The conscious cell

Biology in the 21st century: Natural selection is cognitive selection

Natural selection has a formal definition as the natural process that results in the survival and reproductive success of individuals or groups best adjusted to their environment, leading to the perpetuation of those genetic qualities best suited to that organism's environmental niche. Within conventional Neo-Darwinism, the largest source of those variations that can be selected is presumed to be secondary to random genetic mutations. As these arise, natural selection sustains adaptive traits in the context of a 'struggle for existence'. Consequently, in the 20th century, natural selection was generally portrayed as the primary evolutionary driver. The 21st century offers a comprehensive alternative to Neo-Darwinian dogma within Cognition-Based Evolution. The substantial differences between these respective evolutionary frameworks have been most recently articulated in a revision of Crick's Central Dogma, a former centerpiece of Neo-Darwinism. The argument is now advanced that the concept of natural selection should also be comprehensively reappraised. Cognitive selection is presented as a more precise term better suited to 21st century biology. Since cognition began with life's origin, natural selection represents cognitive selection.

The synchronic, diachronic cell as the holism of consciousness

The cell is both synchronic and diachronic, based on ontogeny and phylogeny, respectively. As experimental evidence for this holism, absent gravitational force, differentiated lung and bone cells devolve, losing their phenotypes, losing their evolutionary status, reverting to their nonlocal status. Thus, when evolution is seen as serial homeostasis, it is homologous with Quantum Entanglement as the nonlocal means of maintaining homeostatic balance between particles. This monadic perspective on consciousness is one-hundred and eighty degrees out of synch with the conventional way of thinking about consciousness as a diad, or mind and brain. There have been many attempts to explain consciousness, virtually all of them based on the brain as mind. The working hypothesis is that consciousness is a holism constituted by the unicell, the lipid cell membrane forming a barrier between inside and outside of the cell's environment as a topology. Conceptually, both the unicell and 'two hands clapping' are holisms, but because the cell is constituted by the ambiguity of negative entropy, and 'one hand clapping' requires two hands, they are both pseudo-holisms, constantly striving to be whole again. In the case of the cell, it is incomplete in the sense that there are factors in the ever-changing environment that can homeostatically complete it. That process results in biochemical modification of specific DNA codes in the egg or sperm so that the offspring is able to adapt in subsequent generations epigenetically. The opportunity to trace the evolution of the breath from humans to fish opens up to the further revelation of the interplay between evolution and geological change, tracing it back to invertebrates, sponges, and ultimately to unicellular organisms. And therein is evidence that the Cosmos itself 'breathes', providing the ultimate celestial fundament for this trail of holisms.

An evaluation of the xenobotic cognitive project: Towards Stage 1 of xenobotic cognition

Xenobot, the world's first biological robot, puts numerous philosophical riddles before us. One among them pertains to the cognitive status of these entities. Are these biological robots cognitive? To evaluate the cognitive status of xenobots and to resolve the puzzle of a single mind emerging from smaller sub-units, in this article, I juxtapose the cognitive capacities of xenobots with that of two other minimal models of cognition, i.e., basal cognition and nonliving active matter cognition. Further, the article underlines the essential cognitive capabilities that xenobots need to achieve to enter what I call stage 1 of xenobotic cognition. Stage 1 is characterized by numerous cognitive mechanisms, which are integral for the survival and cognition of basal organisms. Finally, I suggest that developing xenobots that can reach Stage 1 can help us achieve sophistication in the areas of evolution of the human mind, robotics, biology and medicine, and artificial intelligence (AI).

Ownership psychology as a "cognitive cell" adaptation: A minimalist model of microbial goods theory

Microbes perfect social interactions with intuitive logics and goal-directed reciprocity. These multilevel, cognition-resembling adaptations in Dictyostelid cellular molds enable individual-to-group viability through public/private bacterial farming and dynamic marketspaces. Like humans and animals, Dictyostelid livestock-ownership depends on environmental sensing, cooperation, and competition. Moreover, social-norm policing of cosmopolitan colonies coordinates farmer decisions, phenotypes, and ownership identities with bacteria herding, privatization, and consumption.

