A new biology for a new century

Traces of a Primitive RNA Ring in Current Genomes

(1) Background: Previous theoretical studies have provided arguments for the existence of a circular or hairpin RNA that could have served as a primitive informational and functional molecule at the origin of life. The present article consists of searching in current genomes for RNAs closest to this primitive RNA in terms of the occurrence of similar nucleotide motifs. (2) Methods: In searching for the smallest possible RNA capable of interacting with amino acids in the construction of the peptides of the primitive living world, we found a circular docosamer RNA molecule (length 22), which we called AL (for ALpha or Archetypal Loop). Then, we started to systematically track AL relics in current genomes in the form of motifs like pentamers or pairs of consecutive codons in common with AL. (3) Results: The sequence correspondence between AL and RNA sequences of organisms from different kingdoms of life (Archaea, Bacteria, and Eukarya) was found with high statistical significance, with a frequency gradient depending on both the antiquity of the species and the functional necessity of the genes. (4) Conclusions: Considering the suitability of AL as a candidate for being a primitive sequence, and the evolution of the different species considered, we can consider the AL RNA as a possible actor that favored the appearance of life on Earth.

Cultivation methods and biology of Lentinula edodes

In this study, the biological applications of cultivation methods related to cultivar selection, vegetative growth, and reproductive development in Lentinula edodes cultivation are briefly reviewed to clarify the current situation and inform future developments. The current cultivars widely used in the main production areas are derived from wild strains distributed in northern Asia. The most effective techniques for cultivar identification are molecular markers identified in two nuclear genome datasets and one mitochondrial genome dataset. The current stage of cultivar breeding is at the junction of Breeding 3.0 (biological breeding) and Breeding 4.0 (intelligent breeding). Plant breeder's rights and patents have different emphases on new breeding variety protection, with the former being the most utilized globally. L. edodes is mostly produced on synthetic logs filled with sawdust substrates. Hardwood sawdust comprises approximately 80% of the substrates. The vegetative growth of L. edodes on synthetic logs involves two distinct stages of mycelial colonization and browning. Mycelia mainly perform glycolysis, tricarboxylic acid cycle, and respiratory metabolism reactions to produce energy and intermediates for synthesizing the structural components of hyphae in the vegetative colonization stage. Upon stimulation by physiological and environmental pressures after colonization, mycelia trigger gluconeogenesis, autophagy, and secondary metabolism, increase metabolic flux of pentose phosphate pathway, activate the glyoxylate cycle, and accumulate melanin on the surface of logs to ensure growth and survival. Sexually competent mycelia can form hyphal knots as a result of reprogrammed hyphal branching patterns after a period of vegetative growth (which varies by cultivar) and stimulation by specific environmental factors. Under a genetically encoded developmental program, hyphal knots undergo aggregation, tissue differentiation, primordium formation, meiosis in the hymenium, stipe elongation, basidiospore production and maturation, and cap expansion to form mature fruiting bodies. Growers can achieve good fruiting body shape and high yield by regulating the number of young fruiting bodies and adjusting specific environmental factors. KEY POINTS: • Cultivar selection becomes less with the increasing technological requirement of L. edodes cultivation. • L. edodes mycelia showed different biological events in the mycelial colonization and browning stages. • Specific cultivar breading may be the next milestone in L. edodes cultivation.

Transcending the hegemony of the molecular machine through an organic renewal of biology and biomedicine

The dominant approach to the study of living systems in the 20th century into today has been that of a reductionist approach focused on genetics and biochemistry. The hunt for genes and the elucidation of their biochemical outputs has organized funding in research, educational curricula, academic promotion, and the distribution of prestige through awards. Such reductionism has gone hand in hand with an ontology of the machine. We will discuss how viewing life as if it emanated from a set of molecular machines is the main bottleneck in addressing key questions in biology. We will discuss how moving beyond it is not contingent on new technologies but rather a refreshed perspective of life that can be termed "organic". Furthermore, we suggest that the study of how form arises, morphogenesis, is the key to an organic renewal of biology and biomedicine. Although morphogenesis is currently seen as a subsidiary branch of developmental biology as well as the consequence of molecular patterning processes at the subcellular scale, we will argue that morphology and its self-organizing capacity at the supracellular scale is the fundamental nexus in embryonic development as well as disease. We see the inability to appreciate form through an organic supracellular perspective as the principal bottleneck for making inroads into health issues such as cancer and the chronic disease epidemic.

