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Ibbini Z, Truebano M, Spicer JI, McCoy JCS, Tills O. Dev-ResNet: automated developmental event detection using deep learning. J Exp Biol 2024; 227:jeb247046. [PMID: 38806151 PMCID: PMC11152166 DOI: 10.1242/jeb.247046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/22/2024] [Indexed: 05/30/2024]
Abstract
Delineating developmental events is central to experimental research using early life stages, permitting widespread identification of changes in event timing between species and environments. Yet, identifying developmental events is incredibly challenging, limiting the scale, reproducibility and throughput of using early life stages in experimental biology. We introduce Dev-ResNet, a small and efficient 3D convolutional neural network capable of detecting developmental events characterised by both spatial and temporal features, such as the onset of cardiac function and radula activity. We demonstrate the efficacy of Dev-ResNet using 10 diverse functional events throughout the embryonic development of the great pond snail, Lymnaea stagnalis. Dev-ResNet was highly effective in detecting the onset of all events, including the identification of thermally induced decoupling of event timings. Dev-ResNet has broad applicability given the ubiquity of bioimaging in developmental biology, and the transferability of deep learning, and so we provide comprehensive scripts and documentation for applying Dev-ResNet to different biological systems.
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Affiliation(s)
- Ziad Ibbini
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Manuela Truebano
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - John I. Spicer
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Jamie C. S. McCoy
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Oliver Tills
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
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2
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Barbara L. Resilience and the shift of paradigm in ecology: a new name for an old concept or a different explanatory tool? HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2023; 46:2. [PMID: 38153583 DOI: 10.1007/s40656-023-00600-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/27/2023] [Indexed: 12/29/2023]
Abstract
In the shift from the balance of nature to the flux of nature paradigm, the concept of resilience has gained great traction in ecology. While it has been suggested that the concept of resilience does not imply a genuine departure from the balance of nature paradigm, I shall argue against this stance. To do so, I first show that the balance of nature paradigm and the related conception of a single-state equilibrium relies on what Eliot Sober has named the "Natural State Model (NSM)", suggesting that the NSM has instead been dismissed in the flux of nature paradigm. I then focus on resilience as the main explanatory concept of the flux paradigm. After distinguishing between two main different understandings of "resilience", namely engineering resilience and ecological resilience, I argue that the former is close to the concept of balance or stability and still part of the NSM, while the latter is not. Finally, I claim that ecological resilience is inconsistent with the NSM, concluding that this concept-being incompatible with the NSM-is not part of the balance of nature paradigm but rather a genuinely new explanatory tool.
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Affiliation(s)
- Lara Barbara
- Department of Philosophy, Università del Piemonte Orientale, Vercelli, Italy.
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3
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Yoshida Y. Joint representation: Modeling a phenomenon with multiple biological systems. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2023; 99:67-76. [PMID: 37068423 DOI: 10.1016/j.shpsa.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 03/01/2023] [Accepted: 03/19/2023] [Indexed: 05/30/2023]
Abstract
Biologists often study particular biological systems as models of a phenomenon of interest even if they already know that the phenomenon is produced by diverse mechanisms and hence none of those systems alone can sufficiently represent it. To understand this modeling practice, the present paper provides an account of how multiple model systems can be used to study a phenomenon that is produced by diverse mechanisms. Even if generalizability of results from a single model system is significantly limited, generalizations concerning specific aspects of mechanisms often hold across certain ranges of biological systems, which enables multiple model systems to jointly represent such a phenomenon. Comparing mechanisms that operate in different biological systems as examples of the same phenomenon also facilitates characterization and investigation of individual mechanisms. I also compare my account with two existing accounts of the use of multiple model systems and argue that my account is distinct from and complementary to them.
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Affiliation(s)
- Yoshinari Yoshida
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN, USA, Heller Hall, 271 S 19th Ave #831, Minneapolis, MN 55455, USA.
