Information, Coding, and Biological Function: The Dynamics of Life.

In the mid-20th century, two new scientific disciplines emerged forcefully: molecular biology and information-communication theory. At the beginning, cross-fertilization was so deep that the term genetic code was universally accepted for describing the meaning of triplets of mRNA (codons) as amino acids. However, today, such synergy has not taken advantage of the vertiginous advances in the two disciplines and presents more challenges than answers. These challenges not only are of great theoretical relevance but also represent unavoidable milestones for next-generation biology: from personalized genetic therapy and diagnosis to Artificial Life to the production of biologically active proteins. Moreover, the matter is intimately connected to a paradigm shift needed in theoretical biology, pioneered a long time ago, that requires combined contributions from disciplines well beyond the biological realm. The use of information as a conceptual metaphor needs to be turned into quantitative and predictive models that can be tested empirically and integrated in a unified view. Successfully achieving these tasks requires a wide multidisciplinary approach, including Artificial Life researchers, to address such an endeavour.

Wavelet Analysis of Respiratory Muscle sEMG Signals during the Physiological Breakpoint of Static Dry End-Expiratory Breath-Holding in Naive Apneists: A Pilot Study.

The wavelet spectral characteristics of three respiratory muscle signals (scalenus (SC), parasternal intercostal (IC), and rectus abdominis (RA)) and one locomotor muscle (brachioradialis (BR)) were analyzed in the time-frequency (T-F) domain during voluntary breath-holding (BH), with a focus on the physiological breakpoint that is commonly considered the first involuntary breathing movement (IBM) that signals the end of the easy-going phase of BH. The study was performed for an end-expiratory BH physiological breaking point maneuver on twelve healthy, physically active, naive breath-holders/apneists (six professional athletes; six recreational athletes, and two individuals in the post-COVID-19 period) using surface electromyography (sEMG). We observed individual effects that were dependent on muscle oxygenation and each person's fitness, which were consistent with the mechanism of motor unit (MU) recruitment and the transition of slow-twitch oxidative (type 1) to fast-twitch glycolytic (type 2) muscle fibers. Professional athletes had longer BH durations (BHDs) and strong hypercapnic responses regarding the expiratory RA muscle, which is activated abruptly at higher BHDs in a person-specific range below 250 Hz and is dependent on the BHD. This is in contrast with recreational athletes, who had strong hypoxic responses regarding inspiratory IC muscle, which is activated faster and gradually in the frequency range of 250-450 Hz (independent of the person and BHD). This pilot study preliminarily indicates that it is possible to noninvasively assess the physiological characteristics of skeletal muscles, especially oxygenation, and improve physical fitness tests by determining the T-F features of elevated myoelectric IC and RA activity during BH.

Alzheimer's and Consciousness: How Much Subjectivity Is Objective?

Does Alzheimer Disease show a decline in cognitive functions that relate to the awareness of external reality? In this paper, we will propose a perspective that patients with increasing symptoms of AD show a change in the awareness of subjective versus objective representative axis of reality thus consequently move to a more internal like perception of reality. This paradigm shift suggests that new insights into the dynamicity of the conscious representation of reality in the AD brain may give us new clues to the very early signs of memory and self-awareness impairment that originates from, in our view the microtubules. Dialog between Adso and William, in Umberto Eco's The Name of the Rose, Third Day: Vespers. "But how does it happen," I said with admiration, "that you were able to solve the mystery of the library looking at it from the outside, and you were unable to solve it when you were inside?" "Thus, God knows the world, because He conceived it in His mind, as if it was from the outside, before it was created, and we do not know its rule, because we live inside it, having found it already made."

p-Adic mathematics and theoretical biology.

The principal objective of this article is a brief overview of the main parts of p-adic mathematics, which have already had valuable applications and may have a significant impact in the near future on the further development of some fields of theoretical and mathematical biology. In particular, we present the basics of ultrametrics, p-adic numbers and p-adic analysis, as well as insight into their applications for modeling some cognitive processes, genetic code and protein dynamics. We also argue that ultrametric concepts and p-adic mathematics are natural tools for the viable description of biological systems and phenomena with a hierarchical structure.

On Entropy of Probability Integral Transformed Time Series.

The goal of this paper is to investigate the changes of entropy estimates when the amplitude distribution of the time series is equalized using the probability integral transformation. The data we analyzed were with known properties-pseudo-random signals with known distributions, mutually coupled using statistical or deterministic methods that include generators of statistically dependent distributions, linear and non-linear transforms, and deterministic chaos. The signal pairs were coupled using a correlation coefficient ranging from zero to one. The dependence of the signal samples is achieved by moving average filter and non-linear equations. The applied coupling methods are checked using statistical tests for correlation. The changes in signal regularity are checked by a multifractal spectrum. The probability integral transformation is then applied to cardiovascular time series-systolic blood pressure and pulse interval-acquired from the laboratory animals and represented the results of entropy estimations. We derived an expression for the reference value of entropy in the probability integral transformed signals. We also experimentally evaluated the reliability of entropy estimates concerning the matching probabilities.

p-Adic hierarchical properties of the genetic code.

In this article, we consider p-adic modeling of the standard genetic code and the vertebrate mitochondrial one. To this end, we use 5-adic and 2-adic distance as a mathematical tool to describe closeness (nearness, similarity) between codons as elements of a bioinformation space. Codons which are simultaneously at the smallest 5-adic and 2-adic distance code the same (or similar) amino acid or stop signal. The set of codons is presented as an ultrametric tree as well as a fractal and p-adic network. It is shown that genetic code can be treated as sequential translation between genetic languages. This p-adic approach gives possibility to be applied to sequences of nucleotides of an arbitrary finite length. We present an overview of published and some new results on various p-adic properties of the genetic code.