The Origin(s) of LUCA: Computer Simulation of a New Theory

Carl Woese's thesis of cellular evolution emphasized that the last universal common/cellular ancestor (LUCA) must have evolved by drawing from "global inventions". Yet, existing theories regarding the origin(s) of LUCA have mostly centered upon scenarios that LUCA had evolved mostly independently. In an earlier paper, we advanced a new theory regarding the origin(s) of LUCA that extends Woese's original insights. Our theory centers upon the possibility that different vesicles and protocells can merge with and acquire each other as a form of variation, selection, and retention, driven by wet-and-dry cycles and other similar cyclical processes. In this paper, we use computer simulation to show that under a variety of simulated conditions, LUCA can indeed be produced by our proposed processes. We hope that our study can stimulate laboratory testing of some key hypotheses that vesicles' absorption, acquisition, and merger has indeed been a central force in driving the evolution of LUCA.

The disciplinary matrix of holobiont biology

Uniting life's seen and unseen realms guides a conceptual advance in research.

mSphere of Influence: The power of polymicrobial partnerships in chronic infection research

Chelsey VanDrisse works in the field of microbial physiology, studying how acylation of small molecules and proteins affects the development of Pseudomonas biofilms. In this mSphere of Influence article, she reflects on the paper "Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system" by Jean-Pierre et al. This paper prompted her to reassess her approach to studying antibiotic tolerance and her design of experiments that search for disease-relevant mutants and phenotypes in the laboratory.

Agency as an Inherent Property of Living Organisms

A central characteristic of living organisms is their agency, that is, their intrinsic activity, both in terms of their basic life processes and their behavior in the environment. This aspect is currently a subject of debate and this article provides an overview of some of the relevant publications on this topic. We develop the argument that agency is immanent in living organisms. There is no life without agency. Even the basic life processes are an intrinsic activity, which we call the organismic level of agency. In addition to this we describe several further levels. These capture different qualities that occur or transform during evolution. In addition to the organismic level, we propose an ontogenetic level, a level of directed agency, directed agency with extended flexibility, and a level that includes the capacities to follow preconceived goals. A further property of organisms is their autonomy. It has been shown that the capacity for autonomy changed during evolution. Here we propose that the two organismic properties autonomy and agency are closely related. Enhanced physiological and behavioral autonomy extends the scope of self-generated, flexible actions and reactions. The increase in autonomy through the evolution of a widened scope of behavioral possibilities and versatility in organisms coincides with extended levels of agency. Especially the human organization, including the sophisticated brain, is the basis for an extended level of agency referring to the capacities to follow preconceived goals. However, it is important for the understanding of the phenomenon of agency not only to assume this latter form, but also to look at the different levels of agency.

Epistemic misalignments in microbiome research

We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call "epistemic misalignment." An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epistemic misalignments, due to the different temporal scales that 16S rRNA provides information about and the temporal scales that are required to know about the functionality of some microorganisms. We show how some of these exist in contemporary microbiome science and urge microbiome scientists to take some measures to avoid them, as they may question the credibility of the field as a whole.

