Gene Foundry

Synthetic biology is not a unified field. It involves many disciplines, from molecular genetics to biochemistry, and from engineering to bioinformatics. It includes xenobiological approaches that build and use artificial nucleic acids, metabolic reengineering of existing microbes, maybe using standardized parts and devices, creation of minimal organisms, bio-brick-biochemistry, and attempts to make synthetic organisms from scratch. The contributions to this thematic issue reflect on these scientific activities in synthetic biology and in related fields. They grew out of a workshop on the scientific, philosophical, and social dimensions of synthetic biology, including its research strategies, conceptual apparatus and societal implications. For many, the attraction of synthetic biology is its aim to apply in biology the methods of traditional engineering, especially rational engineering, using standardized components that allow plug-and-play modular design (Canton et al. 2008; Mutalik et al. 2013a, b). Rational engineering contrasts with creating desired systems through trial-and-error experimentation, which includes tried-and-true methods like tinkering and kludging, as well as sophisticated methods like generating and screening massive libraries of high-throughput wet-lab experimental data. Trial-and-error methods in synthetic biology also include familiar and widespread methods like in vitro (or directed) evolution (Yokobayashi et al. 2002), as well as new applications of machine-learning methods to make high-throughput experiments maximally intelligent and efficient (Caschera et al. 2010, 2011). Synthetic biology involves a plurality of experimental research programs. It includes top-down reengineering of existing life forms, for example, to mass-produce products such as pharmaceuticals (Martin et al. 2003) or biofuel (Savage et al. 2008). It also includes bottom-up attempts to create new minimal chemical life or ‘‘protocells’’ using nothing but non-living materials (Rasmussen et al. 2004, 2009a). Both top-down and bottom-up synthetic biology employ the two methods we contrasted above: rational engineering and trial-and-error experimentation. These two distinctions (top-down versus bottom-up, and rational engineering versus trial-and-error experimentation) define four quadrants in Table 1. These quadrants map achievements in synthetic biology and illustrate some of the field’s scientific plurality. Least familiar and least developed is the lower right quadrant of trial-and-error methods for bottomup synthetic biology, though some would argue that this quadrant also shows the most upside potential (e.g., Bedau 2013, this issue).

Reports of the successful creation of artificial life usually garner considerable interest from philosophers. This paper argues that the worries philosophers have about artificial life do not, for the most part, depend on the artificiality of a given organism. In particular advances in synthetic biology will make the distinction between artificial and natural life a difficult and fluid one. Philosophers should hence refrain from making their arguments depend on a distinction between artificial and natural life.

Paving the way for synthetic biology‐based bioremediation in Europe

One way of acknowledging the putative progress of science is to trace its successes with respect to description, manipulation, and genuine innovation. In this regard, the history of genetics can be viewed as an exemplary case study. Indeed, the ground breaking work of Watson and Crick, the remarkable results associated with both describing and manipulating regulatory genes (e.g., early and recent work on Drosophila), and the cutting edge efforts related to nuclear transfer (i.e., cloning) are stunning progress-worthy accomplishments. Yet, there are moral, religious, and social implications of scientific triumphs that may give us pause with respect to ascriptions of progress. For instance, genetic modification, stem cell procurement, reproductive enhancement, and cloning have received a great deal of negative attention from moral, religious, and political factions. These groups have cried foul for a mix of metaphysical, moral, and public policy reasons. There appears, then, to be a somewhat mixed reception with respect to some scientific endeavors and feats—especially those coups commandeered by biotechnology mavens. It is within this mixed reception that the burgeoning field of synthetic biology [SB hereafter] finds itself. Broadly, this discipline’s innovative uniqueness is captured not so much by its goals of (1) modifying organism behavior by modifying existing sets of DNA and (2) producing new sets of DNA to assist in the production of novel tasks, but more so by its focus on creating new organisms from (i) genetic raw material and (ii) from extant parts of living organisms. For example, Ro et al. (2006, Nature) have engineered an E. coli bacterial organism that can produce 10,000 times more artemisinic acid (needed for a certain anti-malarial drug) than the natural bacteria that produces this same chemical. They accomplished this by transplanting into the bacteria particular genes from the wormwood plant and yeast fungus. In a

