A central theory of biology

The quantum cell

There is a consensus that we are conscious of something greater than ourselves, as if we are derived from some other primordial set of principles. Classical or Newtonian physics is based on the Laws of Nature. Conversely, in a recent series of articles, it has been hypothesized that the cell was formed from lipid molecules submerged in the primordial ocean that covered the earth 100 million years after it formed. Since lipids are amphiphiles, with both a positively- and negatively-charged pole, the negatively-charged pole is miscible in water. Under the influence of earth's gravity, the lipid molecules stand up perpendicularly to the surface of the water, packing together until the negative charge neutralizes the Van der Waals force for surface tension, causing the lipid molecules to 'leap' into the micellar form as a sphere with a semi-permeable membrane. Particles in the water freely enter and exit such spheres based on mass action. Over time such protocells evolved Symbiogenesis, encountering factors that posed existential threats, assimilating them to form physiology to maintain homeostatic control. Importantly, when differentiated lung or bone cells are exposed to zero gravity, they lose their phenotypic identity in their evolved state, which has been interpreted as transiting from local to non-local consciousness.

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.

The holism of evolution as consciousness

Quantum Entanglement has been hypothesized to mediate non-local consciousness, underlying which, empirically, is the force of gravity. Upon further reflection, the case can be made for 'the breath' as the physiologic trait that binds all of these properties together, offering further opportunity for hypothesis testing experimentation. Humans have inexplicably made extraordinary intellectual and technical advances within a relatively very short period of time, referred to as the 'great leap forward'. It would be of great value if we could identify how and why we have evolved so rapidly. There is a holotropism that begins with the Big Bang that is centered on the homeostatic control of energy, perpetually referencing the First Principles of Physiology. "The Breath" is how and why our physiology has managed to perpetuate our species, and perhaps why the lung has been 'over-engineered' in order to facilitate the role of breathing in consciousness.

Systems biology of human aging: A Fibonacci time series model

Fractals are everywhere in nature, particularly at the interfaces where matter or energy must be transferred, since they maximize surface area while minimizing energy losses. Temporal fractals have been well studied at micro scales in human biology, but have received comparatively little attention at broader macro scales. In this paper, we describe a fractal time series model of human aging from a systems biology perspective. This model examines how intrinsic aging rates are shaped by entropy and Fibonacci fractal dynamics, with implications for the emergence of key life cycle traits. This proposition is supported by research findings. The finding of an intrinsic aging rate rooted in Fibonacci fractal dynamics represents a new predictive paradigm in evolutionary biology.

The holism of cosmology and consciousness

The greatest unsolved mystery of all is what consciousness is. Torday and Miller have hypothesized that consciousness is the homologous 'equivalent' of our physiology, behaving as our history, providing an algorithm by which evolution can determine how and why to adapt to ever-changing environmental conditions. Complicated physiology was reduced iteratively to the unicell by tracing the cell-cell signaling mechanisms that dealt with emergent threats based on Bayesian statistics. Unlike Darwinian random mutations, the current approach is predicated on structural and functional changes within the context of pre-existing physiologic traits. The cytoskeleton of the cell is a complete representation for all of the phases of life, past, present and future, controlling the Target of Rapamycin gene, which determines all of the stages of life-homeostasis, meiosis and mitosis. Viewed from this perspective, the cell remains at equipoise relative to the Singularity that existed before the Big Bang. The purpose of life is to collect epigenetic marks by pursuing energy flows, not conventional material change due to random mutations. The cytoskeleton universally controls all of the states of the cell - homeostasis, meiosis and mitosis, rendering the status of the cell relative to the prevailing circumstances. Indeed, the cytoskeleton of the cell is a central player in all of the phases of life, past, present and future. The above-described integration of physiology as the cipher for consciousness is quite ingenious as a 'top-down/bottom-up/middle-out' way of ensuring the holism of life and non-life. Recognition of the centrality of the cell has led to a number of novel insights into biology that have been represented by dogma up until now. Consequently, biology has been simplified by shifting from description to mechanism. Based on Ockam's Razor, the cellular approach to evolution is superior to Darwin.

