scholarly journals Integrative emergence in contrast to separating modularity in plant biology: views on systems biology with information, signals and memory at scalar levels from molecules to the biosphere

2021 ◽  
Vol 33 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Ulrich Lüttge
Keyword(s):  
Systems Biology ◽  
Building Blocks ◽  
Plant Biology ◽  
Self Organization ◽  
Modern Aspect ◽  
Whole Plant ◽  
Emergent Systems ◽  
Per Se ◽  
Living Organisms ◽  
Creative Self

AbstractModularity is reductionism and materialism, where modules are considered as building blocks per se. By contrast self-organization of modules in living organisms, like plants, generates the emergence of integrated systems with new properties not predicted by the properties of the modules. This can occur at the hierarchy of a series of scalar levels, where emergent systems become modules for emergence of new systems on the next higher scalar level akin to a hierarchy of networks from molecules, cells and individuals up to the levels of ecosystems, biomes and the entire biosphere or Gaia. The systems on these levels are holobiont-like systems, i.e., central organisms in interaction with all their associated organisms as a unit for selection in evolution. Systems biology, now a modern aspect of plant biology, has started with the advancement of whole-plant physiology in the early 1970s unraveling the roles of signaling for integration and cooperation of parts or modules in the performance of entire plants. Fixation of information in plant memory and emergence from such storage rules the timing of events of emergence. With the enthusiasm promoted by the creative self-organization of modules into the emergence of exciting new systems, biology diverts from the reductionism and materialism of bare modularity. Understanding emergence helps to advance on the rocky paths towards understanding the complexity of life.

scholarly journals Self-replication of a quantum artificial organism driven by single-photon pulses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniel Valente
Keyword(s):  
Self Assembly ◽  
Artificial Life ◽  
Single Photon ◽  
Self Organization ◽  
Physical Systems ◽  
Self Organized ◽  
Living Organisms ◽  
A Chain ◽  
Thermodynamic Mechanism ◽  
Self Replication

AbstractImitating the transition from inanimate to living matter is a longstanding challenge. Artificial life has achieved computer programs that self-replicate, mutate, compete and evolve, but lacks self-organized hardwares akin to the self-assembly of the first living cells. Nonequilibrium thermodynamics has achieved lifelike self-organization in diverse physical systems, but has not yet met the open-ended evolution of living organisms. Here, I look for the emergence of an artificial-life code in a nonequilibrium physical system undergoing self-organization. I devise a toy model where the onset of self-replication of a quantum artificial organism (a chain of lambda systems) is owing to single-photon pulses added to a zero-temperature environment. I find that spontaneous mutations during self-replication are unavoidable in this model, due to rare but finite absorption of off-resonant photons. I also show that the replication probability is proportional to the absorbed work from the photon, thereby fulfilling a dissipative adaptation (a thermodynamic mechanism underlying lifelike self-organization). These results hint at self-replication as the scenario where dissipative adaptation (pointing towards convergence) coexists with open-ended evolution (pointing towards divergence).

scholarly journals Dimerization and oligomerization of DNA-assembled building blocks for controlled multi-motion in high-order architectures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ling Xin ◽  
Xiaoyang Duan ◽  
Na Liu
Keyword(s):  
Building Block ◽  
Degrees Of Freedom ◽  
Building Blocks ◽  
Single Type ◽  
Hierarchical Assembly ◽  
Optical Responses ◽  
Self Association ◽  
Living Organisms ◽  
Order Structures ◽  
Chiral System

AbstractIn living organisms, proteins are organized prevalently through a self-association mechanism to form dimers and oligomers, which often confer new functions at the intermolecular interfaces. Despite the progress on DNA-assembled artificial systems, endeavors have been largely paid to achieve monomeric nanostructures that mimic motor proteins for a single type of motion. Here, we demonstrate a DNA-assembled building block with rotary and walking modules, which can introduce new motion through dimerization and oligomerization. The building block is a chiral system, comprising two interacting gold nanorods to perform rotation and walking, respectively. Through dimerization, two building blocks can form a dimer to yield coordinated sliding. Further oligomerization leads to higher-order structures, containing alternating rotation and sliding dimer interfaces to impose structural twisting. Our hierarchical assembly scheme offers a design blueprint to construct DNA-assembled advanced architectures with high degrees of freedom to tailor the optical responses and regulate multi-motion on the nanoscale.

