Insurgent Science Series

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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. He has written on Euclid’s fifth postulate and the natural science that claims physics as a subset. Sponsored by the Experimental Study Group, and Hindu, Baptist (American), Methodist, Presbyterian and United Church of Christ Chaplaincies, in conjunction with the Institute for the Study of Nature. Part of MIT’s Independent Activities Period. All are welcome! www.isnature.org .

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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.
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Activities of The
activities of the Inhalt Contents Seite Page 2 1 Jahresrückblick und Struktur des KLI Review 2010 and Structure of the KLI 6 2 Projekte Projects 2.1 Bewerbungen / Applications 2.2 Junior Gastwissenschaftler / Junior Visiting Fellows 2.3 Postdoktoranden-Stipendien / Postdoctoral Fellowships 2.4 Senior Stipendiaten / Senior Fellows 2.5 Austausch-Stipendium / Exchange Felllowship 2.6 Gastwissenschaftler / Visiting Scientists 32 3 Wissenschaftliche Veranstaltungen Meetings and Lectures 3.1 Altenberg Workshops 3.2 Symposia 3.3 Rupert Riedl Lecture 3.4 Mittagsdiskussionen / Brown Bag Discussions 50 4 Publikationen Publications 4.1 Vienna Series in Theoretical Biology 4.2 Sammelbände und Bücher / Edited Volumes and Books 4.3 Fachartikel / Professional Papers 4.4 Artikel im Druck / Papers in Press 4.5 Zeitschrift Biological Theory / Journal 4.6 Vorträge und Kongressbeiträge / Scientific Presentations 70 5 Weitere Aktivitäten Further Activities 5.1 EASPLS Graduate Meeting 5.2 Zusätzliche Förderungen Jahresrückblick und Struktur des KLI Review 2010 and Structure of the KLI 61 Through its in-house activities and freshly conceived workshops and seminar series the KLI has uniquely provided a context for rethinking major questions in developmental, cognitive, and evolutionary biology. Stuart Newman, New York Medical College Jahresrückblick und Struktur des KLI Review 2010 and Structure of the KLI 1.1 Jahresrückblick 2010 The Year in Review Der weltweit zu beobachtende Wandel der akademischen Institutionen hat in 3 den letzten Jahren auch Österreich voll erfasst. Das Gespenst der „Nützlichkeit“ geht um. Teils erzwungen, teils in vorauseilendem bürokratischen Eifer bemessen die Universitäten ihre eigenen Leistungen immer mehr nach ökonomistischen Managementkriterien. Die eigentlichen Aufgaben der akademischen Einrichtun- gen – Erkennen, Verstehen, Analyse, Wissen, Kritik, Diskurs, Bildung – die funda- mental auf intellektueller Unabhängigkeit beruhen, werden unter dem Gewicht sogenannter Effizienzkriterien zunehmend zurückgedrängt.
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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.
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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).
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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.
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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.
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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.
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Origination of Organismal Form: the Forgotten Cause in Evolutionary
Origination of Organismal Form: The Forgotten Cause 1 in Evolutionary Theory Gerd B. Müller and Stuart A. Newman Evolutionary biology arose from the age-old desire to understand the origin and the diver- sification of organismal forms. During the past 150 years, the question of how these two as- pects of evolution are causally realized has become a field of scientific inquiry, and the standard answer, encapsulated in a central tenet of Darwinism, is by “variation of traits” and “natural selection.” The modern version of this tenet holds that the continued modifi- cation and inheritance of a basic genetic tool kit for the regulation of developmental processes, directed by mechanisms acting at the population level, has generated the panoply of organismal body plans encountered in nature. This notion is superimposed on a sophisticated, mathematically based population genetics, which became the dominant mode of evolutionary biology in the second half of the twentieth century. As a conse- quence, much of present-day evolutionary theory is concerned with formal accounts of quantitative variation and diversification. Other major branches of evolutionary biology have concentrated on patterns of evolution, ecological factors, and, increasingly, on the associated molecular changes. Indeed, the concern with the “gene” has overwhelmed all other aspects, and evolutionary biology today has become almost synonymous with evolutionary genetics. These developments have edged the field farther and farther away from the second ini- tial theme: the origin of organismal form and structure. The question of why and how cer- . tain forms appear in organismal evolution addresses not what is being maintained (and 0 1 - quantitatively varied) but rather what is being generated in a qualitative sense.
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STUART NEWMAN Is a Professor of Cell Biology
Epigenetics vs. Genetic Determinism An Interview with Stuart Newman Casey Walker: As a cellular biologist, where do you see poor assumptions and bad theory playing themselves out in biogenetic engineering? Stuart Newman: It begins with the false idea that organisms can be designed to specification, or corrected by popping in new genes and popping out bad genes. We see these assumptions in agriculture with genetically engi- neered foods, and with practices such as inserting naturally occurring insecticide proteins into crop plants like corn. There is a prevailing and, in my view, incorrect idea that genes are modular entities with a one-to-one correspon- dence between a function and a gene. My particular inter- est is in how these ideas are being played out in human biology, where we see the same kind of genetic reduction- ism justifying attempts to assign genes to complex condi- tions such as schizophrenia, intelligence, homosexuality, and so forth. Definition of problems in genetic terms obvi- ously leads to calls for genetic solutions with profound con- sequences for human beings and evolution. Although it’s unquestionable that every complex bio- logical condition has a genetic component to it, the media- tion that occurs between the genetic component and the actual behavior or feature is typically quite complex and is a professor of Cell Biology and should militate against taking the reductionist approach. STUART NEWMAN Anatomy at New York Medical College, Valhalla, New York; with Frequently, a gene in one context will influence a condition degrees in chemistry from Columbia University (AB) and the in one way and in a different context will influence the University of Chicago (PhD).
