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From Developmental Constraint to Evolvability
From Developmental Constraint to Evolvability How Concepts Figure in Explanation and Disciplinary Identity Ingo Brigandt Department of Philosophy, University of Alberta 2-40 Assiniboia Hall, Edmonton, AB T6G2E7, Canada [email protected] Abstract The concept of developmental constraint was at the heart of develop- mental approaches to evolution of the 1980s. While this idea was widely used to criticize neo-Darwinian evolutionary theory, critique does not yield an alternative framework that offers evolutionary explanations. In current Evo-devo the concept of constraint is of minor importance, whereas notions as evolvability are at the center of attention. The latter clearly defines an explanatory agenda for evolution- ary research, so that one could view the historical shift from ‘developmental con- straint’ towards ‘evolvability’ as the move from a concept that is a mere tool of criticism to a concept that establishes a positive explanatory project. However, by taking a look at how the concept of constraint was employed in the 1980s, I argue that developmental constraint was not just seen as restricting possibilities (‘con- straining’), but also as facilitating morphological change in several ways. Ac- counting for macroevolutionary transformation and the origin of novel form was an aim of these developmental approaches to evolution. Thus, the concept of de- velopmental constraint was part of a positive explanatory agenda long before the advent of Evo-devo as a genuine scientific discipline. In the 1980s, despite the lack of a clear disciplinary identity, this concept coordinated research among pale- ontologists, morphologists, and developmentally inclined evolutionary biologists. I discuss the different functions that scientific concepts can have, highlighting that instead of classifying or explaining natural phenomena, concepts such as ‘devel- opmental constraint’ and ‘evolvability’ are more important in setting explanatory agendas so as to provide intellectual coherence to scientific approaches. -
Dr. Stuart Newman Declaration
1 SWEENEY, DAVIDIAN, & GREENE LLP James F. Sweeney (SBN 124527) 2 Ben Davidian (SBN 94965) Stephen J. Greene, Jr. (SBN 178098) 3 Stephen R. McCutcheon, Jr. (SBN 191749) 8001 Folsom Boulevard, Ste. 101 4 Sacramento, CA 95826 Telephone: (916) 388-5170 5 Facsimile: (916) 388-0357 6 Attorneys for Real Parties In Interest 7 SUPERIOR COURT OF THE STATE OF CALIFORNIA 8 COUNTY OF SACRAMENTO 9 UNLIMITED JURISDICTION 10 PAUL BERG, Ph.D; ROBERT N. KLEIN; and ) Case No. 04CS01015 11 LARRY GOLDSTEIN ) 8001 ) DECLARATION OF DR. STUART A. S S ACRAMENTO WEENEY 12 ) NEWMAN, PH.D. IN OPPOSITION TO Petitioners, F ) PETITION FOR WRIT OF MANDATE OLSOM A 13 ) AND ALTERNATIVE WRIT OF TTORNEYS AT v. , D ) MANDATE/ORDER TO SHOW CAUSE AVIDIAN B 14 ) , OULEVARD KEVIN SHELLEY, Secretary of State of C ) Hearing Date: August 4, 2004 ALIFORNIA 15 California, ) Time: 1:30 p.m. & ) Dept.: 11 G 16 ) Judge: Hon. Gail Ohanesian L Respondent. AW REENE , ) S UITE 17 ) 95826 GEOFF BRANDT, State Printer; TOM LLP MCCLINTOCK; H. REX GREENE; JOHN M. ) 101 18 ) MORLACH; JUDY NORSIGIAN; FRANCINE ) 19 COETAUX; TINA STEVENS; DOES I through ) X, inclusive; ) 20 ) Real Parties in Interest ) 21 ) 22 23 I, STUART A. NEWMAN, depose, declare, and state as follows: 24 1. I am a member of the faculty in the Department of Cell Biology and Anatomy at 25 the New York Medical College in Valhalla, New York. I am not party to the instant proceeding. 26 If called as a witness, I could competently testify to the following from own personal knowledge. -
The Evolutionary Origin of Digit Patterning
Touro Scholar NYMC Faculty Publications Faculty 11-1-2017 The Evolutionary Origin of Digit Patterning T Stewart Ramray Bhat Stuart Newman New York Medical College Follow this and additional works at: https://touroscholar.touro.edu/nymc_fac_pubs Part of the Developmental Biology Commons, and the Medicine and Health Sciences Commons Recommended Citation Stewart, T., Bhat, R., & Newman, S. (2017). The Evolutionary Origin of Digit Patterning. EvoDevo, 8, 21. https://doi.org/10.1186/s13227-017-0084-8 This Article is brought to you for free and open access by the Faculty at Touro Scholar. It has been accepted for inclusion in NYMC Faculty Publications by an authorized administrator of Touro Scholar. For more information, please contact [email protected]. Stewart et al. EvoDevo (2017) 8:21 DOI 10.1186/s13227-017-0084-8 EvoDevo REVIEW Open Access The evolutionary origin of digit