Self-organization versus Watchmaker: stochastic dynamics of cellular organization

Suberin nanostructures of Malus domestica Borkh. (Rosaceae) pericarp

New data are presented on nanosized suberin structures that directly participate in the formation of suberin deposits into the cell walls of the Malus domestica outer pericarp zone. The nanostructures were spherical formations containing conglomerates of electron-dense nanoparticles (diameter 5-30 nm) in the center. It has been demonstrated for the first time that the site of synthesis of suberin monomers, along with the endoplasmic reticulum (ER), may be the chloroplasts of hypoderm cells. Several possibilities for the transport of suberin nanoparticles have been discovered: via ER cisterns and its subdomains, via Golgi apparatus microvesicles, and via plasma membrane invaginations. The membrane structures of these compartments are directly related to intracytosis, the intracellular movement of suberin monomers; they can carry suberin monomeric precursors of a lipid nature in the membranes themselves or in the tubule's lumen. Either way, fusion with the hydrophobic surface of the suberin plate releases monomers, and they become accessible to apoplastic enzymes that polymerize suberin. It cannot be ruled out that the extremely arid conditions of the steppe ecological zone where the M. domestica grew could have influenced the features of metabolic processes, in particular, activating all possible pathways for the formation of suberin monomers, which make up suberin nanostructures.

Light-Operated Diverse Logic Gates Enabled by Modulating Time-Dependent Fluorescence of Dissipative Self-Assemblies

Light-fueled dissipative self-assembly possesses enormous potential in the field of optical information due to controllable time-dependent optical signals, but remains a great challenge for constructing intelligent light-operated logic circuits due to the limited availability of optical signal inputs and outputs. Herein, a series of light-fueled dissipative self-assembly systems with variable optical signals are reported to realize diverse logic gates by modulating time-dependent fluorescence variations of the loaded fluorophores. Three kinds of alkyl trimethylammonium homologs are employed to co-assemble with a merocyanine-based photoinduced amphiphile separately to construct a series of dissipative self-assemblies, showing unexpectedly different fluorescence control behaviors of loaded fluorophores during light irradiation and thermal relaxation processes. The opposite monotonicity of time-dependent emission intensity is achieved just by changing the excitation wavelength. Furthermore, by varying the types of trimethylammoniums and excitation wavelengths, a robust logic system is accomplished, integrating AND, XNOR, and XOR functions, which provides an effective pathway for advancing information transmission applications.

Mechanisms of pollen wall development in Lysimachia vulgaris

Exine, this complex sporopollenin-containing and highly variable among taxa envelope of the male gametophyte, consists of two layers, ectexine and endexine. We traced in detail the pollen wall development in Lysimachia vulgaris (Primulaceae), with emphasis on driving forces and critical ontogenetic time. By observation on the sequence of the emergent patterns and by analysis of their substructure with TEM, we intended to clarify the obvious and not-obvious ways of exine construction and to find out the common features in pattern development in other representatives in living nature. The ectexine and endexine ontogeny follows the main stages observed in many other species: first, the appearance of microspore plasma membrane invaginations with isotropic contents within, changed later to anisotropic state; then successive appearance of spherical, rod-like, and lamellate units in the periplasmic space. The lamellate endexine appears unusually early in the exine development. All these elements and their aggregations are manifestation of well-known physical phenomena: phase separation and micellar self-assembly. A consideration of similar surface patterns in very remote taxa suggests the participation in their development of some general nature phenomena as the lows of space-filling operations.

Pollen wall development in Impatiens glandulifera: exine substructure and underlying mechanisms

The aim of this study was to investigate in detail the pollen wall ontogeny in Impatiens glandulifera, with emphasis on the substructure and the underlying mechanisms of development. Sporopollenin-containing pollen wall, the exine, consists of two parts, ectexine and endexine. By determining the sequence of developing substructures with TEM, we have in mind to understand in which way the exine substructure is connected with function. We have shown earlier that physical processes of self-assembly and phase separation are universally involved in ectexine development; currently, we try to clear up whether these processes participate in endexine development. The data received were compared with those on other species. The ectexine ontogeny of I. glandulifera followed the main stages observed in many other species, including the late tetrad stage named "Golden gates". It turned out that the same physico-chemical processes act in endexine development, especially expressed in aperture sites. Another peculiar phenomenon observed in exine development was the recurrency of micellar sequence at near-aperture and aperture sites where the periplasmic space is widened. It should be noted that, in the whole, the developmental substructures observed during the tetrad and early post-tetrad period are similar in species with columellate exines. Evidently, these basic physical processes proceed, reiterating again and again in different species, resulting in an enormous variety of exine structures on the base of a relatively modest number of genes. Granular and alveolar exines emerge on the base of the same basic processes but are arrested at spherical and cylindrical micelle mesophases correspondingly.

