Evolution viewed from physics, physiology and medicine

The mega-evolution of life with its three memory systems depends on sender-receiver communication and problem-solving. A narrative review

It should be the ultimate goal of any theory of evolution to delineate the contours of an integrative system to answer the question: How does life (in all its complexity) evolve (which can be called mega-evolution)? But how to plausibly define 'life'? My answer (1994-2023) is: 'life' sounds like a noun, but denotes an activity, and thus is a verb. Life (L) denotes nothing else than the total sum (∑) of all acts of communication (transfer of information) (C) executed by any type of senders-receivers at all their levels (up to at least 15) of compartmental organization: L = ∑C. The 'communicating compartment' is better suited to serve as the universal unit of structure, function and evolution than the cell, the smallest such unit. By paying as much importance to communication activity as to the Central Dogma of molecular biology, a wealth of new insights unfold. The major ones are as follows. (1) Living compartments have not only a genetic memory (DNA), but also a still enigmatic cognitive and an electrical memory system (and thus a triple memory system). (2) Complex compartments can have up to three types of progeny: genetic descendants/children, pupils/learners and electricians. (3) Of particular importance to adaptation, any act of communication is a problem-solving act because all messages need to be decoded. Hence through problem-solving that precedes selection, life itself is the driving force of its own evolution (a very clever but counterintuitive and unexpected logical deduction). Perhaps, this is the 'vital force' philosopher and Nobel laureate (in 1927) Henri Bergson searched for but did not find.

Proposing an integrative, dynamic and transdiagnostic model for addictions: dysregulation phenomena of the three main modes of the predostatic mind

Several theories have been proposed to explain the complex diagnostic aspects related to addiction disorders and their development. Recent frameworks tend to focus on dimensional perspectives of symptoms rather than categorical systems, since substance use disorders are frequently comorbid with other psychiatric and especially personality disorders. However, useful transdiagnostic models that could integrate clinical evaluation derived from neuroscientific theories are lacking. In the present manuscript, the authors propose a model based on a new paradigm, in an attempt to better explain this complex, multifaceted phenomenon. The new paradigm presupposes that emotions and behavior are a response to risk prediction. Individuals make choices and engage in actions to manage potential risks/rewards in order to seek or maintain homeostasis in their internal and external environments - a mechanism that the authors call predostatic (predictive mechanism with homeostatic purpose). The model considers three main modes of the predostatic mind: (1) Alarm Mode, activated by high and/or imminent risk prediction; (2) Seek Mode, activated by long-term risk or reward prediction; and (3) Balance Mode, a self-regulating state of mind related to low risk prediction, a soothing system and a calm state. Addiction is seen as a chronic dysregulation of organism systems leading to internalizing or externalizing phenomena mainly related to the Seek and Alarm Modes, which are persistently activated by reward and risk prediction, respectively, thus hindering Balance. Addiction neuroscience research has shown that chronic drug use or engagement in addictive behaviors can lead to neuroadaptations in the brain reward circuitry, disrupting normal balance and the regulation of reward processes. This dysregulation can contribute to persistent drug-seeking/addictive behaviors despite negative consequences. This newly proposed dynamic and integrative model, named dysregulation based on externalizing and internalizing phenomena of the three main modes of the predostatic mind (DREXI3), proposes six dysregulation dimensions with basic emotional and behavioral symptoms, such as neurophysiological alterations, impulsivity, compulsion, cognitive impairment/psychosis, mood, and anxiety/anger. In this paper, the authors explain the rationale behind DREXI3 and present some hypothetical clinical examples to better illustrate the use of the model in clinical practice. The development of this innovative model could possibly guide tailored treatment interventions in the addiction field.

Making use of noise in biological systems

Disorder and noise are inherent in biological systems. They are required to provide systems with the advantages required for proper functioning. Noise is a part of the flexibility and plasticity of biological systems. It provides systems with increased routes, improves information transfer, and assists in response triggers. This paper reviews recent studies on noise at the genome, cellular, and whole organ levels. We focus on the need to use noise in system engineering. We present some of the challenges faced in studying noise. Optimizing the efficiency of complex systems requires a degree of variability in their functions within certain limits. Constrained noise can be considered a method for improving system robustness by regulating noise levels in continuously dynamic settings. The digital pill-based artificial intelligence (AI)-based platform is the first to implement second-generation AI comprising variability-based signatures. This platform enhances the efficacy of the therapeutic regimens. Systems requiring variability and mechanisms regulating noise are mandatory for understanding biological functions.