patterning Thomas A. Stewart1,2,5*, Ramray Bhat3 and Stuart A. Newman4 Abstract The evolution of tetrapod limbs from paired fns has long been of interest to both evolutionary and developmental biologists. Several recent investigative tracks have converged to restructure hypotheses in this area. First, there is now general agreement that the limb skeleton is patterned by one or more Turing-type reaction–difusion, or reaction–dif- fusion–adhesion, mechanism that involves the dynamical breaking of spatial symmetry. Second, experimental studies in fnned vertebrates, such as catshark and zebrafsh, have disclosed unexpected correspondence between the devel- opment of digits and the development of both the endoskeleton and the dermal skeleton of fns. Finally, detailed mathematical models in conjunction with analyses of the evolution of putative Turing system components have permitted formulation of scenarios for the stepwise evolutionary origin of patterning networks in the tetrapod limb. -
Evolution & Development
DOI: 10.1111/ede.12315 RESEARCH Developmental structuring of phenotypic variation: A case study with a cellular automata model of ontogeny Wim Hordijk1 | Lee Altenberg2 1Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Abstract Austria Developmental mechanisms not only produce an organismal phenotype, but 2University of Hawai‘iatMānoa, they also structure the way genetic variation maps to phenotypic variation. ‘ Honolulu, Hawai i Here, we revisit a computational model for the evolution of ontogeny based on Correspondence cellular automata, in which evolution regularly discovered two alternative Wim Hordijk, Konrad Lorenz Institute for mechanisms for achieving a selected phenotype, one showing high modularity, Evolution and Cognition Research, the other showing morphological integration. We measure a primary variational Martinstrasse 12, 3400 Klosterneuburg, Austria. property of the systems, their distribution of fitness effects of mutation. We find Email: [email protected] that the modular ontogeny shows the evolution of mutational robustness and ontogenic simplification, while the integrated ontogeny does not. We discuss the wider use of this methodology on other computational models of development as well as real organisms. 1 | INTRODUCTION summarize, “almost anything can be changed if it shows phenotypic variation” and “combinations of traits, even The idea that phenotypic variation could ever be those unfavorably correlated, can be changed”). Once the “unbiased” is a historical artifact coming from two main premises of this “pan‐variationism” are accepted, pans- sources: First were the early characterizations of quanti- electionism is the natural conclusion—in other words, if tative genetic variation for single traits or small numbers variation is diffusing in every phenotypic direction, the of traits. -
Evolutionary Morphology, Innovation, and the Synthesis of Evolutionary and Developmental Biology
Biology and Philosophy 18: 309–345, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. Evolutionary Morphology, Innovation, and the Synthesis of Evolutionary and Developmental Biology ALAN C. LOVE Department of History and Philosophy of Science University of Pittsburgh CL 1017 Pittsburgh, PA 15260 U.S.A. E-mail: [email protected] Abstract. One foundational question in contemporary biology is how to ‘rejoin’ evolution and development. The emerging research program (evolutionary developmental biology or ‘evo- devo’) requires a meshing of disciplines, concepts, and explanations that have been developed largely in independence over the past century. In the attempt to comprehend the present separation between evolution and development much attention has been paid to the split between genetics and embryology in the early part of the 20th century with its codification in the exclusion of embryology from the Modern Synthesis. This encourages a characterization of evolutionary developmental biology as the marriage of evolutionary theory and embryology via developmental genetics. But there remains a largely untold story about the significance of morphology and comparative anatomy (also minimized in the Modern Synthesis). Functional and evolutionary morphology are critical for understanding the development of a concept central to evolutionary developmental biology, evolutionary innovation. Highlighting the discipline of morphology and the concepts of innovation and novelty provides an alternative way of conceptualizing the ‘evo’ and the ‘devo’ to be synthesized. Key words: comparative anatomy, developmental genetics, embryology, evolutionary developmental biology, innovation, morphology, novelty, synthesis, typology 1. Introduction and methodology ... problems concerned with the orderly development of the individual are unrelated to those of the evolution of organisms through time .. -