Pollen wall and tapetal development in Cymbalaria muralis: the role of physical processes, evidenced by in vitro modelling

Our aim was to unravel the underlying mechanisms of pollen wall development in Cymbalaria muralis. By determining the sequence of developing substructures with TEM, we intended to compare it with that of other taxa and clarify whether physical processes of self-assembly and phase separation were involved. In parallel, we tried to simulate in vitro the substructures observed in Cymbalaria muralis exine development, using colloidal mixtures, to determine whether purely physical self-assembly processes could replicate them. Exine ontogeny followed the main stages observed in many other species and was initiated by phase separation, resulting in heterogeneity of the homogeneous contents of the periplasmic space around the microspore which is filled with genome-determined substances. At every stage, phase separation and self-assembly come into force, gradually driving the substances through the sequence of mesophases: spherical micelles, columns of spherical micelles, cylindrical micelles arranged in a layer, laminate micelles. The final two of these mesophases define the structure of the columellate ectexine and lamellate endexine respectively. Structures obtained in vitro from colloidal mixtures simulated the developing exine structures. Striking columella-like surface of some abnormal tapetal cells and lamella-like structures in the anther medium confirm the conclusion that pattern generation is a feature of colloidal materials, after genomic control on material contents. Simulation experiments show the high pattern-generating capacity of colloidal interactions.

The Roots of Genetic Coding in Aminoacyl-tRNA Synthetase Duality

Codon-dependent translation underlies genetics and phylogenetic inferences, but its origins pose two challenges. Prevailing narratives cannot account for the fact that aminoacyl-tRNA synthetases (aaRSs), which translate the genetic code, must collectively enforce the rules used to assemble themselves. Nor can they explain how specific assignments arose from rudimentary differentiation between ancestral aaRSs and corresponding transfer RNAs (tRNAs). Experimental deconstruction of the two aaRS superfamilies created new experimental tools with which to analyze the emergence of the code. Amino acid and tRNA substrate recognition are linked to phase transfer free energies of amino acids and arise largely from aaRS class-specific differences in secondary structure. Sensitivity to protein folding rules endowed ancestral aaRS-tRNA pairs with the feedback necessary to rapidly compare alternative genetic codes and coding sequences. These and other experimental data suggest that the aaRS bidirectional genetic ancestry stabilized the differentiation and interdependence required to initiate and elaborate the genetic coding table.

An integral insight into pollen wall development: involvement of physical processes in exine ontogeny in Calycanthus floridus L., with an experimental approach

We aimed to understand the underlying mechanisms of development in the sporopollenin-containing part of the pollen wall, the exine, one of the most complex cell walls in plants. Our hypothesis is that distinct physical processes, phase separation and micellar self-assembly, underpinexine development by taking the molecular building blocks, determined and synthesised by the genome, through several phase transitions. To test this hypothesis, we traced each stage of microspore development in Calycanthus floridus with transmission electron microscopy and then generated in vitro experimental simulations corresponding to every developmental stage. The sequence of structures observed within the periplasmic space around developing microspores starts with spherical units, which are rearranged into columns to then form rod-like units (the young columellae) and, finally, white line centred endexine lamellae. Phase separation precedes each developmental stage. The set of experimental simulations, obtained as self-assembled micellar mesophases formed at the interface between lipid and water compartments, was the same: spherical micelles; columns of spherical micelles; cylindrical micelles; and laminate micelles, separated by gaps, resembling white-lined lamellae. Thus, patterns simulating structures observed at the main stages of exine development in C. floridus were obtained from in vitro experiments, and hence purely physicochemical processes can construct exine-like patterns. This highlights the important part played by physical processes that are not under direct genomic control and share influence on the emerging ultrastructure with the genome during exine development. These findings suggest that a new approach to ontogenetic studies, including a consideration of physical factors, is required for a better understanding of developmental processes.