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Wajzer M. Idealisation, genetic explanations and political behaviours: Notes on the anti-reductionist critique of genopolitics. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2021; 90:275-284. [PMID: 34753069 DOI: 10.1016/j.shpsa.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The rapid development of genetic research, determined, among others, by the requirements of The Human Genome Project, and a gradual reorientation in the perception of the role of nature and culture in the process of shaping complex networks of human relations by some political scientists, result in the increasing application of genetic data and methods in research regarding political behaviours. One of the key philosophical objections against the studies of the genetic foundations of political behaviours is that of excessive reductionism. This is supposed to manifest itself in the inadequate selection of the level of analysis for the explained phenomenon, the incompleteness of explanations and their low utility. My findings show that this objection is not sufficiently supported by contemporary science. Both studies using classical behavioural genetic methodologies and studies using DNA-based methods show that genes most likely play a role in political behaviours. Emphasising the significance of genetic influences in the midst of multiple extra-genetic interactions generates highly idealised explanations. Using the conceptual apparatus of the deformational concept of culture, I have demonstrated that the omission of a number of important extra-genetic influences by researchers is a consequence of focusing on specific causal patterns. This omission, however, does not entail negating the influence of non-genetic factors and, importantly, it may not have to be permanent. Following this approach, if correct, the reductionism of research into the genetic foundations of political behaviours is a standard cognitive procedure applied in science.
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Affiliation(s)
- Mateusz Wajzer
- Faculty of Social Sciences, University of Silesia in Katowice, Bankowa 11, PL, 40007, Katowice, Poland.
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5
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Rivera‐Yoshida N, Hernández‐Terán A, Escalante AE, Benítez M. Laboratory biases hinder Eco‐Evo‐Devo integration: Hints from the microbial world. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 334:14-24. [DOI: 10.1002/jez.b.22917] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Natsuko Rivera‐Yoshida
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de EcologíaUniversidad Nacional Autónoma de México Mexico City Mexico
- Programa de Doctorado en Ciencias BiomédicasUniversidad Nacional Autónoma de México Mexico City Mexico
- Centro de Ciencias de la ComplejidadUniversidad Nacional Autónoma de México Mexico City Mexico
| | - Alejandra Hernández‐Terán
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de EcologíaUniversidad Nacional Autónoma de México Mexico City Mexico
- Programa de Doctorado en Ciencias BiomédicasUniversidad Nacional Autónoma de México Mexico City Mexico
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de EcologíaUniversidad Nacional Autónoma de México Mexico City Mexico
| | - Mariana Benítez
- Laboratorio Nacional de Ciencias de la Sostenibilidad (LANCIS), Instituto de EcologíaUniversidad Nacional Autónoma de México Mexico City Mexico
- Centro de Ciencias de la ComplejidadUniversidad Nacional Autónoma de México Mexico City Mexico
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6
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Love AC, Yoshida Y. Reflections on Model Organisms in Evolutionary Developmental Biology. Results Probl Cell Differ 2019; 68:3-20. [PMID: 31598850 DOI: 10.1007/978-3-030-23459-1_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This chapter reflects on and makes explicit the distinctiveness of reasoning practices associated with model organisms in the context of evolutionary developmental research. Model organisms in evo-devo instantiate a unique synthesis of model systems strategies from developmental biology and comparative strategies from evolutionary biology that negotiate a tension between developmental conservation and evolutionary change to address scientific questions about the evolution of development and the developmental basis of evolutionary change. We review different categories of model systems that have been advanced to understand practices found in the life sciences in order to comprehend how evo-devo model organisms instantiate this synthesis in the context of three examples: the starlet sea anemone and the evolution of bilateral symmetry, leeches and the origins of segmentation in bilaterians, and the corn snake to understand major evolutionary change in axial and appendicular morphology.
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Affiliation(s)
- Alan C Love
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota - Twin Cities, Minneapolis, MN, USA.
