The definitions of information and meaning two possible boundaries between physics and biology.

The standard approach to the definition of the physical quantities has not produced satisfactory results with the concepts of information and meaning. In the case of information we have at least two unrelated definitions, while in the case of meaning we have no definition at all. Here it is shown that both information and meaning can be defined by operative procedures, but it is also pointed out that we need to recognize them as a new type of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because are not subjective features. Here it is proposed to call them nominable entities, i.e., entities which can be specified only by naming their components in their natural order. If the genetic code is not a linguistic metaphor but a reality, we must conclude that information and meaning are real natural entities, and now we must also conclude that they are not equivalent to the quantities and qualities of our present theoretical framework. This gives us two options. One is to extend the definition of physics and say that the list of its fundamental entities must include information and meaning. The other is to say that physics is the science of quantities only, and in this case information and meaning become the exclusive province of biology. The boundary between physics and biology, in short, is a matter of convention, but the existence of information and meaning is not. We can decide to study them in the framework of an extended physics or in a purely biological framework, but we cannot avoid studying them for what they are, i.e., as fundamental components of the fabric of Nature.     

Where is Darwin 200 years later?

The theory of evolution is perceived by many people, particularly but not only in the United States, as a controversial theory not yet fully demonstrated. Yet, that living organisms, including humans, have evolved from ancestors who were very different from them is beyond reasonable doubt, confirmed by at least as much evidence as any other widely accepted scientific theory. I argue that Darwin’s contribution to science goes much beyond the theory of evolution in itself. The theory of natural selection explains the adaptations of organisms, their ‘design’. The ‘Copernican Revolution’ brought the phenomena of the physical universe into the realm of science: explanations by natural causes that can be tested by observation and experiment. However, the scientific revolution that occurred in the 16th and 17th centuries had left the living world out of scientific explanations, because organisms seemingly show that they are ‘designed,’ and thus call for an intentional designer. It was Darwin’s greatest contribution to science, to demonstrate that the adaptations of organisms, their apparent ‘design’, can be explained by natural processes governed by natural laws. At that point, science came into maturity, because all natural phenomena in the universe, living as well as nonliving, could be investigated scientifically, and explained as matter in motion governed by natural laws.     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

Logical puzzles and scientific controversies: The nature of species,viruses and living organisms

In the past, biologists believed that species were stable and permanent entities and they viewed them as natural kinds which, like the chemical elements, exist in nature independently of any human conceptualization. After Darwin, biologists came to accept that species were the products of evolution and natural selection and were not immutable natural kinds.     

A critical approach to the definition of Darwinian units of selection

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.     

From quasi-organism to protolife

Tansley's [Tansley, 1935. The use and abuse of vegetational concepts and terms. Ecology 16, 284–307] “quasi-organism” portrays the ecosystem as an aberration of nature, being neither fully organism nor fully abiotic. The term is untenable, as there can be no semi-metaphor. I approach the issue by examining whether ecosystems, nature, Gaia and communities are phenotypes, that is, as entities upon which natural selection operates and which are expressions of a genotype homologue. The complicated internal structure of atomic particles is suggested as homologues for the nucleotides of nature. It is further suggested that if the superpositions of quantum states of the molecular or cellular levels of a mutualism (community), or “q-gene,” such as a soil bacteria–vegetation complex, could remain coherent for biochemically relevant scales, then these could experience simultaneous adaptive mutations, providing an ensemble upon which natural selection could operate. In general, communities are not phenotypes because they lack a genome homologue. The earth (Gaia) and ecosystems cannot be phenotypes because the physical environment cannot experience adaptive mutation through quantum superposition, and even if they could, the superposition of quantum states of the environment with those of organisms is inconsistent with the treatment of the entanglement of the environment as constituting a measurement. A more tenable characterization of the ecosystem is as an example of a category of emergence that I refer to as protolife, comprising ecosystems, protocells and spiral galaxies. These entities demonstrate the same functions: capturing and transducing energy, sequestering organic matter and ions from the environment, catalyzing the synthesis of its components, protecting the accumulated organic matter from dilution, and self-replicating.     