Physical Determinants in the Evolution of Development
Postprint, July 5, 2012 Physical Determinants in the Evolution of Development Stuart A. Newman Department of Cell Biology and Anatomy New York Medical College, Valhalla, NY 10595 (914) 594-4048 [email protected] One sentence summary: Physical processes mobilized by ancient genes in novel multicellular contexts established morphological templates for subsequent animal evolution. This Week in Science summary: Most animal body plans and morphological motifs arose between 500 and 700 million years ago, during several relatively brief periods of innovation. The genes of the conserved “interaction toolkit,” whose products mediate embryonic morphogenesis and pattern formation, were largely present in the unicellular ancestors of the animals; the next half billion years of evolution failed to generate substantial additional morphological novelty. Stuart Newman reconciles these observations by proposing that physical processes characteristic of chemically and mechanically active soft matter, newly mobilized by the interaction toolkit molecules when they came to function in a multicellular context, originated the motifs of animal form and (with the associated genes), have been the underlying basis of their propagation over the course of evolution. Many of the classic phenomena of early animal development – the formation and folding of distinct germ layers during gastrulation, the convergence and extension movements leading to embryo elongation, the formation of somites (paired blocks of tissue) along the main axis of vertebrate embryos, the generation of the vertebrate limb skeleton, the arrangement of feathers and hairs – have been productively analyzed by mathematical and computational models which treat morphological motifs as expected outcomes of physical process that are generic, i.e., pertaining as well to certain nonliving chemically and mechanically active soft materials (1-6). -
Macroevolutionary Freezing and the Janusian Nature of Evolvability: Is the Evolution (Of Profound Biological Novelty) Going to End?
Biosemiotics https://doi.org/10.1007/s12304-018-9326-y ORIGINAL PAPER Macroevolutionary Freezing and the Janusian Nature of Evolvability: Is the Evolution (of Profound Biological Novelty) Going to End? Jan Toman1 & Jaroslav Flegr1 Received: 30 September 2017 /Accepted: 9 May 2018 # Springer Science+Business Media B.V., part of Springer Nature 2018 Abstract In a macroevolutionary timescale, evolvability itself evolves. Lineages are sorted based on their ability to generate adaptive novelties, which leads to the optimi- zation of their genotype-phenotype map. The system of translation of genetic or epigenetic changes to the phenotype may reach significant horizontal and vertical complexity, and may even exhibit certain aspects of learning behaviour. This continu- ously evolving semiotic system probably enables the origin of complex yet functional and internally compatible adaptations. However, it also has a second, Bdarker^,side.As was pointed out by several authors, the same process gradually reduces the probability of the origination of significant evolutionary novelties. In a similar way to the evolution of societies, teachings, or languages, in which the growing number of internal linkages gradually solidifies their overall structure and the structure or interpretation of their constitutive elements, the evolutionary potential of lineages decreases during biological evolution. Possible adaptations become limited to small Bperipheral^ modifications. According to the Frozen Evolution theory, some of the proximate causes of this Bmacroevolutionary freezing^ are more pronounced or present exclusively in sexual lineages. Sorting based on the highest (remaining) evolvability probably leads to the establishment of certain structural features of complex organisms, e.g. the modular character of their development and morphology. -
Insurgent Science Series