| | - Yoshinari Yoshida
- Department of Philosophy and Minnesota Center for Philosophy of Science, University of Minnesota - Twin Cities, Minneapolis, MN, USA
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Green S, Dietrich MR, Leonelli S, Ankeny RA. 'Extreme' organisms and the problem of generalization: interpreting the Krogh principle. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2018; 40:65. [PMID: 30382416 PMCID: PMC6208786 DOI: 10.1007/s40656-018-0231-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/17/2018] [Indexed: 05/22/2023]
Abstract
Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that "for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied". Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has been developed and used. We interpret the Krogh Principle as a heuristic, i.e., as a recommendation to approach biological problems through organisms where a specific trait or physiological mechanism is expected to be most distinctively displayed or most experimentally accessible. We designate these organisms "Krogh organisms". We clarify the differences between uses of model organisms and non-standard Krogh organisms. Among these is the use of Krogh organisms as "negative models" in biomedical research, where organisms are chosen for their dissimilarity to human physiology. Importantly, the representational scope of Krogh organisms and the generalizability of their characteristics are not fixed or assumed but explored through experimental studies. Research on Krogh organisms is steeped in the comparative method characteristic of zoology and comparative physiology, in which studies of biological variation produce insights into general physiological constraints. Accordingly, we conclude that the Krogh principle exemplifies the advantages of studying biological variation as a strategy to produce generalizable insights.
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Affiliation(s)
- Sara Green
- Department of Science Education, University of Copenhagen, Copenhagen, Denmark
| | - Michael R. Dietrich
- Department of History and Philosophy of Science, University of Pittsburgh, Pittsburgh, USA
| | - Sabina Leonelli
- Department of Sociology, Philosophy and Anthropology, University of Exeter, Exeter, UK
| | - Rachel A. Ankeny
- School of Humanities, University of Adelaide, Adelaide, Australia
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8
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Green S, Dietrich MR, Leonelli S, Ankeny RA. 'Extreme' organisms and the problem of generalization: interpreting the Krogh principle. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2018. [PMID: 30382416 DOI: 10.1007/s40656-017-0165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Many biologists appeal to the so-called Krogh principle when justifying their choice of experimental organisms. The principle states that "for a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied". Despite its popularity, the principle is often critiqued for implying unwarranted generalizations from optimal models. We argue that the Krogh principle should be interpreted in relation to the historical and scientific contexts in which it has been developed and used. We interpret the Krogh Principle as a heuristic, i.e., as a recommendation to approach biological problems through organisms where a specific trait or physiological mechanism is expected to be most distinctively displayed or most experimentally accessible. We designate these organisms "Krogh organisms". We clarify the differences between uses of model organisms and non-standard Krogh organisms. Among these is the use of Krogh organisms as "negative models" in biomedical research, where organisms are chosen for their dissimilarity to human physiology. Importantly, the representational scope of Krogh organisms and the generalizability of their characteristics are not fixed or assumed but explored through experimental studies. Research on Krogh organisms is steeped in the comparative method characteristic of zoology and comparative physiology, in which studies of biological variation produce insights into general physiological constraints. Accordingly, we conclude that the Krogh principle exemplifies the advantages of studying biological variation as a strategy to produce generalizable insights.
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Affiliation(s)
- Sara Green
- Department of Science Education, University of Copenhagen, Copenhagen, Denmark.
| | - Michael R Dietrich
- Department of History and Philosophy of Science, University of Pittsburgh, Pittsburgh, USA
| | - Sabina Leonelli
- Department of Sociology, Philosophy and Anthropology, University of Exeter, Exeter, UK
| | - Rachel A Ankeny
- School of Humanities, University of Adelaide, Adelaide, Australia
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9
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Nuño de la Rosa L. Computing the Extended Synthesis: Mapping the Dynamics and Conceptual Structure of the Evolvability Research Front. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:395-411. [DOI: 10.1002/jez.b.22741] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/11/2017] [Accepted: 03/24/2017] [Indexed: 11/12/2022]
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10
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Liao BK, Oates AC. Delta-Notch signalling in segmentation. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:429-447. [PMID: 27888167 PMCID: PMC5446262 DOI: 10.1016/j.asd.2016.11.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/20/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor. Here, we discuss vertebrate segmentation with particular emphasis on the role of the Notch intercellular signalling pathway. We introduce vertebrate segmentation and Notch signalling, pointing out historical milestones, then describe existing models for the Notch pathway in the synchronization of noisy neighbouring oscillators, and a new role in the modulation of gene expression wave patterns. We ask what functions Notch signalling may have in arthropod segmentation and explore the relationship between Notch-mediated lateral inhibition and synchronization. Finally, we propose open questions and technical challenges to guide future investigations into Notch signalling in segmentation.
