A biological relativity view of the relationships between genomes and phenotypes

Personalized redox biology: Designs and concepts

Personalized interventions are regarded as a next-generation approach in almost all fields of biomedicine, such as clinical medicine, exercise, nutrition and pharmacology. At the same time, an increasing body of evidence indicates that redox processes regulate, at least in part, multiple aspects of human physiology and pathology. As a result, the idea of applying personalized redox treatments to improve their efficacy has gained popularity among researchers in recent years. The aim of the present primer-style review was to highlight some crucial yet underappreciated methodological, statistical, and interpretative concepts within the redox biology literature, while also providing a physiology-oriented perspective on personalized redox biology. The topics addressed are: (i) the critical issue of investigating the potential existence of inter-individual variability; (ii) the importance of distinguishing a genuine and consistent response of a subject from a chance finding; (iii) the challenge of accurately quantifying the effect of a redox treatment when dealing with 'extreme' groups due to mathematical coupling and regression to the mean; and (iv) research designs and analyses that have been implemented in other fields, and can be reframed and exploited in a redox biology context.

Cancer as a form of life: Musings of the cancer and evolution symposium

Advanced cancer is one of the major problems in oncology as currently, despite the recent technological and scientific advancements, the mortality of metastatic disease remains very high at 70-90%. The field of oncology is in urgent need of novel ideas in order to improve quality of life and prognostic of cancer patients. The Cancer and Evolution Symposium organized online October 14-16, 2020 brought together a group of specialists from different fields that presented innovative strategies for better understanding, preventing, diagnosing, and treating cancer. Today still, the main reasons behind the high incidence and mortality of advanced cancer are, on one hand, the paucity of funding and effort directed to cancer prevention and early detection, and, on the other hand, the lack of understanding of the cancer process itself. I argue that besides being a disease, cancer is also a form of life, and, this frame of reference may provide a fresh look on this complex process. Here, I provide a different angle to several contemporary cancer theories discussing them from the perspective of "cancer-forms of life" (i.e. bionts) point of view. The perspectives and the several "bionts" introduced here, by no means exclusive or comprehensive, are just a shorthand that will hopefully encourage the readers, to further explore the contemporary oncology theoretical landscape.

How the Toxin got its Toxicity

Venom systems are functional and ecological traits, typically used by one organism to subdue or deter another. A predominant subset of their constituent molecules—“toxins”—share this ecological function and are therefore molecules that mediate interactions between organisms. Such molecules have been referred to as “exochemicals.” There has been debate within the field of toxinology concerning the evolutionary pathways leading to the “recruitment” of a gene product for a toxic role within venom. We review these discussions and the evidence interpreted in support of alternate pathways, along with many of the most popular models describing the origin of novel molecular functions in general. We note that such functions may arise with or without gene duplication occurring and are often the consequence of a gene product encountering a novel “environment,” i.e., a range of novel partners for molecular interaction. After stressing the distinction between “activity” and “function,” we describe in detail the results of a recent study which reconstructed the evolutionary history of a multigene family that has been recruited as a toxin and argue that these results indicate that a pluralistic approach to understanding the origin of novel functions is advantageous. This leads us to recommend that an expansive approach be taken to the definition of “neofunctionalization”—simply the origins of a novel molecular function by any process—and “recruitment”—the “weaponization” of a molecule via the acquisition of a toxic function in venom, by any process. Recruitment does not occur at the molecular level or even at the level of gene expression, but only when a confluence of factors results in the ecological deployment of a physiologically active molecule as a toxin. Subsequent to recruitment, the evolutionary regime of a gene family may shift into a more dynamic form of “birth-and-death.” Thus, recruitment leads to a form of “downwards causation,” in which a change at the ecological level at which whole organisms interact leads to a change in patterns of evolution at the genomic level.