Cellular evolution of language

The evolutionary origin of language remains unknown despite many efforts to determine the origin of this signature human trait. Based on epigenetic inheritance, the current article hypothesizes that language evolved from cell-cell communication as the basis for generating structure and function embryologically and phylogenetically, as did all physiologic traits. Beginning with lipids forming the first micelle, a vertical integration of the evolved properties of the cell, from multicellular organisms to the introduction of cholesterol into the cell membrane, to the evolution of the peroxisome, the water-land transition and duplication of the βAdrenergic Receptor, the evolution of endothermy, leading to bipedalism, freeing the forelimbs for toolmaking and language, selection pressure for myelinization of the central nervous system to facilitate calcium flux, bespeaks human expression, culminating in the evolution of civilization. This process is epitomized by the Area of Broca as the structural-functional site for both motor control and language formation. The mechanistic interrelationship between motor control and language formation is underscored by the role of FoxP2 gene expression in both bipedalism and language. The effect of endothermy on bipedalism, freeing the forelimbs for toolmaking and language as the vertical integration from Cosmology to Physiology as the basis for language bespeaks human expression.

Consciousness, Redux

There have been many attempts to explain consciousness, ranging from Plato's archetypes, to Descartes' 'Mind-Body Dualism', and more recently to Chalmers' Qualia, and Andy Clarke's extended mind. Yet none of these conceptualizations of consciousness provide empiric evidence for what consciousness actually constitutes. The present hypothesis is that Consciousness is a product of the Singularity/Big Bang resulting from the endogenization of factors in the environment that have formed our physiology. Understanding the origin of consciousness as the Consciousness of the Singularity/Big Bang requires that it diachronically cuts across space-time. Consciousness functions based on the same data operating system as Cosmology. We can transcend consciousness and approach Consciousness by authoring our own software once we recognize this fundamental, mechanistic interrelationship.

Reappraising the exteriorization of the mammalian testes through evolutionary physiology

A number of theories have been proposed to explain the exteriorization of the testicles in most mammalian species. None of these provide a consistent account for the wide variety of testicular locations found across the animal kingdom. It is proposed that testicular location is the result of coordinate action of testicular tissue ecologies to sustain preferential states of homeostatic equipoise throughout evolutionary development in response to the advent of endothermy.

Biological evolution as defense of 'self'

Although the origin of self-referential consciousness is unknown, it can be argued that the instantiation of self-reference was the commencement of the living state as phenomenal experientiality. As self-referential cognition is demonstrated by all living organisms, life can be equated with the sustenance of cellular homeostasis in the continuous defense of 'self'. It is proposed that the epicenter of 'self' is perpetually embodied within the basic cellular form in which it was instantiated. Cognition-Based Evolution argues that all of biological and evolutionary development represents the perpetual autopoietic defense of self-referential basal cellular states of homeostatic preference. The means by which these states are attained and maintained is through self-referential measurement of information and its communication. The multicellular forms, either as biofilms or holobionts, represent the cellular attempt to achieve maximum states of informational distinction and energy efficiency through individual and collective means. In this frame, consciousness, self-consciousness and intelligence can be identified as forms of collective cellular phenotype directed towards the defense of fundamental cellular self-reference.

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.

Unitary Physiology

The common relationships among a great variety of biological phenomena seem enigmatic when considered solely at the level of the phenotype. The deep connections in physiology, for example, between the effects of maternal food restriction in utero and the subsequent incidence of metabolic syndrome in offspring, the effects of microgravity on cell polarity and reproduction in yeast, stress effects on jellyfish, and their endless longevity, or the relationship between nutrient abundance and the colonial form in slime molds, are not apparent by phenotypic observation. Yet all of these phenomena are ultimately determined by the Target of Rapamycin (TOR) gene and its associated signaling complexes. In the same manner, the unfolding of evolutionary physiology can be explained by a comparable application of the common principle of cell-cell signaling extending across complex developmental and phylogenetic traits. It is asserted that a critical set of physiologic and phenotypic adaptations emanated from a few crucial, ancestral receptor gene duplications that enabled the successful terrestrial transition of vertebrates from water to land. In combination, mTor and its cognate receptors and a few crucial genetic duplications provide a mechanistic common denominator across a diverse spectrum of biological responses. The proper understanding of their purpose yields a unified concept of physiology and its evolutionary development. © 2018 American Physiological Society. Compr Physiol 8:761-771, 2018.