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Evo-Devo, Devo-Evo, and Devgen-Popgen
Biology and Philosophy 18: 347–352, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. Evo-Devo, Devo-Evo, and Devgen-Popgen SCOTT F. GILBERT Department of Biology Martin Research Laboratories Swarthmore College Swarthmore, PA 19081 U.S.A. E-mail: [email protected] In his guest editorial in Evolution and Development, “Evo-devo or Devo-evo – Does It Matter?”, Brian Hall (2000) concluded that Evo-devo and Devo-evo are not the same and that it mattered a great deal. According to Hall, Evo-devo is continuous with the evolutionary embryology of the nineteenth century and is a way of integrating proximate and ultimate causes for the origin of pheno- types. The interactions of evolutionary biology and developmental biology, he believes, should produce emergent properties not found in either parent discipline. Interactions tend to do that, whether inside the embryo or inside academia. While Evo-devo is merely the expansion of developmental biology into a new area, Hall views developmental evolutionary biology (Devo-evo) as constituting something more revolutionary. According to Hall, Devo-evo sees the neo-Darwinian view of evolution (the Modern Synthesis) as incom- plete and in need of complementation by developmental biology. Moreover, such a new synthesis “would not place primary emphasis on genes as the only units of evolutionary change.” I have been asked to comment on this matter, and I find that Hall and I differ with respect to these definitions. I think that Hall’s definition of Devo- evo has two parts, and that these parts do not necessarily have to go together.
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Darwin's Doubt
Advancing the Scientific Debate In Paperback Now with a New Epilogue Purchase today at www.DarwinsDoubt.com Darwin’s Doubt: A Discussion Guide Introduction This discussion guide is designed to facilitate the use of Stephen Meyer’s book Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design in small groups, adult education classes, and book discussion clubs. The guide contains brief summaries of each chapter grouped into eight total discussion sessions. Each discussion session also contains discussion questions for the chapters covered by that session. Permission is hereby granted to distribute and reproduce this guide in whole or in part for non- commercial educational use, provided that: (1) the original source is credited; (2) any copies display the web addresses for Discovery Institute’s Center for Science and Culture (www.discovery.org/csc), IntelligentDesign.org (www.intelligentdesign.org), and the official Darwin’s Doubt website (www.darwinsdoubt.com); and (3) the copies are distributed free of charge. Contents Session 1 (p. 4) Prologue; Chapter 1: Darwin’s Nemesis; Chapter 2: The Burgess Bestiary Session 2 (p. 7) Chapter 3: Soft Bodies and Hard Facts; Chapter 4: The Not Missing Fossils? Session 3 (p. 10) Chapter 5: The Genes Tell the Story?; Chapter 6: The Animal Tree of Life; Chapter 7: Punk Eek! Session 4 (p. 14) Chapter 8: The Cambrian Information Explosion; Chapter 9: Combinatorial Inflation; Chapter 10: The Origin of Genes and Proteins Session 5 (p. 18) Chapter 11: Assume a Gene; Chapter 12: Complex Adaptations and the Neo- Darwinian Math Session 6 (p.
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Meiogenics: Synthetic Biology Meets Transhumanism
Meiogenics: Synthetic Biology Meets Transhumanism Some enthusiasts of synthetic biology envision technologies that would “improve” humans—and, perhaps, create useful “subhumans.” BY STUART A. NEWMAN Synthetic biology is a collection of virus-proof.”4 In a similar vein, Drew If you could complement evolution techniques, and research and busi- Endy, a synthetic biology researcher with a secondary path, decode a ge- ness agendas, that includes the con- formerly at MIT and now at Stanford, nome, take it off-line to the level of struction of DNA sequences that asked rhetorically in an interview information…we can then design encode protein or RNA molecules with a New Yorker reporter, “What if whatever we want, and recompile which assemble into macromolecu- we could liberate ourselves from the it…At that point, you can make dis- lar complexes, biochemical circuits tyranny of evolution by being able to posable biological systems that don’t and networks with known or novel design our own offspring?”5 have to produce offspring.”7 functions; the substitution of chemi- One difference from earlier eugen- With the objective thus being cally synthesized DNA or DNA ana- ic fantasies is that synthetic biologists “meiogenics” (from the Greek μείον: logues for their natural counterparts now know enough to realize that it less), that is, the creation of useful in order to change cell behavior and/ would be hundreds of times more subhumans, many barriers to imple- or produce novel products; and at- likely to botch an embryo’s genome menting such programs fall aside. Ex- tempts to define and construct basic by gene manipulation techniques isting regulatory regimes on human living systems from minimal sets of than to come up with an improve- experimentation pertain to what are molecules.1 Synthetic biology has ment.
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