Golden Braid Research Articles

Some strategies for teaching a course based on Gödel, Escher, Bach

In 1979, Douglas Hofstadter published a Pulitzer prizewinning classic, Gödel, Escher, Bach: an eternal golden braid [1], henceforward referred to as GEB. I have presented a course at La Salle University based on GEB eleven times during the last twenty-one years. From these experiences, I present below some useful strategies for instructors who are interested in teaching a course where at least half of GEB is covered in some depth.

GB3.0: a platform for plant bio-design that connects functional DNA elements with associated biological data.

Modular DNA assembly simplifies multigene engineering in Plant Synthetic Biology. Furthermore, the recent adoption of a common syntax to facilitate the exchange of plant DNA parts (phytobricks) is a promising strategy to speed up genetic engineering. Following this lead, here, we present a platform for plant biodesign that incorporates functional descriptions of phytobricks obtained under pre-defined experimental conditions, and systematically registers the resulting information as metadata for documentation. To facilitate the handling of functional descriptions, we developed a new version (v3.0) of the GoldenBraid (GB) webtool that integrates the experimental data and displays it in the form of datasheets. We report the use of the Luciferase/Renilla (Luc/Ren) transient agroinfiltration assay in Nicotiana benthamiana as a standard to estimate relative transcriptional activities conferred by regulatory phytobricks, and show the consistency and reproducibility of this method in the characterization of a synthetic phytobrick based on the CaMV35S promoter. Furthermore, we illustrate the potential for combinatorial optimization and incremental innovation of the GB3.0 platform in two separate examples, (i) the development of a collection of orthogonal transcriptional regulators based on phiC31 integrase and (ii) the design of a small genetic circuit that connects a glucocorticoid switch to a MYB/bHLH transcriptional activation module.

A modular toolbox for gRNA-Cas9 genome engineering in plants based on the GoldenBraid standard.

BackgroundThe efficiency, versatility and multiplexing capacity of RNA-guided genome engineering using the CRISPR/Cas9 technology enables a variety of applications in plants, ranging from gene editing to the construction of transcriptional gene circuits, many of which depend on the technical ability to compose and transfer complex synthetic instructions into the plant cell. The engineering principles of standardization and modularity applied to DNA cloning are impacting plant genetic engineering, by increasing multigene assembly efficiency and by fostering the exchange of well-defined physical DNA parts with precise functional information.ResultsHere we describe the adaptation of the RNA-guided Cas9 system to GoldenBraid (GB), a modular DNA construction framework being increasingly used in Plant Synthetic Biology. In this work, the genetic elements required for CRISPRs-based editing and transcriptional regulation were adapted to GB, and a workflow for gRNAs construction was designed and optimized. New software tools specific for CRISPRs assembly were created and incorporated to the public GB resources site.ConclusionsThe functionality and the efficiency of gRNA–Cas9 GB tools were demonstrated in Nicotiana benthamiana using transient expression assays both for gene targeted mutations and for transcriptional regulation. The availability of gRNA–Cas9 GB toolbox will facilitate the application of CRISPR/Cas9 technology to plant genome engineering.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-016-0101-2) contains supplementary material, which is available to authorized users.