Multivariate selection and the making and breaking of mutational pleiotropy

The role of mutations have been subject to many controversies since the formation of the Modern Synthesis of evolution in the early 1940ties. Geneticists in the early half of the twentieth century tended to view mutations as a limiting factor in evolutionary change. In contrast, natural selection was largely viewed as a “sieve” whose main role was to sort out the unfit but which could not create anything novel alone. This view gradually changed with the development of mathematical population genetics theory, increased appreciation of standing genetic variation and the discovery of more complex forms of selection, including balancing selection. Short-term evolutionary responses to selection are mainly influenced by standing genetic variation, and are predictable to some degree using information about the genetic variance–covariance matrix (G) and the strength and form of selection (e. g. the vector of selection gradients, β). However, predicting long-term evolution is more challenging, and requires information about the nature and supply of novel mutations, summarized by the mutational variance–covariance matrix (M). Recently, there has been increased attention to the role of mutations in general and M in particular. Some evolutionary biologists argue that evolution is largely mutation-driven and claim that mutation bias frequently results in mutation-biased adaptation. Strong similarities between G and M have also raised questions about the non-randomness of mutations. Moreover, novel mutations are typically not isotropic in their phenotypic effects and mutational pleiotropy is common. Here I discuss the evolutionary origin and consequences of mutational pleiotropy and how multivariate selection directly shapes G and indirectly M through changed epistatic relationships. I illustrate these ideas by reviewing recent literature and models about correlational selection, evolution of G and M, sexual selection and the fitness consequences of sexual antagonism.

Modern physiology vindicates Darwin's Dream

New Findings

What is the topic of this review?

Revisiting the 2013 article ‘Physiology is rocking the foundations of evolutionary biology’.

What advances does it highlight?

The discovery that the genome is not isolated from the soma and the environment, and that there is no barrier preventing somatic characteristics being transmitted to the germline, means that Darwin's pangenetic ideas become relevant again.

Abstract

Charles Darwin spent the last decade of his life collaborating with physiologists in search of the biological processes of evolution. He viewed physiology as the way forward in answering fundamental questions about inheritance, acquired characteristics, and the mechanisms by which organisms could achieve their ends and survival. He collaborated with 19th century physiologists, notably John Burdon‐Sanderson and George Romanes, in his search for the mechanisms of transgenerational inheritance. The discovery that the genome is not isolated from the soma and the environment, and that there is no barrier preventing somatic characteristics being transmitted to the germline, means that Darwin's pangenetic ideas become relevant again. It is time for 21st century physiology to come to the rescue of evolutionary biology. This article outlines research lines by which this could be achieved.

Complexification of eukaryote phenotype: Adaptive immuno-cognitive systems as unique Gödelian block chain distributed ledger

The digitization of inheritable information in the genome has been called the 'algorithmic take-over of biology'. The McClintock discovery that viral software based transposable elements that conduct cut-paste (transposon) and copy-paste (retrotransposon) operations are needed for genomic evolvability underscores the truism that only software can change software and also that viral hacking by internal and external bio-malware is the Achilles heel of genomic digital systems. There was a paradigm shift in genomic information processing with the Adaptive Immune System (AIS) 500 mya followed by the Mirror Neuron System (MNS), latterly mostly in primate brains, which reaches its apogee in human social cognition. The AIS and MNS involve distinctive Gödelian features of self-reference (Self-Ref) and offline virtual self-representation (Self-Rep) for complex self-other interaction with prodigious open-ended capacity for anticipative malware detection and novelty production within a unique blockchain distributed ledger (BCDL). The role of self-referential information processing, often considered to be central to the sentient self with origins in the immune system 'Thymic self', is shown to be part of the Gödel logic behind a generator-selector framework at a molecular level, which exerts stringent selection criteria to maintain genomic BCDL. The latter manifests digital and decentralized record keeping where no internal or external bio-malware can compromise the immutability of the life's building blocks and no novel blocks can be added that is not consistent with extant blocks. This is demonstrated with regard to somatic hypermutation with novel anti-body production in the face of external non-self antigen attacks.

Autopoiesis, Thermodynamics, and the Natural Drift of Living Beings: Another Way to the New Evolutionary Synthesis

The New Evolutionary Synthesis (NES) groups a series of theories that, departing from the gene-centric approach of Modern Synthesis evolutionary theory (MS), place the organism as the central agent of evolution. Two versions of NES, each one with advantages and disadvantages, can be distinguished in this regard; the restrictive NES and the comprehensive NES. Comparatively, the comprehensive NES is a more robust theoretical construction than the restrictive one because it comes grounded on a general, thermodynamically informed theory of living beings (something that the restrictive NES lacks). However, due to its strong teleological commitments, the comprehensive NES has serious problems fitting with modern science’s methodological framework; a problem that the restrictive version, with no explicit commitment to teleology, does not face. In this paper, we propose the autopoietic approach to evolution as a way of integrating these two versions of NES, combining the theoretical robustness of the comprehensive view with the methodological appropriateness of the restrictive one. The autopoietic approach, we show, offers a non-teleological, organism-centered theory of evolution, namely the natural drift theory (NDT), and a grounding on a thermodynamic theory of living beings, namely the embodied autopoietic theory (EAT). We conclude that, from the programmatic point of view, an autopoietic (NDT plus EAT) approach to evolution offers a promising way to develop the NES project.