Two decades of functional-structural plant modelling: now addressing fundamental questions in systems biology and predictive ecology

BACKGROUND

Functional-structural plant models (FSPMs) explore and integrate relationships between a plant's structure and processes that underlie its growth and development. In the last 20 years, scientists interested in functional-structural plant modelling have expanded greatly the range of topics covered and now handle dynamical models of growth and development occurring from the microscopic scale, and involving cell division in plant meristems, to the macroscopic scales of whole plants and plant communities.

SCOPE

The FSPM approach occupies a central position in plant science; it is at the crossroads of fundamental questions in systems biology and predictive ecology. This special issue of Annals of Botany features selected papers on critical areas covered by FSPMs and examples of comprehensive models that are used to solve theoretical and applied questions, ranging from developmental biology to plant phenotyping and management of plants for agronomic purposes. Altogether, they offer an opportunity to assess the progress, gaps and bottlenecks along the research path originally foreseen for FSPMs two decades ago. This review also allows discussion of current challenges of FSPMs regarding (1) integration of multidisciplinary knowledge, (2) methods for handling complex models, (3) standards to achieve interoperability and greater genericity and (4) understanding of plant functioning across scales.

CONCLUSIONS

This approach has demonstrated considerable progress, but has yet to reach its full potential in terms of integration and heuristic knowledge production. The research agenda of functional-structural plant modellers in the coming years should place a greater emphasis on explaining robust emergent patterns, and on the causes of possible deviation from it. Modelling such patterns could indeed fuel both generic integration across scales and transdisciplinary transfer. In particular, it could be beneficial to emergent fields of research such as model-assisted phenotyping and predictive ecology in managed ecosystems.

Are Synapse-Like Structures a Possible Way for Crosstalk of Cancer with Its Microenvironment?

The failure of therapies directed at targets within cancer cells highlight the necessity for a paradigm change in cancer therapy. The attention of researchers has shifted towards the disruption of cancer cell interactions with the tumor microenvironment. A typical example of such a disruption is the immune checkpoint cancer therapy that disrupts interactions between the immune and the cancer cells. The interaction of cancer antigens with T cells occurs in the immunological synapses. This is characterized by several special features, i.e., the proximity of the immune cells and their target cells, strong intercellular adhesion, and secretion of signaling cytokines into the intercellular cleft. Earlier, we hypothesized that the cancer-associated fibroblasts interacting with cancer cells through a synapse-like adhesion might play an important role in cancer tumors. Studies of the interactions between cancer cells and cancer-associated fibroblasts showed that their clusterization on the membrane surface determined their strength and specificity. The hundreds of interacting pairs are involved in the binding that may indicate the formation of synapse-like structures. These interactions may be responsible for successful metastasis of cancer cells, and their identification and disruption may open new therapeutic possibilities.

Unsolvable Problems of Biology: It Is Impossible to Create Two Identical Organisms, to Defeat Cancer, or to Map Organisms onto Their Genomes

The review is devoted to unsolvable problems of biology. 1) Problems unsolvable due to stochastic mutations occurring during DNA replication that make it impossible to create two identical organisms or even two identical complex cells (Sverdlov, E. D. (2009) Biochemistry (Moscow), 74, 939-944) and to "defeat" cancer. 2) Problems unsolvable due to multiple interactions in complex systems leading to the appearance of unpredictable emergent properties that prevent establishment of unambiguous relationships between the genetic architecture and phenotypic manifestation of the genome and make impossible to predict with certainty responses of the organism, its parts, or pathological processes to external factors. 3) Problems unsolvable because of the uncertainty principle and observer effect in biology, due to which it is impossible to obtain adequate information about cells in their tissue microenvironment by isolating and analyzing individual cells. In particular, we cannot draw conclusions on the properties of stem cells in their niches based on the properties of stem cell cultures. A strategy is proposed for constructing the pattern most closely approximated to the relationship of genotypes with their phenotypes by designing networks of intermediate phenotypes (endophenotypes).