Disruptive Texts: Case Narratives As Research Inspirations

Academy of Management ReviewVol. 42, No. 1 What Inspires the Academy: Book Reviews and Beyond?Disruptive Texts: Case Narratives As Research InspirationsDanny MillerDanny MillerHEC Montreal and University of AlbertaPublished Online:7 Jan 2016https://doi.org/10.5465/amr.2015.0418AboutSectionsView articleView Full TextPDF/EPUB ToolsDownload CitationsAdd to favoritesTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail View articleREFERENCESAnderson R., Reeb D. 2003. Founding-family ownership and firm performance: Evidence from the S&P 500. Journal of Finance, 58: 1301–1328. Google ScholarAnderson T., Warkov S. 1961. Organizational size and functional complexity. American Sociological Review, 26: 23–28. Google ScholarBarney J. 1991. Firm resources and sustained competitive advantage. Journal of Management, 17: 99–120. Google ScholarChandler A. D. 1990. Scale and scope: The dynamics of industrial capitalism. Boston: Harvard University Press. Google ScholarChild J. 1973. Parkinson’s progress: Accounting for the number of specialists in organizations. Administrative Science Quarterly, 18: 328–329. Google ScholarGalbraith J. R. 1973. Designing complex organizations. Reading, MA: Addison-Wesley. Google ScholarHofstadter D. R. 1979. Gödel, Escher, Bach: An eternal golden braid. New York: Random House. Google ScholarKhandwalla P. 1973. Viable and effective organizational designs of firms. Academy of Management Journal, 16: 481–495.Link , Google ScholarLe Breton-Miller I., Miller D. 2015. The paradox of resource vulnerability: Considerations for organizational curatorship. Strategic Management Journal, 36: 397–415. Google ScholarLevine J. 1999. The rise and fall of the House of Barneys: A family tale of chutzpah, glory, and greed. New York: Morrow. Google ScholarMcNichols T. J. 1967. Policy making and executive action (3rd ed.). New York: McGraw-Hill. Google ScholarMerton R. K. 1968. Social theory and social structure. New York: Simon & Schuster. Google ScholarMiller D. 1981. Toward a new contingency approach: The search for organizational gestalts. Journal of Management Studies, 18: 1–27. Google ScholarMiller D. 2003. An asymmetry-based view of advantage. Strategic Management Journal, 24: 961–976. Google ScholarMiller D. 2007. Paradigm prison. Strategic Organization, 5: 177–184. Google ScholarMiller D., Eisenstat R., Foote N. 2002. Strategy from the inside out: Building capability-creating organizations. California Management Review, 44(1): 37–54. Google ScholarMiller D., Friesen P. 1984. Organizations: A quantum view. Englewood Hills, NJ: Prentice-Hall. Google ScholarMiller D., Le Breton-Miller I. 2005. Managing for the long run: Lessons in competitive advantage from great family businesses. Boston: Harvard Business School Publishing. Google ScholarMintzberg H. 1973. Strategy making in three modes. California Management Review, 16(2): 44–53. Google ScholarMintzberg H. 1979. The structuring of organizations: A synthesis of the research. Englewood Cliffs, NJ: Prentice-Hall. Google ScholarPhillips N., Hardy C. 2002. Discourse analysis: Investigating processes of social construction. Beverly Hills, CA: Sage. Google ScholarPugh D. S., Hickson D. J., Hinings C. R. 1969. An empirical taxonomy of structures of work organizations. Administrative Science Quarterly, 14: 115–126. Google ScholarPugh D. S., Hickson D. J., Hinings C. R., Turner C. 1968. Dimensions of organization structure. Administrative Science Quarterly, 13: 65–105. Google ScholarRushing W. 1967–68. The effects of industry, size and division of labor on administration. Administrative Science Quarterly, 12: 273–295. Google ScholarRushing W. 1976. Two patterns of industrial administration. Human Organization, 10: 32–39. Google ScholarShapiro D. 1965. Neurotic styles. New York: Basic Books. Google ScholarStarbuck W. H. 1981. A trip to view the elephants and rattlesnakes in the garden of Aston. In A. Van de Ven & W. Joyce (Eds.), Perspectives on organization design and behavior: 167–198. New York: Oxford. Google ScholarTeece D. J., Pisano G., Shuen A. 1997. Dynamic capabilities and strategic management. Strategic Management Journal, 18: 509–533. Google ScholarTerrien F., Mills D. 1955. The effect of size on the changing structure of organizations. American Sociological Review, 20: 11–13. Google ScholarThompson J. D. 1967. Organizations in action. New York: McGraw-Hill. Google ScholarFiguresReferencesRelatedDetailsCited byOrganizing Refugee Camps: “Respected Space” and “Listening Posts”Marlen de la Chaux, Helen Haugh and Royston Greenwood25 June 2018 | Academy of Management Discoveries, Vol. 4, No. 2 Vol. 42, No. 1 Permissions Metrics in the past 12 months History Published online 7 January 2016 Published in print 1 January 2017 Information© Academy of Management ReviewI would like to thank my wife, Isabelle Le Breton-Miller, for suggesting the thesis of this essay, and Jean Bartunek, for her encouragement and inspired comments.Download PDF

Software-assisted stacking of gene modules using GoldenBraid 2.0 DNA-assembly framework.