Correspondence insights into the role of genes in cell functionality. Comments on "The gene: An appraisal" by K. Baverstock

One of the most important goals of the post-genomic era is to understand the different sources of molecular information that regulate the functional and structural architecture of cells. In this regard, Prof. K. Baverstock underscores in his recent article "The gene: An appraisal" (Baverstock, 2021) that genes are not the leading elements in cellular functionality, inheritance and evolution. As a consequence, the theory of evolution based on the Neo-Darwinian synthesis, is inadequate for today's scientific evidence. Conversely, the author contends that life processes viewed on the basis of thermodynamics, complex system dynamics and self-organization provide a new framework for the foundations of Biology. I consider it necessary to comment on some essential aspects of this relevant work, and here I present a short overview of the main non-genetic sources of biomolecular order and complexity that underline the molecular dynamics and functionality of cells. These sources generate different processes of complexity, which encompasses from the most elementary levels of molecular activity to the emergence of systemic behaviors, and the information necessary to sustain them is not contained in the genome.

Improving Diuretic Response in Heart Failure by Implementing a Patient-Tailored Variability and Chronotherapy-Guided Algorithm

Heart failure is a major public health problem, which is associated with significant mortality, morbidity, and healthcare expenditures. A substantial amount of the morbidity is attributed to volume overload, for which loop diuretics are a mandatory treatment. However, the variability in response to diuretics and development of diuretic resistance adversely affect the clinical outcomes. Morevoer, there exists a marked intra- and inter-patient variability in response to diuretics that affects the clinical course and related adverse outcomes. In the present article, we review the mechanisms underlying the development of diuretic resistance. The role of the autonomic nervous system and chronobiology in the pathogenesis of congestive heart failure and response to therapy are also discussed. Establishing a novel model for overcoming diuretic resistance is presented based on a patient-tailored variability and chronotherapy-guided machine learning algorithm that comprises clinical, laboratory, and sensor-derived inputs, including inputs from pulmonary artery measurements. Inter- and intra-patient signatures of variabilities, alterations of biological clock, and autonomic nervous system responses are embedded into the algorithm; thus, it may enable a tailored dose regimen in a continuous manner that accommodates the highly dynamic complex system.

Cellular Darwinism: Regulatory networks, stochasticity, and selection in cancer development

There are strong parallels between the evolutionary origin of species within populations of organisms and new concepts for the origin of cancers within cell populations in the tissues of the body. The analogy is that cancers can be regarded as a new somatic species developing within the host organism. In both cases, understanding the processes involved requires a multi-scale analysis, including higher-level control of genetic and epigenetic changes. A key to developing successful therapeutic strategies will be to identify the processes that control heterogeneity in tissues. These include processes outside the currently dominant theory of evolution, i.e. the Modern Synthesis. Specifically, organisms can partially direct both genetic and epigenetic changes through the harnessing of chance. The loci and rates of mutation and of genome reorganisation are forms of targeted functional reorganisation of genomes. They are more likely to result in functional reorganisations compared to the slow accumulation of point mutations.

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.

Stochasticity Versus Determinacy in Neurobiology: From Ion Channels to the Question of the "Free Will"

If one accepts that decisions are made by the brain and that neuronal mechanisms obey deterministic physical laws, it is hard to deny what some brain researchers postulate, such as "We do not do what we want, but we want what we do" and "We should stop talking about freedom. Our actions are determined by physical laws." This point of view has been substantially supported by spectacular neurophysiological experiments demonstrating action-related brain activity (readiness potentials, blood oxygen level-dependent signals) occurring up to several seconds before an individual becomes aware of his/her decision to perform the action. This report aims to counter the deterministic argument for the absence of free will by using experimental data, supplemented by computer simulations, to demonstrate that biological systems, specifically brain functions, are built on principle randomness, which is introduced already at the lowest level of neuronal information processing, the opening and closing of ion channels. Switching between open and closed states follows physiological laws but also makes use of randomness, which is apparently introduced by Brownian motion - principally unavoidable under all life-compatible conditions. Ion-channel stochasticity, manifested as noise, function is not smoothed out toward higher functional levels but can even be amplified by appropriate adjustment of the system's non-linearities. Examples shall be given to illustrate how stochasticity can propagate from ion channels to single neuron action potentials to neuronal network dynamics to the interactions between different brain nuclei up to the control of autonomic functions. It is proposed that this intrinsic stochasticity helps to keep the brain in a flexible state to explore diverse alternatives as a prerequisite of free decision-making.