Multidimensional Complexity of Cancer. Simple Solutions Are Needed

Cancer is a complex system. Tumor complexity is determined not only by genetic and epigenetic heterogeneity, but also by a huge number of interactions between cancer and normal cells. The heterogeneity and complexity of a tumor causes failure of molecular targeting therapy as a tool for fighting cancer. This review considers the concepts of malignant tumors as organisms that have common characteristics despite all heterogeneity. This leads to the idea that one of the most promising strategies for fighting cancer is the use of the patient's immune system.

The Semiosis of "Side Effects" in Genetic Interventions

Genetic interventions, which include transgenic engineering, gene editing, and other forms of genome modification aimed at altering the information "in" the genetic code, are rapidly increasing in power and scale. Biosemiotics offers unique tools for understanding the nature, risks, scope, and prospects of such technologies, though few in the community have turned their attention specifically in this direction. Bruni (2003, 2008) is an important exception. In this paper, I examine how we frame the concept of "side effects" that result from genetic interventions and how the concept stands up to current perspectives of the role of organism activity in development. I propose that once the role of living systems in constructing and modifying the informational value of their various developmental resources is taken into account, the concept of a "side effect" will need to be significantly revised. Far from merely a disturbance brought about in a senseless albeit complex system, a biosemiotic view would take "side effects" as at least sometimes the organism's active re-organization in order to accommodate or make use of novelty. This insight is nascent in the work of developmental plasticity and niche construction theory (West-Eberhard 2003; Odling-Smee et al. 2003), but it is brought into sharper focus by the explicitly interpretive perspective offered by biosemiotics. Understanding the "side effects" of genetic interventions depends in part on being able to articulate when and where unexpected consequences are a result of semiotic activity at various levels within the system. While a semiotic interpretation of "side effects" puts into question the naive attitude that would see all unintended side effects as indications of disturbance in system functionality, it certainly does not imply that such side effects are of no concern for the viability of the organisms in the system. As we shall see, the fact that such interventions do not respect the translation of information that occurs in multi-level biological systems ensures that disruption is still likely. But it does unprivilege the human agent as the sole generator of meaning and information in the products of biotechnology, with important consequences on how we understand our relationship with other species.

Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions

A unique myocardial characteristic is its ability to grow/remodel in order to adapt; this is determined partly by genes and partly by the environment and the milieu intérieur. In the "post-genomic" era, a need is emerging to elucidate the physiologic functions of myocardial genes, as well as potential adaptive and maladaptive modulations induced by environmental/epigenetic factors. Genome sequencing and analysis advances have become exponential lately, with escalation of our knowledge concerning sometimes controversial genetic underpinnings of cardiovascular diseases. Current technologies can identify candidate genes variously involved in diverse normal/abnormal morphomechanical phenotypes, and offer insights into multiple genetic factors implicated in complex cardiovascular syndromes. The expression profiles of thousands of genes are regularly ascertained under diverse conditions. Global analyses of gene expression levels are useful for cataloging genes and correlated phenotypes, and for elucidating the role of genes in maladies. Comparative expression of gene networks coupled to complex disorders can contribute insights as to how "modifier genes" influence the expressed phenotypes. Increasingly, a more comprehensive and detailed systematic understanding of genetic abnormalities underlying, for example, various genetic cardiomyopathies is emerging. Implementing genomic findings in cardiology practice may well lead directly to better diagnosing and therapeutics. There is currently evolving a strong appreciation for the value of studying gene anomalies, and doing so in a non-disjointed, cohesive manner. However, it is challenging for many-practitioners and investigators-to comprehend, interpret, and utilize the clinically increasingly accessible and affordable cardiovascular genomics studies. This survey addresses the need for fundamental understanding in this vital area.

Getting personal: can systems medicine integrate scientific and humanistic conceptions of the patient?