Synthetic biology is an interdisciplinary subject in which biologists, engineers and computer scientists collaborate with the aim to synthesize new organisms and engineer them to perform tasks, which the respective organism does not perform in nature. Synthetic biology overlaps with nanobiotechnology not only in certain technical aspects, but also concerning social, safety and ethical impacts. Both disciplines act at the intersection of biology and technology and challenge the boundary between living and non-living matter, as it has been understood hitherto. Possible applications for example in medicine and the danger for abuse in bioterrorism are common to synthetic biology and nanobiotechnology. We want to examine ethical and social implications of synthetic biology in comparison to nanobiotechnology. Thereby we aim to contribute to a better understanding of which issues are specific to nanobiotechnology and which are shared with other approaches in the field.

Synthetic biology is built on genetic engineering and principles of design engineering, which provides control over the biological functions of interest. This chapter explores the uses, processes, and applications of genetic engineering in synthetic biology. The chapter provides a brief history and course of development of the field of synthetic biology and genetic engineering and their unbreakable association. Next, the chapter delves into materials and methods and the applications of synthetic biology. This includes discussing the generally used components of genetic engineering to design new functions into organisms and even the general steps that are part of any synthetic biology experiment. Lastly, the chapter also explains the use of the materials and methodology discussed in solving a specific problem related to amodel mentioned in the paper titled"Development of Integrase-mediated differentiation circuits to improve evolutionary stability in E. coli." It explains how by using genetic engineering a synthetic biology-related problem was solved efficiently.

The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.

Artificial Life Next Generation Perspectives: Echoes from the 2018 Conference in Tokyo.

February 01 2020 Trompe L'oeil and Financial Risk in the Age of Paper Maggie M. Cao Maggie M. Cao Maggie M. Cao is the David G. Frey Assistant Professor of Art History at the University of North Carolina, Chapel Hill. She is the author of The End of Landscape in Nineteenth-Century America (University of California Press, 2018). Her research focuses on the intersections of art with histories of technology, natural science, and economics in the eighteenth and nineteenth centuries. Search for other works by this author on: This Site Google Scholar Author and Article Information Maggie M. Cao Maggie M. Cao is the David G. Frey Assistant Professor of Art History at the University of North Carolina, Chapel Hill. She is the author of The End of Landscape in Nineteenth-Century America (University of California Press, 2018). Her research focuses on the intersections of art with histories of technology, natural science, and economics in the eighteenth and nineteenth centuries. Online Issn: 1536-0105 Print Issn: 1526-3819 © 2020 by Grey Room, Inc. and the Massachusetts Institute of Technology.2020Grey Room, Inc. and the Massachusetts Institute of Technology. Grey Room (2020) (78): 6–33. https://doi.org/10.1162/grey_a_00287 Cite Icon Cite Permissions Share Icon Share Facebook Twitter LinkedIn MailTo Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Search Site Citation Maggie M. Cao; Trompe L'oeil and Financial Risk in the Age of Paper. Grey Room 2020; (78): 6–33. doi: https://doi.org/10.1162/grey_a_00287 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsGrey Room Search Advanced Search This content is only available as a PDF. © 2020 by Grey Room, Inc. and the Massachusetts Institute of Technology.2020Grey Room, Inc. and the Massachusetts Institute of Technology. Article PDF first page preview Close Modal You do not currently have access to this content.

Most of the reports on synthetic biology include not only familiar topics like biosafety and biosecurity but also a chapter on 'ethical concerns'; a variety of diffuse topics that are interrelated in some way or another. This article deals with these 'ethical concerns'. In particular it addresses issues such as the intrinsic value of life and how to deal with 'artificial life', and the fear that synthetic biologists are tampering with nature or playing God. Its aim is to analyse what exactly is the nature of the concerns and what rationale may lie behind them. The analysis concludes that the above-mentioned worries do not give genuine cause for serious concern. In the best possible way they are interpreted as slippery slope arguments, yet arguments of this type need to be handled with care. It is argued that although we are urged to be especially vigilant we do not have sufficiently cogent reasons to assume that synthetic biology will cause such fundamental hazards as to warrant restricting or refraining from research in this field.