How prokaryotes 'encode' their environment: Systemic tools for organizing the information flow

An important issue related to code biology concerns the cell's informational relationships with the environment. As an open self-producing system, a great variety of inputs and outputs are necessary for the living cell, not only consisting of matter and energy but also involving information flows. The analysis here of the simplest cells will involve two basic aspects. On the one side, the molecular apparatuses of the prokaryotic signaling system, with all its variety of environmental signals and component pathways (which have been called 1-2-3 Component Systems), including the role of a few second messengers which have been pointed out in bacteria too. And in the other side, the gene transcription system as depending not only on signaling inputs but also on a diversity of factors. Amidst the continuum of energy, matter, and information flows, there seems to be evidence for signaling codes, mostly established around the arrangement of life-cycle stages, in large metabolic changes, or in the relationships with conspecifics (quorum sensing) and within microbial ecosystems. Additionally, and considering the complexity growth of signaling systems from prokaryotes to eukaryotes, four avenues or "roots" for the advancement of such complexity would come out. A comparative will be established in between the signaling strategies and organization of both kinds of cellular systems. Finally, a new characterization of "informational architectures" will be proposed in order to explain the coding spectrum of both prokaryotic and eukaryotic signaling systems. Among other evolutionary aspects, cellular strategies for the construction of novel functional codes via the intermixing of informational architectures could be related to the persistence of retro-elements with obvious viral ancestry.

From cholesterol to consciousness

The nature of consciousness has been debated for centuries. It can be understood as part and parcel of the natural progression of life from unicellular to multicellular, calcium fluxes mediating communication within and between cells. Consciousness is the vertical integration of calcium fluxes, mediated by the Target of Rapamycin gene integrated with the cytoskeleton. The premise of this paper is that there is a fundamental physiologic integration of the organism with the environment that constitutes consciousness.

A systems approach to physiologic evolution: From micelles to consciousness

A systems approach to evolutionary biology offers the promise of an improved understanding of the fundamental principles of life through the effective integration of many biologic disciplines. It is presented that any critical integrative approach to evolutionary development involves a paradigmatic shift in perspective, more than just the engagement of a large number of disciplines. Critical to this differing viewpoint is the recognition that all biological processes originate from the unicellular state and remain permanently anchored to that phase throughout evolutionary development despite their macroscopic appearances. Multicellular eukaryotic development can, therefore, be viewed as a series of connected responses to epiphenomena that proceeds from that base in continuous iterative maintenance of collective cellular homeostatic equipoise juxtaposed against an ever-changing and challenging environment. By following this trajectory of multicellular eukaryotic evolution from within unicellular First Principles of Physiology forward, the mechanistic nature of complex physiology can be identified through a step-wise analysis of a continuous arc of vertebrate evolution based upon serial exaptations.

The evolution of "Life": A Metadarwinian integrative approach

It is undeniably very logical to first formulate an unambiguous definition of “Life” before engaging in defining the parameters instrumental to Life's evolution. Because nearly everybody assumes, erroneously in my opinion, that catching Life's essence in a single sentence is impossible, this way of thinking remained largely unexplored in evolutionary theory. Upon analyzing what exactly happens at the transition from “still alive” to “just dead,” the following definition emerged. What we call “Life” (L) is an activity. It is nothing other than the total sum (∑) of all communication acts (C) executed, at moment t, by entities organized as sender-receiver compartments: L = ∑C Such “living” entities are self-electrifying and talking ( = communicating) aggregates of fossil stardust operating in an environment heavily polluted by toxic calcium. Communication is a multifaceted, complex process that is seldom well explained in introductory textbooks of biology. Communication is instrumental to adaptation because, at the cellular level, any act of communication is in fact a problem-solving act. It can be logically deduced that not Natural Selection itself but communication/problem-solving activity preceding selection is the universal driving force of evolution. This is against what textbooks usually claim, although doubt on the status of Natural Selection as driving force has been around for long. Finally, adopting the sender-receiver with its 2 memory systems (genetic and cognitive, both with their own rules) and 2 types of progeny (”physical children” and “pupils”) as the universal unit of architecture and function of all living entities, also enables the seamless integration of cultural and organic evolution, another long-standing tough problem in evolutionary theory. Paraphrasing Theodosius Dobzhansky, the very essence of biology is: “Nothing in biology and evolutionary theory makes sense except in the light of the ability of living matter to communicate, and by doing so, to solve problems.”