Harmony in a panpsychist world

Experiences tend to be followed by states for which they provide normative reasons. Such harmonious correlations cry out for explanation. Theories that answer or diminish these cries thereby achieve an advantage over theories that do neither. I argue that the main lines of response to these cries that are available to biological theorists-theorists who hold (roughly) that conscious subjects are generally biological entities-are problematic. And I argue that panpsychism-which holds (roughly) that conscious subjects are ubiquitous in nature-provides an attractive response to these explanatory cries. Taken together, these considerations underwrite a kind of 'psychophysical fine-tuning' argument in support of panpsychism, one that is reminiscent of cosmological fine-tuning arguments in favor of multiverse hypotheses.

Competitive Coherence Generates Qualia in Bacteria and Other Living Systems

The relevance of bacteria to subjective experiences or qualia is underappreciated. Here, I make four proposals. Firstly, living systems traverse sequences of active states that determine their behaviour; these states result from competitive coherence, which depends on connectivity-based competition between a Next process and a Now process, whereby elements in the active state at time n+1 are chosen between the elements in the active state at time n and those elements in the developing n+1 state. Secondly, bacteria should help us link the mental to the physical world given that bacteria were here first, are highly complex, influence animal behaviour and dominate the Earth. Thirdly, the operation of competitive coherence to generate active states in bacteria, brains and other living systems is inseparable from qualia. Fourthly, these qualia become particularly important to the generation of active states in the highest levels of living systems, namely, the ecosystem and planetary levels.

Biomolecular Basis of Cellular Consciousness via Subcellular Nanobrains

Cells emerged at the very beginning of life on Earth and, in fact, are coterminous with life. They are enclosed within an excitable plasma membrane, which defines the outside and inside domains via their specific biophysical properties. Unicellular organisms, such as diverse protists and algae, still live a cellular life. However, fungi, plants, and animals evolved a multicellular existence. Recently, we have developed the cellular basis of consciousness (CBC) model, which proposes that all biological awareness, sentience and consciousness are grounded in general cell biology. Here we discuss the biomolecular structures and processes that allow for and maintain this cellular consciousness from an evolutionary perspective.

Cognition in some surprising places

The most widely accepted view in the biopsychological sciences is that the cognitive functions that are diagnostic of mental operations, sentience or, more commonly, consciousness emerged fairly late in evolution, most likely in the Cambrian period. Our position dovetails with James's below - subjectivity, feeling, consciousness has a much longer evolutionary history, one that goes back to the first appearance of life. The Cellular Basis of Consciousness (CBC) model is founded on the presumption that sentience and life are coterminous; that all organisms, based on inherent cellular activities via processes that take place in excitable membranes of their cells, are sentient, have subjective experiences and feelings. These, in turn, guide the context-relevant behaviors essential for their survival in often hostile environments in constant flux. The CBC framework is reductionistic, mechanistic, and calls for bottom-up research programs into the evolutionary origin of biological consciousness.

Sentience and Consciousness in Single Cells: How the First Minds Emerged in Unicellular Species

A reductionistic, bottom-up, cellular-based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. It emerges as an inherent feature of, and contemporaneously with, the very first life-forms. All other varieties of mentation are the result of evolutionary mechanisms based on this singular event. Therefore, all forms of sentience and consciousness evolve from this original instantiation in prokaryotes. It has also been identified that three cellular structures and mechanisms that likely play critical roles here are excitable membranes, oscillating cytoskeletal polymers, and structurally flexible proteins. Finally, basic biophysical principles are proposed to guide those processes that underly the emergence of supracellular sentience from cellular sentience in multicellular organisms.

Life before LUCA

We see the last universal common ancestor of all living organisms, or LUCA, at the evolutionary separation of the Archaea from the Eubacteria, and before the symbiotic event believed to have led to the Eukarya. LUCA is often implicitly taken to be close to the origin of life, and sometimes this is even stated explicitly. However, LUCA already had the capacity to code for many proteins, and had some of the same bioenergetic capacities as modern organisms. An organism at the origin of life must have been vastly simpler, and this invites the question of how to define a living organism. Even if acceptance of the giant viruses as living organisms forces the definition of LUCA to be revised, it will not alter the essential point that LUCA should be regarded as a recent player in the evolution of life.

