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Journal: Progress in biophysics and molecular biology


We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H- W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion - life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.

Concepts: DNA, Gene, Genetics, Bacteria, Evolution, Organism, Species, Paleontology


Therapeutic activity of antibiotics is noteworthy, as they are used in the treatment of microbial infections. Regardless of their utility, there has been a steep decrease in the number of drug candidates due to antibiotic resistance, an inevitable consequence of noncompliance with the full therapeutic regimen. A variety of resistant species like MDR (Multi-Drug Resistant), XDR (Extensively Drug-Resistant) and PDR (Pan Drug-Resistant) species have evolved, but discovery pipeline has already shown signs of getting dried up. Therefore, the need for newer antibiotics is of utmost priority to combat the microbial infections of future times. Peptides have some interesting features like minimal side effect, high tolerability and selectivity towards specific targets, which would help them successfully comply with the stringent safety standards set for clinical trials. In this review, we attempt to present the state of the art in the discovery of peptide-based antimicrobials from a design perspective.


We present a plausible account of the origin of the archetypal vertebrate bauplan. We offer a theoretical reconstruction of the geometrically regular structure of the blastula resulting from the sequential subdivision of the egg, followed by mechanical deformations of the blastula in subsequent stages of gastrulation. We suggest that the formation of the vertebrate bauplan during development, as well as fixation of its variants over the course of evolution, have been constrained and guided by global mechanical biases. Arguably, the role of such biases in directing morphology-though all but neglected in previous accounts of both development and macroevolution-is critical to any substantive explanation for the origin of the archetypal vertebrate bauplan. We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis-currently an elusive goal-will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences.

Concepts: Critical thinking, Mathematics, Developmental biology, Geometry, Vertebrate, Analytic geometry, Geometric progression, Body plan


The earliest indications for paternally induced transgenerational effects from the environment to future generations were based on a small number of long-term epidemiological studies and some empirical observations. Only recently have experimental animal models and a few analyses on human data explored the transgenerational nature of phenotypic changes observed in offspring. Changes include multiple metabolic disorders, cancer and other chronic diseases. These phenotypes cannot always be explained by Mendelian inheritance, DNA mutations or genetic damage. Hence, a new compelling theory on epigenetic inheritance is gaining interest, providing new concepts that extend Darwin’s evolutionary theory. Epigenetic alterations or “epimutations” are being considered to explain transgenerational inheritance of parentally acquired traits. The responsible mechanisms for these epimutations include DNA methylation, histone modification, and RNA-mediated effects. This review explores the literature on a number of time-dependent environmentally induced epigenetic alterations, specifically those from dietary exposures. We suggest a role for the male germ line as one of nature’s tools to capture messages from our continuously changing environment and to transfer this information to subsequent generations. Further, we open the discussion that the paternally inherited epigenetic information may contribute to evolutionary adaptation.

Concepts: DNA, Gene, Genetics, Natural selection, Evolution, Histone, Biology, DNA repair


Epigenetic inheritance refers to changes in gene expression that are heritable across generations but are not caused by changes in the DNA sequence. Many environmental factors are now known to cause epigenetic changes, including the presence of pathogens, parasites, harmful chemicals and other stress factors. There is increasing evidence that transcriptional reprograming caused by epigenetic modifications can be passed from parents to offspring. Indeed, diseases such as cancer can occur in the offspring due to epigenetically-inherited gene expression profiles induced by stress experienced by the parent. Empirical studies to investigate the role of epigenetics in trans-generational gene regulation and disease require appropriate model organisms. In this review, we argue that selected insects can be used as models for human diseases with an epigenetic component because the underlying molecular mechanisms (DNA methylation, histone acetylation and the expression of microRNAs) are evolutionarily conserved. Insects offer a number of advantages over mammalian models including ethical acceptability, short generation times and the potential to investigate complex interacting parameters such as fecundity, longevity, gender ratio, and resistance to pathogens, parasites and environmental stress.

