible after all, and jointly enable significant progress on the mind–body problem. (shrink)

Catholic integralism is a tradition of thought which insists upon the ideal nature of political arrangements on which the Church can mandate the State to advance the supernatural good of the baptized. Thomas Pink, one of the foremost defenders, has proposed controversially that these arrangements are ideal because the Church possesses rights to civil coercive authority. But I argue this fact would not entail – by itself – the ideal nature of those arrangements. To the contrary, I argue that integralism (...) is unjust, even assuming Pink’s claims are true. The integralist ideal necessarily involves violating moral duties toward unbaptized citizens. Integralism does so in imposing differential civic burdens upon baptized/unbaptized citizens and in implying that non-Catholics might be rightly excluded from power merely on account of religious beliefs, both without just cause. I conclude by showing that readings of the relevant Catholic teaching can be given which are non-integralist. (shrink)

This document presents the Bonn PRINTEGER Consensus Statement: Working with Research Integrity—Guidance for research performing organisations. The aim of the statement is to complement existing instruments by focusing specifically on institutional responsibilities for strengthening integrity. It takes into account the daily challenges and organisational contexts of most researchers. The statement intends to make research integrity challenges recognisable from the work-floor perspective, providing concrete advice on organisational measures to strengthen integrity. The statement, which was concluded February 7th 2018, provides guidance on (...) the following key issues: § 1.Providing information about research integrity § 2.Providing education, training and mentoring § 3.Strengthening a research integrity culture § 4.Facilitating open dialogue § 5.Wise incentive management § 6.Implementing quality assurance procedures § 7.Improving the work environment and work satisfaction § 8.Increasing transparency of misconduct cases § 9.Opening up research § 10.Implementing safe and effective whistle-blowing channels § 11.Protecting the alleged perpetrators § 12.Establishing a research integrity committee and appointing an ombudsperson § 13.Making explicit the applicable standards for research integrity. (shrink)

We describe a strategy for integration of data that is based on the idea of semantic enhancement. The strategy promises a number of benefits: it can be applied incrementally; it creates minimal barriers to the incorporation of new data into the semantically enhanced system; it preserves the existing data (including any existing data-semantics) in their original form (thus all provenance information is retained, and no heavy preprocessing is required); and it embraces the full spectrum of data sources, types, models, (...) and modalities (including text, images, audio, and signals). The result of applying this strategy to a given body of data is an evolving Dataspace that allows the application of a variety of integration and analytic processes to diverse data contents. We conceive semantic enhancement (SE) as a lightweight and flexible process that leverages the richness of the structured contents of the Dataspace without adding storage and processing burdens to what, in the intelligence domain, will be an already storage- and processing-heavy starting point. SE works not by changing the data to which it is applied, but rather by adding an extra semantic layer to this data. We sketch how the semantic enhancement approach can be applied consistently and in cumulative fashion to new data and data-models that enter the Dataspace. (shrink)

This paper examines the integration and unification of the philosophy and psychology of well-being. For the most part, these disciplines investigate well-being without reference to each other. In recent years, however, with the maturing of each discipline, there have been a growing number of calls to integrate the two. While such calls are welcome, what it means to integrate well-being philosophy and psychology can vary greatly depending on one’s theoretical and practical ends. The aim of this paper is to (...) provide a novel conceptual framework for thinking about integrating well-being philosophy and psychology that systematically categorizes different kinds of integration projects. We divide existing attempts in the literature into three broad categories according to the perspective from which the integration takes place: (1) top-down meta-theoretical unification; (2) psychological integration within philosophy; and (3) philosophical integration within psychology. These categories are then broken down into various further subcategories. Our aim in providing this framework is both to facilitate the assessment and comparison of existing integration attempts and to provide a roadmap for future integration attempts. For each category, we discuss one or two representative examples of the approaches. By doing so, we hope to generate interest in the wide variety of existing integration projects, as well as to generate discussion concerning the benefits and pitfalls of different approaches. (shrink)

Cognitive integration is a defining yet overlooked feature of our intellect that may nevertheless have substantial effects on the process of knowledge-acquisition. To bring those effects to the fore, I explore the topic of cognitive integration both from the perspective of virtue reliabilism within externalist epistemology and the perspective of extended cognition within externalist philosophy of mind and cognitive science. On the basis of this interdisciplinary focus, I argue that cognitive integration can provide a minimalist yet adequate (...) epistemic norm of subjective justification: so long as the agent’s belief-forming process has been integrated in his cognitive character, the agent can be justified in holding the resulting beliefs merely by lacking any doubts there was something wrong in the way he arrived at them. Moreover, since both externalist philosophy of mind and externalist epistemology treat the process of cognitive integration in the same way, we can claim that epistemic cognitive characters may extend beyond our organismic cognitive capacities to the artifacts we employ or even to other agents we interact with. This move is not only necessary for accounting for advanced cases of knowledge that is the product of the operation of epistemic artifacts or the interactive activity of research teams, but it can further lead to interesting ramifications both for social epistemology and philosophy of science. (shrink)

I investigate the status of subjectivity in Integrated Information Theory. This leads me to examine if Integrated Information Theory can answer the hard problem of consciousness. On itself, Integrated Information Theory does not seem to constitute an answer to the hard problem, but could be combined with panpsychism to yield a more satisfying theory of consciousness. I will show, that even if Integrated Information Theory employs the metaphysical machinery of panpsychism, Integrated Information would still suffer from a different problem, not (...) being able to account for the subjective character of consciousness. (shrink)