The Molecular Apgar Score: A Key to Unlocking Evolutionary Principles

One of the first "tools" used for systematically evaluating successful newborn transitional physiology at birth was the Apgar Score, devised by Virginia Apgar in 1953. This objective assessment tool allowed clinicians to immediately gauge the relative success of a newborn infant making the transition from the in utero liquid immersive environment to the ex utero gas environment in the delivery room during the first minutes after birth. The scoring system, although eponymous, is generally summarized as an acronym based on Appearance, Pulse, Grimace, Activity, and Respiration, criteria evaluated and scored at 1 and 5 min after birth. This common clinical appraisal is a guide for determining the elements of integrated physiology involved as the infant makes the transition from a "sea water" environment of 3% oxygen to a "land" environment in 21% oxygen. Appearance determines the perfusion of the skin with oxygenated blood-turning it pink; Pulse is the rate of heart beat, reflecting successful oxygen delivery to organs; Grimace, or irritability, is a functional marker for nervous system integration; Activity represents locomotor capacity; and, of course, Respiration represents pulmonary function as well as the successful neuro-feedback-mediated drive to breathe, supplying oxygen by inspiring atmospheric gas. Respiration, locomotion, and metabolism are fundamental processes adapted for vertebrate evolution from a water-based to an atmosphere-based life and are reflected by the Apgar Score. These physiologic processes last underwent major phylogenetic changes during the water-land transition some 300-400 million years ago, during which specific gene duplications occurred that facilitated terrestrial adaptation, in particular the parathyroid hormone-related protein receptor, the β-adrenergic receptor, and the glucocorticoid receptor. All these genetic traits and the gene regulatory networks they comprise represent the foundational substructure of the Apgar Score. As such, these molecular elements can be examined using a Molecular Apgar evaluation of keystone evolutionary events that predict successful evolutionary adaptation of physiologic functions necessary for neonatal transition and survival.

Phenotype as Agent for Epigenetic Inheritance

The conventional understanding of phenotype is as a derivative of descent with modification through Darwinian random mutation and natural selection. Recent research has revealed Lamarckian inheritance as a major transgenerational mechanism for environmental action on genomes whose extent is determined, in significant part, by germ line cells during meiosis and subsequent stages of embryological development. In consequence, the role of phenotype can productively be reconsidered. The possibility that phenotype is directed towards the effective acquisition of epigenetic marks in consistent reciprocation with the environment during the life cycle of an organism is explored. It is proposed that phenotype is an active agent in niche construction for the active acquisition of epigenetic marks as a dominant evolutionary mechanism rather than a consequence of Darwinian selection towards reproductive success. The reproductive phase of the life cycle can then be appraised as a robust framework in which epigenetic inheritance is entrained to affect growth and development in continued reciprocal responsiveness to environmental stresses. Furthermore, as first principles of physiology determine the limits of epigenetic inheritance, a coherent justification can thereby be provided for the obligate return of all multicellular eukaryotes to the unicellular state.

The Unicellular State as a Point Source in a Quantum Biological System

A point source is the central and most important point or place for any group of cohering phenomena. Evolutionary development presumes that biological processes are sequentially linked, but neither directed from, nor centralized within, any specific biologic structure or stage. However, such an epigenomic entity exists and its transforming effects can be understood through the obligatory recapitulation of all eukaryotic lifeforms through a zygotic unicellular phase. This requisite biological conjunction can now be properly assessed as the focal point of reconciliation between biology and quantum phenomena, illustrated by deconvoluting complex physiologic traits back to their unicellular origins.

Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow

As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses.

Life and evolution as physics

What is evolution and why does it exist in the biological, geophysical and technological realms — in short, everywhere? Why is there a time direction — a time arrow — in the changes we know are happening every moment and everywhere? Why is the present different than the past? These are questions of physics, about everything, not just biology. The answer is that nothing lives, flows and moves unless it is driven by power. Physics sheds light on the natural engines that produce the power destroyed by the flows, and on the free morphing that leads to flow architectures naturally and universally. There is a unifying tendency across all domains to evolve into flow configurations that provide greater access for movement. This tendency is expressed as the constructal law of evolutionary flow organization everywhere. Here I illustrate how this law of physics accounts for and unites the life and evolution phenomena throughout nature, animate and inanimate.

The Cell as the First Niche Construction

Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as 'internal' Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology.