The New Era of Cancer Cytogenetics and Cytogenomics

The promises of the cancer genome sequencing project, combined with various -omics technologies, have raised questions about the importance of cancer cytogenetic analyses. It is suggested that DNA sequencing provides high resolution, speed, and automation, potentially replacing cytogenetic testing. We disagree with this reductionist prediction. On the contrary, various sequencing projects have unexpectedly challenged gene theory and highlighted the importance of the genome or karyotype in organizing gene network interactions. Consequently, profiling the karyotype can be more meaningful than solely profiling gene mutations, especially in cancer where karyotype alterations mediate cellular macroevolution dominance. In this chapter, recent studies that illustrate the ultimate importance of karyotype in cancer genomics and evolution are briefly reviewed. In particular, the long-ignored non-clonal chromosome aberrations or NCCAs are linked to genome or chromosome instability, genome chaos is linked to genome reorganization under cellular crisis, and the two-phased cancer evolution reconciles the relationship between genome alteration-mediated punctuated macroevolution and gene mutation-mediated stepwise microevolution. By further synthesizing, the concept of karyotype coding is discussed in the context of information management. Altogether, we call for a new era of cancer cytogenetics and cytogenomics, where an array of technical frontiers can be explored further, which is crucial for both basic research and clinical implications in the cancer field.

A plea for the ultimate optimism: Cognitive biology as a foundation for a worldview

Homo sapiens' cultural evolution has far outpaced its biological evolution and led us into an impasse.

Extremophilic red algae as models for understanding adaptation to hostile environments and the evolution of eukaryotic life on the early earth

Extremophiles have always garnered great interest because of their exotic lifestyles and ability to thrive at the physical limits of life. In hot springs environments, the Cyanidiophyceae red algae are the only photosynthetic eukaryotes able to live under extremely low pH (0-5) and relatively high temperature (35ºC to 63ºC). These extremophiles live as biofilms in the springs, inhabit acid soils near the hot springs, and form endolithic populations in the surrounding rocks. Cyanidiophyceae represent a remarkable source of knowledge about the evolution of extremophilic lifestyles and their genomes encode specialized enzymes that have applied uses. Here we review the evolutionary origin, taxonomy, genome biology, industrial applications, and use of Cyanidiophyceae as genetic models. Currently, Cyanidiophyceae comprise a single order (Cyanidiales), three families, four genera, and nine species, including the well-known Cyanidioschyzon merolae and Galdieria sulphuraria. These algae have small, gene-rich genomes that are analogous to those of prokaryotes they live and compete with. There are few spliceosomal introns and evidence exists for horizontal gene transfer as a driver of local adaptation to gain access to external fixed carbon and to extrude toxic metals. Cyanidiophyceae offer a variety of commercial opportunities such as phytoremediation to detoxify contaminated soils or waters and exploitation of their mixotrophic lifestyles to support the efficient production of bioproducts such as phycocyanin and floridosides. In terms of exobiology, Cyanidiophyceae are an ideal model system for understanding the evolutionary effects of foreign gene acquisition and the interactions between different organisms inhabiting the same harsh environment on the early Earth. Finally, we describe ongoing research with C. merolae genetics and summarize the unique insights they offer to the understanding of algal biology and evolution.

Recent Approaches for Downplaying Antibiotic Resistance: Molecular Mechanisms

Antimicrobial resistance (AMR) is a ubiquitous public health menace. AMR emergence causes complications in treating infections contributing to an upsurge in the mortality rate. The epidemic of AMR in sync with a high utilization rate of antimicrobial drugs signifies an alarming situation for the fleet recovery of both animals and humans. The emergence of resistant species calls for new treatments and therapeutics. Current records propose that health drug dependency, veterinary medicine, agricultural application, and vaccination reluctance are the primary etymology of AMR gene emergence and spread. Recently, several encouraging avenues have been presented to contest resistance, such as antivirulent therapy, passive immunization, antimicrobial peptides, vaccines, phage therapy, and botanical and liposomal nanoparticles. Most of these therapies are used as cutting-edge methodologies to downplay antibacterial drugs to subdue the resistance pressure, which is a featured motive of discussion in this review article. AMR can fade away through the potential use of current cutting-edge therapeutics, advancement in antimicrobial susceptibility testing, new diagnostic testing, prompt clinical response, and probing of new pharmacodynamic properties of antimicrobials. It also needs to promote future research on contemporary methods to maintain host homeostasis after infections caused by AMR. Referable to the microbial ability to break resistance, there is a great ultimatum for using not only appropriate and advanced antimicrobial drugs but also other neoteric diverse cutting-edge therapeutics.

