Why control an experiment?: From empiricism, via consciousness, toward Implicate Order.

Empirical research is based on observation and experimentation. Yet, experimental controls are essential for overcoming our sensory limits and generating reliable, unbiased and objective results.

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.

Prevention of perinatal nicotine-induced bone marrow mesenchymal stem cell myofibroblast differentiation by augmenting the lipofibroblast phenotype.

Perinatal nicotine exposure drives the differentiation of alveolar lipofibroblasts (LIFs), which are critical for lung injury repair, to myofibroblasts (MYFs), which are the hallmark of chronic lung disease. Bone marrow-derived mesenchymal stem cells (BMSCs) are important players in lung injury repair; however, how these cells are affected with perinatal nicotine exposure and whether these can be preferentially driven to a lipofibroblastic phenotype are not known. We hypothesized that perinatal nicotine exposure would block offspring BMSCs lipogenic differentiation, driving these cells toward a MYF phenotype. Since peroxisome proliferator activated-receptor γ (PPARγ) agonists can prevent nicotine-induced MYF differentiation of LIFs, we further hypothesized that the modulation of PPARγ expression would inhibit nicotine's myogenic effect on BMSCs. Sprague Dawley dams were perinatally administered nicotine (1 mg/kg bodyweight) with or without the potent PPARγ agonist rosiglitazone (RGZ), both administered subcutaneously. At postnatal day 21, BMSCs were isolated and characterized morphologically, molecularly, and functionally for their lipogenic and myogenic potentials. Perinatal nicotine exposure resulted in decreased oil red O staining, triolein uptake, expression of PPARγ, and its downstream target gene adipocyte differentiation-related protein by BMSCs, but enhanced α-smooth muscle actin and fibronectin expression, and activated Wnt signaling, all features indicative of their inhibited lipogenic, but enhanced myogenic potential. Importantly, concomitant treatment with RGZ virtually blocked all of these nicotine-induced morphologic, molecular, and functional changes. Based on these data, we conclude that BMSCs can be directionally induced to differentiate into the lipofibroblastic phenotype, and PPARγ agonists can effectively block perinatal nicotine-induced MYF transdifferentiation, suggesting a possible molecular therapeutic approach to augment BMSC's lung injury/repair potential.

On the evolution of the pulmonary alveolar lipofibroblast.

The pulmonary alveolar lipofibroblast was first reported in 1970. Since then its development, structure, function and molecular characteristics have been determined. Its capacity to actively absorb, store and 'traffic' neutral lipid for protection of the alveolus against oxidant injury, and for the active supply of substrate for lung surfactant phospholipid production have offered the opportunity to identify a number of specialized functions of these strategically placed cells. Namely, Parathyroid Hormone-related Protein (PTHrP) signaling, expression of Adipocyte Differentiation Related Protein, leptin, peroxisome proliferator activator receptor gamma, and the prostaglandin E2 receptor EP2- which are all stretch-regulated, explaining how and why surfactant production is 'on-demand' in service to ventilation-perfusion matching. Because of the central role of the lipofibroblast in vertebrate lung physiologic evolution, it is a Rosetta Stone for understanding how and why the lung evolved in adaptation to terrestrial life, beginning with the duplication of the PTHrP Receptor some 300 mya. Moreover, such detailed knowledge of the workings of the lipofibroblast have provided insight to the etiology and effective treatment of Bronchopulmonary Dysplasia based on physiologic principles rather than on pharmacology.

Vitamin D supplementation blocks pulmonary structural and functional changes in a rat model of perinatal vitamin D deficiency.

Whereas epidemiological data strongly link vitamin D (VD) deficiency to childhood asthma, the underlying molecular mechanisms remain unknown. Although VD is known to stimulate alveolar epithelial-mesenchymal interactions, promoting perinatal lung maturation, whether VD supplementation during this period protects against childhood asthma has not been demonstrated experimentally. Using an in vivo rat model, we determined the effects of perinatal VD deficiency on overall pulmonary function and the tracheal contraction as a functional marker of airway contractility. One month before pregnancy, rat dams were put on either a no cholecalciferol-added or a 250, 500, or 1,000 IU/kg cholecalciferol-added diet, which was continued throughout pregnancy and lactation. At postnatal day 21, offspring plasma 25(OH)D levels and pulmonary function (whole body plethysmography and tracheal contraction response to acetylcholine) were determined. 25(OH)D levels were lowest in the no cholecalciferol-supplemented group, increasing incrementally in response to cholecalciferol supplementation. Compared with the 250 and 500 IU/kg VD-supplemented groups, the no cholecalciferol-supplemented group demonstrated a significant increase in airway resistance following methacholine challenge. However, the cholecalciferol deficiency-mediated increase in tracheal contractility in the cholecalciferol-depleted group was only blocked by supplementation with 500 IU/kg cholecalciferol. Therefore, in addition to altering alveolar epithelial-mesenchymal signaling, perinatal VD deficiency also alters airway contractility, providing novel insights to asthma pathogenesis in perinatally VD-deficient offspring. Perinatal VD supplementation at 500 IU/kg appears to effectively block these effects of perinatal VD deficiency in the rat model used, providing a strong clinical rationale for effective perinatal VD supplementation for preventing childhood asthma.

