scholarly journals Downward causation by information control in micro-organisms

2011 ◽  
Vol 2 (1) ◽  
pp. 26-41 ◽  
Author(s):  
Luc Jaeger ◽  
Erin R. Calkins
Keyword(s):  
Operating System ◽  
Synthetic Biology ◽  
Living Systems ◽  
Functional Equivalence ◽  
Information Control ◽  
Top Down ◽  
Adaptive Selection ◽  
Feedback Information ◽  
Protein World ◽  
Micro Organisms

The concepts of functional equivalence classes and information control in living systems are useful to characterize downward (or top-down) causation by feedback information control in synthetic biology. Herein, we re-analyse published experiments of microbiology and synthetic biology that demonstrate the existence of several classes of functional equivalence in microbial organisms. Classes of functional equivalence from the bacterial operating system, which processes and controls the information encoded in the genome, can readily be interpreted as strong evidence, if not demonstration, of top-down causation (TDC) by information control. The proposed biological framework reveals how this type of causality is put in action in the cellular operating system. Considerations on TDC by information control and adaptive selection can be useful for synthetic biology by delineating the irreducible set of properties that characterizes living systems. Through a ‘retro-synthetic’ biology approach, these considerations could contribute to identifying the constraints behind the emergence of molecular complexity during the evolution of an ancient RNA/peptide world into a modern DNA/RNA/protein world. In conclusion, we propose TDCs by information control and adaptive selection as the two types of downward causality absolutely necessary for life.

scholarly journals Top-down causation and emergence: some comments on mechanisms

2011 ◽  
Vol 2 (1) ◽  
pp. 126-140 ◽  
Author(s):  
George F. R. Ellis
Keyword(s):  
Causal Power ◽  
Physical World ◽  
Human Mind ◽  
Information Control ◽  
Top Down ◽  
Bottom Up ◽  
Adaptive Selection ◽  
Abstract Entities ◽  
The Mind ◽  
Medical Healthcare

Both bottom-up and top-down causation occur in the hierarchy of structure and causation. A key feature is multiple realizability of higher level functions, and consequent existence of equivalence classes of lower level variables that correspond to the same higher level state. Five essentially different classes of top-down influence can be identified, and their existence demonstrated by many real-world examples. They are: algorithmic top-down causation; top-down causation via non-adaptive information control, top-down causation via adaptive selection, top-down causation via adaptive information control and intelligent top-down causation (the effect of the human mind on the physical world). Through the mind, abstract entities such as mathematical structures have causal power. The causal slack enabling top-down action to take place lies in the structuring of the system so as to attain higher level functions; in the way the nature of lower level elements is changed by context, and in micro-indeterminism combined with adaptive selection. Understanding top-down causation can have important effects on society. Two cases will be mentioned: medical/healthcare issues, and education—in particular, teaching reading and writing. In both cases, an ongoing battle between bottom-up and top-down approaches has important consequences for society.

scholarly journals Top-down causation by information control: from a philosophical problem to a scientific research programme

2008 ◽  
Vol 5 (27) ◽  
pp. 1159-1172 ◽  
Author(s):  
G Auletta ◽  
G.F.R Ellis ◽  
L Jaeger
Keyword(s):  
Feedback Control ◽  
Biological Systems ◽  
Scientific Research ◽  
Research Programme ◽  
Equivalence Classes ◽  
Philosophical Problem ◽  
Functional Equivalence ◽  
Information Control ◽  
Top Down ◽  
Different Types

It has been claimed that different types of causes must be considered in biological systems, including top-down as well as same-level and bottom-up causation, thus enabling the top levels to be causally efficacious in their own right. To clarify this issue, the important distinctions between information and signs are introduced here and the concepts of information control and functional equivalence classes in those systems are rigorously defined and used to characterize when top-down causation by feedback control happens, in a way that is testable. The causally significant elements we consider are equivalence classes of lower level processes, realized in biological systems through different operations having the same outcome within the context of information control and networks.