GoldenBraid (GB) is a modular DNA assembly technology for plant multigene engineering based on type IIS restriction enzymes. GB speeds up the assembly of transcriptional units from standard genetic parts and facilitates the stacking of several genes within the same T-DNA in few days. GBcloning is software-assisted with a set of online tools. The GBDomesticator tool assists in the adaptation of DNA parts to the GBstandard. The combination of GB-adapted parts to build new transcriptional units is assisted by the GB TU Assembler tool. Finally, the assembly of multigene modules is simulated by the GB Binary Assembler. All the software tools are available at www.gbcloning.org . Here, we describe in detail the assembly methodology to create a multigene construct with three transcriptional units for polyphenol metabolic engineering in plants.

A Study of Replicators and Hypercycles by Hofstadter's Typogenetics

A Typogenetics is a formal system designed to study origins of life from a “primordial soup” of DNA molecules, enzymes and other building materials. It was introduced by Hofstadter (1979) in his seminal book Dialogues with Gödel, Escher, Bach: An Eternal Golden Braid. Autoreplicating molecules and systems of mutually replicating and catalyzing molecules (autoreplicators and hypercycles) are modeled in the present paper in a form composed of two strands of symbols. These strands are vehicle of two fold information: The first one corresponds to information that is transferred by strands. The second type of information specifies a process of strand replication. The used replicating molecules - strands are created by an approach closely related to evolutionary algorithms. While a small hypercycle of two molecules mutually supporting their reproduction can be created without extreme difficulties, it is nearly impossible to create a hypercycle involving more than 4 autoreplicators at once. This paper demonstrates that larger hypercycles can be created by an optimization and inclusion of new molecules into a smaller hypercycle. Such a sequential construction of hypercycles can substantially reduce the combinatorial complexity in comparison with a simultaneous optimization of single components of a large hypercycle.

The Asheel-Terrapin Interviews

In the CALICO '96 Keynote Address Don Fischer cited two unpublished papers, "The Asheel-Terrapin Interviews:" "Interview #1: The Desert" and "Interview #2: LISLO and IPPBID." The following article offers these two fictive interviews for the first time in published form. The author first presented "Interview #1: The Desert" in November 1981 as a skit at a luncheon meeting in the Air Force Academy Officer's Club. The luncheon was part of the pre-conference session on computers and foreign language teaching held at the Air Force Academy during the 1981 Annual Meeting of the American Council on the Teaching of Foreign Languages (ACTFL). He wrote "Interview #2: LISLO and IPPBID" about the same time but does not recall presenting it at the luncheon. "Interview #1" was a credo on the nature of language learning and teaching, which, collectively, the writer had been doing for about twenty years at the time he wrote the piece. "Interview #2" was a personal cognitive manifesto about language learning and technology. The only update needed after some sixteen years of technological change is to refer to multimedia rather than videodisc in the second interview. Admirers of Gödel, Escher, Bach: An Eternal Golden Braid (Hofstadter 1979) should note that in French "Achilles" is pronounced more or less like Asheel.

GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules

Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop (“braid”) topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described.

Perception, action, and experience: Unraveling the golden braid

Much of our human mental life looks to involve a seamless unfolding of perception, action and experience: a golden braid in which each element twines intimately with the rest. We see the very world we act in and we act in the world we see. But more than this, visual experience presents us with the world in a way apt for the control and fine guidance of action. Or so it seems. Milner and Goodale's [Milner, D., Goodale, M. (1995). The visual brain in action. Oxford: Oxford University Press; Milner, A., Goodale, M. (2006). Epilogue: Twelve years on. In Milner, A., Goodale, M. (Ed.), The visual brain in action (2nd ed., pp. 207–252). Oxford: Oxford University Press] influential work on the dual visual systems hypothesis casts doubt on certain versions of this intuitive vision. It does so by prising apart the twining strands of conscious visual perception and the fine control of visuomotor action. Such a bold proposal is of major interest both to cognitive science and philosophy. In what follows I first clarify the major claims that the bold proposal involves, then examine three sets of worries and objections. The first set concern some important matters of detail. The second set concern a certain kind of conceptual or philosophical worry to the effect that the perception/action model unfairly equates visual experience itself with what are in fact certain elements within visual experience. The third set concern the very idea of conscious experience as a well-defined conceptual or experimental target. I conclude that the boldest versions of the Dual Visual Systems (2VS) story underestimate the variety and richness of visual experience, but that the general picture of visual uptake as a fragmented, multi-stream, multipurpose adaptation is correct, and still revealing after all these years.