Nebulized PPARγ agonists: a novel approach to augment neonatal lung maturation and injury repair in rats.

BACKGROUND: By stimulating lipofibroblast maturation, parenterally administered peroxisome proliferator-activated receptor γ (PPARγ) agonists promote lung homeostasis and injury repair in the neonatal lung. In this study, we determined whether PPARγ agonists could be delivered effectively via nebulization to neonates, and whether this approach would also protect against hyperoxia-induced lung injury. METHODS: One-day old Sprague-Dawley rat pups were administered PPARγ agonists rosiglitazone (RGZ, 3 mg/kg), pioglitazone (PGZ, 3 mg/kg), or the diluent, via nebulization every 24 h; animals were exposed to 21% or 95% O2 for up to 72 h. Twenty-four and 72 h following initial nebulization, the pups were sacrificed for lung tissue and blood collection to determine markers of lung maturation, injury repair, and RGZ and PGZ plasma levels. RESULTS: Nebulized RGZ and PGZ enhanced lung maturation in both males and females, as evidenced by the increased expression of markers of alveolar epithelial and mesenchymal maturation. This approach also protected against hyperoxia-induced lung injury, since hyperoxia-induced changes in bronchoalveolar lavage cell and protein contents and lung injury markers were all blocked by nebulized PGZ. CONCLUSION: Nebulized PPARγ agonist administration promotes lung maturation and prevents neonatal hyperoxia-induced lung injury in both males and females.

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 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 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.

Symbiogenesis redicts the monism of the cosmos.

Symbiogenesis has been systematically exploited to understand consciousness as the aggregate of our physiology. The Symbiogenic mechanism for assimilation of factors in the environment formulates the continuum from inside the cell to the Cosmos, both consciousness and cosmology complying with the Laws of Nature. Since Symbiogenesis is 'constructive', whereas eliminating what threatens us is 'destructive', why do we largely practice Symbiogenesis? Hypothetically, Symbiogenesis recursively simulates the monism of our origin, recognizing 'something bigger than ourselves'. That perspective explains many heretofore unexplained aspects of consciousness, such as mind, epigenetic inheritance, physiology, behaviors, social systems, mathematics, the Arts, from an a priori perspective. Moreover, there is an energetic continuum from Newtonian to Quantum Mechanics, opening up to a novel way of understanding the 'true nature of our being', not as 'materialism', but instead being the serial homeostatic control of energy. The latter is consistent with the spirit of Claude Bernard and Walter B. Cannon's perspectives on physiology. Such a paradigm shift is overdue, given that materialism is causing the destruction of the Earth and ourselves.

The mobius strip, the cell, and soft logic mathematics.

The cell-cell signaling mechanisms that are the basis for all of physiology have been used to trace evolution back to the unicellular state, and beyond, to the "First Principles of Physiology". And since our physiology derives from the Cosmos based on Symbiogenesis, it has been hypothesized that the cell behaves like a functional Mobius Strip, having no 'inside or outside' cell membrane surface - it is continuous with the Cosmos, its history being codified from Quantum Entanglement to Newtonian Mechanics, affording the cell consciousness and unconsciousness/subconsciousness as a continuum for the first time. Similarly, Klein and Maimon have concluded that their 'Soft Logic' mathematics also constitutes a Mobius Strip, using both a real number axis, combined with a zero axis, numerically representing cognition. This is congruent with the cell as 'two-tiered' consciousness, the first tier being the real-time interface between the cell membrane and its environment; the second tier constituting integrated physiology, referencing the consciousness of the Cosmos. Thus, there is coherence between physiology, consciousness and mathematics for the first time.

Sex-specific perinatal nicotine-induced asthma in rat offspring.