Artificial pollen walls simulated by the tandem processes of phase separation and self-assembly in vitro

Despite numerous attempts to elucidate the developmental mechanisms responsible for the observed diversity of pollen and spore walls, the processes involved remained obscure until the structures observed during exine development were recognized as a sequence of self-assembling micellar mesophases. To confirm this, a series of in vitro experiments was undertaken in which exine-like patterns were generated in colloidal mixtures by self-assembly, without any genomic participation. The intention was to test whether all the main types of exine structure could be simulated experimentally. Mixtures of substances, analogous to those involved in microspore development, were left undisturbed while water evaporated and self-assembly occurred. We varied the substances, their combinations and concentrations, and the physical constraints to make the experiments closer to the situation in nature. The resulting dry films were then examined using transmission electron microscopy. A variety of microstructures, simulating the full range of exine types, was obtained by micellar self-assembly. Moreover, the signs of related physicochemical process (i.e. phase separation) were also observed. Simple, energy-efficient, physical-chemical interactions, phase separation and self-assembly, are capable of generating exine-like patterns, providing evidence that these processes share control of exine formation with the well-documented program of gene expression.

Mimicking pollen and spore walls: self-assembly in action

BACKGROUND AND AIMS

Decades of research have attempted to elucidate the underlying developmental mechanisms that give rise to the enormous diversity of pollen and spore exines. The organization of the exine starts with the establishment of an elaborate glycocalyx within which the subsequent accumulation of sporopollenin occurs. Ontogenetic studies using transmission electron microscopy of over 30 species from many different groups have shown that the sequence of structures observed during development of the exine corresponds to the sequence of self-assembling micellar mesophases (including liquid crystals) observed at increasing concentrations of surfactants. This suggested that self-assembly plays an important part in exine pattern determination. Some patterns resembling separate layers of spore and pollen grain walls have been obtained experimentally, in vitro, by self-assembly. However, to firmly establish this idea, columellate and granulate exines, the most widespread forms, needed to be simulated experimentally.

METHODS

We used our original method, preparing mixtures of substances analogous to those known to occur in the periplasmic space of developing microspores, then leaving the mixtures undisturbed for specific periods of time to allow the process of self-assembly to occur. We developed our method further by using new substances analogous to those present in the periplasmic space and performing the experiments in a thin layer, more closely resembling the dimensions of the periplasmic space.

KEY RESULTS

The artificial microstructures obtained from our in vitro self-assembly experiments closely resembled the main types of exines, including tectate-columellate, granulate, alveolate and structureless, and permitted comparison with both developing and mature microspore walls. Compared with the previous attempts, we managed to simulate columellate and granulate exines, including lamellate endexine.

CONCLUSIONS

Our results show that simple physico-chemical interactions are able to generate patterns resembling those found in exines, supporting the idea that exine development in nature involves an interplay between the genome and self-assembly.

Assembling the thickest plant cell wall: exine development in Echinops (Asteraceae, Cynareae)

The exceptionally complex exine of Echinops, representing a significant investment of energy, develops from an elaborate glycocalyx which establishes, by self-assembly, a multi-layered system of micelles upon which sporopollenin polymerizes. We report on pollen development in two species of Echinops (Asteraceae, Cynareae) studied using transmission and scanning electron microscopy with an emphasis on the organisation and development of the massive sporoderm (maximum thickness 18 μm). The major events of exine deposition during the tetrad stage follow the now familiar sequence of self-assembling micellar mesophases and the subsequent incorporation of sporopollenin, observed here as: (1) spherical units with light cores; (2) columns of spherical units with dark cores; (3) large branched macromolecules arranged in a dendritic, three-dimensional network of long alveoli; and (4) alveoli with electron-transparent cores and dense walls. Later, (5) the primexine exhibits an elongated-alveolate pattern in which the alveoli have electron-dense cores and lighter exteriors. When (6) the thick inner columellae make contact with the outer primexine, sporopollenin accumulation in the cores of the primexine alveolae establishes continuity between the inner and outer columellae. In the free microspore stage, (7) the foot layer and first lamellae of the endexine appear (8). The endexine lamellae then increase in number and massive accumulation of sporopollenin occurs on all exine elements, making individual elements such as tectal spines, more pronounced. These and earlier findings, as well as experimental simulations of exine development, show that pollen wall morphogenesis involves a subtle interplay of gene-driven biological processes and physico-chemical factors offering abundant opportunities for the generation of complex, taxon-specific patterns.