To Control the Uncontrollable

2017 ◽  
Author(s):  
Shuge Wei
Keyword(s):  
Information Control ◽  
Top Down ◽  
Treaty Port ◽  
The Government ◽  
Treaty Ports

Chapter 3 highlights the Nationalist government’s attempts to build an international propaganda system and to control the extraterritoriality-protected treaty-port papers from 1928 to 1932.The top-down information control exercised by the party-led propaganda system conflicted with the liberal journalism practiced in the treaty ports. Unable to achieve diplomatic progress in abolishing extraterritoriality, the Nanjing government made inroads into the extraterritorial system in specific fronts. Press control was one of them. By issuing postal bans, deporting journalists, and reviewing treaties with foreign cable companies, the government sought to strengthen its censorship power. It also adapted to the treaty-port press environment by camouflaging the party’s involvement through transnational covers.

Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1252-1254 ◽  
Author(s):  
Petra Schwille
Keyword(s):  
Synthetic Biology ◽  
Life Science ◽  
Biological Systems ◽  
Living Systems ◽  
Design Features ◽  
Literal Interpretation ◽  
Bottom Up ◽  
Systematic Construction ◽  
Science Discipline ◽  
Recent Developments

How synthetic can “synthetic biology” be? A literal interpretation of the name of this new life science discipline invokes expectations of the systematic construction of biological systems with cells being built module by module—from the bottom up. But can this possibly be achieved, taking into account the enormous complexity and redundancy of living systems, which distinguish them quite remarkably from design features that characterize human inventions? There are several recent developments in biology, in tight conjunction with quantitative disciplines, that may bring this literal perspective into the realm of the possible. However, such bottom-up engineering requires tools that were originally designed by nature’s greatest tinkerer: evolution.

scholarly journals Top-down causation: an integrating theme within and across the sciences?

2011 ◽  
Vol 2 (1) ◽  
pp. 1-3 ◽  
Author(s):  
George F. R. Ellis ◽  
Denis Noble ◽  
Timothy O'Connor
Keyword(s):  
Downward Causation ◽  
Top Down ◽  
Adaptive Selection ◽  
The World ◽  
Key Factor ◽  
Holistic Concept ◽  
Scientific Context ◽  
Semantic Frames ◽  
Whole Systems

This issue of the journal is focused on ‘top-down (downward) causation'. The words in this title, however, already raise or beg many questions. Causation can be of many kinds. They form our ways of ordering our scientific understanding of the world, all the way from the reductive concept of cause as elementary objects exerting forces on each other, through to the more holistic concept of attractors towards which whole systems move, and to adaptive selection taking place in the context of an ecosystem. As for ‘top’ and ‘down’, in the present scientific context, these are clearly metaphorical, as some of the articles in this issue of the journal make clear. Do we therefore know what we are talking about? The meeting at the Royal Society on which this set of papers is based included philosophers as well as scientists, and some of those (Jeremy Butterfield, Barry Loewer, Alan Love, Samir Okasha and Eric Scerri) have contributed articles to this issue. We would like also to thank those (Claus Kiefer, Peter Menzies, Jerome Feldman and David Papineau) who contributed only to the discussion meeting. Their contributions were also valuable, both at the meeting and by influencing the articles that have been written by others. We include a glossary with this introduction, composed by one of us (O'Connor). The clarification of the use of words and their semantic frames is an important role of philosophy, and this was evident in the discussions at the meeting and is now evident in many of the articles published here. Moreover, philosophical analysis is not limited to the papers by the professional philosophers. The idea of top-down causation is intimately related to concepts of emergence; indeed, it is a key factor in strong theories of emergence.