Anticodon sequence determines the impact of mistranslating tRNAAla variants

Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAla and the anticodon plays no role in charging, tRNAAla variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAla anticodon variants on the growth of Saccharomyces cerevisiae. Overall, 36 tRNAAla anticodon variants decreased growth in single- or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C-rich anticodons resulted in larger growth deficits than A/U-rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAla anticodon variants.

Integrated intracellular organization and its variations in human iPS cells

Understanding how a subset of expressed genes dictates cellular phenotype is a considerable challenge owing to the large numbers of molecules involved, their combinatorics and the plethora of cellular behaviours that they determine1,2. Here we reduced this complexity by focusing on cellular organization-a key readout and driver of cell behaviour3,4-at the level of major cellular structures that represent distinct organelles and functional machines, and generated the WTC-11 hiPSC Single-Cell Image Dataset v1, which contains more than 200,000 live cells in 3D, spanning 25 key cellular structures. The scale and quality of this dataset permitted the creation of a generalizable analysis framework to convert raw image data of cells and their structures into dimensionally reduced, quantitative measurements that can be interpreted by humans, and to facilitate data exploration. This framework embraces the vast cell-to-cell variability that is observed within a normal population, facilitates the integration of cell-by-cell structural data and allows quantitative analyses of distinct, separable aspects of organization within and across different cell populations. We found that the integrated intracellular organization of interphase cells was robust to the wide range of variation in cell shape in the population; that the average locations of some structures became polarized in cells at the edges of colonies while maintaining the 'wiring' of their interactions with other structures; and that, by contrast, changes in the location of structures during early mitotic reorganization were accompanied by changes in their wiring.

Question-driven stepwise experimental discoveries in biochemistry: two case studies

Philosophers of science diverge on the question what drives the growth of scientific knowledge. Most of the twentieth century was dominated by the notion that theories propel that growth whereas experiments play secondary roles of operating within the theoretical framework or testing theoretical predictions. New experimentalism, a school of thought pioneered by Ian Hacking in the early 1980s, challenged this view by arguing that theory-free exploratory experimentation may in many cases effectively probe nature and potentially spawn higher evidence-based theories. Because theories are often powerless to envisage workings of complex biological systems, theory-independent experimentation is common in the life sciences. Some such experiments are triggered by compelling observation, others are prompted by innovative techniques or instruments, whereas different investigations query big data to identify regularities and underlying organizing principles. A distinct fourth type of experiments is motivated by a major question. Here I describe two question-guided experimental discoveries in biochemistry: the cyclic adenosine monophosphate mediator of hormone action and the ubiquitin-mediated system of protein degradation. Lacking underlying theories, antecedent data bases, or new techniques, the sole guides of the two discoveries were respective substantial questions. Both research projects were similarly instigated by theory-free exploratory experimentation and continued in alternating phases of results-based interim working hypotheses, their examination by experiment, provisional hypotheses again, and so on. These two cases designate theory-free, question-guided, stepwise biochemical investigations as a distinct subtype of the new experimentalism mode of scientific enquiry.

A mathematical analysis of focal adhesion lifetimes and their effect on cell motility

By analyzing the distributions of focal adhesion (FA) lifetimes from different cell types, we found that a gamma distribution best matched the experimental distributions. In all but one case, it was a unimodal, non-symmetric gamma distribution. We used a mathematical model of cell motion to help understand the mechanics and data behind the FA lifetime distributions. The model uses a detach-rate function to determine how long an FA will persist before it detaches. The detach-rate function that produced distributions with a best-fit gamma curve that closely matched that of the data was both force and time dependent. Using the data gathered from the matching simulations, we calculated both the cell speed and mean FA lifetime and compared them. Where available, we also compared this relationship to that of the experimental data and found that the simulation reasonably matches it in most cases. In both the simulations and experimental data, the cell speed and mean FA lifetime are related, with longer mean lifetimes being indicative of slower speeds. We suspect that one of the main predictors of cell speed for migrating cells is the distribution of the FA lifetimes.