Concepts: DNA, Gene, Genetics, Gene expression, Bacteria, Histone, Epigenetics, DNA methylation


The brain is composed of electrically excitable neuronal networks regulated by the activity of voltage-gated ion channels. Further portraying the molecular composition of the brain, however, will not reveal anything remotely reminiscent of a feeling, a sensation or a conscious experience. In classical physics, addressing the mind-brain problem is a formidable task because no physical mechanism is able to explain how the brain generates the unobservable, inner psychological world of conscious experiences and how in turn those conscious experiences steer the underlying brain processes toward desired behavior. Yet, this setback does not establish that consciousness is non-physical. Modern quantum physics affirms the interplay between two types of physical entities in Hilbert space: unobservable quantum states, which are vectors describing what exists in the physical world, and quantum observables, which are operators describing what can be observed in quantum measurements. Quantum no-go theorems further provide a framework for studying quantum brain dynamics, which has to be governed by a physically admissible Hamiltonian. Comprising consciousness of unobservable quantum information integrated in quantum brain states explains the origin of the inner privacy of conscious experiences and revisits the dynamic timescale of conscious processes to picosecond conformational transitions of neural biomolecules. The observable brain is then an objective construction created from classical bits of information, which are bound by Holevo’s theorem, and obtained through the measurement of quantum brain observables. Thus, quantum information theory clarifies the distinction between the unobservable mind and the observable brain, and supports a solid physical foundation for consciousness research.


Forty years ago a causal therapy of autism was offered which has never been tried out by the therapeutic profession. It predictably is so effective that even members of other mirror-competent bonding species can be healed from their “physiological autism.” Niklas Luhmann belonged to the therapy’s supporters and Leo Szilard had anticipated it in fiction 30 years earlier. The Ottersberg Lectures on Philosophy revived it through the enthusiasm and cooperation of the youthful audience.

Concepts: Physiology, Sociology


Controversial, sensational and often contradictory scientific reports have triggered active debates over the biological effects of electromagnetic fields (EMFs) in literature and mass media the last few decades. This could lead to confusion and distraction, subsequently hampering the development of a univocal conclusion on the real hazards caused by EMFs on humans. For example, there are lots of publications indicating that EMF can induce apoptosis and DNA strand-breaks in cells. On the other hand, these effects could rather be beneficial, in that they could be effectively harnessed for treatment of various disorders, including cancer. This review discusses and analyzes the results of various in vitro, in vivo and epidemiological studies on the effects of non-ionizing EMFs on cells and organs, including the consequences of exposure to the low and high frequencies EM spectrum. Emphasis is laid on the analysis of recent data on the role of EMF in the induction of oxidative stress and DNA damage. Additionally, the impact of EMF on the reproductive system has been discussed, as well as the relationship between EM radiation and blood cancer. Apart from adverse effects, the therapeutic potential of EMFs for clinical use in different pathologies is also highlighted.


Computational models in biology and biomedical science are often constructed to aid people’s understanding of phenomena or to inform decisions with socioeconomic consequences. Model credibility is the willingness of people to trust a model’s predictions and is often difficult to establish for computational biology models. A 3 × 3 matrix has been proposed to allow such models to be categorised with respect to their testability and epistemic foundation in order to guide the selection of an appropriate process of validation to supply evidence to establish credibility. Three approaches to validation are identified that can be deployed depending on whether a model is deemed untestable, testable or lies somewhere in between. In the latter two cases, the validation process involves the quantification of uncertainty which is a key output. The issues arising due to the complexity and inherent variability of biological systems are discussed and the creation of ‘digital twins’ proposed as a means to alleviate the issues and provide a more robust, transparent and traceable route to model credibility and acceptance.

Concepts: Scientific method, Natural selection, Biology, Physics, Semantics, Philosophy of science, Control theory, Logic


The origin of the incessant rhythmical heartbeat and the mechanism of muscle contraction have fascinated scientists over centuries. This short review outlines physiological explanations that were discussed in the 19th century starting with Albrecht von Haller (1708-1777), an 18th century physiologist who proposed that the heart has an intrinsic irritability. He argued that under normal conditions the inflow of blood stimulates the heart muscle to contract by mechanical touch and distension. Johannes Müller (1800-1858, physiologist in Bonn and Berlin) contended that the influence of the sympathetic nerve, specifically the activity of intracardiac ganglia, is the foremost cause of the heartbeat. Walter H. Gaskell and Theodor Engelmann (physiologists in Cambridge and Utrecht, respectively) independently criticized this neurogenic theory. They reported experimental evidence that supported the myogenic theory of the origin of the heartbeat, which has been accepted since about 1900. The concept of cardiac mechano-sensitivity, which can be traced back to A. von Haller, is currently resurging. Concerning mechanisms of contraction, Edward A. Schäfer (1850-1935), histologist and physiologist in Edinburgh, described differences between cardiac and skeletal muscle and coined the term sarcomere. Based on microscopic studies of cross-striated muscle, Schäfer outlined a detailed and plausible mechanism of muscle contraction in 1892. He put forward that during muscle shortening the “clear part of the muscle substance” (actin) might pass into longitudinal canals, which exist between the “sarcous elements” (myosin). His model foresaw fundamental elements of the sliding filament model, which was discovered by the Huxleys about 60 years later.