A Topological Look at the Quantum Hall Effect

The amazingly precise quantization of Hall conductance in a two-dimensional electron gas can be understood in terms of a topological invariant known as the Chern number.

Agency

Drawing on lessons from computing and theories of strange loops, this paper attempts to redefine the notion of agency within the context of cultural production, as a starting point toward solving the agency-structure dilemma in social and cultural theory.

Imaginary Numbers: an anthology of marvelous mathematical stories, diversions, poems, and musings, edited by William Frucht. Pp. 327. £12.50. 2000. ISBN 0 471 39341 X (John Wiley & Sons).

Imaginary Numbers: an anthology of marvelous mathematical stories, diversions, poems, and musings, edited by William Frucht. Pp. 327. £12.50. 2000. ISBN 0 471 39341 X (John Wiley & Sons). - Volume 85 Issue 504

Autoreplicators and hypercycles in typogenetics

A simplified formal system typogenetics, closely related to concepts of molecular genetics and introduced by Hofstadter in his seminal book Dialogues with G ö del, Escher, Bach: An Eternal Golden Braid [Basic books, New York, 1979 (Chapters XVI and XVII)] is discussed. Concepts of autoreplicators and hypercycles, defined within typogenetics, belong to basic entities in current perception of artificial life. A metaphor of chemical reactions (chemostat) is applied to study emergence of autoreplicators and hypercycles. The initial version of evolutionary approach, designed for construction of autoreplicators, is able to produce only small hypercycles composed of two or at most three autoreplicators. An emergence of larger hypercycles represents extremely complicated combinatorial optimization problem. Therefore, we turn our attention to a sequential technique of their construction, where a smaller hypercycle is enlarged by another autoreplicator. Both components are thus integrated into one hypercycle. This method of successive construction of hypercycles substantially reduces combinatorial complexity of the original approach where whole hypercycles are simultaneously optimized.

Imaginary numbers: an anthology of marvelous mathematical stories, diversions, poems, and musings

Italo Calvino: The Form of Space. Rudy Rucker: A New Golden Age. Lewis Carroll: A Serpent with Corners (from A Tangled Tale). J. A. Lindon: A Positive Reminder. Raymond Smullyan: How Kazir Won His Wife. Alan Lightman: 11 May 1905 (from Einstein's Dreams). Roald Hoffman: Why Does Disorder Increase in the Same Direction of Time as That in Which the Universe Expands? Philip K. Dick: The Golden Man. Hilbert Schenck: The Morphology of the Kirkham Wreck. Abner Shimony: Resolution of the Paradox: A Philosophical Puppet Play. Piet Hein: Parallelism. Douglas Hofstadter Prelude...(from Godel, Escher, Bach: An Eternal Golden Braid). Stanislaw Lem: The Third Sally, or The Dragons of Probability (from The Seven Sallies of Trurl and Klapaucius). Edwin Abbott Abbott: Concerning Irregular Figures (from Flatland). Andrew Marvell: The Definition of Love. A. K. Dewdney: On Fiddib Har (from The Planiverse: Computer Contact with a Two--Dimensional World). Martin Gardner: The Church of the Fourth Dimension. Stanislaw Lem: The Extraordinary Hotel, or the Thousand and First Journey of Ion the Quiet. Anonymous: Ten Weary, Footsore Travelers. Racter: From The Policeman's Beard Is Half--Constructed. William Gibson: Burning Chrome. Fritz Leiber: Gonna Roll the Bones. Wislawa Szymborska: A Word on Statistics. Tommaso Landolfi: Giovanni and His Wife. Joe Haldeman: The Private War of Private Jacob. Jorge Luis Borges: The Library of Babel. Christian Bok: Enantiomorphosis (A Natural History of Mirrors). Connie Willis: Schwarzschild Radius. Siv Cedering: Letter from Caroline Herschel (1750--1848). Yevgeny Zamyatin: From We. J. G. Ballard: The Garden of Time. Acknowledgments. Permission Acknowledgments.