From endosymbiosis to holobionts: Evaluating a conceptual legacy

In her influential 1967 paper, Lynn Margulis synthesized a range of data to support the idea of endosymbiosis. Building on the success of this work, she applied the same methodology to promote the role of symbiosis more generally in evolution. As part of this broader project, she coined the term 'holobiont' to refer to a unified entity of symbiont and host. This concept is now applied with great gusto in microbiome research, and often implies not just a physiological unit but also various senses of an evolving system. My analysis will track how Margulis came to propose the term, its current use in microbiome research, and how those applications link back to Margulis. I then evaluate what contemporary use says about Margulis's legacy for microbiome research.

The Transition to Minimal Consciousness through the Evolution of Associative Learning

The minimal state of consciousness is sentience. This includes any phenomenal sensory experience - exteroceptive, such as vision and olfaction; interoceptive, such as pain and hunger; or proprioceptive, such as the sense of bodily position and movement. We propose unlimited associative learning (UAL) as the marker of the evolutionary transition to minimal consciousness (or sentience), its phylogenetically earliest sustainable manifestation and the driver of its evolution. We define and describe UAL at the behavioral and functional level and argue that the structural-anatomical implementations of this mode of learning in different taxa entail subjective feelings (sentience). We end with a discussion of the implications of our proposal for the distribution of consciousness in the animal kingdom, suggesting testable predictions, and revisiting the ongoing debate about the function of minimal consciousness in light of our approach.

Microorganism and filamentous fungi drive evolution of plant synapses

In the course of plant evolution, there is an obvious trend toward an increased complexity of plant bodies, as well as an increased sophistication of plant behavior and communication. Phenotypic plasticity of plants is based on the polar auxin transport machinery that is directly linked with plant sensory systems impinging on plant behavior and adaptive responses. Similar to the emergence and evolution of eukaryotic cells, evolution of land plants was also shaped and driven by infective and symbiotic microorganisms. These microorganisms are the driving force behind the evolution of plant synapses and other neuronal aspects of higher plants; this is especially pronounced in the root apices. Plant synapses allow synaptic cell–cell communication and coordination in plants, as well as sensory-motor integration in root apices searching for water and mineral nutrition. These neuronal aspects of higher plants are closely linked with their unique ability to adapt to environmental changes.

Strasburger's legacy to mitosis and cytokinesis and its relevance for the Cell Theory

Eduard Strasburger was one of the most prominent biologists contributing to the development of the Cell Theory during the nineteenth century. His major contribution related to the characterization of mitosis and cytokinesis and especially to the discovery of the discrete stages of mitosis, which he termed prophase, metaphase and anaphase. Besides his observations on uninucleate plant and animal cells, he also investigated division processes in multinucleate cells. Here, he emphasised the independent nature of mitosis and cytokinesis. We discuss these issues from the perspective of new discoveries in the field of cell division and conclude that Strasburger's legacy will in the future lead to a reformulation of the Cell Theory and that this will accommodate the independent and primary nature of the nucleus, together with its complement of perinuclear microtubules, for the organisation of the eukaryotic cell.

Horizontal gene transfers with or without cell fusions in all categories of the living matter

This article reviews the history of widespread exchanges of genetic segments initiated over 3 billion years ago, to be part of their life style, by sphero-protoplastic cells, the ancestors of archaea, prokaryota, and eukaryota. These primordial cells shared a hostile anaerobic and overheated environment and competed for survival. "Coexist with, or subdue and conquer, expropriate its most useful possessions, or symbiose with it, your competitor" remain cellular life's basic rules. This author emphasizes the role of viruses, both in mediating cell fusions, such as the formation of the first eukaryotic cell(s) from a united crenarchaeon and prokaryota, and the transfer of host cell genes integrated into viral (phages) genomes. After rising above the Darwinian threshold, rigid rules of speciation and vertical inheritance in the three domains of life were established, but horizontal gene transfers with or without cell fusions were never abolished. The author proves with extensive, yet highly selective documentation, that not only unicellular microorganisms, but the most complex multicellular entities of the highest ranks resort to, and practice, cell fusions, and donate and accept horizontally (laterally) transferred genes. Cell fusions and horizontally exchanged genetic materials remain the fundamental attributes and inherent characteristics of the living matter, whether occurring accidentally or sought after intentionally. These events occur to cells stagnating for some 3 milliard years at a lower yet amazingly sophisticated level of evolution, and to cells achieving the highest degree of differentiation, and thus functioning in dependence on the support of a most advanced multicellular host, like those of the human brain. No living cell is completely exempt from gene drains or gene insertions.