RATIONALE, AIMS AND OBJECTIVES

The practicing doctor, and most obviously the primary care clinician who encounters the full complexity of patients, faces several fundamental but intrinsically related theoretical and practical challenges - strongly actualized by so-called medically unexplained symptoms (MUS) and multi-morbidity. Systems medicine, which is the emerging application of systems biology to medicine and a merger of molecular biomedicine, systems theory and mathematical modelling, has recently been proposed as a primary care-centered strategy for medicine that promises to meet these challenges. Significantly, it has been proposed to do so in a way that at first glance may seem compatible with humanistic medicine. More specifically, it is promoted as an integrative, holistic, personalized and patient-centered approach. In this article, we ask whether and to what extent systems medicine can provide a comprehensive conceptual account of and approach to the patient and the root causes of health problems that can be reconciled with the concept of the patient as a person, which is an essential theoretical element in humanistic medicine.

METHODS

We answer this question through a comparative analysis of the theories of primary care doctor Eric Cassell and systems biologist Denis Noble.

RESULTS AND CONCLUSIONS

We argue that, although systems biological concepts, notably Noble's theory of biological relativity and downward causation, are highly relevant for understanding human beings and health problems, they are nevertheless insufficient in fully bridging the gap to humanistic medicine. Systems biologists are currently unable to conceptualize living wholes, and seem unable to account for meaning, value and symbolic interaction, which are central concepts in humanistic medicine, as constraints on human health. Accordingly, systems medicine as currently envisioned cannot be said to be integrative, holistic, personalized or patient-centered in a humanistic medical sense.

Genes without prominence: a reappraisal of the foundations of biology

The sequencing of the human genome raises two intriguing questions: why has the prediction of the inheritance of common diseases from the presence of abnormal alleles proved so unrewarding in most cases and how can some 25 000 genes generate such a rich complexity evident in the human phenotype? It is proposed that light can be shed on these questions by viewing evolution and organisms as natural processes contingent on the second law of thermodynamics, equivalent to the principle of least action in its original form. Consequently, natural selection acts on variation in any mechanism that consumes energy from the environment rather than on genetic variation. According to this tenet cellular phenotype, represented by a minimum free energy attractor state comprising active gene products, has a causal role in giving rise, by a self-similar process of cell-to-cell interaction, to morphology and functionality in organisms, which, in turn, by a self-similar process entailing Darwin's proportional numbers are influencing their ecosystems. Thus, genes are merely a means of specifying polypeptides: those that serve free energy consumption in a given surroundings contribute to cellular phenotype as determined by the phenotype. In such natural processes, everything depends on everything else, and phenotypes are emergent properties of their systems.

Membrane "potential-omics": toward voltage imaging at the cell population level in roots of living plants

Genetically encoded voltage-sensitive fluorescent proteins (VSFPs) are being used in neurobiology as non-invasive tools to study synchronous electrical activities in specific groups of nerve cells. Here we discuss our efforts to adapt this "light-based electrophysiology" for use in plant systems. We describe the production of transgenic plants engineered to express different versions of VSFPs that are targeted to the plasma membrane and internal membranes of root cells. The aim is to optically record concurrent changes in plasma membrane potential in populations of cells and at multiple membrane systems within single cells in response to various stimuli in living plants. Such coordinated electrical changes may globally orchestrate cell behavior to elicit successful reactions of the root as a whole to varying and unpredictable environments. Findings from membrane "potential-omics" can eventually be fused with data sets from other "omics" approaches to forge the integrated and comprehensive understanding that underpins the concept of systems biology.

On some recent insights in Integral Biomathics

This paper summarizes the results in Integral Biomathics obtained to this moment and provides an outlook for future research in the field.

Downward causes and appropriate abstractions: Alternative argument for Noble's position

In his article of this issue, Denis Noble argues that causation can occur at and between any scales - rather than levels - in nature. I agree with this conclusion, but do not find his reasoning fully persuasive. I offer an independent but related argument for his position, which focuses on the role of the process of abstraction in identifying and understanding a phenomenon. My aim is to give the reader another way to think about causal talk within the framework of Systems Biology.