Life Is Simple-Biologic Complexity Is an Epiphenomenon

Life originated from unicellular organisms by circumventing the Second Law of Thermodynamics using the First Principles of Physiology, namely negentropy, chemiosmosis and homeostatic regulation of calcium and lipids. It is hypothesized that multicellular organisms are merely contrivances or tools, used by unicellular organisms as agents for the acquisition of epigenetic inheritance. The First Principles of Physiology, which initially evolved in unicellular organisms are the exapted constraints that maintain, sustain and perpetuate that process. To ensure fidelity to this mechanism, we must return to the first principles of the unicellular state as the determinants of the primary level of selection pressure during the life cycle. The power of this approach is reflected by examples of its predictive value. This perspective on life is a "game changer", mechanistically rendering transparent many dogmas, teleologies and tautologies that constrain the current descriptive view of Biology.

On the Evolution of the Mammalian Brain

Hobson and Friston have hypothesized that the brain must actively dissipate heat in order to process information (Hobson et al., 2014). This physiologic trait is functionally homologous with the first instantation of life formed by lipids suspended in water forming micelles- allowing the reduction in entropy (heat dissipation). This circumvents the Second Law of Thermodynamics permitting the transfer of information between living entities, enabling them to perpetually glean information from the environment, that is felt by many to correspond to evolution per se. The next evolutionary milestone was the advent of cholesterol, embedded in the cell membranes of primordial eukaryotes, facilitating metabolism, oxygenation and locomotion, the triadic basis for vertebrate evolution. Lipids were key to homeostatic regulation of calcium, forming calcium channels. Cell membrane cholesterol also fostered metazoan evolution by forming lipid rafts for receptor-mediated cell-cell signaling, the origin of the endocrine system. The eukaryotic cell membrane exapted to all complex physiologic traits, including the lung and brain, which are molecularly homologous through the function of neuregulin, mediating both lung development and myelinization of neurons. That cooption later exapted as endothermy during the water-land transition (Torday, 2015a), perhaps being the functional homolog for brain heat dissipation and conscious/mindful information processing. The skin and brain similarly share molecular homologies through the “skin-brain” hypothesis, giving insight to the cellular-molecular “arc” of consciousness from its unicellular origins to integrated physiology. This perspective on the evolution of the central nervous system clarifies self-organization, reconciling thermodynamic and informational definitions of the underlying biophysical mechanisms, thereby elucidating relations between the predictive capabilities of the brain and self-organizational processes.

The Emergence of Physiology and Form: Natural Selection Revisited

Natural Selection describes how species have evolved differentially, but it is descriptive, non-mechanistic. What mechanisms does Nature use to accomplish this feat? One known way in which ancient natural forces affect development, phylogeny and physiology is through gravitational effects that have evolved as mechanotransduction, seen in the lung, kidney and bone, linking as molecular homologies to skin and brain. Tracing the ontogenetic and phylogenetic changes that have facilitated mechanotransduction identifies specific homologous cell-types and functional molecular markers for lung homeostasis that reveal how and why complex physiologic traits have evolved from the unicellular to the multicellular state. Such data are reinforced by their reverse-evolutionary patterns in chronic degenerative diseases. The physiologic responses of model organisms like Dictyostelium and yeast to gravity provide deep comparative molecular phenotypic homologies, revealing mammalian Target of Rapamycin (mTOR) as the final common pathway for vertical integration of vertebrate physiologic evolution; mTOR integrates calcium/lipid epistatic balance as both the proximate and ultimate positive selection pressure for vertebrate physiologic evolution. The commonality of all vertebrate structure-function relationships can be reduced to calcium/lipid homeostatic regulation as the fractal unit of vertebrate physiology, demonstrating the primacy of the unicellular state as the fundament of physiologic evolution.