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Book reviews

Book reviewed in this article:Comparative Statistical Inference, 2nd ed. By Vic Barnett.The Mismeasure of Man. By Stephen J. Gould.Statistics in Britain 1865–1930: The Social Construction of Scientific Knowledge. By Donald A. MacKenzieStochastic Models for Social Processes, 3rd ed. By David J. Bartholomew.Gödel, Escher, Bach: An Eternal Golden Braid. By Douglas R. Hofstadter.The Hut 6 Story. By Gordon Welchman

Tangled Hierarchies: Gödel, Escher, Bach and <i>Gravity's Rainbow</i> (An Abstract of Work in Progress)

Douglas Hofstadter tells us in Godel, Escher, Bach: An Eternal Golden Braid (1979) that the rapid development of computer technology in the past two decades has brought about a new kind of perspective on just what thought is--its powers and weaknesses, as well as its idiosyncracies. This has been made possible through computer experimentation with what he calls "alien, yet hand-tailored forms of thought--or approximations of thought." The results of this experimentation are reflected in the theory and designs developed in the artificial intelligence (AI) field, and many of these developments are considered at some length in Godel, Escher, Bach.

Formal Axiomatic Systems and Computer-Generated Theorems

One of the main topics of discussion in Douglas Hofstadter’s Pulitzer-prize-win-ning book Godei, Escher, Bach: An Eternal Golden Braid is the concept of deriving theorems in a formal system. To give his readers a better idea of what a formal system is, Hofstadter discusses a simple example of such a system, called the MIU system. Although the example may not have been designed for instructional use, to a teacher of mathematics it seems ready-made for the classroom. Indeed, the MIU system can not only provide an instructional unit on some important topics in mathematics, it can also be used to lead students to investigate some fascinating ideas from computer science and artificial intelligence. The present article will describe the MIU system and indicate a number of possible uses for it in the mathematics classroom.

Gödel, Escher, Bach: An Eternal Golden Braid

Back to table of contents Previous article Next article ArticleNo AccessGödel, Escher, Bach: An Eternal Golden BraidLESTER S. KINGLESTER S. KINGSearch for more papers by this authorPublished Online:1 Apr 2006https://doi.org/10.1176/ajp.138.4.542AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InEmail "Gödel, Escher, Bach: An Eternal Golden Braid." American Journal of Psychiatry, 138(4), p. 542 Access content To read the fulltext, please use one of the options below to sign in or purchase access. Personal login Institutional Login Sign in via OpenAthens Purchase Save for later Item saved, go to cart PPV Articles - American Journal of Psychiatry $35.00 Add to cart PPV Articles - American Journal of Psychiatry Checkout Please login/register if you wish to pair your device and check access availability. Not a subscriber? Subscribe Now / Learn More PsychiatryOnline subscription options offer access to the DSM-5 library, books, journals, CME, and patient resources. This all-in-one virtual library provides psychiatrists and mental health professionals with key resources for diagnosis, treatment, research, and professional development. Need more help? PsychiatryOnline Customer Service may be reached by emailing [email protected] or by calling 800-368-5777 (in the U.S.) or 703-907-7322 (outside the U.S.). FiguresReferencesCited byDetailsCited ByIssues in Mental Health Nursing, Vol. 12, No. 3 Volume 138Issue 4 April 1981Pages 542-542 Metrics PDF download History Published online 1 April 2006 Published in print 1 April 1981

Book Reviews

Book reviewed in this article:ROTHENBERG, A. The Emerging Goddess (The Creative Process in Art, Science, and Other Fields).HOFSTADTER, DOUGLAS R. Godel, Escher, Bach: An Eternal Golden Braid.