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.

Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution

Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.

Second-Generation Digital Health Platforms: Placing the Patient at the Center and Focusing on Clinical Outcomes

Artificial intelligence (AI) digital health systems have drawn much attention over the last decade. However, their implementation into medical practice occurs at a much slower pace than expected. This paper reviews some of the achievements of first-generation AI systems, and the barriers facing their implementation into medical practice. The development of second-generation AI systems is discussed with a focus on overcoming some of these obstacles. Second-generation systems are aimed at focusing on a single subject and on improving patients' clinical outcomes. A personalized closed-loop system designed to improve end-organ function and the patient's response to chronic therapies is presented. The system introduces a platform which implements a personalized therapeutic regimen and introduces quantifiable individualized-variability patterns into its algorithm. The platform is designed to achieve a clinically meaningful endpoint by ensuring that chronic therapies will have sustainable effect while overcoming compensatory mechanisms associated with disease progression and drug resistance. Second-generation systems are expected to assist patients and providers in adopting and implementing of these systems into everyday care.

Overcoming Compensatory Mechanisms toward Chronic Drug Administration to Ensure Long-Term, Sustainable Beneficial Effects

Chronic administration of drugs leads to the activation of compensatory mechanisms that may inhibit some of their activity and induce unwanted toxicity. These mechanisms are an obstacle for maintaining a sustainable effect for many chronic medications. Pathways that adapt to the burden induced by chronic drugs, whether or not related to the underlying disease, can lead to a partial or complete loss of effect. Variability characterizes many biological systems and manifests itself as large intra- and inter-individual differences in the response to drugs. Circadian rhythm-based chronotherapy is further associated with variability in responses noted among patients. This paper reviews current knowledge regarding the loss of effect of chronic medications and the range of variabilities that have been described in responses and loss of responses. Establishment of a personalized platform for overcoming these prohibitive mechanisms is presented as a model for ensuring long-term sustained medication effects. This novel platform implements personalized variability signatures and individualized circadian rhythms for preventing and opposing the prohibitive effect of the compensatory mechanisms induced by chronic drug administration.

Introducing the 21st Century's New Four Horsemen of the Coronapocalypse

As the world struggles through the COVID-19 pandemic, we should also be asking what systems-level measures will be needed to prevent this or even worse disasters from happening in the future. We argue that the pandemic is merely one of potentially myriad and pleiomorphic future global disasters generated by the same underlying dynamical system. We explain that there are four broad but easily identifiable systemic, pathologically networked conditions that are hurtling civilization toward potential self-destruction. As long as these conditions are not resolved, we should consider catastrophe as an inevitable emergent endpoint from the dynamics. All four conditions can be reversed with collective action to begin creating an enduring and thriving post- COVID-19 world. This will require maximal application of the precautionary principle.

Order Through Disorder: The Characteristic Variability of Systems

Randomness characterizes many processes in nature, and therefore its importance cannot be overstated. In the present study, we investigate examples of randomness found in various fields, to underlie its fundamental processes. The fields we address include physics, chemistry, biology (biological systems from genes to whole organs), medicine, and environmental science. Through the chosen examples, we explore the seemingly paradoxical nature of life and demonstrate that randomness is preferred under specific conditions. Furthermore, under certain conditions, promoting or making use of variability-associated parameters may be necessary for improving the function of processes and systems.

A consideration of physiological regulation from the perspective of Bayesian enactivism

How the animal regulates its internal environment is a central question in physiology. In recent years, the account of biological functions known as Bayesian enactivism has been extended from neuroscience to address processes of physiological regulation. Enactivism understands sensory action cycles of perception and behaviour to entail expectations of the causes of sensations received from the environment. Enactivism is Bayesian in that the organism strives to update expectations to better match the sensations it experiences through actions. The review starts with a brief examination of the historical development of the concepts of homeostasis, homeorhesis and allostasis. To better align the historical concepts of physiological regulation with Bayesian enactivism it is suggested that homeorhesis and allostasis function as opposing effectors modulating, respectively, robustness and plasticity of phenotype to render homeostatic balance of the animal with its changing environment. In this formulation, the expectations of the environment embedded within the form and functions of the animal that develop under homeorhetic control during morphogenesis and morphostasis are updated by allostasis to better match the animal's phenotype with its contemporary environment. Just as morphogens shape development and persistence of anatomical form during morphogenesis and morphostasis, anticipatory behaviours can be understood to structure the animal's pattern of environmental engagement in a manner that shapes the development and persistence of homeostasis. Further empirical and theoretical analyses should help clarify whether homeorhesis and allostasis are aspects of a common underlying process or are opposing effectors mediating a Bayesian dialogue between expectation and experience.