Recently, we have suggested that down-regulation of homeostatic mesenchymal peroxisome proliferator-activated receptor γ signaling after in utero nicotine exposure might contribute to asthma. Here, we have exploited an in vivo rat model of asthma to determine if the effects of perinatal nicotine exposure on offspring pulmonary function and mesenchymal markers of airway contractility in both tracheal and lung parenchymal tissue are sex specific, and whether the protection afforded by the peroxisome proliferator-activated receptor γ agonist, rosiglitazone (RGZ), against the perinatal nicotine-induced effect on offspring lung is also sex specific. Pregnant rat dams received placebo, nicotine, or nicotine plus RGZ daily from Embryonic Day 6 until Postnatal Day 21, at which time lung resistance, compliance, tracheal contractility, and the expression of structural and functional mesenchymal markers of pulmonary contractility were determined. Compared with control animals, perinatal nicotine exposure caused a significant increase in airway resistance and a decrease in airway compliance after a methacholine challenge in both male and female offspring, with more pronounced changes in the males. In contrast to this, the effects of perinatal nicotine exposure on acetylcholine-induced tracheal constriction, along with the expression of its mesenchymal markers, were observed exclusively in the male offspring. Concomitant treatment with RGZ normalized the nicotine-induced alterations in pulmonary function in both sexes, as well as the male-specific effects on acetylcholine-induced tracheal constriction, along with the affected mesenchymal markers. These data suggest that perinatal nicotine exposure causes sex-specific perinatal cigarette smoke exposure-induced asthma, providing a powerful phenotypic model for unequivocally determining the underlying nature of the cell molecular mechanism for this disease.

Evolution and Cell Physiology. 1. Cell signaling is all of biology.

I hypothesize that the First Principles of Physiology (FPPs) were co-opted during the vertebrate transition from water to land, beginning with the acquisition of cholesterol by eukaryotes, facilitating unicellular evolution over the course of the first 4.5 billion years of the Earth's history, in service to the reduction in intracellular entropy, far from equilibrium. That mechanism was perpetuated by the advent of cholesterol in the cell membrane of unicellular eukaryotes, ultimately giving rise to the metazoan homologs of the gut, lung, kidney, skin, bone, and brain. Parathyroid hormone-related protein (PTHrP), whose cognate receptor underwent a gene duplication during the transition from fish to amphibians, facilitated gas exchange for the water-to-land transition, since PTHrP is necessary for the formation of lung alveoli: deletion of the PTHrP gene in mice causes the offspring to die within a few minutes of birth due to the absence of alveoli. Moreover, PTHrP is central to the development and homeostasis of the kidney, skin, gut, bone, and brain. Therefore, duplication of the PTHrP receptor gene is predicted to have facilitated the molecular evolution of all the necessary traits for land habitation through a common cellular and molecular motif. Subsequent duplication of the ß-adrenergic receptor gene permitted blood pressure control within the lung microvasculature, allowing further evolution of the lung by increasing its surface area. I propose that such gene duplications were the result of shear stress on the microvasculature, locally generating radical oxygen species that caused DNA mutations, giving rise to duplication of the PTHrP and ß-adrenergic receptor genes. I propose that one can determine the FPPs by systematically tracing the molecular homologies between the lung, skin, kidney, gut, bone, and brain across development, phylogeny, and pathophysiology as a type of "reverse evolution." By tracing such relationships back to unicellular organisms, one can use the underlying principles to predict homeostatic failure as disease, thereby also potentially forming the basis for maneuvers that can treat or even prevent such failure.

Perinatal nicotine-induced transgenerational asthma.

Asthma is a major public health hazard worldwide. Its transgenerational inheritance has been inferred from epidemiological studies. More recently, using nicotine as a proxy for maternal smoking, we have demonstrated that an asthma-like phenotype can be inherited by rat offspring for up to two generations, i.e., multigenerationally, after the initial intrauterine exposure. We hypothesized that asthma transmission to offspring following perinatal nicotine exposure is not restricted up to F2 generation, but it also extends to subsequent generations. To test this hypothesis, using a well-established rat model of nicotine exposure-induced childhood asthma, we determined if perinatal nicotine exposure of F0 gestating dams would transmit asthma transgenerationally to F3 offspring. We now extend our findings to third-generation offspring, including abnormal pulmonary function, particularly as it relates to the occurrence in the upper airway exclusively in males, and to its effects on molecular functional markers (fibronectin and peroxisome proliferator-activated receptor γ), previously shown to be consistent with the asthma phenotype, herein expressed in fibroblasts isolated from the lung. These data, for the first time, demonstrate the transgenerational transmission of the asthma phenotype to F3 offspring following perinatal nicotine exposure of F0 dams.

Evolutionary biology redux.

This article offers a novel, enlightened concept for determining the mechanism of evolution. It is based on homeostasis, which distinguishes life from non-life and as such is the universal mechanism for the evolution of all living organisms. This view of evolution is logical, mechanistic, non-scalar, predictive, testable, and falsifiable, and it illuminates the epistemological relationships between physics and biology, ontogeny and phylogeny, development and aging, ultimate and proximate causation, health and disease. In addition to validating Haeckel's biogenetic law and Lamarckian epigenetics, reflecting the enabling value of the cellular approach, this perspective also expresses the evolutionary process at the cell-molecular level, since the mechanism of cell communication itself is universal in biology, in keeping with a Kuhnian paradigm shift. This approach may even elucidate the nature and evolution of consciousness as a manifestation of the cellular continuum from unicellular to multicellular life. We need such a functional genomic mechanism for the process of evolution if we are to make progress in biology and medicine. Like Copernican heliocentrism, a cellular approach to evolution may fundamentally change humankind's perceptions about our place in the universe.

