Philosophy of thermodynamics.

Thermodynamics is regarded as a universal but not foundational theory because its laws for macroscopic quantities have not been derived from microscopic entities. Thus, to root thermodynamics into the fundamental substance, atomism is revived, thinking that the light quantum is the indivisible and permanent element. Assuming the same basic building blocks constitute everything, the state of any system can be quantified by entropy, the logarithmic probability measure multiplied by Boltzmann's constant.

Chiral conformity emerges from the least-time free energy consumption.

The prevalence of chirally pure biological polymers is often assumed to stem from some slight preference for one chiral form at the origin of life. Likewise, the predominance of matter over antimatter is presumed to follow from some subtle bias for matter at the dawn of the universe. However, rather than being imposed from the start, handedness standards in societies emerged to make things work.

The Fundamental Nature of Motives.

Decision-making is described as a natural process, one among others, consuming free energy in the least time. The thermodynamic tenet explains why data associated with decisions display the same patterns as any other data: skewed distributions, sigmoidal cumulative curves, oscillations, and even chaos. Moreover, it is shown that decision-making is intrinsically an intractable process because everything depends on everything else.

Statistical Physics of Evolving Systems.

Evolution is customarily perceived as a biological process. However, when formulated in terms of physics, evolution is understood to entail everything. Based on the axiom of everything comprising quanta of actions (e.

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.

Epidemic as a natural process.

Mathematical epidemiology is a well-recognized discipline to model infectious diseases. It also provides guidance for public health officials to limit outbreaks. Nevertheless, epidemics take societies by surprise every now and then, for example, when the Ebola virus epidemic raged seemingly unrestrained in Western Africa.

Discourse on order vs. disorder.

The second law of thermodynamics is on one hand understood to account for irrevocable flow of energy from the top down, on the other hand it is seen to imply irreversible increase of disorder. This tension between the 2 stances is resolved in favor of the free energy consumption when entropy is derived from the statistical mechanics of open systems. The change in entropy is shown to map directly to the decrease in free energy without any connotation attached to disorder.

On the Character of Consciousness.

The human brain is a particularly demanding system to infer its nature from observations. Thus, there is on one hand plenty of room for theorizing and on the other hand a pressing need for a rigorous theory. We apply statistical mechanics of open systems to describe the brain as a hierarchical system in consuming free energy in least time.

On the divide between animate and inanimate.

Vitalism was abandoned already for a long time ago, yet the impression that animate beings differ in some fundamental way from inanimate objects continues to thrive. Here, we argue that scale free patterns, found throughout nature, present convincing evidence that this demarcation is only imaginary. Therefore, all systems ought to be regarded alike, i.

Genes without prominence: a reappraisal of the foundations of biology.

The sequencing of the human genome raises two intriguing questions: why has the prediction of the inheritance of common diseases from the presence of abnormal alleles proved so unrewarding in most cases and how can some 25 000 genes generate such a rich complexity evident in the human phenotype? It is proposed that light can be shed on these questions by viewing evolution and organisms as natural processes contingent on the second law of thermodynamics, equivalent to the principle of least action in its original form. Consequently, natural selection acts on variation in any mechanism that consumes energy from the environment rather than on genetic variation. According to this tenet cellular phenotype, represented by a minimum free energy attractor state comprising active gene products, has a causal role in giving rise, by a self-similar process of cell-to-cell interaction, to morphology and functionality in organisms, which, in turn, by a self-similar process entailing Darwin's proportional numbers are influencing their ecosystems.

The significance of sex.

Sexual and asexual modes of proliferation are associated with advantages and disadvantages, yet a profound percept that would account for both ways of reproduction is missing. On the basis of the 2nd law of thermodynamics we find that both sexual and asexual reproduction can be regarded as a means to consume free energy in least time. Parthenogenesis is a fast way to consume a rich repository of free energy, e.

Discovery and structural characterization of a phospholamban-binding cyclic peptide and design of novel inhibitors of phospholamban.

The interplay between cardiac sarcoplasmic Ca(2+)ATPase and phospholamban is a key regulating factor of contraction and relaxation in the cardiac muscle. In heart failure, aberrations in the inhibition of sarcoplasmic Ca(2+)ATPase by phospholamban are associated with anomalies in cardiac functions. In experimental heart failure models, modulation of the interaction between these two proteins has been shown to be a potential therapeutic approach.