Cell-cell channels, viruses, and evolution: via infection, parasitism, and symbiosis toward higher levels of biological complexity

Between prokaryotic cells and eukaryotic cells there is dramatic difference in complexity which represents a problem for the current version of the cell theory, as well as for the current version of evolution theory. In the past few decades, the serial endosymbiotic theory of Lynn Margulis has been confirmed. This results in a radical departure from our understanding of living systems: the eukaryotic cell represents de facto"cells-within-cell." Higher order "cells-within-cell" situations are obvious at the eukaryotic cell level in the form of secondary and tertiary endosymbiosis, or in the male and female gametophytes of higher plants. The next challenge of the current version of the cell theory is represented by the fact that the multicellular fungi and plants are, in fact, supracellular assemblies as their cells are not physically separated from each other. Moreover, there are also examples of alliances and mergings between multicellular organisms. Infection, especially the viral one, but also bacterial and fungal infections, followed by symbiosis, is proposed to act as the major force that drives the biological evolution toward higher complexity.

On prokaryotic intelligence: strategies for sensing the environment

The adaptive relationship with the environment is a sine qua non condition for any intelligent system. Discussions on the nature of cellular intelligence, however, have not systematically pursued yet the question of whether there is a fundamental way of sensing the environment, which may characterize prokaryotic cells, or not. The molecular systems found in bacterial signaling are extremely diverse, ranging from very simple transcription regulators (single proteins comprising just two domains) to the multi-component, multi-pathway signaling cascades that regulate crucial stages of the cell cycle, such as sporulation, biofilm formation, dormancy, pathogenesis or flagellar biosynthesis. The combined complexity of the environment and of the cellular way of life is reflected as a whole in the aggregate of signaling elements: an interesting power-law relationship emerges in that regard. In a basic taxonomy of bacterial signaling systems, the first level of complexity corresponds to the simplest regulators, the "one-component systems" (OCSs), which are defined as proteins that contain known or predicted input and output domains but lack histidine kinase and receiver domains. They are evolutionary precursors of the "two-component systems" (TCSs), which include histidine protein-kinase receptors and an independent response regulator, and are considered as the central signaling paradigm within prokaryotic organisms. The addition of independent receptors begets further functional complexity: thus, "three-component systems" (ThCSs) should be applied to those two-component systems that incorporate an extra non-kinase receptor to activate the protein-kinase. Further, the combined information processing functions (cross-talk) and integrative dynamics that OCS, TCS and ThCS may achieve together in the prokaryotic cell have to be depicted, as well as the relationship of these informational functions with the life cycle organization and its checkpoints. Finally, the extent to which formal models would capture the ongoing relationship of the living cell with its medium has to be gauged, in the light of both the complexity of molecular recognition events and the impredicative nature of living systems.

Reflections on 'plant neurobiology'

Plant neurobiology, a new and developing area in the plant sciences, is a meeting place for scientists concerned with exploring how plants perceive signs within their environment and convert them into internal electro-chemical ('plant neurobiological') signals. These signals, in turn, permit rapid modifications of physiology and development that help plants adjust to changes in their environment. The use of the epithet 'neurobiology' in the context of plant life has, however, led to misunderstanding about the aims, content, and scope of this topic. This difficulty is possibly due to the terminology used, since this is often unfamiliar in the context of plants. In the present article, the scope of plant neurobiology is explored and some of analogical and metaphorical aspects of the subject are discussed. One approach to reconciling possible problems of using the term 'plant neurobiology' and, at the same time, of analysing information transfer in plants and the developmental processes which are regulated thereby, is through Living Systems Theory (LST). This theory specifically directs attention to the means by which information is gathered and processed, and then dispersed throughout the hierarchy of organisational levels of the plant body. Attempts to identify the plant 'neural' structures point to the involvement of the vascular tissue - xylem and phloem - in conveying electrical impulses generated in zones of special sensitivity to receptive locations throughout the plant in response to mild stress. Vascular tissue therefore corresponds, at the level of organismic organisation, with the informational 'channel and net' subsystem of LST.