Pollen wall ontogeny in Polemonium caeruleum (Polemoniaceae) and suggested underlying mechanisms of development

By a detailed ontogenetic study of Polemonium caeruleum pollen, tracing each stage of development at high TEM resolution, we aim to understand the establishment of the pollen wall and to unravel the mechanisms underlying sporoderm development. The main steps of exine ontogeny in Polemonium caeruleum, observed in the microspore periplasmic space, are spherical units, gradually transforming into columns, then to rod-like units (procolumellae), the appearance of the initial tectum, growth of columellae in height and tectum in thickness and initial sporopollenin accumulation on them, the appearance of the endexine lamellae and of dark-contrasted particles on the tectum, the appearance of a sponge-like layer and of the intine in aperture sites, the appearance of the foot layer on the base of the sponge-like layer and of spinules on the tectum, and massive sporopollenin accumulation. This sequence of developmental events fits well to the sequence of self-assembling micellar mesophases. This gives (together with earlier findings and experimental exine simulations) strong evidence that genome and self-assembly probably share control of exine formation. It is highly probable that self-assembly is an intrinsic instrument of evolution.

Adaptive self-organization in the embryo: its importance to adult anatomy and to tissue engineering

The anatomy of healthy humans shows much minor variation, and twin‐studies reveal at least some of this variation cannot be explained genetically. A plausible explanation is that fine‐scale anatomy is not specified directly in a genetic programme, but emerges from self‐organizing behaviours of cells that, for example, place a new capillary where it happens to be needed to prevent local hypoxia. Self‐organizing behaviour can be identified by manipulating growing tissues (e.g. putting them under a spatial constraint) and observing an adaptive change that conserves the character of the normal tissue while altering its precise anatomy. Self‐organization can be practically useful in tissue engineering but it is limited; generally, it is good for producing realistic small‐scale anatomy but large‐scale features will be missing. This is because self‐organizing organoids miss critical symmetry‐breaking influences present in the embryo: simulating these artificially, for example, with local signal sources, makes anatomy realistic even at large scales. A growing understanding of the mechanisms of self‐organization is now allowing synthetic biologists to take their first tentative steps towards constructing artificial multicellular systems that spontaneously organize themselves into patterns, which may soon be extended into three‐dimensional shapes.

Self-assembly as the underlying mechanism for exine development in Larix decidua D. C

Our findings suggest a new approach to pollen ontogenetic investigations, entailing consideration of physical factors, which enable a better understanding of exine developmental processes. The sporopollenin-containing part of the pollen wall-the exine-is one of the most complex cell walls in plants. By tracing each stage of microspore development in Larix decidua with TEM, we aimed to understand the underlying mechanisms of its exine establishment. Our hypothesis is that self-assembly interferes with exine development. Our specific aim is to generate experimental simulations of the exine developmental pattern. The sequence of events leading to exine development includes the appearance of spherical units in the periplasmic space, their rearrangement into radial columns, and the appearance of white-lined endexine lamellae. The final accumulation of sporopollenin proceeds in the post-tetrad period. The sequence of self-assembling micellar mesophases corresponds with that of the developmental events: spherical micelles; columns of spherical micelles; and laminate micelles separated by strata of water and visible as white-lined lamellae in TEM. Several patterns, simulating structures at different stages of exine development in Larix, were obtained from in vitro experiments. Purely physicochemical processes of self-assembly, which are not under direct genetic control, play an important role in exine development and share control with the genome. These findings suggest that a new approach to ontogenetic investigations, entailing consideration of physical factors (e.g., cell tensegrity), is required for a better understanding of developmental processes.

An improved Akt reporter reveals intra- and inter-cellular heterogeneity and oscillations in signal transduction

Akt is a key node in a range of signal transduction cascades and play a critical role in diseases such as cancer and diabetes. Fluorescently-tagged Akt reporters have been used to discern Akt localisation, yet it has not been clear how well these tools recapitulate the behaviour of endogenous Akt proteins. Here, we observed that fusion of eGFP to Akt2 impaired both its insulin-stimulated plasma membrane recruitment and its phosphorylation. Endogenous-like responses were restored by replacing eGFP with TagRFP-T. The improved response magnitude and sensitivity afforded by TagRFP-T-Akt2 over eGFP-Akt2 enabled monitoring of signalling outcomes in single cells at physiological doses of insulin with subcellular resolution and revealed two previously unreported features of Akt biology. In 3T3-L1 adipocytes, stimulation with insulin resulted in recruitment of Akt2 to the plasma membrane in a polarised fashion. Additionally, we observed oscillations in plasma membrane localised Akt2 in the presence of insulin with a consistent periodicity of 2 min. Our studies highlight the importance of fluorophore choice when generating reporter constructs and shed light on new Akt signalling responses that may encode complex signalling information.This article has an associated First Person interview with the first author of the paper.