scholarly journals Self-reproducing catalyst drives repeated phospholipid synthesis and membrane growth

2015 ◽  
Vol 112 (27) ◽  
pp. 8187-8192 ◽  
Author(s):  
Michael D. Hardy ◽  
Jun Yang ◽  
Jangir Selimkhanov ◽  
Christian M. Cole ◽  
Lev S. Tsimring ◽  
...  
Keyword(s):  
Lipid Synthesis ◽  
Building Blocks ◽  
Phospholipid Bilayer ◽  
Phospholipid Synthesis ◽  
Synthetic Membranes ◽  
Design And Synthesis ◽  
Membrane Growth ◽  
Membrane Bound ◽  
Living Organisms ◽  
Dynamic Structures

Cell membranes are dynamic structures found in all living organisms. There have been numerous constructs that model phospholipid membranes. However, unlike natural membranes, these biomimetic systems cannot sustain growth owing to an inability to replenish phospholipid-synthesizing catalysts. Here we report on the design and synthesis of artificial membranes embedded with synthetic, self-reproducing catalysts capable of perpetuating phospholipid bilayer formation. Replacing the complex biochemical pathways used in nature with an autocatalyst that also drives lipid synthesis leads to the continual formation of triazole phospholipids and membrane-bound oligotriazole catalysts from simpler starting materials. In addition to continual phospholipid synthesis and vesicle growth, the synthetic membranes are capable of remodeling their physical composition in response to changes in the environment by preferentially incorporating specific precursors. These results demonstrate that complex membranes capable of indefinite self-synthesis can emerge when supplied with simpler chemical building blocks.

Core-modified porphyrins: novel building blocks in chemistry

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Aleksey E. Kuznetsov
Keyword(s):  
Periodic Table ◽  
Building Blocks ◽  
Effective Strategy ◽  
Research Groups ◽  
Structures And Properties ◽  
Porphyrin Core ◽  
Living Organisms ◽  
New Compounds ◽  
Related Compounds ◽  
Nitrogen Phosphorus

Abstract Various (metallo)porphyrins and related compounds have been intensively investigated by different research groups due to their extremely important role in living organisms along with their versatile applications in technology. The design of novel porphyrinoids by core-modification, or substitution of pyrrole nitrogens, with the elements of other groups of the Periodic Table has been considered as a highly promising methodology for tuning structures and properties of porphyrinoids and thus opening new possible applications for them. Much effort has been given to the modifications of the porphyrin core with elements of the main groups, namely O, S, Se (chalcogens), and the heavier congener of nitrogen, phosphorus. In general, the porphyrin core modification by replacing nitrogens with heteroatoms is a promising and effective strategy for obtaining new compounds with unusual structures and properties (optical, electrochemical, coordinating, etc.) as well as reactivity. These novel molecules can also be employed as promising building or construction blocks in various applications in the nanotechnology area.

Haematite–water system on Mars and its possible role in chemical evolution

2007 ◽  
Vol 6 (4) ◽  
pp. 267-271 ◽  
Author(s):  
Avnish Kumar Arora ◽  
Varsha Tomar ◽  
Aarti ◽  
K.T. Venkateswararao ◽  
Kamaluddin
Keyword(s):  
Chemical Evolution ◽  
Water System ◽  
American Chemical Society ◽  
Building Blocks ◽  
Chemical Society ◽  
Geological Evidence ◽  
Water On Mars ◽  
Western Regional ◽  
Living Organisms ◽  
Aqueous Conditions