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Affiliation(s)
- Bo-Kai Liao
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Andrew C Oates
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK; Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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11
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Doronin YK, Tiunov AV, Kalistratova EN. Changes in elemental and isotopic composition accompanying larval growth and metamorphosis of the moor frog. Russ J Dev Biol 2017. [DOI: 10.1134/s1062360417010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Grosso JR, Baldo D, Vera Candioti F. Heterochronic changes during embryonic development of neotropical foam nesting frogs (genus Leptodactylus). ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2016.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Candioti FV, Grosso J, Haad B, Pereyra MO, Bornschein MR, Borteiro C, Costa P, Kolenc F, Pie MR, Proaño B, Ron S, Stanescu F, Baldo D. Structural and Heterochronic Variations During the Early Ontogeny in Toads (Anura: Bufonidae). HERPETOLOGICAL MONOGRAPHS 2016. [DOI: 10.1655/herpmonographs-d-16-00004.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lowe JWE. Normal development and experimental embryology: Edmund Beecher Wilson and Amphioxus. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 57:44-59. [PMID: 27054569 DOI: 10.1016/j.shpsc.2016.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/26/2016] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
This paper concerns the concept of normal development, and how it is enacted in experimental procedures. To that end, I use an historical case study to assess the three ways in which normal development is and has been produced, used, and interpreted in the practice of experimental biology. I argue that each of these approaches involves different processes of abstraction, which manage biological variation differently. I then document the way in which Edmund Beecher Wilson, a key contributor to late-nineteenth century experimental embryology, approached the study of normal development and show that his work does not fit any of the three established categories in the taxonomy. On the basis of this new case study, I present a new interpretation of normal development as a methodological norm which operates as a technical condition in various experimental systems. I close by suggesting the questions, and ways of investigating developmental biology, that are opened up by this perspective.
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Affiliation(s)
- James W E Lowe
- Department of Sociology, Philosophy and Anthropology, and Egenis, The Centre for the Study of Life Sciences, University of Exeter, UK.
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Lowe JWE. Managing variation in the investigation of organismal development: problems and opportunities. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2015; 37:449-73. [PMID: 26452776 DOI: 10.1007/s40656-015-0089-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 09/14/2015] [Indexed: 05/24/2023]
Abstract
This paper aims to clarify the consequences of new scientific and philosophical approaches for the practical-theoretical framework of modern developmental biology. I highlight normal development, and the instructive-permissive distinction, as key parts of this framework which shape how variation is conceptualised and managed. Furthermore, I establish the different dimensions of biological variation: the units, temporality and mode of variation. Using the analytical frame established by this, I interpret a selection of examples as challenges to the instructive-permissive distinction. These examples include the phenomena of developmental plasticity and transdifferentiation, the role of the microbiome in development, and new methodological approaches to standardisation and the assessment of causes. Furthermore, I argue that investigations into organismal development should investigate the effects of a wider range of kinds of variation including variation in the units, modes and temporalities of development. I close by examining various possible opportunities for producing and using normal development free of the assumptions of the instructive-permissive distinction. These opportunities are afforded by recent developments, which include new ways of producing standards incorporating more natural variation and being based on function rather than structure, and the ability to produce, store, and process large quantities of data.
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Affiliation(s)
- James W E Lowe
- Department of Sociology, Philosophy and Anthropology, and Egenis, The Centre for the Study of Life Sciences, University of Exeter, Byrne House, St. German's Road, Exeter, Devon, EX4 4PJ, UK.