Non-biodegradable biopolymers from renewable resources: perspectives and impacts

In recent years the biotechnological production of bulk biopolymers has focused on the synthesis of biodegradable polymers to replace their non-biodegradable counterparts derived from fossil resources. Examples include polyhydroxyalkanoates and polylactic acid, which act as substitutes for polyolefins. By contrast, the biotechnological production of non-biodegradable polymers from renewable resources has so far been scarcely considered, probably because this idea contradicts the paradigm that all natural compounds are biodegradable. Polythioesters, which were recently described as new biopolymers, do not follow this paradigm because although they are produced by bacteria, they are persistent to microbial degradation. Mankind has a need for both non-biodegradable and biodegradable polymers and methods to produce them from renewable resources will be of great value.     

Architectures of biological complexity

Three features contribute to the complexity of an entity: numberof parts, their order, and their iteration. Many functionalbiological entities are complex when measured by those attributes,and although they are produced in tree-like architectures, theorganizational structures that permit them to function are inthe form of hierarchies. Natural hierarchies can be thoughtof as organizing structures that are emergent properties ofcomplex functional entities, and which are transformed fromtrees by process networks. For example, hierarchies are observedin the architecture of metazoan bodies (the somatic hierarchy)and in the biotic structure of ecogeographic units (the ecologicalhierarchy). As the metazoan developmental genome is quite complexand has been evolved through tree-like processes, it must harborat least one hierarchy, which is most clearly indicated in thedevelopmental processes that create the somatic hierarchy. Formulticellular organisms, the processes that serve to transformtrees of gene expression events into a somatic hierarchy haveproduced complicated signaling networks whose histories canprobably be recovered in general outline.     

Sustainable management of planted landscapes: lessons from Japan

In Japan, 42?% of forests are planted forests, and most of them were established after World War II (1950–1980) to meet increased wood demands. Although Japanese planted forests are now reaching their planned harvest age, they have not been managed, and their restoration is now being discussed. Japanese foresters have not cut their own forests, and the country’s high wood demands have been met by imports during recent decades. The decline of young forests due to the stagnation of forestry activity is suggested to be partly responsible for the nation-wide decline in early-successional species, which is referred to as the “second crisis of biodiversity.” As a timber-importing nation, it is suggested that Japan has underused the nation’s own forests and has overused forests elsewhere. A revival of Japanese plantation forestry may contribute to the restoration of early-successional species because young planted forests are likely to provide suitable habitats. Furthermore, only 30?% of the current planted forests in Japan will be needed to meet the expected future domestic demand for lumber and plywood without imports. The remaining 70?% of the current planted forests may be restored to natural forests with or without harvesting. The history of Japanese planted forests suggests that some natural trees/forests should be retained, even in the landscapes that specialize in wood production, because part of the planted forests may be economically marginalized in the future, and their restoration to natural forests would then be needed.     

Adaptation and novelty: teleological explanations in evolutionary biology

Knives, birds' wings, and mountain slopes are used for certain purposes: cutting, flying, and climbing. A bird's wings have in common with knives that they have been 'designed' for the purpose they serve, which purpose accounts for their existence, whereas mountain slopes have come about by geological processes independently of their uses for climbing. A bird's wings differ from a knife in that they have not been designed or produced by any conscious agent; rather, the wings, like the slopes, are outcomes of natural processes without any intentional causation. Evolutionary biologists use teleological language and teleological explanations. I propose that this use is appropriate, because teleological explanations are hypotheses that can be subject to empirical testing. The distinctiveness of teleological hypotheses is that they account for the existence of a feature in terms of the function it serves; for example, wings have evolved and persist because flying is beneficial to birds by increasing their chances of surviving and reproducing. Features of organisms that are explained with teleological hypotheses include structures, such as wings; processes, such as development from egg to adult; and behaviours, such as nest building. A proximate explanation of these features is the function they serve; an ultimate explanation that they all share is their contribution to the reproductive fitness of the organisms. I distinguish several kinds of teleological explanations, such as natural and artificial, as well as bounded and unbounded, some of which but not others apply to biological explanations.     