AbstractRecent findings on the presence of water on Mars (Baker, V.R. (2006). Geomorphological evidence for water on Mars. Elements2(3), 139–143; DeJong, E. (2006). Geological evidence of the presence of water on Mars. Abstracts from the 40th Western Regional Meeting of the American Chemical Society, Anaheim, CA, January, 2006, pp. 22–25. American Chemical Society, Washington, DC; McSween, H.Y. Jr. (2006). Water on Mars. Elements2(3), 135–137; Mitrofanov, I.G. (2005). Water explorations on Mars. Priroda9, 34–43) strongly suggest that there existed a period of chemical evolution eventually leading to life processes on primitive Mars (Kanavarioti, A. & Maneinelli, R.L. (1990). Could organic matter have been preserved on Mars for 3.5 billion years. Icarus84, 196–202). Owing to the adverse conditions, it is quite likely that the process of chemical evolution would have been suppressed and any living organisms that formed would have become extinct over time on Mars. The presence of water as a necessity for the survival of living organisms and the presence of grey haematite, originated under aqueous conditions, have led us to investigate the possible role of haematite in the chemical evolution on Mars. Our observations suggest that iron oxide hydroxide (FeOOH), a precursor of haematite, has a much higher binding affinity towards ribose nucleotides (the building blocks of RNA) than the haematite itself. This would mean that during the process of haematite formation, especially through the probable process of Fe3+ hydrolysis by aqueous ammonia, the precursors of haematite might have played a significant role in the processes leading to chemical evolution and the possible origin of life on Mars.

scholarly journals A developmental biologist’s journey to rediscover the Zen of plant physiology

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 264 ◽  
Author(s):  
José R. Dinneny
Keyword(s):  
Plant Physiology ◽  
Human Population ◽  
Holistic Approach ◽  
Normal Function ◽  
Plant Biology ◽  
Form And Function ◽  
Adaptive Mechanisms ◽  
Basic Concepts ◽  
Living Organisms ◽  
And Function

Physiology, which is often viewed as a field of study distinct from development, is technically defined as the branch of biology that explores the normal function of living organisms and their parts. Because plants normally develop continuously throughout their life, plant physiology actually encompasses all developmental processes. Viewing plant biology from a physiologist’s perspective is an attempt to understand the interconnectedness of development, form, and function in the context of multidimensional complexity in the environment. To meet the needs of an expanding human population and a degrading environment, we must understand the adaptive mechanisms that plants use to acclimate to environmental change, and this will require a more holistic approach than is used by current molecular studies. Grand challenges for studies on plant physiology require a more sophisticated understanding of the environment that plants grow in, which is likely to be at least as complex as the plant itself. Moving the lab to the field and using the field for inspiration in the lab need to be expressly promoted by the community as we work to apply the basic concepts learned through reductionist approaches toward a more integrated and realistic understanding of the plant.

Ordered Assembling of Size and Shape Selected Nanocrystals

1998 ◽  
Vol 4 (S2) ◽  
pp. 728-729
Author(s):  
Z.L. Wang
Keyword(s):  
Organic Molecules ◽  
Three Dimensional ◽  
Building Blocks ◽  
Organic Coating ◽  
Self Organization ◽  
Functional Specificity ◽  
Orientation Order ◽  
Self Assembled ◽  
Superlattice Structures ◽  
Physical And Chemical

Nanoparticles and the physical and chemical functional specificity and selectivity they possess, suggest them as ideal building blocks for two- and three-dimensional cluster self-assembled superlattice structures, in which the particles behave as well-defined molecular matter and they are arranged with long-range translation and even orientation order [1]. Self-assembled arrays involve self-organization into monolayers, thin films, and superlattices of size-selected nanoclusters encapsulated in protective compact organic coating. The macroscopic properties of the nanocrystal superlattice (NCS) are determined not only by the properties of each individual particle but by the coupling/interaction between nanocrystals interconnected and isolated by a monolayer of thin organic molecules.Periodic packing of nanocrystals is different from the 3-D packing of atoms. First, to an excellent approximation atoms are spherical, while nanoparticles can be faceted polyhedra, thus, the 3-D packing of particles can be critically affected by their shapes and sizes.

