Evo-devo: a science of dispositions

Austin, Christopher J.

doi:10.1007/s13194-016-0166-9

Cited by 15 publications

(13 citation statements)

References 90 publications

(47 reference statements)

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“…In this paper, we have shown the utility of approaching pressing biological questions by appealing to metaphysical notions. Our approach follows a growing tendency in contemporary biological and philosophical research that consists in combining scientific practice with the use of the metaphysical discourse to clarify some scientific debates (Boogerd et al, 2005;Dupré, 2012Dupré, , 2015Mumford and Tugby, 2013;Guay and Pradeu, 2014;Austin, 2016Austin, , 2017Waters, 2017;Austin and Nuño de la Rosa, 2018;Nicholson and Dupré, 2018;Laplane et al, 2019;Triviño, 2019). Concretely, we have shown how approaching the concept of holobiont adaptation by appealing to the notions of emergence and inter-identity allows to shed light on some of the perceived issues in contemporary hologenome literature.…”

Section: Resultsmentioning

confidence: 99%

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

Suárez

Triviño

2020

Front. Psychol.

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Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.

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Section: Resultsmentioning

confidence: 99%

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

Suárez

Triviño

2020

Front. Psychol.

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“…Discovering new genes associated with anatomical phenotypes, such as limb and fin development leads to a clear understanding of the underlying molecular mechanisms for anatomical development. Moreover, such discoveries support the progress of emerging evolutionary developmental biology (evo-devo) studies [2, 52]. Computational prediction of candidate genes for anatomical entities is rare compared to predicting genes for molecular mechanisms and functions, but the need for accurate methods is evident based on the low number of gene annotations currently available for the majority of anatomical entities.…”

Section: Discussionmentioning

confidence: 99%

Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities

Fernando

Mabee

Zeng

2020

Preprint

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Results 41According to candidate gene prediction performance evaluations tested under four different 42 semantic similarity calculation methods (Lin, Resnik, Schlicker, and Wang), the integrated 43 networks showed better receiver operating characteristic (ROC) and precision-recall curve 44 performances than PPI networks for both zebrafish and mouse. 45 Conclusion 46Integration of existing experimental knowledge about gene-anatomical entity relationships with 47 PPI networks via anatomy ontology improves the network quality, which makes them better 48 optimized for predicting candidate genes for anatomical entities. 49 50 molecular and phenotypic functions of proteins is a cornerstone in molecular 68 biology. In particular, understanding the genes associated with the formation of anatomical 69 structures, also termed 'anatomical entities', is essential in developmental biology [1][2][3][4]. The 70 majority of genes associated with anatomical entities are obtained using wet-lab methods, such 71 as gene knockout [5, 6], gene knockdown [7], and overexpression [8, 9]. These methods, 72 however, are time-consuming and require significant resources, and thus only a few genes may 73 be associated with the development of a particular anatomical entity, though there are likely 74 many more genes involved. 75Alternatively, computational prediction methods for discovering gene-anatomical entity 76 associations can be employed because of their higher speed and low resource consumption. 77Sequence similarity-based function prediction is such an example, which is widely used to 78 predict the molecular functions of proteins [10, 11]. However, using it to predict anatomical 79 associations of genes is questionable, because anatomical entities develop from a combination of 80 several biological pathways that include proteins with diverse molecular functions and sequences 81[12]. On the other hand, protein-protein interaction (PPI) networks can be used to predict 82 candidate genes for anatomical entities, based on the assumption that proteins that regulate the 83 same term or function are more likely to physically interact with each other [13, 14]. PPI 84 networks represent such interactions as graphs where proteins are represented by nodes and their 85 interactions are represented by edges. PPI networks have been widely used in predicting 86 candidate genes for human disease phenotypes [15][16][17]. Therefore, PPI networks are suitable for 87 predicting candidate genes associated with anatomical entities. However, the challenge with PPI 88 network-based candidate gene prediction is improving the accuracy of the predictions [13,[18][19][20][21], which is low because of the poor quality of the large-scale PPI network data sets [14, 21-90 23]. PPI networks are generated by experimental methods such as yeast two-hybrid assay and 91 high-throughput mass-spectrometric protein complex identification (HMS-PCI), which can 92 generate false positive interactions [19]. Furthermore, PPI networks for model organisms are still 93incomplete ...

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“…Importantly, however, the generative potential which is mapped-out in these morphospaces are reflections of the intrinsic capacities of these modules, capacities which channel the exploration of these spaces over evolutionary time (see the chapter on -Inherency‖). As multiply realised, intrinsic centres of specified potentiality that both conform and constrain the character of morphological regularities in the phylogenetic record, developmental modules are best conceptualised dispositionally (Austin 2017). …”

Section: Modularitymentioning

confidence: 99%

“…The set of potential manifestations of a developmental system's multi-track disposition may form a continuous, gradient-like stratification of phenotypic variation -as exemplified in the ‗reaction norms' of experimental genetics -or consist of a collection of discrete phenotypic forms (so-called ‗polyphenisms'). Thus the developmental dispositions of these systems cannot be individuated according to their generative competency with respect to the production of a single, particularised phenotypic end-state, but rather to their potential to produce an entire -phenotypic repertoire‖ (Austin 2017). …”

Section: Plasticitymentioning

confidence: 99%

“…Evo-devo's investigation into the developmental structure of the modality of morphology -the possibility and impossibility of organismal form, as well as the directionality and speed of morphological changes -has led to the utilisation of dispositional concepts that emphasise the ‗inherency' of the evolutionary process, its proclivity to privilege particular pathways (see the chapter on -Inherency‖). In this sense, and in contrast to the perspective of the Modern Synthesis, evo-devo can be described as a -science of dispositions‖ (Austin 2017). …”

Section: Introduction: Evo-devo As a Science Of Dispositionsmentioning

confidence: 99%

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Dispositional Properties in Evo-Devo

Austin

Rosa

2018

Evolutionary Developmental Biology

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In identifying intrinsic molecular chance and extrinsic adaptive pressures as the only causally relevant factors in the process of evolution, the theoretical perspective of the Modern Synthesis had a major impact on the perceived tenability of an ontology of dispositional properties. However, since the late 1970s, an increasing number of evolutionary biologists have challenged the descriptive and explanatory adequacy of this -chance alone, extrinsic only‖ understanding of evolutionary change. Because morphological studies of homology, convergence, and teratology have revealed a space of possible forms and phylogenetic trajectories that is considerably more restricted than expected, evo-devo has focused on the causal contribution of intrinsic developmental processes to the course of evolution. Evo-devo's investigation into the developmental structure of the modality of morphology -including both the possibility and impossibility of organismal form -has led to the utilisation of a number of dispositional concepts that emphasise the tendency of the evolutionary process to change along certain routes. In this sense, and in contrast to the perspective of the Modern Synthesis, evo-devo can be described as a -science of dispositions.‖ This chapter discusses the recent philosophical literature on dispositional properties in evo-devo, exploring debates about both the metaphysical and epistemological aspects of the central dispositional concepts utilised in contemporary evo-devo (e.g., variability, modularity, robustness, plasticity, and evolvability) and addressing the epistemological question of how dispositional properties challenge existing explanatory models in evolutionary biology.

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Evo-devo: a science of dispositions

Cited by 15 publications

References 90 publications

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities

Dispositional Properties in Evo-Devo

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