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.

Consciousness, embodied Quantum Entanglement.

We have systematically misconstrued the nature of consciousness by overlooking our own physiology as that awareness. The following is a way to rectify this error through a deep understanding of what life 'means' in order to further advance our knowledge of who and what we are. The evolution of consciousness from the cell membrane to physiology is revealed by the effect of microgravity on phenotypic identity, revealing the two levels of consciousness experimentally. As does the classic Double-Slit experiment, exposing the dual way in which consciousness functions as both the day-to-day of the cell membrane and the transcendent property of our physiology.

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.

Perinatal nicotine exposure induces asthma in second generation offspring.

BACKGROUND: By altering specific developmental signaling pathways that are necessary for fetal lung development, perinatal nicotine exposure affects lung growth and differentiation, resulting in the offsprings' predisposition to childhood asthma; peroxisome proliferator-activated receptor gamma (PPARγ) agonists can inhibit this effect. However, whether the perinatal nicotine-induced asthma risk is restricted to nicotine-exposed offspring only; whether it can be transmitted to the next generation; and whether PPARγ agonists would have any effect on this process are not known. METHODS: Time-mated Sprague Dawley rat dams received either placebo or nicotine (1 mg/kg, s.c.), once daily from day 6 of gestation to postnatal day (PND) 21. Following delivery, at PND21, generation 1 (F1) pups were either subjected to pulmonary function tests, or killed to obtain their lungs, tracheas, and gonads to determine the relevant protein markers (mesenchymal contractile proteins), global DNA methylation, histone 3 and 4 acetylation, and for tracheal tension studies. Some F1 animals were used as breeders to generate F2 pups, but without any exposure to nicotine in the F1 pregnancy. At PND21, F2 pups underwent studies similar to those performed on F1 pups. RESULTS: Consistent with the asthma phenotype, nicotine affected lung function in both male and female F1 and F2 offspring (maximal 250% increase in total respiratory system resistance, and 84% maximal decrease in dynamic compliance following methacholine challenge; P < 0.01, nicotine versus control; P < 0.05, males versus females; and P > 0.05, F1 versus F2), but only affected tracheal constriction in males (51% maximal increase in tracheal constriction following acetylcholine challenge, P < 0.01, nicotine versus control; P < 0.0001, males versus females; P > 0.05, F1 versus F2); nicotine also increased the contractile protein content of whole lung (180% increase in fibronectin protein levels, P < 0.01, nicotine versus control, and P < 0.05, males versus females) and isolated lung fibroblasts (for example, 45% increase in fibronectin protein levels, P < 0.05, nicotine versus control), along with decreased PPARγ expression (30% decrease, P < 0.05, nicotine versus control), but only affected contractile proteins in the male trachea (P < 0.05, nicotine versus control, and P < 0.0001, males versus females). All of the nicotine-induced changes in the lung and gonad DNA methylation and histone 3 and 4 acetylation were normalized by the PPARγ agonist rosiglitazone except for the histone 4 acetylation in the lung. CONCLUSIONS: Germline epigenetic marks imposed by exposure to nicotine during pregnancy can become permanently programmed and transferred through the germline to subsequent generations, a ground-breaking finding that shifts the current asthma paradigm, opening up many new avenues to explore.

Evolution, gravity, and the topology of consciousness.

It has previously been hypothesized that consciousness is the aggregate of our evolutionary history, forged by ontogeny and phylogeny via cell-cell communications. In an on-going effort to identify the serial pre-adaptations that gave rise to consciousness, certain fundamental properties of the emerging cell are addressed herein. Evolution is topologic because it began as a phase transition caused by gravity attracting lipid molecules, spontaneously forming micelles submersed in the ocean that covered the primordial Earth, forming a surface boundary between the exterior Cosmos and the interior of micelles. Such protocells comply with the First Principles of Physiology-negative entropy, chemiosmosis and homeostasis-the first two principles being deterministic, the last being probabilistic, bestowing them with far more than just random chance. The mechanism of cellular evolution is based on exaptations of sequentially earlier and earlier genetic traits, working in reverse from present-day physiology all the way back to the unicellular state, which is homologous with mathematical 'knots'. Ironically, that relationship is evidence for the ontologic and epistemologic primacy of the cell, which supersedes mathematics and physics as manifestations of the Implicate Order since a conscious cell can conceive of a circle, but an unconscious circle is not able to conceive of a cell.