Insurgent Science Series Highlighting challenging developments in the conception of nature and science Friday, January 16 th at 1:30 in 68-181 A Pattern Language for Animal Form Stuart Newman Animal body plans and organs emerged during several bursts of concentrated evolutionary change between 500 and 600 million years ago. Many of the key regulatory genes for animal development existed in single-celled ancestors, took on new functions in the multicellular state, and remained relatively unchanged during the explosive diversification of form. This talk will present a theory for the origination of multicellular form in which the major driving force consists of the physical laws inherent to organisms’ mesoscopic materials rather than, as the standard conception of biological evolution holds, genetic change driven by chance. Dr. Newman is professor of cell biology and anatomy at New York Medical College. He specializes in cellular and molecular mechanisms of vertebrate limb development, physical mechanisms of morphogenesis, and evolution of developmental mechanisms. Wednesday, January 28 th at 1:30pm in 4-231 A Bigger Physics Michael Augros As Erwin Schrödinger wrote in 1951, “The isolated knowledge obtained by a group of specialists in a narrow field has in itself no value whatsoever, but only in its synthesis with all the rest of knowledge”. What could it mean to ‘synthesize’ all of natural science? To what extent is such a thing possible? Why is it desirable? Whose job is it? And how would it relate to mathematics? Come join Dr. Augros to explore the possibility of a general theory of nature. Dr. Augros is a philosopher of science who teaches at the Center for Higher Studies in Thornwood, New York. -
Stuart A. Newman New York Medical College International Centre For
Physico-genetic processes of animal development and evolution Stuart A. Newman New York Medical College International Centre for Theoretical Studies Bangalore Program on “Living Matter” April 16, 2018 The Ediacaran and Cambrian Explosions ~570 Mya ~1 Bya ~4 Bya http://geologycafe.com/ The Holozoans Ruiz-Trillo et al. TIG 2007 Monosiga Capsaspora Mesomycetozoea One or more of the extant holozoans and by inference, the unicellular ancestors of the metazoans, contain(ed) genes specifying cadherins, C-type lectins, Notch and Wnt pathway components, Hedgehog and other members of the metazoan developmental-genetic toolkit which eventually came to mediate cell-cell interactions (a.k.a. the “interaction toolkit”). King et al., Nature 451:783; 2008 Shalchian-Tabrizi et al., PLoS ONE 3:e2098; 2008 Sebé-Pedrós et al. eLife 2: e01287; 2013 Origination of highly disparate animal body plans occurred with a pre-existing genetic toolkit and was compressed in time. What additional causal agency was involved? Toolkit-based functionalities in unicellular ancestors of the metazoans Innovation of classical cadherins in the metazoans permitted cells to move autonomously without disrupting the cohesion of the cell mass This created “liquid tissues”: a category of biogeneric matter “Generic” mechanisms of development Form- and pattern-generating processes common to living and nonliving (mesoscale, viscoelastic, excitable) systems “Biogeneric” materials and mechanisms of development Multicellular materials in which cellular systems behave similarly to certain nonliving materials, but utilizing evolved, cell-based response functions Biogeneric materials exhibit forms and patterns resembling those characteristic of generic processes. Some novel genes were associated with emergence of novel biogeneric materials Protocadherins Cell clusters Classical cadherins, Wnt “Liquid tissues” Peroxidasin Vang/Stbm (PCP) (basement “Liquid crystalline” tissues membrane) Planar tissues Galectins, fibronectin, EMT, mesenchyme tenascin SAN Phil. -
The Newman Application and the Uspto's Unnecessary Response Patentability of Humans and Human Embryos
Copyright © 2006, Chicago-Kent Journal of Intellectual Property THE NEWMAN APPLICATION AND THE USPTO'S UNNECESSARY RESPONSE PATENTABILITY OF HUMANS AND HUMAN EMBRYOS Sefin M. Coughlin* Background Inventor Stuart Newman filed an application drawn to human/animal chimeric organisms, embryos and methods of making and using the same.1 Newman's application was not necessarily filed to acquire a patent on this invention, but to serve as a de facto petition to the U.S. Patent and Trademark Office (USPTO) to clarify the Office's stance on the patentability of this and similar controversial inventions.2 Newman opposes patenting such inventions, because they could lead to the unethical use and treatment of human animal chimeras, e.g. in drug testing.3 The USPTO, while refusing to give Newman an advisory opinion, and despite having plenty of other more mundane reasons to reject the Newman application4 , accommodated him by rejecting his claims for not being drawn to a statutorily permitted subject matter, i.e. stating that 5 