5. Robots and artificial life

2018 ◽  
Author(s):  
Margaret A. Boden
Keyword(s):  
Artificial Life ◽  
Biological Systems ◽  
Evolutionary Programming ◽  
Self Organization ◽  
Big Business ◽  
Practical Applications ◽  
Living Organisms ◽  
Self Organizing

Artificial life (A-Life) models biological systems. Like AI, it has both technological and scientific aims. ‘Robots and artificial life’ explains that A-Life is integral to AI, because all the intelligence we know about is found in living organisms. AI technologists turn to biology in developing practical applications of many kinds, including robots, evolutionary programming, and self-organizing devices. Robots are quintessential examples of AI, having high visibility and being hugely ingenious—and very big business, too. Evolutionary AI, although widely used, is less well known. Self-organizing machines are even less familiar. Nevertheless, in the quest to understand self-organization, AI has been as useful to biology as biology has been to AI.

scholarly journals Précis of Simple heuristics that make us smart

2000 ◽  
Vol 23 (5) ◽  
pp. 727-741 ◽  
Author(s):  
Peter M. Todd ◽  
Gerd Gigerenzer
Keyword(s):  
Animal Behavior ◽  
Information Search ◽  
Building Blocks ◽  
Decision Makers ◽  
Sequential Search ◽  
Simple Rules ◽  
Living Organisms ◽  
Deep Thought ◽  
Mental Resources ◽  
Simple Heuristics

How can anyone be rational in a world where knowledge is limited, time is pressing, and deep thought is often an unattainable luxury? Traditional models of unbounded rationality and optimization in cognitive science, economics, and animal behavior have tended to view decision-makers as possessing supernatural powers of reason, limitless knowledge, and endless time. But understanding decisions in the real world requires a more psychologically plausible notion of bounded rationality. In Simple heuristics that make us smart (Gigerenzer et al. 1999), we explore fast and frugal heuristics – simple rules in the mind's adaptive toolbox for making decisions with realistic mental resources. These heuristics can enable both living organisms and artificial systems to make smart choices quickly and with a minimum of information by exploiting the way that information is structured in particular environments. In this précis, we show how simple building blocks that control information search, stop search, and make decisions can be put together to form classes of heuristics, including: ignorance-based and one-reason decision making for choice, elimination models for categorization, and satisficing heuristics for sequential search. These simple heuristics perform comparably to more complex algorithms, particularly when generalizing to new data – that is, simplicity leads to robustness. We present evidence regarding when people use simple heuristics and describe the challenges to be addressed by this research program.

scholarly journals Self-Organization of Motor-Propelled Cytoskeletal Filaments at Topographically Defined Borders

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Alf Månsson ◽  
Richard Bunk ◽  
Mark Sundberg ◽  
Lars Montelius
Keyword(s):  
Molecular Motor ◽  
Direct Consequence ◽  
Self Organization ◽  
Test Model ◽  
Structured Surfaces ◽  
Microstructured Surfaces ◽  
Living Organisms ◽  
Edge Tracing ◽  
Motor Density

Self-organization phenomena are of critical importance in living organisms and of great interest to exploit in nanotechnology. Here we describe in vitro self-organization of molecular motor-propelled actin filaments, manifested as a tendency of the filaments to accumulate in high density close to topographically defined edges on nano- and microstructured surfaces. We hypothesized that this “edge-tracing” effect either (1) results from increased motor density along the guiding edges or (2) is a direct consequence of the asymmetric constraints on stochastic changes in filament sliding direction imposed by the edges. The latter hypothesis is well captured by a model explicitly defining the constraints of motility on structured surfaces in combination with Monte-Carlo simulations [cf. Nitta et al. (2006)] of filament sliding. In support of hypothesis 2 we found that the model reproduced the edge tracing effect without the need to assume increased motor density at the edges. We then used model simulations to elucidate mechanistic details. The results are discussed in relation to nanotechnological applications and future experiments to test model predictions.

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