Multi-Cellular Immunological Interactions Associated With COVID-19 Infections

To rapidly prognosticate and generate hypotheses on pathogenesis, leukocyte multi-cellularity was evaluated in SARS-CoV-2 infected patients treated in India or the United States (152 individuals, 384 temporal observations). Within hospital (<90-day) death or discharge were retrospectively predicted based on the admission complete blood cell counts (CBC). Two methods were applied: (i) a "reductionist" one, which analyzes each cell type separately, and (ii) a "non-reductionist" method, which estimates multi-cellularity. The second approach uses a proprietary software package that detects distinct data patterns generated by complex and hypothetical indicators and reveals each data pattern's immunological content and associated outcome(s). In the Indian population, the analysis of isolated cell types did not separate survivors from non-survivors. In contrast, multi-cellular data patterns differentiated six groups of patients, including, in two groups, 95.5% of all survivors. Some data structures revealed one data point-wide line of observations, which informed at a personalized level and identified 97.8% of all non-survivors. Discovery was also fostered: some non-survivors were characterized by low monocyte/lymphocyte ratio levels. When both populations were analyzed with the non-reductionist method, they displayed results that suggested survivors and non-survivors differed immunologically as early as hospitalization day 1.

An ensemble approach to the structure-function problem in microbial communities

The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.

Evolutionary Approaches to Innovation, the Firm, and the Dynamics of Industries

We examine the progress of the evolutionary research on innovation, the firm, and the dynamics of industries in the last four decades. The paper acknowledges that the themes related to knowledge and technological regimes, the evolutionary processes leading to innovation, and the long-term dynamics of technologies have generated, and still remain, relevant research trajectories. The same can be said for the research trajectories on organizational and dynamic capabilities, evolutionary strategies, vertical integration, diversification, niche construction, and authority and power in organizations. Important progress has also been made in understanding the evolutionary trajectories of industries, the link between industry architecture and industry dynamics, the types of knowledge of entrants, the role of focal and vertical spinouts, the relevance of institutions and sectoral innovation systems in industry dynamics, and the catch-up process by firms from latecomer countries. We argue that future developments in the evolutionary camp should continue to be characterized by eclecticism and multidisciplinarity, as well as by the integration of different methodologies from cases to stylized facts, quantitative analyses, appreciative theorizing, and formal modelling. We conclude with an analysis of the main methodologies used by evolutionary scholars and a discussion of the road ahead.

Regulating Expression of Mistranslating tRNAs by Readthrough RNA Polymerase II Transcription

Transfer RNA (tRNA) variants that alter the genetic code increase protein diversity and have many applications in synthetic biology. Since the tRNA variants can cause a loss of proteostasis, regulating their expression is necessary to achieve high levels of novel protein. Mechanisms to positively regulate transcription with exogenous activator proteins like those often used to regulate RNA polymerase II (RNAP II)-transcribed genes are not applicable to tRNAs as their expression by RNA polymerase III requires elements internal to the tRNA. Here, we show that tRNA expression is repressed by overlapping transcription from an adjacent RNAP II promoter. Regulating the expression of the RNAP II promoter allows inverse regulation of the tRNA. Placing either Gal4- or TetR–VP16-activated promoters downstream of a mistranslating tRNA^Ser variant that misincorporates serine at proline codons in Saccharomyces cerevisiae allows mistranslation at a level not otherwise possible because of the toxicity of the unregulated tRNA. Using this inducible tRNA system, we explore the proteotoxic effects of mistranslation on yeast cells. High levels of mistranslation cause cells to arrest in the G1 phase. These cells are impermeable to propidium iodide, yet growth is not restored upon repressing tRNA expression. High levels of mistranslation increase cell size and alter cell morphology. This regulatable tRNA expression system can be applied to study how native tRNAs and tRNA variants affect the proteome and other biological processes. Variations of this inducible tRNA system should be applicable to other eukaryotic cell types.

