Beyond Biobricks: Synthesizing Synergistic Biochemical Systems from the Bottom-up

Engineers who attempt to discover and optimize the behavior of complex biochemical systems face a dauntingly difficult task. This is especially true if the systems are governed by multiple qualitative and quantitative variables that have non-linear response functions and that interact synergistically. The synthetic biology community has responded to this difficulty by promoting the use of standard biological parts called BioBricks , which are supposed to make biology into traditional engineering and enable engineers to program living organisms in the same way a computer scientists can program a computer . But the BioBricks research program faces daunting hurdles, because the nonlinearity and synergy found throughout biochemical systems generates lots of unpredictable emergent properties. This talk describes an alternative vision of how to engineer complex biochemical systems, according to which we would refashion engineering to fit biology (rather than the other way around). The resulting method (termed Predictive Design Technology or PDT) is a robot- and computer-driven automatic and autonomous implementation of traditional Edisonian science. The PDT method is described and illustrated in application to a number of practical biochemical design tasks, including (2) optimizing combination drug therapies, (2) optimizing cargo capacity of liposomes that self-assemble from complex amphiphile mixtures, (3) optimizing the liposomal formulation of insoluble drugs, and (4) optimizing in vitro protein expression.https://pdxscholar.library.pdx.edu/systems_science_seminar_series/1040/thumbnail.jp

Open problems in artificial life

This article lists fourteen open problems in artificial life, each of which is a grand challenge requiring a major advance on a fundamental issue for its solution. Each problem is briefly explained, and, where deemed helpful, some promising paths to its solution are indicated

Topology and Evolution of Technology Innovation Networks

The web of relations linking technological innovation can be fairly described in terms of patent citations. The resulting patent citation network provides a picture of the large-scale organization of innovations and its time evolution. Here we study the patterns of change of patents registered by the US Patent and Trademark Office (USPTO). We show that the scaling behavior exhibited by this network is consistent with a preferential attachment mechanism together with a Weibull-shaped aging term. Such attachment kernel is shared by scientific citation networks, thus indicating an universal type of mechanism linking ideas and designs and their evolution. The implications for evolutionary theory of innovation are discussed.Comment: 6 pages, 5 figures, submitted to Physical Review

Social and ethical checkpoints for bottom-up synthetic biology, or protocells

An alternative to creating novel organisms through the traditional “top-down” approach to synthetic biology involves creating them from the “bottom up” by assembling them from non-living components; the products of this approach are called “protocells.” In this paper we describe how bottom-up and top-down synthetic biology differ, review the current state of protocell research and development, and examine the unique ethical, social, and regulatory issues raised by bottom-up synthetic biology. Protocells have not yet been developed, but many expect this to happen within the next five to ten years. Accordingly, we identify six key checkpoints in protocell development at which particular attention should be given to specific ethical, social and regulatory issues concerning bottom-up synthetic biology, and make ten recommendations for responsible protocell science that are tied to the achievement of these checkpoints

Can unrealistic computer models illuminate theoretical biology

Questions about the important essential properties of biological systems are both di cult to answer and worthwhile to try to answer. Here are three examples of deep open questions in theoretical biology: 1. Is robust multi-level emergent activity anintrinsic property of certain homeostatic self-organizing systems like cells or organisms, and if so, how is this possible? 2. Is open-ended adaptive evolution an intrinsic property of certain evolving systems like the biosphere, and if so, how? 3. Is unbounded complexity or diversity growth an intrinsic property of certain evolving systems like the biosphere, and if so, how? These questions concern apparent fundamental properties of living systems|properties which, furthermore, seem to be shared bymany other complex adaptive systems, such as the global economy. It is especially hard to address these questions, largely because they concern the global emergent behavior of overwhelmingly complex systems. One way to pursue answers is with a certain sort of unrealistic computational model. Although this may sound paradoxical, I shall argue that, properly understood, it makes perfect sense. I could not agree more when Levin et al. [10] say that \[i]maginative and e cient computational approaches are essential in dealing with the overwhelming complexity of biological systems " (p. 341). There are at least two quite di erent kinds of computational models of complex biological systems. One strives for maximal delity to the details of particular natural systems, exploiting prodigious computer power to push the envelope on micro-mechanical realism. But I a

Four Puzzles about Life

To surmount the notorious difficulties of defining life, we should evaluate theories of life not by whether they provide necessary and sufficient conditions for our current preconceptions about life but by how well they explain living phenomena and how satisfactorily they resolve puzzles about life. On these grounds, the theory of life as supple adaptation (Bedau 1996) gets support from its natural and compelling resolutions of the following four puzzles: (1) How are different forms of life at different levels of the vital hierarchy related? (2) Is there a continuum between life and non-life? (3) Does life essentially concern a living entity's material composition or its form? (4) Are life and mind intrinsically connected

Pluralism About How Wholes Emerge From Parts

Any investigation of the relationship between wholes and parts must face the concept of emergence, but that concept has a chequered history in both philosophy and science. The talk illustrated a pluralistic and pragmatic way to evaluate concepts of emergence and applied it to a number of familiar conceptions of emergence. It focused on weak emergence, which is a hallmark of what we can call &#8216;complex wholes&#8217;, composed of nothing but certain parts organized in certain ways, whose behaviour is nothing more than the organized activity of their parts, while the underlying causal network is highly parallel, nonlinear, and synergistic, so that the behaviour of wholes cannot be derived from the behaviour of isolated parts. Complex wholes evoke terms like &#8216;holism&#8217;, &#8216;surplus&#8217;, &#8216;synergy&#8217;, &#8216;situatedness&#8217;, and &#8216;activity&#8217;. Bedau examined three kinds of complex wholes involving life: (1) a verbal Program-Metabolism-Container model of the origin of minimal chemical life, (2) a precise computational system that exhibits life-like global behaviour, and (3) the wet experiments in bottom-up synthetic biology laboratories that combine nonliving materials to create new and unfamiliar forms of life (or &#8216;protocells&#8217;). Mark A. Bedau is professor of philosophy and humanities at Reed College, Editor-in-Chief of the journal Artificial Life, and regular visiting professor in the PhD program &#8216;Foundations and Ethical Implications of the Life Sciences&#8217; at the European School of Molecular Medicine in Milan, Italy. His interdisciplinary collaborations have recently produced a number of books, including Emergence (2008, with Paul Humphreys), The Nature of Life (2010, with Carol Cleland), Protocells: Bridging Nonliving and Living Matter (2009, with Rasmussen et al), and The Ethics of Protocells: Moral and Social Implications of Creating Life in the Laboratory (2009, with Emily Parke). He is currently writing a book about the emergence and open-ended evolution of life, mind, and technology.Mark A. Bedau, Pluralism About How Wholes Emerge From Parts, lecture, ICI Berlin, 28 February 2013, part 1, video recording, mp4, 21:02 <https://doi.org/10.25620/e130228

Dynamics of the environment for adaptation in static resource models

We measure the environment that is relevant to a population&apos;s adaptation as the information-theoretic uncertainty of the distribution of local environmental states that the adapting population experiences. Then w