Is the cell really a machine?

Nicholson, Daniel J.

doi:10.1016/j.jtbi.2019.06.002

Cited by 127 publications

(85 citation statements)

References 155 publications

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“…In fact, we found that protein-protein reactivity networks showed characteristics of exponential networks thus lie in between power law (antibody-antigen) and randomly sampled networks. Indeed, in agreement with previous extensive literature on proteinprotein interaction networks, we confirmed the existence of hubs in protein-protein interaction (Kupiec, 2010;Nicholson, 2019;Stelzl et al, 2005). However, on the level of interaction motifs, such hubs were not as pronounced leading to a tree-branch-like structure (exponential degree distribution) as opposed to a power law degree distribution.…”

Section: Antibody-antigen Recognition Is Overall Oligoreactive With Isupporting

confidence: 91%

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

Akbar

Jeliazkov

Robert

et al. 2019

Preprint

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Antibody recognition of antigen relies on the specific interaction of amino acids at the paratopeepitope interface. A long-standing question in the fields of immunology and structural biology is whether paratope-epitope interaction is predictable. A fundamental premise for the predictability of paratope-epitope binding is the existence of structural units that are universally shared among antibody-antigen binding complexes. Here, we identified structural interaction motifs, which together compose a vocabulary of paratope-epitope binding that is shared among investigated antibody-antigen complexes. The vocabulary (i) is finite with less than 10 4 motifs, (ii) mediates specific and non-redundant interactions between paratope-epitope pairs, (iii) is immunity-specific (distinct from the motif vocabulary used by non-immune protein-protein interactions), and (iv) enables the machine learning prediction of paratope or epitope. The discovery of a vocabulary of paratope-epitope interaction demonstrates the learnability and predictability of paratope-epitope interaction.

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Section: Antibody-antigen Recognition Is Overall Oligoreactive With Isupporting

confidence: 91%

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

Akbar

Jeliazkov

Robert

et al. 2019

Preprint

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“…Cells are empirically revealing themselves to be inherently dynamic, self-organising systems that respond stochastically and nonlinearly to environmental stimuli (Nicholson 2019). Considering a plant cell, 1/f scaling is interesting, because it reveals long-lasting correlations or long-range spatial coherence in a growing cell system, which is similar to the behaviour close to critical points (Bédard et al 2006).…”

Section: Discussionmentioning

confidence: 99%

Extracellular ionic fluxes suggest the basis for cellular life at the 1/f ridge of extended criticality

Pietruszka

Olszewska

2020

Eur Biophys J

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The criticality hypothesis states that a system may be poised in a critical state at the boundary between different types of dynamics. Previous studies have suggested that criticality has been evolutionarily selected, and examples have been found in cortical cell cultures and in the human nervous system. However, no one has yet reported a single-or multi-cell ensemble that was investigated ex vivo and found to be in the critical state. Here, the precise 1/f noise was found for pollen tube cells of optimum growth and for the physiological ("healthy") state of blood cells. We show that the multi-scale processes that arise from the so-called critical phenomena can be a fundamental property of a living cell. Our results reveal that cell life is conducted at the border between order and disorder, and that the dynamics themselves drive a system towards a critical state. Moreover, a temperature-driven re-entrant state transition, manifest in the form of a Lorentz resonance, was found in the fluctuation amplitude of the extracellular ionic fluxes for the ensemble of elongating pollen tubes of Nicotiana tabacum L. or Hyacintus orientalis L. Since this system is fine-tuned for rapid expansion to reach the ovule at a critical temperature which results in fertilisation, the core nature of criticality (long-range coherence) offers an explanation for its potential in cell growth. We suggest that the autonomous organisation of expansive growth is accomplished by self-organised criticality, which is an orchestrated instability that occurs in an evolving cell. "Symbols are very adept at hiding the truth." (Dan Brown)

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“…mechanical components, and reassembling it, without the watch ceasing to exist. 17 Conversely, an organism cannot normally persist if it is decomposed into parts because, as some people have argued, the nature of organisms is such that their persistence conditions are radically different from those that make machines possible (Nicholson, 2013(Nicholson, , 2019. Of course, this does not mean that organisms do not tolerate any kind of replacements in their parts without losing their identity.…”

Section: The Inter-identity Of the Holobiontmentioning

confidence: 99%

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

Suárez

Triviño

2020

Front. Psychol.

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Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.

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Is the cell really a machine?

Cited by 127 publications

References 155 publications

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

Extracellular ionic fluxes suggest the basis for cellular life at the 1/f ridge of extended criticality

What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems

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