The results of the Sixty-Fourth William Lowell Putnam Mathematical Competition, held December 6, 2003, follow. They have been determined in accordance with the regulations governing the Competition. The contest is supported by the William Lowell Putnam Prize Fund for the Promotion of Scholarship, an endowment established by Mrs. Putnam in memory of her husband. The annual Competition is held under the auspices of the Mathematical Association of America. The first prize, $25,000, was awarded to the Department of Mathematics of the Massachusetts Institute of Technology. The members of the winning team were Reid W. Barton, Daniel M. Kane, and Yevgeny K. Zaytman; each was awarded a prize of $1,000. The second prize, $20,000, was awarded to the Department of Mathematics of Harvard University. The members of the winning team were Gabriel D. Carroll, George Lee, Jr., and Alexander B. Schwartz; each was awarded a prize of $800. The third prize, $15,000, was awarded to the Department of Mathematics of Duke University. The members of the winning team were David G. Arthur, Nikifor C. Bliznashki, and Oaz Nir; each was awarded a prize of $600. The fourth prize, $10,000, was awarded to the Department of Mathematics of the California Institute of Technology. The members of the winning team were Zhihao Liu, Po-Ru Loh, and Po-Shen Loh; each was awarded a prize of $400. The fifth prize, $5,000, was awarded to the Department of Mathematics of Harvey Mudd College. The members of the winning team were David J. Gaebler, Jason Murcko, and Andrew G. Niedermaier; each was awarded a prize of $200. The five highest ranking individual contestants, the Putnam Fellows, in alphabetical order, were Reid W. Barton, Massachusetts Institute of Technology; Ana Caraiani, Princeton University; Gabriel D. Carroll, Harvard University; Ralph C. Furmaniak, University of Waterloo; and Daniel M. Kane, Massachusetts Institute of Technology. Each receives an award of $2,500. The next eleven highest ranking contestants, in alphabetical order, were: David G. Arthur, Duke University; Robert M. Barrington Leigh, University of Toronto; Alex R. Fink, University of Calgary; Andrei Jorza, Harvard University; Suehyun Kwon, Princeton University; Ian Tuan-Yen Le, Harvard University; Ricky I. Liu, Harvard University; Po-Ru Loh, California Institute of Technology; Sevak Mkrtchyan, University of Pittsburgh; David A. G. Pritchard, Massachusetts Institute of Technology; and Emanuel I. Stoica, Massachusetts Institute of Technology. Each receives an award of $1,000. The next ten highest ranking contestants, in alphabetical order, were: Vladimir Barzov, Massachusetts Institute of Technology; Michael C. Catlin, Harvard University; Benjamin J. Conlee, Harvard University; Stefan L. Hornet, Princeton University; George Lee, Jr., Harvard University; Po-Shen Loh, California Institute of Technology; Vladimir S. Novakovski, Harvard University; Zhongtao Wu, Massachusetts Institute of Technology; Rumen I. Zarev, California Institute of Technology; and Yevgeny K. Zaytman, Massachusetts Institute of Technology. Each receives an award of $250.