Does Darwin’s Naturalization Hypothesis Explain Fish Invasions?

Darwin’s naturalization hypothesis predicts that introduced species tend not to invade areas containing congeneric native species, because they would otherwise compete with their close relatives and would likely encounter predators and pathogens that can attack them. An opposing view is that introduced species should succeed in areas where native congeners are present because they are more likely to share traits that pre-adapt them to their new environment. A test of both these hypotheses using data on fish introductions from several independent regions fails to support either viewpoints. In contrast to studies of nonindigenous plants, our results suggest that taxonomic affiliation is not an important general predictor of fish invasion success.     

Visual homing: an insect perspective

The ability to learn the location of places in the world and to revisit them repeatedly is crucial for all aspects of animal life on earth. It underpins animal foraging, predator avoidance, territoriality, mating, nest construction and parental care. Much theoretical and experimental progress has recently been made in identifying the sensory cues and the computational mechanisms that allow insects (and robots) to find their way back to places, while the neurobiological mechanisms underlying navigational abilities are beginning to be unravelled in vertebrate and invertebrate models. Studying visual homing in insects is interesting, because they allow experimentation and view-reconstruction under natural conditions, because they are likely to have evolved parsimonious, yet robust solutions to the homing problem and because they force us to consider the viewpoint of navigating animals, including their sensory and computational capacities.     

The hypoxic microenvironment: A determinant of cancer stem cell evolution

Tumors are often viewed as unique entities with specific behaviors. However, tumors are a mixture of differentially evolved subpopulations of cells in constant Darwinian evolution, selecting the fittest clone and allowing it to outgrow the rest. As in the natural environment, the niche defines the properties the fittest clones must possess. Therefore, there can be multiple fit clones because of the various microenvironments inside a single tumor. Hypoxia is considered to be a major feature of the tumor microenvironment and is a potential contributor to the cancer stem cell (CSC) phenotype and its enhanced tumorigenicity. The acidic microenvironment around hypoxic cells is accompanied by the activation of a subset of proteases that contribute to metastasis. Because of aberrant angiogenesis and the inaccessibility of their locations, hypoxic cells are less likely to accumulate therapeutic concentrations of chemotherapeutics that can lead to therapeutic resistance. Therefore, the targeting of the hypoxic CSC niche in combination with chemotherapy may provide a promising strategy for eradicating CSCs. In this review, we examine the cancer stem cell hypothesis and its relationship to the microenvironment, specifically to hypoxia and the subsequent metabolic switch and how they shape tumor behavior.     

Sub-aerial biofilms as blockers of solar radiation: spectral properties as tools to characterise material-relevant microbial growth

Sub-aerial biofilms (SABs) are ubiquitous microbial communities that develop at the interface between hard surfaces and the atmosphere. Inherent SAB “core-settlers” include phototrophic algae, cyanobacteria, heterotrophic bacteria and microcolonial fungi (MCF). SABs do not simply cover hard surfaces; they interact with them in myriads of ways and bind to the underlying substrate. Secretion of extracellular mucilage aids adhesion, while organic acids and acidic polysaccharides weather the surface. As protection against solar radiation, many members of the SAB consortia produce shielding pigments while the phototrophic inhabitants are laden with photosynthetic pigments. All absorb light of many wavelengths and in addition, the cells themselves scatter light. Both effects change the spectra of incoming radiation (including wavelengths that are converted to electricity by photovoltaic cells) and decrease its intensity. To quantify these effects on SABs as complex entities of organisms and pigments, we measured the spectral properties of model and natural biofilms transferred to glass. Here we show that SABs growing on solar panels and other substrates scatter incident radiation between 250 nm up to 1800 nm and block up to 70% of its transmission. Model biofilms have the advantage that their microbial components can be “tuned” to resemble natural ones of different compositions thus providing a novel materials-testing tool.     

Rediscovery of known natural compounds: nuisance or goldmine?