claims "embracing" humans and human embryos are not patentable. The primary basis of this rejection was an interpretation of Congress' intent regarding patenting humans, 6 which was later confirmed by the addition of a provision to the Consolidated Appropriations Act of 2004, forbidding the patenting of "human organisms".7 While the rationale for this rejection is plausible, it and the legislation are unnecessary and problematic. There is no need to specifically prevent the patenting of a human being or a human embryo. First, human beings and embryos are unpatentable subject matter in any case because they are not novel or made by man, as required for patentability.8 Second, there is currently no commercial reason to patent a genetically modified near-human. -
Canalization and Robustness - Evolutionary Biology - Oxford Bibliog
Canalization and Robustness - Evolutionary Biology - Oxford Bibliog... http://www.oxfordbibliographies.com/view/document/obo-978019994... Canalization and Robustness Thomas Flatt, Günter Wagner LAST MODIFIED: 27 JUNE 2018 DOI: 10.1093/OBO/9780199941728-0109 Introduction Canalization describes the phenomenon whereby particular genotypes exhibit reduced phenotypic sensitivity or variation (i.e., increased robustness) in response to mutations and/or to environmental changes relative to other genotypes. Canalization is a variational property of genotypes: it implies a reduced potential or propensity of the phenotype, produced by this genotype, to vary in response to genetic or environmental change. The terms “canalization,” “robustness” and “buffering” are typically used interchangeably; today, “robustness” is perhaps more commonly used than “canalization.” The concept of canalization was first introduced by Conrad Hal Waddington in the 1940s; around the same time, Ivan Ivanovich Schmalhausen came up with essentially the same concept (see Books and Early History of the Canalization Concept). Their main conjecture was the existence of a special kind of stabilizing selection, so-called canalizing selection, which favors genotypes that deviate least from the trait optimum (e.g., the fitness optimum), by selecting for genetic mechanisms that suppress phenotypic variation caused by mutations (genetic canalization) or by environmental perturbations or changes (environmental canalization). The concept of canalization is closely related to the phenomenon of genetic assimilation, that is, the idea that previously hidden, cryptic genetic variants can become phenotypically expressed following an environmental or genetic perturbation and increase in frequency by selection. General Overviews Early experimental evidence for the existence of canalization and genetic assimilation is reviewed in depth by Scharloo 1991, the first comprehensive review paper in the field. -
The International Journal of Developmental Biology
Int. J. Dev. Biol. 53: 663-671 (2009) DEVELOPMENTALTHE INTERNATIONAL JOURNAL OF doi: 10.1387/ijdb.072553cc BIOLOGY www.intjdevbiol.com Limb pattern, physical mechanisms and morphological evolution - an interview with Stuart A. Newman CHENG MING CHUONG* Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA ABSTRACT Stuart A. Newman grew up in New York City. He received a Bachelor of Arts from Columbia University and obtained a Ph.D. in chemical physics from the University of Chicago in 1970. He did post-doctoral studies in several institutions and disciplines with a focus on theoretical and developmental biology. He had a rich experience interacting with people like Stuart Kauffman, Arthur Winfree, Brian Goodwin, and John W. Saunders, Jr. He was also exposed to many interesting experimental models of development. These early experiences fostered his interest in biological pattern formation. He joined the State University of New York at Albany as a junior faculty member when Saunders was still there. With his physical science background, Newman’s approach to limb bud patterning was refreshing. In his major Science paper in 1979, he and H.L. Frisch proposed a model showing how reaction-diffusion can produce chemical standing waves to set up limb skeletal patterns. He then used limb bud micromass cultures for further develop- ment and testing of the model. Extending earlier ideas, he developed a comprehensive framework for the role of physical mechanisms (diffusion, differential adhesion, oscillation, dynamical multistability, reaction diffusion, mechano-chemical coupling, etc.) in morphogenesis. He also applied these mechanisms to understand the origin of multicellularity and evolution of novel body plans.