The microbiome impacts host hybridization and speciation

Microbial symbiosis and speciation profoundly shape the composition of life's biodiversity. Despite the enormous contributions of these two fields to the foundations of modern biology, there is a vast and exciting frontier ahead for research, literature, and conferences to address the neglected prospects of merging their study. Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation. Though microorganisms were proposed to impact animal speciation a century ago, the weight of the evidence supporting this view has now reached a tipping point.

Why Should Clinical Autopsies Continue to Exist?

At some point in history, medicine was integrated with pathology, more precisely, with pathological anatomy [...].

The Origin(s) of Cell(s): Pre-Darwinian Evolution from FUCAs to LUCA : To Carl Woese (1928-2012), for his Conceptual Breakthrough of Cellular Evolution

The coming of the Last Universal Cellular Ancestor (LUCA) was the singular watershed event in the making of the biotic world. If the coming of LUCA marked the crossing of the "Darwinian Threshold", then pre-LUCA evolution must have been Pre-Darwinian and at least partly non-Darwinian. But how did Pre-Darwinian evolution before LUCA actually operate? I broaden our understanding of the central mechanism of biological evolution (i.e., variation-selection-inheritance) and then extend this broadened understanding to its natural starting point: the origin(s) of the First Universal Cellular Ancestors (FUCAs) before LUCA. My hypothesis centers upon vesicles' making-and-remaking as variation and competition as selection. More specifically, I argue that vesicles' acquisition and merger, via breaking-and-repacking, proto-endocytosis, proto-endosymbiosis, and other similar processes had been a central force of both variation and selection in the pre-Darwinian epoch. These new perspectives shed important new light upon the origin of FUCAs and their subsequent evolution into LUCA.

The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype

The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.

Biology transcends the limits of computation

Cognition-sensing and responding to the environment-is the unifying principle behind the genetic code, origin of life, evolution, consciousness, artificial intelligence, and cancer. However, the conventional model of biology seems to mistake cause and effect. According to the reductionist view, the causal chain in biology is chemicals → code → cognition. Despite this prevailing view, there are no examples in the literature to show that the laws of physics and chemistry can produce codes, or that codes produce cognition. Chemicals are just the physical layer of any information system. In contrast, although examples of cognition generating codes and codes controlling chemicals are ubiquitous in biology and technology, cognition remains a mystery. Thus, the central question in biology is: What is the nature and origin of cognition? In order to elucidate this pivotal question, we must cultivate a deeper understanding of information flows. Through this lens, we see that biological cognition is volitional (i.e., deliberate, intentional, or knowing), and while technology is constrained by deductive logic, living things make choices and generate novel information using inductive logic. Information has been called "the hard problem of life' and cannot be fully explained by known physical principles (Walker et al., 2017). The present paper uses information theory (the mathematical foundation of our digital age) and Turing machines (computers) to highlight inaccuracies in prevailing reductionist models of biology, and proposes that the correct causation sequence is cognition → code → chemicals.

Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same?

Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.

Transfer RNAs: diversity in form and function

As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.

Drug overdose deaths, addiction neuroscience and the challenges of translation

In this article, we argue that the rapid rise in drug overdose deaths in America is a tragedy that draws attention to fundamental conceptual and experimental problems in addiction science that have significant human consequences. Despite enormous economic investment, political support and claims to have revolutionised addiction medicine, neurobiological models are yet to produce a treatment for substance addiction. This is partly, we claim, because neurobiology is unable to explain essential features of addiction and relapse that neurobehavioral models of addiction are better placed to investigate. We show how addiction neuroscience turned to long-term memory to explain the chronicity of addiction and persistent relapses long after neurochemical traces have left the body. The turn to memory may in time help to close the translational gap facing addiction medicine, but it is our view in this article that the primary value of memory theory lays in its potential to create new critical friendships between biological and social sciences that are attuned to the lived experience and suffering of stigmatised people. The value of the memory turn may rest upon the capacity of these critical friendships to wean addiction science off its long-term dependence on disease concepts of human distress.