The Role of Mutation Bias in Adaptive Evolution

Mutational input is the ultimate source of genetic variation, but mutations are not thought to affect the direction of adaptive evolution. Recently, critics of standard evolutionary theory have questioned the random and non-directional nature of mutations, claiming that the mutational process can be adaptive in its own right. We discuss here mutation bias in adaptive evolution. We find little support for mutation bias as an independent force in adaptive evolution, although it can interact with selection under conditions of small population size and when standing genetic variation is limited, entirely consistent with standard evolutionary theory. We further emphasize that natural selection can shape the phenotypic effects of mutations, giving the false impression that directed mutations are driving adaptive evolution.

The N-space Episenome unifies cellular information space-time within cognition-based evolution

Self-referential cellular homeostasis is maintained by the measured assessment of both internal status and external conditions based within an integrated cellular information field. This cellular field attachment to biologic information space-time coordinates environmental inputs by connecting the cellular senome, as the sum of the sensory experiences of the cell, with its genome and epigenome. In multicellular organisms, individual cellular information fields aggregate into a collective information architectural matrix, termed a N-space Episenome, that enables mutualized organism-wide information management. It is hypothesized that biological organization represents a dual heritable system constituted by both its biological materiality and a conjoining N-space Episenome. It is further proposed that morphogenesis derives from reciprocations between these inter-related facets to yield coordinated multicellular growth and development. The N-space Episenome is conceived as a whole cell informational projection that is heritable, transferable via cell division and essential for the synchronous integration of the diverse self-referential cells that constitute holobionts.

The Dynamical Emergence of Biology From Physics: Branching Causation via Biomolecules

Biology differs fundamentally from the physics that underlies it. This paper proposes that the essential difference is that while physics at its fundamental level is Hamiltonian, in biology, once life has come into existence, causation of a contextual branching nature occurs at every level of the hierarchy of emergence at each time. The key feature allowing this to happen is the way biomolecules such as voltage-gated ion channels can act to enable branching logic to arise from the underlying physics, despite that physics per se being of a deterministic nature. Much randomness occurs at the molecular level, which enables higher level functions to select lower level outcomes according to higher level needs. Intelligent causation occurs when organisms engage in deduction, enabling prediction and planning. This is possible because ion channels enable action potentials to propagate in axons. The further key feature is that such branching biological behavior acts down to cause the underlying physical interactions to also exhibit a contextual branching behavior.

Harnessing stochasticity: How do organisms make choices?

Choice in the behavior of organisms involves novelty, which may be unpredictable. Yet in retrospect, we can usually provide a rationale for the choice. A deterministic view of life cannot explain this. The solution to this paradox is that organisms can harness stochasticity through which they can generate many possible solutions to environmental challenges. They must then employ a comparator to find the solution that fits the challenge. What therefore is unpredictable in prospect can become comprehensible in retrospect. Harnessing stochastic and/or chaotic processes is essential to the ability of organisms to have agency and to make choices.

Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution

Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.

Was the Watchmaker Blind? Or Was She One-Eyed?

The question whether evolution is blind is usually presented as a choice between no goals at all ('the blind watchmaker') and long-term goals which would be external to the organism, for example in the form of special creation or intelligent design. The arguments either way do not address the question whether there are short-term goals within rather than external to organisms. Organisms and their interacting populations have evolved mechanisms by which they can harness blind stochasticity and so generate rapid functional responses to environmental challenges. They can achieve this by re-organising their genomes and/or their regulatory networks. Epigenetic as well as DNA changes are involved. Evolution may have no foresight, but it is at least partially directed by organisms themselves and by the populations of which they form part. Similar arguments support partial direction in the evolution of behavior.

The metaphysics of evolution

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. It then explores the implications of process metaphysics for conceptualizing evolution. After explaining what it is for an organism to be a process, the paper takes up the Hull/Ghiselin thesis of species as individuals and explores the conditions under which a species or lineage could constitute an individual process. It is argued that only sexual species satisfy these conditions, and that within sexual species the degree of organization varies. This, in turn, has important implications for species' evolvability. One important moral is that evolution will work differently in different biological domains.