The capricious character of nature.

The on-going whole genome sequencing and whole cell assays of metabolites and proteins imply that complex systems could ultimately be mastered by perfecting knowledge into great detail. However, courses of nature are inherently intractable because flows of energy and their driving forces depend on each other. Thus no data will suffice to predict precisely the outcomes of e.

Looking for the Last Universal Common Ancestor (LUCA).

Genomic sequences across diverse species seem to align towards a common ancestry, eventually implying that eons ago some universal antecedent organism would have lived on the face of Earth. However, when evolution is understood not only as a biological process but as a general thermodynamic process, it becomes apparent that the quest for the last universal common ancestor is unattainable. Ambiguities in alignments are unavoidable because the driving forces and paths of evolution cannot be separated from each other.

Natural patterns of energy dispersal.

Universal patterns such as power-law dependences, skewed distributions, tree-like structures, networks and spirals are associated with energy dispersal processes using the principle of least action. Also ubiquitous temporal courses such as sigmoid growth, bifurcations and chaos are ascribed to the decrease of free energy in the least time. Moreover, emergence of natural standards such as the common genetic code and chirality consensus of amino acids are understood to follow from the quest to maximize the dispersal of energy.

Ecological succession as an energy dispersal process.

Ecological succession is described by the 2nd law of thermodynamics. According to the universal law of the maximal energy dispersal, an ecosystem evolves toward a stationary state in its surroundings by consuming free energy via diverse mechanisms. Species are the mechanisms that conduct energy down along gradients between repositories of energy which consist of populations at various thermodynamic levels.

Natural hierarchy emerges from energy dispersal.

Hierarchical organization of 'systems within systems' is an apparent characteristic of nature. For many biotic and abiotic systems it is known how the nested structural and functional order builds up, yet the general principle why matter evolves to hierarchies has remained unfamiliar to many. We clarify that increasingly larger integrated systems result from the quest to decrease free energy according to the 2nd law of thermodynamics.

Gaia again.

The ideas of the Gaia hypothesis from the 1960s are today largely included in global ecology and Earth system sciences. The interdependence between biosphere, oceans, atmosphere and geosphere is well-established by data from global monitoring. Nevertheless the theory underlying the holistic view of the homeostatic Earth has remained obscure.

The driving force behind genomic diversity.

Eukaryote genomes contain excessively introns, intergenic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of increasing entropy. According to thermodynamics of open systems, genomes evolve toward diversity by various mechanisms that increase, decrease and distribute genomic material in response to thermodynamic driving forces.

Roots of diversity relations.

The species-area relationship is one of the central generalizations in ecology; however, its origin has remained a puzzle. Since ecosystems are understood as energy transduction systems, the regularities in species richness are considered to result from ubiquitous imperatives in energy transduction. From a thermodynamic point of view, organisms are transduction mechanisms that distribute an influx of energy down along the steepest gradients to the ecosystem's diverse repositories of chemical energy, that is, populations of species.

Natural distribution.

Log-normal distributions describe data from diverse disciplines of science. However, the fundamental basis of log-normal distributions is unknown. We suggest that the skewed distributions are outcomes of natural processes i.

Evidence of molecular alignment fluctuations in aqueous dilute liquid crystalline media.

Protein dynamics can be studied by NMR measurements of aqueous dilute liquid crystalline samples. However, the measured residual dipolar couplings are sensitive not only to internal fluctuations but to all changes in internuclear vectors relative to the laboratory frame. We show that side-chain fluctuations and bond librations in the ps-ns time scale perturb the molecular shape and charge distribution of a small globular protein sufficiently to cause a noticeable variation in the molecular alignment.

Structural basis and evolutionary origin of actin filament capping by twinfilin.

Dynamic reorganization of the actin cytoskeleton is essential for motile and morphological processes in all eukaryotic cells. One highly conserved protein that regulates actin dynamics is twinfilin, which both sequesters actin monomers and caps actin filament barbed ends. Twinfilin is composed of two ADF/cofilin-like domains, Twf-N and Twf-C.

Natural process--natural selection.

Life is supported by a myriad of chemical reactions. To describe the overall process we have formulated entropy for an open system undergoing chemical reactions. The entropy formula allows us to recognize various ways for the system to move towards more probable states.