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From Nanomachine to Nanobrain, Information Processing at a Molecular Scale
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From Nanomachine to Nanobrain, Information Processing at a Molecular Scale

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 14013

Special Issue Editor

Dr. Youri Timsit

E-Mail Website1 Website2
Guest Editor
Mediterranean Institute of Oceanography UM 110, Aix-Marseille Université, CNRS, IRD, Campus de Luminy, 13288 Marseille, France
Interests: structural biology; DNA; ribosome; ribosomal proteins; chromatin folding; structural transitions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nanomachines are the culmination of a conception of Life that took its roots in the second half of the 20th century, with the appearance of molecular biology. While this metaphor highlights the extraordinary properties of biological macromolecules, it is in line with the dominant ideology of the 21st century, which considers life (and human) according to its model of economic production. From slot to learning machines, the semantic field of machines irrevocably brings us back to an anthropomorphic concept of manufactured objects whose functions are to efficiently accomplish a repetitive task. However, can living beings from their smallest to their highest level of organization be compared to machines? Can this metaphor bias our understanding of biology, mislead us on the notion of function, and divert our attention from the essential properties of molecules that do not fit into the concept of the machine?

Unlike living beings, machines have severe limitations, which were masterfully illustrated in Charlie Chaplin's film "Modern Times". Everyone remembers the highly comical effect that a feeding machine can produce without feedback. Much less funny is to observe the ecological disasters caused by machines and their great designers. Like Chaplin, metazoans understood early on that they needed sensorimotor circuits to synchronize and adapt their motions to their fluctuating environment. What about LUCA and the subsequent unicellular life forms? Many unicellular organisms such as Amoeba, Paramecium, and Physarum polycephalum exhibit indeed complex behaviors although they do not possess nervous circuits. Recent studies have also shown that organelles such as ribosomes possess complex r-protein networks that probably play a role equivalent to that of nervous circuits, at a molecular scale. Has life developed molecular circuits that perform the roles of nervous systems in single cells or even organelles? Although artificial intelligence is very much in vogue today, focusing on “natural intelligence” and its earlier forms can be promising in many areas, from antibiotic resistance to nanotechnology. Thus, this Special Issue proposes to explore the properties of molecular networks involved in information processing.

Dr. Youri Timsit
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Published Papers (3 papers)

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Review

20 pages, 3177 KiB  
Review
From Molecular Recognition to the “Vehicles” of Evolutionary Complexity: An Informational Approach
by Pedro C. Marijuán and Jorge Navarro
Int. J. Mol. Sci. 2021, 22(21), 11965; https://doi.org/10.3390/ijms222111965 - 04 Nov 2021
Cited by 8 | Viewed by 1739
Abstract
Countless informational proposals and models have explored the singular characteristics of biological systems: from the initial choice of information terms in the early days of molecular biology to the current bioinformatic avalanche in this “omic” era. However, this was conducted, most often, within [...] Read more.
Countless informational proposals and models have explored the singular characteristics of biological systems: from the initial choice of information terms in the early days of molecular biology to the current bioinformatic avalanche in this “omic” era. However, this was conducted, most often, within partial, specialized scopes or just metaphorically. In this paper, we attempt a consistent informational discourse, initially based on the molecular recognition paradigm, which addresses the main stages of biological organization in a new way. It considers the interconnection between signaling systems and information flows, between informational architectures and biomolecular codes, between controlled cell cycles and multicellular complexity. It also addresses, in a new way, a central issue: how new evolutionary paths are opened by the cumulated action of multiple variation engines or mutational ‘vehicles’ evolved for the genomic exploration of DNA sequence space. Rather than discussing the possible replacement, extension, or maintenance of traditional neo-Darwinian tenets, a genuine informational approach to evolutionary phenomena is advocated, in which systemic variation in the informational architectures may induce differential survival (self-construction, self-maintenance, and reproduction) of biological agents within their open ended environment. Full article
(This article belongs to the Special Issue From Nanomachine to Nanobrain, Information Processing at a Molecular Scale)
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49 pages, 7495 KiB  
Review
Towards the Idea of Molecular Brains
by Youri Timsit and Sergeant-Perthuis Grégoire
Int. J. Mol. Sci. 2021, 22(21), 11868; https://doi.org/10.3390/ijms222111868 - 01 Nov 2021
Cited by 20 | Viewed by 4689
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This [...] Read more.
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors. Full article
(This article belongs to the Special Issue From Nanomachine to Nanobrain, Information Processing at a Molecular Scale)
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15 pages, 2432 KiB  
Review
Biomolecular Basis of Cellular Consciousness via Subcellular Nanobrains
by František Baluška, William B. Miller, Jr. and Arthur S. Reber
Int. J. Mol. Sci. 2021, 22(5), 2545; https://doi.org/10.3390/ijms22052545 - 03 Mar 2021
Cited by 29 | Viewed by 6654
Abstract
Cells emerged at the very beginning of life on Earth and, in fact, are coterminous with life. They are enclosed within an excitable plasma membrane, which defines the outside and inside domains via their specific biophysical properties. Unicellular organisms, such as diverse protists [...] Read more.
Cells emerged at the very beginning of life on Earth and, in fact, are coterminous with life. They are enclosed within an excitable plasma membrane, which defines the outside and inside domains via their specific biophysical properties. Unicellular organisms, such as diverse protists and algae, still live a cellular life. However, fungi, plants, and animals evolved a multicellular existence. Recently, we have developed the cellular basis of consciousness (CBC) model, which proposes that all biological awareness, sentience and consciousness are grounded in general cell biology. Here we discuss the biomolecular structures and processes that allow for and maintain this cellular consciousness from an evolutionary perspective. Full article
(This article belongs to the Special Issue From Nanomachine to Nanobrain, Information Processing at a Molecular Scale)
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