Heterochrony as Diachronically Modified Cell-Cell Interactions

Heterochrony is an enabling concept in evolution theory that metaphorically captures the mechanism of biologic change due to mechanisms of growth and development. The spatio-temporal patterns of morphogenesis are determined by cell-to-cell signaling mediated by specific soluble growth factors and their cognate receptors on nearby cells of different germline origins. Subsequently, down-stream production of second messengers generates patterns of form and function. Environmental upheavals such as Romer’s hypothesized drying up of bodies of water globally caused the vertebrate water-land transition. That transition caused physiologic stress, modifying cell-cell signaling to generate terrestrial adaptations of the skeleton, lung, skin, kidney and brain. These tissue-specific remodeling events occurred as a result of the duplication of the Parathyroid Hormone-related Protein Receptor (PTHrPR) gene, expressed in mesodermal fibroblasts in close proximity to ubiquitously expressed endodermal PTHrP, amplifying this signaling pathway. Examples of how and why PTHrPR amplification affected the ontogeny, phylogeny, physiology and pathophysiology of the lung are used to substantiate and further our understanding through insights to the heterochronic mechanisms of evolution, such as the fish swim bladder evolving into the vertebrate lung, interrelated by such functional homologies as surfactant and mechanotransduction. Instead of the conventional description of this phenomenon, lung evolution can now be understood as adaptive changes in the cellular-molecular signaling mechanisms underlying its ontogeny and phylogeny.

The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life

All eukaryotic organisms are holobionts representing complex collaborations between the entire microbiome of each eukaryote and its innate cells. These linked constituencies form complex localized and interlocking ecologies in which the specific microbial constituents and their relative abundance differ substantially according to age and environmental exposures. Rapid advances in microbiology and genetic research techniques have uncovered a significant previous underestimate of the extent of that microbial contribution and its metabolic and developmental impact on holobionts. Therefore, a re-calibration of the neonatal period is suggested as a transitional phase in development that includes the acquisition of consequential collaborative microbial life from extensive environmental influences. These co-dependent, symbiotic relationships formed in the fetal and neonatal stages extend into adulthood and even across generations.

What We Talk About When We Talk About Evolution

Currently, the biologic sciences are a Tower of Babel, having become so highly specialized that one discipline cannot effectively communicate with another. A mechanism for evolution that integrates development and physiologic homeostasis phylogenetically has been identified—cell-cell interactions. By reducing this process to ligand-receptor interactions and their intermediate down-stream signaling partners, it is possible, for example, to envision the functional homologies between such seemingly disparate structures and functions as the lung alveolus and kidney glomerulus, the skin and brain, or the skin and lung. For example, by showing the continuum of the lung phenotype for gas exchange at the cell-molecular level, being selected for increased surface area by augmenting lung surfactant production and function in lowering surface tension, we have determined an unprecedented structural-functional continuum from proximate to ultimate causation in evolution. It is maintained that tracing the changes in structure and function that have occurred over both the short-term history of the organism (as ontogeny), and the long-term history of the organism (as phylogeny), and how the mechanisms shared in common can account for both biologic stability and novelty, will provide the key to understanding the mechanisms of evolution. We need to better understand evolution from its unicellular origins as the Big Bang of biology.

Homeostasis as the Mechanism of Evolution

Homeostasis is conventionally thought of merely as a synchronic (same time) servo-mechanism that maintains the status quo for organismal physiology. However, when seen from the perspective of developmental physiology, homeostasis is a robust, dynamic, intergenerational, diachronic (across-time) mechanism for the maintenance, perpetuation and modification of physiologic structure and function. The integral relationships generated by cell-cell signaling for the mechanisms of embryogenesis, physiology and repair provide the needed insight to the scale-free universality of the homeostatic principle, offering a novel opportunity for a Systems approach to Biology. Starting with the inception of life itself, with the advent of reproduction during meiosis and mitosis, moving forward both ontogenetically and phylogenetically through the evolutionary steps involved in adaptation to an ever-changing environment, Biology and Evolution Theory need no longer default to teleology.

Pleiotropy as the Mechanism for Evolving Novelty: Same Signal, Different Result

In contrast to the probabilistic way of thinking about pleiotropy as the random expression of a single gene that generates two or more distinct phenotypic traits, it is actually a deterministic consequence of the evolution of complex physiology from the unicellular state. Pleiotropic novelties emerge through recombinations and permutations of cell-cell signaling exercised during reproduction based on both past and present physical and physiologic conditions, in service to the future needs of the organism for its continued survival. Functional homologies ranging from the lung to the kidney, skin, brain, thyroid and pituitary exemplify the evolutionary mechanistic strategy of pleiotropy. The power of this perspective is exemplified by the resolution of evolutionary gradualism and punctuated equilibrium in much the same way that Niels Bohr resolved the paradoxical duality of light as Complementarity.