Discourse on order vs. disorder

Responses to commentaries on "The gene: An appraisal"

The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance.

The Gene: An appraisal

The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics, and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.

Is the tendency to maximise energy distribution an optimal collective activity for biological purposes? A proposal for a global principle of biological organization

Our purpose is to address the biological problem of finding foundations of the organization in the collective activity among cell networks in the nervous system, at the meso/macroscale, giving rise to cognition and consciousness. But in doing so, we encounter another problem related to the interpretation of methods to assess the neural interactions and organization of the neurodynamics, because thermodynamic notions, which have precise meaning only under specific conditions, have been widely employed in these studies. The consequence is that apparently contradictory results appear in the literature, but these contradictions diminish upon the considerations of the specific circumstances of each experiment. After clarifying some of these controversial points and surveying some experimental results, we propose that a necessary condition for cognition/consciousness to emerge is to have available enough energy, or cellular activity; and a sufficient condition is the multiplicity of configurations in which cell networks can communicate, resulting in non-uniform energy distribution, the generation and dissipation of energy gradients due to the constant activity. The diversity of sensorimotor processing of higher animals needs a flexible, fluctuating web on neuronal connections, and we review results supporting such multiplicity of configurations among brain regions associated with conscious awareness and healthy brain states. These ideas may reveal possible fundamental principles of brain organization that could be extended to other natural phenomena and how healthy activity may derive to pathological states.

The gene: An appraisal

The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.

The Matter of Time

About a century ago, in the spirit of ancient atomism, the quantum of light was renamed the photon to suggest that it is the fundamental element of everything. Since the photon carries energy in its period of time, a flux of photons inexorably embodies a flow of time. Thus, time comprises periods as a trek comprises legs. The flows of quanta naturally select optimal paths (i.e., geodesics) to level out energy differences in the least amount of time. The corresponding flow equations can be written, but they cannot be solved. Since the flows affect their driving forces, affecting the flows, and so on, the forces (i.e., causes) and changes in motions (i.e., consequences) are inseparable. Thus, the future remains unpredictable. However, it is not all arbitrary but rather bounded by free energy. Eventually, when the system has attained a stationary state where forces tally, there are no causes and no consequences. Since there are no energy differences between the system and its surroundings, the quanta only orbit on and on. Thus, time does not move forward either but circulates.

Cellular senomic measurements in Cognition-Based Evolution

All living entities are cognitive and dependent on ambiguous information. Any assessment of that imprecision is necessarily a measuring function. Individual cells measure information to sustain self-referential homeostatic equipoise (self-identity) in juxtaposition to the external environment. The validity of that information is improved by its collective assessment. The reception of cellular information obliges thermodynamic reactions that initiate a self-reinforcing work channel. This expresses as natural cellular engineering and niche constructions which become the complex interrelated tissue ecologies of holobionts. Multicellularity is collaborative cellular information management directed towards the optimization of information quality through its collective measured assessment. Biology and its evolution can now be re-framed as the continuous process of self-referential cellular measurement in the perpetual defense of individual cellular self-identities through the collective form.

Introducing the 21st Century's New Four Horsemen of the Coronapocalypse

As the world struggles through the COVID-19 pandemic, we should also be asking what systems-level measures will be needed to prevent this or even worse disasters from happening in the future. We argue that the pandemic is merely one of potentially myriad and pleiomorphic future global disasters generated by the same underlying dynamical system. We explain that there are four broad but easily identifiable systemic, pathologically networked conditions that are hurtling civilization toward potential self-destruction. As long as these conditions are not resolved, we should consider catastrophe as an inevitable emergent endpoint from the dynamics. All four conditions can be reversed with collective action to begin creating an enduring and thriving post- COVID-19 world. This will require maximal application of the precautionary principle.

The relationship between gunshot-residue particle size and Boltzmann distribution

Gunshot-residue (GSR) particles usually form spherical structures, have special dimensions, and a composition that consists of burned and partially unburned matter with a 0.5–50-µm diameter (sometimes larger). The GSR particle-size distributions have been argued to be caused by the effects of equilibrium-surface distributions during formation and have not yet been correlated with a theoretical analysis or probability distribution. This study proposes a model to explain the GSR particle-size distribution quantitatively. Based on the data, and, as predicted by our model, the number of GSR particles decreases proportionally to the inverse square of the GSR particle size as the particle size increases. This result occurs because of the abundance of microstructures that are encountered in the GSR particles.