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16
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Diogo R, Smith CM, Ziermann JM. Evolutionary developmental pathology and anthropology: A new field linking development, comparative anatomy, human evolution, morphological variations and defects, and medicine. Dev Dyn 2015; 244:1357-74. [DOI: 10.1002/dvdy.24336] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 08/10/2015] [Accepted: 08/12/2015] [Indexed: 01/24/2023] Open
Affiliation(s)
- Rui Diogo
- Department of Anatomy; Howard University College of Medicine; Washington DC
| | | | - Janine M. Ziermann
- Department of Anatomy; Howard University College of Medicine; Washington DC
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17
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Fusco G. For a new dialogue between theoretical and empirical studies in evo-devo. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Meicenheimer RD. The plastochron index: still useful after nearly six decades. AMERICAN JOURNAL OF BOTANY 2014; 101:1821-35. [PMID: 25366849 DOI: 10.3732/ajb.1400305] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The plastochron index (PI) introduced by Erickson and Michelini in 1957 provides a solution to a long-standing problem, of how to measure time in growing plant populations, such that the occurrence of critical developmental events can be more readily detected, compared, and analyzed, than if chronologic time is used. The PI reduces the rather large variation associated with chronologic time in measuring such events by taking advantage of the growth characteristics of stem organs that repeat at regular intervals (the plastochron) and has found widespread application in botanical research. The original formulation and derivation of the PI and associated leaf plastochron index (LPI) is reviewed. Additional formulations that have been developed to overcome some of the limitations of the original PI formulation are examined. Major advancements that have been achieved in understanding the physiology, growth, and development of agriculturally important and current model plant species are reviewed to illustrate how various researchers have used the PI in such studies. Potential uses to which the PI and LPI might be applied in emerging frontiers of plant science are suggested. A searchable bibliography of most all the primary research studies that cite the original PI article is provided.
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Minelli A, Baedke J. Model organisms in evo-devo: promises and pitfalls of the comparative approach. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2014; 36:42-59. [PMID: 25515263 DOI: 10.1007/s40656-014-0004-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/16/2014] [Indexed: 06/04/2023]
Abstract
Evolutionary developmental biology (evo-devo) is a rapidly growing discipline whose ambition is to address questions that are of relevance to both evolutionary biology and developmental biology. This field has been increasingly progressing as a new and independent comparative science. However, we argue that evo-devo's comparative approach is challenged by several metaphysical, methodological and socio-disciplinary issues related to the foundation of heuristic functions of model organisms and the possible criteria to be adopted for their selection. In addition, new tools have to be developed to deal with newly chosen model organisms. Therefore, we present a modelling framework suitable to integrate data on individual variation into evo-devo studies on new model organisms and thus to compensate for current idealization practices deliberately suppressing variation.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35131, Padova, Italy,
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21
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Affiliation(s)
- Jessica A. Bolker
- Department of Biological Sciences; University of New Hampshire; Durham NH 03824 USA
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22
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Plutynski A. Cancer and the goals of integration. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:466-76. [PMID: 23582848 DOI: 10.1016/j.shpsc.2013.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cancer is not one, but many diseases, and each is a product of a variety of causes acting (and interacting) at distinct temporal and spatial scales, or "levels" in the biological hierarchy. In part because of this diversity of cancer types and causes, there has been a diversity of models, hypotheses, and explanations of carcinogenesis. However, there is one model of carcinogenesis that seems to have survived the diversification of cancer types: the multi-stage model of carcinogenesis. This paper examines the history of the multistage theory, and uses the theory as a case study in the limits and goals of unification as a theoretical virtue, comparing and contrasting it with "integrative" research.
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Affiliation(s)
- Anya Plutynski
- University of Utah, Department of Philosophy, 215 S. Central Campus Dr., 402 CTIHB, Salt Lake City, UT 84112, United States.
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23
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Baedke J. The epigenetic landscape in the course of time: Conrad Hal Waddington's methodological impact on the life sciences. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:756-773. [PMID: 23932231 DOI: 10.1016/j.shpsc.2013.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/27/2013] [Accepted: 06/14/2013] [Indexed: 06/02/2023]
Abstract
It seems that the reception of Conrad Hal Waddington's work never really gathered speed in mainstream biology. This paper, offering a transdisciplinary survey of approaches using his epigenetic landscape images, argues that (i) Waddington's legacy is much broader than is usually recognized--it is widespread across the life sciences (e.g. stem cell biology, developmental psychology and cultural anthropology). In addition, I will show that (ii) there exist as yet unrecognized heuristic roles, especially in model building and theory formation, which Waddington's images play within his work. These different methodological facets envisioned by Waddington are used as a natural framework to analyze and classify the manners of usage of epigenetic landscape images in post-Waddingtonian 'landscape approaches'. This evaluation of Waddington's pictorial legacy reveals that there are highly diverse lines of traditions in the life sciences, which are deeply rooted in Waddington's methodological work.