Fundamental awareness: A framework for integrating science, philosophy and metaphysics

The ontologic framework of Fundamental Awareness proposed here assumes that non-dual Awareness is foundational to the universe, not arising from the interactions or structures of higher level phenomena. The framework allows comparison and integration of views from the three investigative domains concerned with understanding the nature of consciousness: science, philosophy, and metaphysics. In this framework, Awareness is the underlying reality, not reducible to anything else. Awareness and existence are the same. As such, the universe is non-material, self-organizing throughout, a holarchy of complementary, process driven, recursive interactions. The universe is both its own first observer and subject. Considering the world to be non-material and comprised, a priori, of Awareness is to privilege information over materiality, action over agency and to understand that qualia are not a “hard problem,” but the foundational elements of all existence. These views fully reflect main stream Western philosophical traditions, insights from culturally diverse contemplative and mystical traditions, and are in keeping with current scientific thinking, expressible mathematically.

Dynamic self-guiding analysis of Alzheimer's disease

We applied a self-guiding evolutionary algorithm to initiate the synthesis of the Alzheimer's disease-related data and literature. A protein interaction network associated with amyloid-beta precursor protein (APP) and a seed model that treats Alzheimer's disease as progressive dysregulation of APP-associated signaling were used as dynamic “guides” and structural “filters” in the recursive search, analysis, and assimilation of data to drive the evolution of the seed model in size, detail, and complexity. Analysis of data and literature across sub-disciplines and system-scale discovery platforms suggests a key role of dynamic cytoskeletal connectivity in the stability, plasticity, and performance of multicellular networks and architectures. Chronic impairment and/or dysregulation of cell adhesions/synapses, cytoskeletal networks, and/or reversible epithelial-to-mesenchymal-like transitions, which enable and mediate the stable and coherent yet dynamic and reconfigurable multicellular architectures, may lead to the emergence and persistence of the disordered, wound-like pockets/microenvironments of chronically disconnected cells. Such wound-like microenvironments support and are supported by pro-inflammatory, pro-secretion, de-differentiated cellular phenotypes with altered metabolism and signaling. The co-evolution of wound-like microenvironments and their inhabitants may lead to the selection and stabilization of degenerated cellular phenotypes, via acquisition of epigenetic modifications and mutations, which eventually result in degenerative disorders such as cancer and Alzheimer's disease.

Materiomics: an -omics approach to biomaterials research

The past fifty years have seen a surge in the use of materials for clinical application, but in order to understand and exploit their full potential, the scientific complexity at both sides of the interface--the material on the one hand and the living organism on the other hand--needs to be considered. Technologies such as combinatorial chemistry, recombinant DNA as well as computational multi-scale methods can generate libraries with a very large number of material properties whereas on the other side, the body will respond to them depending on the biological context. Typically, biological systems are investigated using both holistic and reductionist approaches such as whole genome expression profiling, systems biology and high throughput genetic or compound screening, as already seen, for example, in pharmacology and genetics. The field of biomaterials research is only beginning to develop and adopt these approaches, an effort which we refer to as "materiomics". In this review, we describe the current status of the field, and its past and future impact on the biomedical sciences. We outline how materiomics sets the stage for a transformative change in the approach to biomaterials research to enable the design of tailored and functional materials for a variety of properties in fields as diverse as tissue engineering, disease diagnosis and de novo materials design, by combining powerful computational modelling and screening with advanced experimental techniques.

