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Life
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Synthetic Biology: From Living Computers to Terraformation
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Synthetic Biology: From Living Computers to Terraformation

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Synthetic Biology and Systems Biology".

Deadline for manuscript submissions: closed (31 October 2018) | Viewed by 37432

Special Issue Editor

Prof. Dr. Ricard Solé

E-Mail Website
Guest Editor
1. ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Barcelona, 08003, Spain
2. Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico, (USA)
Interests: synthetic evolutionary transitions; liquid–solid brains; biological computation; origins and evolution of cognition; biosphere terraformation

Special Issue Information

Dear Colleagues,

Over the last two decades, synthetic biology has emerged as a novel field with major impact on both basic science and biomedical research. By moving beyond the classical approaches of genetic engineering, synthetic circuits implemented within living cells allow to redesign nature from the molecular and cellular levels to multicellular scales. Because of its potential to change the behavior of living systems, synthetic biology also provides a new avenue to interrogate nature. Synthetic microorganisms have been built to explore cooperation and conflict in microbial interactions as well as the rise of multicellularity. Complex computational tasks have also been created de novo and used to expand the cognitive potential of cellular assemblies. In parallel with all these already promising results, synthetic biology is being considered as a potential path to artificially modify microbiomes and even terraform Mars biosphere.

The objective of the present Special Issue of Life is to bring together original research and reviews on synthetic biology with a special emphasis on its current and future role in understanding the origins of living complexity on multiple scales. The broad scope of this Special Issue encompasses a diverse range of topics, including:

  • Computation in living cells and tissues
  • Engineering synthetic transitions
  • Engineering cognitive innovations
  • Synthetic evolutionary ecology
  • Synthetic transitions from parasitism to mutualism
  • Synthetic microbiomes
  • Planetary terraformation

Prof. Dr. Ricard Solé
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • synthetic biology
  • evolutionary innovations
  • synthetic ecosystems
  • biological computation
  • terraformation

Published Papers (6 papers)

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Research

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12 pages, 2318 KiB  
Article
Dynamical Task Switching in Cellular Computers
by Angel Goñi-Moreno, Fernando de la Cruz, Alfonso Rodríguez-Patón and Martyn Amos
Life 2019, 9(1), 14; https://doi.org/10.3390/life9010014 - 26 Jan 2019
Cited by 4 | Viewed by 4834
Abstract
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the [...] Read more.
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discuss the potential for future work in this area. Full article
(This article belongs to the Special Issue Synthetic Biology: From Living Computers to Terraformation)
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22 pages, 941 KiB  
Article
Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems
by Bernat Corominas-Murtra
Life 2019, 9(1), 9; https://doi.org/10.3390/life9010009 - 15 Jan 2019
Cited by 7 | Viewed by 4179
Abstract
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, [...] Read more.
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10 − 13 J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1 kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it. Full article
(This article belongs to the Special Issue Synthetic Biology: From Living Computers to Terraformation)
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Review