The Pathogenesis of Tuberculosis-The Koch Phenomenon Reinstated

Research on the pathogenesis of tuberculosis (TB) has been hamstrung for half a century by the paradigm that granulomas are the hallmark of active disease. Human TB, in fact, produces two types of granulomas, neither of which is involved in the development of adult type or post-primary TB. This disease begins as the early lesion; a prolonged subclinical stockpiling of secreted mycobacterial antigens in foamy alveolar macrophages and nearby highly sensitized T cells in preparation for a massive necrotizing hypersensitivity reaction, the Koch Phenomenon, that produces caseous pneumonia that is either coughed out to form cavities or retained to become the focus of post-primary granulomas and fibrocaseous disease. Post-primary TB progresses if the antigens are continuously released and regresses when they are depleted. This revised paradigm is supported by nearly 200 years of research and suggests new approaches and animal models to investigate long standing mysteries of human TB and vaccines that inhibit the early lesion to finally end its transmission.

Complexity in Biological Organization: Deconstruction (and Subsequent Restating) of Key Concepts

The “magic” word complexity evokes a multitude of meanings that obscure its real sense. Here we try and generate a bottom-up reconstruction of the deep sense of complexity by looking at the convergence of different features shared by complex systems. We specifically focus on complexity in biology but stressing the similarities with analogous features encountered in inanimate and artefactual systems in order to track an integrative path toward a new “mainstream” of science overcoming the actual fragmentation of scientific culture.

A comprehensive framework for considering additional unintended consequences in economic evaluation

Background

In recent years there has been a growth in economic evaluations that consider indirect health benefits to populations due to advances in mathematical modeling. In addition, economic evaluations guidelines have suggested the inclusion of impact inventories to include non-health direct and indirect consequences. We aim to bring together this literature, together with the broader literature on internalities and externalities to propose a comprehensive approach for analysts to identify and characterize all unintended consequences in economic evaluations.

Methods

We present a framework to assist analysts identify and characterize additional costs and effects beyond that of direct health impact primarily intended to be influenced by the intervention/technology. We build on previous checklists to provide analysts with a comprehensive framework to justify the inclusion or exclusion of effects, supporting the use of current guidelines, to ensure any unintended effects are considered. We illustrate this framework with examples from immunization. These were identified from a previous systematic review, PhD thesis work, and general search scoping in PubMed databases.

Results

We present a comprehensive framework to consider additional consequences, exemplified by types and categories. We bring this and other guidance together to assist analysts identify possible unintended consequences whether taking a provider or societal perspective.

Conclusions

Although there are many challenges ahead to standardize the inclusion of additional consequences in economic evaluation, we hope by moving beyond generic statements to reporting against a comprehensive framework of additional effects we can support further consistency in this aspect of cost-effectiveness analysis going forward.

Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life

(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singular docosameric RNA molecule, we call the ALPHA sequence. Then, we searched for any relics of the peptides made from ALPHA in sequences deposited in the different public databases. (3) Results: Sequence matching between ALPHA and sequences from organisms among the earliest forms of life on Earth were found at high statistical relevance. We hypothesize that the frequency of appearance of relics from ALPHA sequence in present genomes has a functional necessity. (4) Conclusions: Given the fitness of ALPHA as a supportive sequence of the framework of all existing theories, and the evolution of Archaea and giant viruses, it is anticipated that the unique properties of this singular archetypal ALPHA sequence should prove useful as a model matrix for future applications, ranging from synthetic biology to DNA computing.