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Affiliation(s)
- Jan Baedke
- Department of Philosophy I, Ruhr University Bochum, Universitätsstr. 150, D-44801 Bochum, Germany.
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Andrews RM, Brandley MC, Greene VW. Developmental sequences of squamate reptiles are taxon specific. Evol Dev 2013; 15:326-43. [DOI: 10.1111/ede.12042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robin M. Andrews
- Department of Biological Sciences; Virginia Polytechnic Institute and State University; Blacksburg VA 24061 USA
| | - Matthew C. Brandley
- School of Biological Sciences (A08); University of Sydney; Sydney NSW 2006 Australia
| | - Virginia W. Greene
- Department of Biological Sciences; Virginia Polytechnic Institute and State University; Blacksburg VA 24061 USA
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Wang Z, Pang X, Wu W, Wang J, Wang Z, Wu R. MODELING PHENOTYPIC PLASTICITY IN GROWTH TRAJECTORIES: A STATISTICAL FRAMEWORK. Evolution 2013; 68:81-91. [DOI: 10.1111/evo.12263] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 08/10/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Zhong Wang
- Center for Computational Biology; Beijing Forestry University; Beijing 100083 China
| | - Xiaoming Pang
- Center for Computational Biology; Beijing Forestry University; Beijing 100083 China
| | - Weimiao Wu
- Center for Computational Biology; Beijing Forestry University; Beijing 100083 China
| | - Jianxin Wang
- Center for Computational Biology; Beijing Forestry University; Beijing 100083 China
| | - Zuoheng Wang
- Division of Biostatistics; Yale University; New Haven Connecticut 06510
| | - Rongling Wu
- Center for Computational Biology; Beijing Forestry University; Beijing 100083 China
- Center for Statistical Genetics; Pennsylvania State University; Hershey Pennsylvania 17033
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Minelli A, Fusco G. Developmental plasticity and the evolution of animal complex life cycles. Philos Trans R Soc Lond B Biol Sci 2010; 365:631-40. [PMID: 20083638 DOI: 10.1098/rstb.2009.0268] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Metazoan life cycles can be complex in different ways. A number of diverse phenotypes and reproductive events can sequentially occur along the cycle, and at certain stages a variety of developmental and reproductive options can be available to the animal, the choice among which depends on a combination of organismal and environmental conditions. We hypothesize that a diversity of phenotypes arranged in developmental sequence throughout an animal's life cycle may have evolved by genetic assimilation of alternative phenotypes originally triggered by environmental cues. This is supported by similarities between the developmental mechanisms mediating phenotype change and alternative phenotype determination during ontogeny and the common ecological condition that favour both forms of phenotypic variation. The comparison of transcription profiles from different developmental stages throughout a complex life cycle with those from alternative phenotypes in closely related polyphenic animals is expected to offer critical evidence upon which to evaluate our hypothesis.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131 Padova, Italy.
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Fusco G, Minelli A. Phenotypic plasticity in development and evolution: facts and concepts. Introduction. Philos Trans R Soc Lond B Biol Sci 2010; 365:547-56. [PMID: 20083631 PMCID: PMC2817147 DOI: 10.1098/rstb.2009.0267] [Citation(s) in RCA: 249] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This theme issue pursues an exploration of the potential of taking into account the environmental sensitivity of development to explaining the evolution of metazoan life cycles, with special focus on complex life cycles and the role of developmental plasticity. The evolution of switches between alternative phenotypes as a response to different environmental cues and the evolution of the control of the temporal expression of alternative phenotypes within an organism's life cycle are here treated together as different dimensions of the complex relationships between genotype and phenotype, fostering the emergence of a more general and comprehensive picture of phenotypic evolution through a quite diverse sample of case studies. This introductory article reviews fundamental facts and concepts about phenotypic plasticity, adopting the most authoritative terminology in use in the current literature. The main topics are types and components of phenotypic variation, the evolution of organismal traits through plasticity, the origin and evolution of phenotypic plasticity and its adaptive value.
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Affiliation(s)
- Giuseppe Fusco
- Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131 Padova, Italy.
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