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17 pages, 36310 KiB  
Review
Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities
by Daniel Rodríguez Amor and Martina Dal Bello
Life 2019, 9(1), 22; https://doi.org/10.3390/life9010022 - 26 Feb 2019
Cited by 37 | Viewed by 11086
Abstract
Microbial cooperation pervades ecological scales, from single-species populations to host-associated microbiomes. Understanding the mechanisms promoting the stability of cooperation against potential threats by cheaters is a major question that only recently has been approached experimentally. Synthetic biology has helped to uncover some of [...] Read more.
Microbial cooperation pervades ecological scales, from single-species populations to host-associated microbiomes. Understanding the mechanisms promoting the stability of cooperation against potential threats by cheaters is a major question that only recently has been approached experimentally. Synthetic biology has helped to uncover some of these basic mechanisms, which were to some extent anticipated by theoretical predictions. Moreover, synthetic cooperation is a promising lead towards the engineering of novel functions and enhanced productivity of microbial communities. Here, we review recent progress on engineered cooperation in microbial ecosystems. We focus on bottom-up approaches that help to better understand cooperation at the population level, progressively addressing the challenges of tackling higher degrees of complexity: spatial structure, multispecies communities, and host-associated microbiomes. We envisage cooperation as a key ingredient in engineering complex microbial ecosystems. Full article
(This article belongs to the Special Issue Synthetic Biology: From Living Computers to Terraformation)
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17 pages, 543 KiB  
Review
Synthetic Mutualism and the Intervention Dilemma
by Jai A. Denton and Chaitanya S. Gokhale
Life 2019, 9(1), 15; https://doi.org/10.3390/life9010015 - 28 Jan 2019
Cited by 8 | Viewed by 5577
Abstract
Ecosystems are complex networks of interacting individuals co-evolving with their environment. As such, changes to an interaction can influence the whole ecosystem. However, to predict the outcome of these changes, considerable understanding of processes driving the system is required. Synthetic biology provides powerful [...] Read more.
Ecosystems are complex networks of interacting individuals co-evolving with their environment. As such, changes to an interaction can influence the whole ecosystem. However, to predict the outcome of these changes, considerable understanding of processes driving the system is required. Synthetic biology provides powerful tools to aid this understanding, but these developments also allow us to change specific interactions. Of particular interest is the ecological importance of mutualism, a subset of cooperative interactions. Mutualism occurs when individuals of different species provide a reciprocal fitness benefit. We review available experimental techniques of synthetic biology focused on engineered synthetic mutualistic systems. Components of these systems have defined interactions that can be altered to model naturally occurring relationships. Integrations between experimental systems and theoretical models, each informing the use or development of the other, allow predictions to be made about the nature of complex relationships. The predictions range from stability of microbial communities in extreme environments to the collapse of ecosystems due to dangerous levels of human intervention. With such caveats, we evaluate the promise of synthetic biology from the perspective of ethics and laws regarding biological alterations, whether on Earth or beyond. Just because we are able to change something, should we? Full article
(This article belongs to the Special Issue Synthetic Biology: From Living Computers to Terraformation)
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Other

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15 pages, 1146 KiB  
Opinion
Real-World Synthetic Biology: Is It Founded on an Engineering Approach, and Should It Be?
by Jamie A. Davies
Life 2019, 9(1), 6; https://doi.org/10.3390/life9010006 - 07 Jan 2019
Cited by 12 | Viewed by 7168
Abstract
Authors often assert that a key feature of 21st-century synthetic biology is its use of an ‘engineering approach’; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even [...] Read more.
Authors often assert that a key feature of 21st-century synthetic biology is its use of an ‘engineering approach’; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey of synthetic biology projects that have reached, or are near to, commercial application outside laboratories shows that they showed very few of these attributes. Instead, they featured much trial and error, and the use of specialized, custom components and assays. What is more, consideration of the special features of living systems suggest that a conventional engineering approach will often not be helpful. The article concludes that the engineering approach may be useful in some projects, but it should not be used to define or constrain synthetic biological endeavour, and that in fact the conventional engineering has more to gain by expanding and embracing more biological ways of working. Full article
(This article belongs to the Special Issue Synthetic Biology: From Living Computers to Terraformation)
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6 pages, 601 KiB  
Perspective
The Hidden Charm of Life
by Manuel Porcar
Life 2019, 9(1), 5; https://doi.org/10.3390/life9010005 - 07 Jan 2019
Cited by 2 | Viewed by 3943
Abstract
Synthetic biology is an engineering view on biotechnology, which has revolutionized genetic engineering. The field has seen a constant development of metaphors that tend to highlight the similarities of cells with machines. I argue here that living organisms, particularly bacterial cells, are not [...] Read more.
Synthetic biology is an engineering view on biotechnology, which has revolutionized genetic engineering. The field has seen a constant development of metaphors that tend to highlight the similarities of cells with machines. I argue here that living organisms, particularly bacterial cells, are not machine-like, engineerable entities, but, instead, factory-like complex systems shaped by evolution. A change of the comparative paradigm in synthetic biology from machines to factories, from hardware to software, and from informatics to economy is discussed. Full article
(This article belongs to the Special Issue Synthetic Biology: From Living Computers to Terraformation)
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