Characteristics of the Airway Microbiome of Cystic Fibrosis Patients

Microbiota as an integral component of human body is actively investigated, including by massively parallel sequencing. However, microbiomes of lungs and sinuses have become the object of scientific attention only in the last decade. For patients with cystic fibrosis, monitoring the state of respiratory tract microorganisms is essential for maintaining lung function. Here, we studied the role of sinuses and polyps in the formation of respiratory tract microbiome. We identified Proteobacteria in the sinuses and samples from the lower respiratory tract (even in childhood). In some cases, they were accompanied by potentially dangerous basidiomycetes. The presence of polyps did not affect formation of the sinus microbiome. Proteobacteria are decisive in reducing the biodiversity of lung and sinus microbiomes, which correlated with the worsening of the lung function indicators. Soft mutations in the CFTR gene contribute to the formation of safer microbiome even in heterozygotes with class I mutations.

Special Issue “Kinetic Theory and Swarming Tools to Modeling Complex Systems—Symmetry problems in the Science of Living Systems”—Editorial and Research Perspectives

This editorial paper presents a special issue devoted to the development of mathematical tools from kinetic and swarms theory to the modeling and simulations of the dynamics of living systems constituted by very many interacting living entities. Applications refer to several fields: collective learning, behavioral economy, multicellular systems, vehicular traffic, and human crowds. A forward look to research perspectives is focused on the conceptual links between swarms methods and the kinetic theory approach.

Beyond the modern synthesis: A framework for a more inclusive biological synthesis

Many theorists in recent years have been calling for evolutionary biology to move beyond the Modern Synthesis - the paradigm that has long provided the theoretical backbone for the discipline. Terms like "postmodern synthesis," "integrative synthesis," and "extended evolutionary synthesis" have been invoked by various critics in connection with the many recent developments that pose deep challenges - even contradictions - to the traditional model and underscore the need for an update, or a makeover. However, none of these critics, to this author's knowledge, has to date offered an explicit alternative that could provide a unifying theoretical paradigm for our vastly increased knowledge about living systems and the history of life on Earth (but see Noble 2015, 2017). This paper briefly summarizes the case against the Modern Synthesis and its many amendments over the years, and a new paradigm is proposed, called an "Inclusive Biological Synthesis," which, it is argued, can provide a more general framework for the biological sciences. The focus of this framework is the fundamental nature of life as a contingent dynamic process - an always at-risk "survival enterprise." The ongoing, inescapable challenge of earning a living in a given environmental context - biological survival and reproduction - presents an existential problem to which all biological phenomena can be related and comprehended. They and their "parts" can be analyzed in relation to ethologist Niko Tinbergen's four key questions. Some basic properties and guiding assumptions related to this alternative paradigm are also identified.

Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics

The apparent lack of success in curing cancer that was evidenced in the last four decades of molecular medicine indicates the need for a global re-thinking both its nature and the biological approaches that we are taking in its solution. The reductionist, one gene/one protein method that has served us well until now, and that still dominates in biomedicine, requires complementation with a more systemic/holistic approach, to address the huge problem of cross-talk between more than 20,000 protein-coding genes, about 100,000 protein types, and the multiple layers of biological organization. In this perspective, the relationship between the chromatin network organization and gene expression regulation plays a fundamental role. The elucidation of such a relationship requires a non-linear thermodynamics approach to these biological systems. This change of perspective is a necessary step for developing successful 'tumour-reversion' therapeutic strategies.

Is the cell really a machine?

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.

Toward a rapid method for the study of biodiversity in cold environments: the characterization of psychrophilic yeasts by MALDI-TOF mass spectrometry

To investigate the potential of matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF/MS) as a platform to support biodiversity and phylogenetic studies of psychrophilic yeasts in cold environments, the technique was employed to rapidly characterize and distinguish three psychrophilic yeasts (Rhodotorula mucilaginosa, Naganishia vishniacii, and Dioszegia cryoxerica) from three mesophilic counterparts (Saccharomyces cerevisiae Cry Havoc, S. cerevisiae California V Ale, and S. pastorianus). A detailed workflow for providing reproducible mass spectral fingerprints of low molecular weight protein/peptide features specific to the organisms studied is presented. The potential of this approach as a tool in the study of biodiversity, systematics, and phylogeny of psychrophilic microorganisms is highlighted.