Synthetic biology is concerned with applying the engineering paradigm of systems design to biological systems in order to produce predictable and robust systems with novel functionalities that do not exist in nature. The circuit-like connectivity of biological parts and their ability to collectively process logical operations was first appreciated nearly 50 years ago. This inspired attempts to describe biological regulation schemes with mathematical models and to apply circuit analogies from established frameworks in electrical engineering(McAdams & Arkin A,2000). Meanwhile, breakthroughs in genomic research and genetic engineering (e.g., recombinant DNA technology) were supplying the inventory and methods necessary to physically construct and assemble biomolecular parts. As a result, synthetic biology was born with the broad goal of engineering or “wiring” biological circuitry—be it genetic, protein, viral, pathway, or genomic—for manifesting logical forms of cellular control. Synthetic biology, equipped with the engineering-driven approaches of modularization, rationalization, and modeling, has progressed rapidly and generated an ever-increasing suite of genetic devices and biological modules. synthetic biology is seeking to use and expand the mechanisms that control biological organisms using engineering approaches. These approaches will be applied on all scales of biological complexity: from the basic units to novel interactions between these units to novel multi-component modules that generate complex logical behaviour, and even to completely or partially engineered cells(McAdams & Shapiro,1995). Bringing the engineering paradigm to biology will allow us to apply existing biological knowledge to biotechnological problems in a much more rational and systematic way than has previously been possible, and at the same time to expand the scope of what can be achieved this way. The introduction of design principles such as modularity of parts, standardization of parts and devices according to internationally recognized criteria, and the adaptation of available abstract design procedures to biological systems, coupled to novel technological breakthroughs that allow the decoupling of design and fabrication, will fundamentally change our current concepts of how to manipulate biological systems. In this sense, synthetic biology is not primarily a “discovery science”, but is ultimately about a new way of making things. By adapting natural biological mechanisms to the requirements of an engineering approach, the possibilities for re-assembling biological systems in a designed way will increase tremendously. While several of the fundamental scientific issues and current applied objectives of synthetic biology overlap with those in other, more mature fields, especially

Gram-negative, rod-shaped Pseudomonas putida bacteria may be found in a variety of biological environments. This ubiquity can be attributed to its extraordinarily adaptable metabolism, ability to endure physicochemical stress, and propensity to survive in unfavorable conditions. These traits have led to an increase in interest in microorganisms for industrial usage, also associated with studying has advanced quickly in recent years. Strong motivators in this regard include use of inexpensive waste streams and sustainable feedstocks for manufacturing with added value compounds along with continual advancement of Systematic biology of this bacterium and genetic strain engineering. Here, provide a summary of current developments and future directions P. putida is used as a cell factory in genetic engineering, computer systems, and synthetic biology

There has been considerable interest in computer viruses since they first appeared in 1981, and especially in the past few years as they have reached epidemic numbers in many personal computer environments. Viruses have been written about as a security problem, as a social problem, and as a possible means of performing useful tasks in a distributed computing environment. However, only recently have some scientists begun to ask if computer viruses are not a form of artificial life—a self-replicating organism. Simply because computer viruses do not exist as organic molecules may not be sufficient reason to dismiss the classification of this form of “vandalware” as a form of life. This paper begins with a description of how computer viruses operate and their history, and of the various ways computer viruses are structured. It then examines how viruses meet properties associated with life as defined by some researchers in the area of artificial life and self-organizing systems. The paper concludes with some comments directed toward the definition of artificially “alive” systems and experimentation.

This book brings together contributions to the Fourth Artificial Life Workshop, held at the Massachusetts Institute of Technology in the summer of 1994. July 6-8, 1994 · The Massachusetts Institute of Technology The field of artificial life has recently emerged through the interaction of research in biology, physics, parallel computing, artificial intelligence, and complex adaptive systems. The goal is to understand, through synthetic experiments, the organizational principles underlying the dynamics (usually the nonlinear dynamics) of living systems. This book brings together contributions to the Fourth Artificial Life Workshop, held at the Massachusetts Institute of Technology in the summer of 1994. Topics include: Self-organization and emergent functionality • Definitions of life • Origin of life • Self-reproduction • Computer viruses • Synthesis of "the living state." • Evolution and population genetics • Coevolution and ecological dynamics • Growth, development, and differentiation • Organization and behavior of social and colonial organisms • Animal behavior • Global and local ecosystems and their intersections • Autonomous agents (mobile robots and software agents) • Collective intelligence ("swarm" intelligence) • Theoretical biology • Philosophical issues in A-life (from ontology to ethics) • Formalisms and tools for A-life research • Guidelines and safeguards for the practice of A-life. Bradford Books imprint