Developmental Systems Theory: What Does It Explain, and How Does It Explain It?
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Downloaded to Major Neurons and Is Thereby Capable of Communicating Its State to the Outside World’ (2006, 396F.)
1 Review Article for Progress in Biophysics and Molecular Biology, Volume 131, December, 2017, Special Issue: Integral Biomathics: “The Necessary Conjunction of the Western and Eastern Thought Traditions for Exploring the Nature of Mind and Life" (Guest Editors: Plamen L. Simeonov, Arran Gare, Koichiro Matsuno and Abir U. Igamberdiev, pp.61-91. https://doi.org/10.1016/j.pbiomolbio.2017.08.010 Chreods, Homeorhesis and Biofields: FINDING THE RIGHT PATH FOR SCIENCE THROUGH DAOISM1 Arran Gare Abstract: C.H. Waddington’s concepts of ‘chreods’ (canalized paths of development) and ‘homeorhesis’ (the tendency to return to a path), each associated with ‘morphogenetic fields’, were conceived by him as a contribution to complexity theory. Subsequent developments in complexity theory have largely ignored Waddington’s work and efforts to advance it. Waddington explained the development of the concept of chreod as the influence on his work of Alfred North Whitehead’s process philosophy, notably, the concept of concrescence as a self-causing process. Processes were recognized as having their own dynamics, rather than being explicable through their components or external agents. Whitehead recognized the tendency to think only in terms of such ‘substances’ as a bias of European thought, claiming in his own philosophy ‘to approximate more to some strains of Indian, or Chinese, thought, than to western Asiatic, or European, thought.’ Significantly, the theoretical biologist who comes closest to advancing Waddington’s research program, also marginalized, -
Getting Ab Ovo Developmental Processes Intelligible Using
and S etic ys th te n m y s S B t i n o Current Synthetic and Systems e l o r r g u y C Biology Spriet, et al., Curr Synthetic Sys Biol 2015, 3:1 ISSN: 2332-0737 DOI: 10.4172/2332-0737.1000118 Review Article Open Access Getting ab ovo Developmental Processes Intelligible Using Metaphors, Microscopy and Paradigms Spriet C1, Cailliau K2 and Bodart JF2* 1Université de Lille, Sciences et Technologies, TISBio, UMR 8576, FR3688 CNRS, Villeneuve d´Ascq, France 2Université de Lille, Sciences et Technologies, Régulation des Signaux de Division Team, UMR 8576 CNRS, Villeneuve d´Ascq, France *Corresponding author: Jean-François Bodart, Université de Lille, Sciences et Technologies, TISBio, UMR 8576, FR3688 CNRS, Villeneuve d´Ascq, France, Tel: 33320436867; E-mail: [email protected] Rec Date: February 22, 2015, Acc Date: March 13, 2015, Pub Date: March 16, 2015 Copyright: © 2015 Spriet C, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Developmental biology is a field fertile in metaphors and paradigms, and offers a playground rich of possibilities for various technologies. The underlying mechanisms for developmental biology processes have challenged science and imagination for centuries. Herein we propose a non-exhaustive incursion into three major concepts in the field: self-organization, pattern organization and mechanical forces. Observations and views issued from synthetic and systems biology are discussed to move towards a more comprehensive and accurate "landscape" of the very early steps of embryogenesis. -
Released March 2021
Released March 2021 EVALUATION REPORT FOR THE NATIONAL CANCER INSTITUTE CANCER SYSTEMS BIOLOGY CONSORTIUM Hannah Dueck, Ph.D. Shannon Hughes, Ph.D. Dan Gallahan, Ph.D. NCI Division of Cancer Biology June 15, 2020 (Executive summary and Appendix 5 – Additional Data added August 2020) 1 Released March 2021 Table of Contents Executive Summary ........................................................................................................................... 3 Goal 1: Advance understanding of mechanisms that underlie fundamental processes in cancer .................................... 3 Goal 2: Support the broad application of systems biology approaches in cancer research .............................................. 3 Goal 3: Support the growth of a strong and stable research community in cancer systems biology ................................ 4 Introduction ...................................................................................................................................... 5 Evaluation Purpose and Charge to the External Panel .................................................................................5 Introduction to the CSBC ............................................................................................................................6 Goal 1: Advance the understanding of mechanisms that underlie fundamental processes in cancer ... 7 CSBC scientific advances .............................................................................................................................8 Dissemination -
Associating Cellular Epigenetic Models with Human Phenotypes