Hsp90 binds microtubules and is involved in the reorganization of the microtubular network in angiosperms

Microtubules (MTs) are essential for many processes in plant cells. MT-associated proteins (MAPs) influence MT polymerization dynamics and enable them to perform their functions. The molecular chaperone Hsp90 has been shown to associate with MTs in animal and plant cells. However, the role of Hsp90-MT binding in plants has not yet been investigated. Here, we show that Hsp90 associates with cortical MTs in tobacco cells and decorates MTs in the phragmoplast. Further, we show that tobacco Hsp90_MT binds directly to polymerized MTs in vitro. The inhibition of Hsp90 by geldanamycin (GDA) severely impairs MT re-assembly after cold-induced de-polymerization. Our results indicate that the plant Hsp90 interaction with MTs plays a key role in cellular events, where MT re-organization is needed.

Order without design

Experimental reality in molecular and cell biology, as revealed by advanced research technologies and methods, is manifestly inconsistent with the design perspective on the cell, thus creating an apparent paradox: where do order and reproducibility in living systems come from if not from design?

I suggest that the very idea of biological design (whether evolutionary or intelligent) is a misconception rooted in the time-honored and thus understandably precious error of interpreting living systems/organizations in terms of classical mechanics and equilibrium thermodynamics. This error, introduced by the founders and perpetuated due to institutionalization of science, is responsible for the majority of inconsistencies, contradictions, and absurdities plaguing modern sciences, including one of the most startling paradoxes - although almost everyone agrees that any living organization is an open nonequilibrium system of continuous energy/matter flow, almost everyone interprets and models living systems/organizations in terms of classical mechanics, equilibrium thermodynamics, and engineering, i.e., in terms and concepts that are fundamentally incompatible with the physics of life.

The reinterpretation of biomolecules, cells, organisms, ecosystems, and societies in terms of open nonequilibrium organizations of energy/matter flow suggests that, in the domain of life, order and reproducibility do not come from design. Instead, they are natural and inevitable outcomes of self-organizing activities of evolutionary successful, and thus persistent, organizations co-evolving on multiple spatiotemporal scales as biomolecules, cells, organisms, ecosystems, and societies. The process of self-organization on all scales is driven by economic competition, obeys empirical laws of nonequilibrium thermodynamics, and is facilitated and, thus, accelerated by memories of living experience persisting in the form of evolutionary successful living organizations and their constituents.

Scale-free flow of life: on the biology, economics, and physics of the cell

The present work is intended to demonstrate that most of the paradoxes, controversies, and contradictions accumulated in molecular and cell biology over many years of research can be readily resolved if the cell and living systems in general are re-interpreted within an alternative paradigm of biological organization that is based on the concepts and empirical laws of nonequilibrium thermodynamics. In addition to resolving paradoxes and controversies, the proposed re-conceptualization of the cell and biological organization reveals hitherto unappreciated connections among many seemingly disparate phenomena and observations, and provides new and powerful insights into the universal principles governing the emergence and organizational dynamics of living systems on each and every scale of biological organizational hierarchy, from proteins and cells to economies and ecologies.

Chromatin: linking structure and function in the nucleolus

The nucleolus is an informative model structure for studying how chromatin-regulated transcription relates to nuclear organisation. In this review, we describe how chromatin controls nucleolar structure through both the modulation of rDNA activity by convergently-evolved remodelling complexes and by direct effects upon rDNA packaging. This packaging not only regulates transcription but may also be important for suppressing internal recombination between tandem rDNA repeats. The identification of nucleolar histone chaperones and novel chromatin proteins by mass spectrometry suggests that structure-specific chromatin components remain to be characterised and may regulate the nucleolus in novel ways. However, it also suggests that there is considerable overlap between nucleolar and non-nucleolar-chromatin components. We conclude that a fuller understanding of nucleolar chromatin will be essential for understanding how gene organisation is linked with nuclear architecture.

The PDZ domain as a complex adaptive system

Specific protein associations define the wiring of protein interaction networks and thus control the organization and functioning of the cell as a whole. Peptide recognition by PDZ and other protein interaction domains represents one of the best-studied classes of specific protein associations. However, a mechanistic understanding of the relationship between selectivity and promiscuity commonly observed in the interactions mediated by peptide recognition modules as well as its functional meaning remain elusive. To address these questions in a comprehensive manner, two large populations of artificial and natural peptide ligands of six archetypal PDZ domains from the synaptic proteins PSD95 and SAP97 were generated by target-assisted iterative screening (TAIS) of combinatorial peptide libraries and by synthesis of proteomic fragments, correspondingly. A comparative statistical analysis of affinity-ranked artificial and natural ligands yielded a comprehensive picture of known and novel PDZ ligand specificity determinants, revealing a hitherto unappreciated combination of specificity and adaptive plasticity inherent to PDZ domain recognition. We propose a reconceptualization of the PDZ domain in terms of a complex adaptive system representing a flexible compromise between the rigid order of exquisite specificity and the chaos of unselective promiscuity, which has evolved to mediate two mutually contradictory properties required of such higher order sub-cellular organizations as synapses, cell junctions, and others – organizational structure and organizational plasticity/adaptability. The generalization of this reconceptualization in regard to other protein interaction modules and specific protein associations is consistent with the image of the cell as a complex adaptive macromolecular system as opposed to clockwork.

Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuitry

A large body of experimental evidence indicates that the specific molecular interactions and/or chemical conversions depicted as links in the conventional diagrams of cellular signal transduction and metabolic pathways are inherently probabilistic, ambiguous and context-dependent. Being the inevitable consequence of the dynamic nature of protein structure in solution, the ambiguity of protein-mediated interactions and conversions challenges the conceptual adequacy and practical usefulness of the mechanistic assumptions and inferences embodied in the design charts of cellular circuitry. It is argued that the reconceptualization of molecular recognition and cellular organization within the emerging interpretational framework of self-organization, which is expanded here to include such concepts as bounded stochasticity, evolutionary memory, and adaptive plasticity offers a significantly more adequate representation of experimental reality than conventional mechanistic conceptions do. Importantly, the expanded framework of self-organization appears to be universal and scale-invariant, providing conceptual continuity across multiple scales of biological organization, from molecules to societies. This new conceptualization of biological phenomena suggests that such attributes of intelligence as adaptive plasticity, decision-making, and memory are enforced by evolution at different scales of biological organization and may represent inherent properties of living matter.

Nanoscopic medicine: the next frontier

The extraordinary progress that has taken place in cell science and optical nanoscale microscopy has led recently to the concept of medical nanoscopy. Here, we lay out a concept for developing live cell nanoscopy into a comprehensive diagnostic and therapeutic scheme referred to as nanoscopic medicine, which integrates live cell nanoscopy with the structural and functional studies of nanoscopic protein machines (NPMs), the systems biology of NPMs, fluorescent labeling, nanoscopic analysis, and nanoscopic intervention, in order to advance the medical frontier toward the nanoscopic fundament of the cell. It aims at the diagnosis and therapy of diseases by directly visualizing, analyzing, and modifying NPMs and their networks in living cells and tissues.

Self-organization versus Watchmaker: Molecular motors and protein translocation

Generation of directional movement at the molecular scale is a phenomenon crucial for biological organization and dynamics. It is traditionally described in mechanistic terms, in consistency with the conventional machine-like image of the cell. The designated and highly specialized protein machines and molecular motors are presumed to bring about most of cellular motion. A review of experimental data suggests, however, that uncritical adherence to mechanistic interpretations may limit the ability of researchers to comprehend and model biology. Specifically, this article illustrates that the interpretation of molecular motors and protein translocation in terms of stochasticity and self-organization appears to provide a more adequate and fruitful conceptual framework for understanding of biological organization at the molecular scale.

Implications of 'postmodern biology' for pathology: the Cell Doctrine

Recent insights regarding stem cells, repression and de-repression of gene expression, and the application of Complexity Theory to cell and molecular biology require a re-evaluation of many long-held dogmas regarding the nature of the human body in health and disease. Greater than expected cell plasticity, trafficking of cells between organs, 'cellular uncertainty', stochasticity of cell origins and fates, and a reconsideration of Cell Doctrine itself all logically follow from these observations and conceptual approaches. In this paper, these themes will be considered and some implications for the investigative pathologist will be explored.

Checking and fixing the cellular nanomachinery: towards medical nanoscopy

Most diseases, regardless of their diverse etiologies, manifest themselves as defects of cellular proteins. Cellular proteins have been recently shown to form specific complexes exerting their functions as if they were nanoscopic machines. Such nanoscopic protein machines cooperate in functional modules, yielding extended, highly compartmentalized networks. The classical resolution limits of fluorescence microscopy have also been recently overcome, opening the nanometer domain to live-cell imaging. Together, progress in functional proteomics and live-cell imaging provide novel possibilities for directly analyzing and modifying nanoscopic protein machines in living cells and tissues.