Living Technology: Exploiting Life's Principles in Technology

2010 ◽  
Vol 16 (1) ◽  
pp. 89-97 ◽  
Author(s):  
Mark A. Bedau ◽  
John S. McCaskill ◽  
Norman H. Packard ◽  
Steen Rasmussen
Keyword(s):  
Synthetic Biology ◽  
Artificial Life ◽  
Evolvable Hardware ◽  
Top Down ◽  
Bottom Up ◽  
Chemical Systems ◽  
The Social ◽  
Living Organisms ◽  
Electronic Chemical ◽  
Core Features

The concept of living technology—that is, technology that is based on the powerful core features of life—is explained and illustrated with examples from artificial life software, reconfigurable and evolvable hardware, autonomously self-reproducing robots, chemical protocells, and hybrid electronic-chemical systems. We define primary (secondary) living technology according as key material components and core systems are not (are) derived from living organisms. Primary living technology is currently emerging, distinctive, and potentially powerful, motivating this review. We trace living technology's connections with artificial life (soft, hard, and wet), synthetic biology (top-down and bottom-up), and the convergence of nano-, bio-, information, and cognitive (NBIC) technologies. We end with a brief look at the social and ethical questions generated by the prospect of living technology.

scholarly journals Opportunities, Challenges, and Future Considerations for Top-Down Governance for Biosecurity and Synthetic Biology

2021 ◽  
pp. 37-58
Author(s):  
R. Alexander Hamilton ◽  
Ruth Mampuys ◽  
S. E. Galaitsi ◽  
Aengus Collins ◽  
Ivan Istomin ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Genetic Engineering ◽  
Dna Sequencing ◽  
Environmental Sustainability ◽  
Gene Editing ◽  
Dual Use ◽  
Top Down ◽  
Modern Biology ◽  
The Creation

AbstractSynthetic biology promises to make biology easier to engineer (Endy 2005), enabling more people in less formal research settings to participate in modern biology. Leveraging advances in DNA sequencing and synthesis technologies, genetic assembly methods based on standard biological parts (e.g. BioBricks), and increasingly precise gene-editing tools (e.g. CRISPR), synthetic biology is helping increase the reliability of and accessibility to genetic engineering. Although potentially enabling tremendous opportunities for the advancement of the global bioeconomy, opening new avenues for the creation of health, wealth and environmental sustainability, the possibility of a more ‘democratic’ (widely accessible) bioengineering capability could equally yield new opportunities for accidental, unintended or deliberate misuse. Consequently, synthetic biology represents a quintessential ‘dual-use’ biotechnology – a technology with the capacity to enable significant benefits and risks (NRC 2004).

scholarly journals Expanding the Fluorine Chemistry of Living Systems Using Engineered Polyketide Synthase Pathways

Science ◽  
2013 ◽  
Vol 341 (6150) ◽  
pp. 1089-1094 ◽  
Author(s):  
Mark C. Walker ◽  
Benjamin W. Thuronyi ◽  
Louise K. Charkoudian ◽  
Brian Lowry ◽  
Chaitan Khosla ◽  
...  
Keyword(s):  
Natural Products ◽  
Synthetic Biology ◽  
Natural Product ◽  
Polyketide Synthase ◽  
Building Blocks ◽  
Living Systems ◽  
Synthetic Compounds ◽  
Fluorinated Building Blocks

Organofluorines represent a rapidly expanding proportion of molecules that are used in pharmaceuticals, diagnostics, agrochemicals, and materials. Despite the prevalence of fluorine in synthetic compounds, the known biological scope is limited to a single pathway that produces fluoroacetate. Here, we demonstrate that this pathway can be exploited as a source of fluorinated building blocks for introduction of fluorine into natural-product scaffolds. Specifically, we have constructed pathways involving two polyketide synthase systems, and we show that fluoroacetate can be used to incorporate fluorine into the polyketide backbone in vitro. We further show that fluorine can be inserted site-selectively and introduced into polyketide products in vivo. These results highlight the prospects for the production of complex fluorinated natural products using synthetic biology.

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