PERSPECTIVES EPIGENETICS loci changing DNA methylation consistently OPINION in multiple individuals but also that these changes select for specific genes within Associating cellular epigenetic the genome that may have importance for disease risk or aetiology. Despite what sound like positive results models with human phenotypes of these EWAS approaches, we7,8 and others9,10 have noted that this typical EWAS Tuuli Lappalainen and John M. Greally approach suffers from multiple problems. Abstract | Epigenetic association studies have been carried out to test the These problems can be grouped into two categories: the robust identification of hypothesis that environmental perturbations trigger cellular reprogramming, with molecular (usually DNA methylation) downstream effects on cellular function and phenotypes. There have now been differences associated with the phenotype numerous studies of the potential molecular mediators of epigenetic changes by studied, and the interpretability of these epigenome-wide association studies (EWAS). However, a challenge for the field is results. The robustness issue is the typical the interpretation of the results obtained. We describe a second-generation EWAS focus of reviews addressing the problems of designing and carrying out EWAS7,9,10 approach, which focuses on the possible cellular models of epigenetic and usually includes discussion of cohort perturbations, studied by rigorous analysis and interpretation of genomic data. selection, statistical approaches used when Thus refocused, epigenetics research aligns with the field of functional genomics dealing with high‑dimensional data and to provide insights into environmental and genetic influences on phenotypic caution about the technical artefacts that 11–13 variation in humans. can occur in all genome‑wide studies . -
Small Intestinal Tuft Cell Specification and Behavior in Homeostasis and Intestinal Inflammatory Disease
SMALL INTESTINAL TUFT CELL SPECIFICATION AND BEHAVIOR IN HOMEOSTASIS AND INTESTINAL INFLAMMATORY DISEASE By Amrita Banerjee Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University In partial fulfillment of the requirements For the degree of DOCTOR OF PHILOSOPHY in Cell and Developmental Biology May 10, 2019 Nashville, TN Approved: Guoqiang Gu, Ph.D. Christopher Wright, D.Phil. Robert J. Coffey, M.D. Christopher Williams, M.D., Ph.D. Ken S. Lau, Ph.D. For my family, without whose support this work would not have been possible. ii ACKNOWLEDGEMENTS I am deeply indebted to my mentor Dr. Ken Lau for his support and guidance during my five years in his lab. He has afforded me every opportunity to develop my research, writing, and computational skills. He encourages me to think deeply about my experiments without forgetting about the big picture. My progress in all aspects of my training are due to his patience and tutelage. Thank you for giving me the freedom to explore my intellectual curiosity as well as the support to ensure that I did not go astray. I would like to thank my committee members: my chair Dr. Guoqiang Gu, my co-chair Dr. Chris Wright, Dr. Robert Coffey, and Dr. Christopher Williams for their many years of guidance and encouragement. From my first class with Dr. Gu, he has always expressed a willingness to offer his mentorship and assistance in making me a better scientist. I am grateful to Dr. Wright for acting as the co-chair of my committee and providing his support to ensure that everything remained on track. -
Embryology and the Evolutionary Synthesis: Waddington, Development and Genetics
Embryology and the Evolutionary Synthesis: Waddington, Development and Genetics. by Paul Dominic Lewin. Submitted in accordance with the requirements for the degree of Doctor of Philosophy. University of Leeds Department of Philosophy. September, 1998. The candidate confirms that the work submitted is his own and that appropriate credit has been given where reference has been made to the work of others. -11- Abstract. The role of embryology, genetics and morphology witllln mid twentieth century evolution theory, is discussed in the context of the growth to dominance of natural selection as the orthodox mechanism of adaptive evolution. The unification of neo Mendelian heredity and neo-Darwinian selection theory, is descnbed as the core of modem synthetic neo-Darwinism as it emerged in 1930s mathematical population genetics. As selectionism strengthened witllln synthetic neo-Darwinism, embryological development was excluded from its traditional causal role in adaptive evolution witllln the "old synthesis" of Haeckelian recapitulation and neo-Lamarckian inheritance. A two-tier embryology was created, as embryology was understood to deal separately with the experimental analysis of ontogenetic development, and the historical descriptive analysis of phylogenetic lineages. Neither tier informed the other, or played any direct causal role in the mechanism of the creation of adaptive evolutionary novelty. That adaptive evolutionary mechanism was entirely the preside of natural selection. However, as the selectionist synthesis hardened in the 1940s, late nineteenth century Darwinists' concerns over the hereditary fixation of highly specific adaptive somatic modifications resurfaced. Consequently, the strategic defence of the synthetic theory against any resurgence of neo-Lamarckian heredity, involved an appeal to the principles of modem synthesis developmentalism; namely, the developmentalist syntheses of Waddington and Schmalhausen.