The biogenic approach to cognition

After half a century of cognitive revolution we remain far from agreement about what cognition is and what cognition does. It was once thought that these questions could wait until the data were in. Today there is a mountain of data, but no way of making sense of it. The time for tackling the fundamental issues has arrived. The biogenic approach to cognition is introduced not as a solution but as a means of approaching the issues. The traditional, and still predominant, methodological stance in cognitive inquiry is what I call the anthropogenic approach: assume human cognition as the paradigm and work 'down' to a more general explanatory concept. The biogenic approach, on the other hand, starts with the facts of biology as the basis for theorizing and works 'up' to the human case by asking psychological questions as if they were biological questions. Biogenic explanations of cognition are currently clustered around two main frameworks for understanding biology: self-organizing complex systems and autopoiesis. The paper describes the frameworks and infers from them ten empirical principles--the biogenic 'family traits'--that constitute constraints on biogenic theorizing. Because the anthropogenic approach to cognition is not constrained empirically to the same degree, I argue that the biogenic approach is superior for approaching a general theory of cognition as a natural phenomenon.

Development of mitochondrial gene replacement therapy

Many "classic" mitochondrial diseases have been described that arise from single homoplasmic mutations in mitochondrial DNA (mtDNA). These diseases typically affect nonmitotic tissues (brain, retina, muscle), present with variable phenotypes, can appear sporadically, and are untreatable. Evolving evidence implicates mtDNA abnormalities in diseases such as Alzheimer's, Parkinson's, and type II diabetes, but specific causal mutations for these conditions remain to be defined. Understanding the mtDNA genotype-phenotype relationships and developing specific treatment for mtDNA-based diseases is hampered by inability to manipulate the mitochondrial genome. We present a novel protein transduction technology ("protofection") that allows insertion and expression of the human mitochondrial genome into mitochondria of living cells. With protofection, the mitochondrial genotype can be altered, or exogenous genes can be introduced to be expressed and either retained in mitochondria or be directed to other organelles. Protofection also delivers mtDNA in vivo, opening the way to rational development of mitochondrial gene replacement therapy of mtDNA-based diseases.

Plant synapses: actin-based domains for cell-to-cell communication

For many years it has been known that plants perform rapid long-distance signalling using classical action potentials that have impacts on diverse processes in plants. Plants also synthesize numerous neuronal molecules and fulfill some criteria for intelligent behaviour. Analysis of recent breakthrough data from ecophysiology studies has revealed that plant roots can discriminate between 'self' and 'non-self'; in animals, this ability to discriminate is dependent on the activities of neuronal synapses. Here, we propose that plant cells establish modes of information exchange between each other that have properties in common with neuronal synapses. Moreover, plants also assemble adhesive contacts that orchestrate cell-to-cell communication between the host cells when challenged with pathogens, parasites and potential symbionts. We propose that these adhesive contacts resemble the immunological synapses found in animals.

Bionformation: untangling the networks of life

The growth of numerous subdisciplines at the interface between biology and computer science paves the way for reconsidering the special relationship between information and life. In this sense, the term 'bioinformation' appears as an integrative notion that is useful to promote a new understanding of the heterogeneous networkings that characterize life. Two conceptual avenues are explored here: representation and symmetry. It is argued that the special organization of the living cell, based on the overlapping of both sequential and 'amorphous' architectures, endlessly strives to fill in the occurring 'functional voids' or symmetry breakings; and it endlessly produces physiological networkings and evolutionary novelties as a byproduct. Characterizing the special dynamics inherent in the living cell may be a precondition for understanding the information-production processes on which other emergent informational entities are based, particularly, nervous systems and societies.