Do all natural compounds have a distinct biological activity, or are most of them merely biosynthetic debris? Many natural compounds have important biological functions, and certainly many more of the ample 200,000 currently known will ultimately prove to be more than just 'secondary metabolites'. The question is how to select the most promising candidates for potential new drugs. 'Rediscovery' of known natural compounds is regarded as a nuisance or disappointment by scientists involved with the identification of novel compounds. The other side of the coin, however, is that the discovery that a particular compound occurs in unrelated species can be a valuable clue toward the identification of a novel receptor or enzyme. Here, we put forward the hypothesis that when a natural compound occurs in unrelated species, it must have an important biological function by interacting with a specific molecular target. This is because it is extremely improbable that in nature one particular compound is synthesized in totally unrelated species for no reason at all. For many compounds occurring in unrelated species, it is already known that they act on specific molecular targets. For others, it is just known that they occur in different species. In some cases, biological activities are known but not the underlying mechanisms of action. It is from this category of compounds that important discoveries are likely to be made. Some (around 70) of them were identified. They represent important clues from nature offering an alternative approach to the classical screening of large numbers of compounds.     

Mosquito feeding affects larval behaviour and development in a moth

Organisms are attacked by different natural enemies present in their habitat. While enemies such as parasitoids and predators will kill their hosts/preys when they successfully attack them, enemies such as micropredators will not entirely consume their prey. However, they can still have important consequences on the performance and ecology of the prey, such as reduced growth, increased emigration, disease transmission. In this paper, we investigated the impact of a terrestrial micropredator, the yellow fever mosquito Aedes aegypti, on its unusual invertebrate host, the Egyptian cotton leaf worm, Spodoptera littoralis. Larvae developing in presence of mosquitoes showed a slower development and reached a smaller pupal weight when compared to a control without mosquitoes, apparently because of a reduced feeding time for larvae. In addition, larvae tended to leave the plant in presence of mosquitoes.These results suggest that mosquitoes act as micropredators and affects lepidopteran larvae behaviour and development. Ecological impacts such as higher risks of food depletion and longer exposure to natural enemies are likely to be costly consequences. The importance of this phenomenon in nature - the possible function as last resort when vertebrates are unavailable - and the evolutionary aspects are discussed.     

Psychiatric classifications: validity and utility

Despite historical assumptions to the contrary, there is little evidence that the majority of recognized mental disorders are separated by natural boundaries. Diagnostic categories defined by their clinical syndromes should be regarded as ‘valid’ only if they have been shown to be truly discrete entities. Most diagnostic concepts in psychiatry have not been demonstrated to be valid in this sense, though many possess ‘utility’ by virtue of the information they convey about presenting symptoms, outcome, treatment response and, in some instances, aetiology. While researchers in genetics, neurobiology and population epidemiology are increasingly more likely to adopt a continuum/dimensional view of the variation in symptomatology, clinicians prefer to hold on to the categorical approach embodied in current classifications such as ICD‐10 and DSM‐5. Both points of view have plausible justification in their respective contexts, but the way forward may be in their conceptual reconciliation.     

The effects of biologically active substances in medicinal plants on the metabolic activity of neutrophils

Neutrophils are the typical effector cells of the innate immune response because they are the first leukocytes to be recruited to an inflammatory site where they engulf invading microorganisms and destroy them by multiple oxidative and non-oxidative mechanisms. The destructive potential of neutrophils requires the tight control of their recruitment into tissue compartments and the production of inflammatory mediators such as reactive oxygen species. These oxidants can be highly toxic not only for infectious agents but also for neighbouring host tissues resulting in various autoimmune and inflammatory diseases. Thus, a significant attention in medicine is paid to approaches designed to modulate the metabolic activity of neutrophils. Synthetic steroid and non-steroid compounds with adverse side effects are commonly used for this purpose. The effects of natural substances which can modulate the metabolic activity of neutrophils and which simultaneously would not exert any significant unfavourable side effects have recently been investigated. Suitable candidates for this purpose might be compounds contained in herbs. These include especially polysaccharides and polyphenols, but also terpenes. The aim of the present paper is to summarize contemporary knowledge on the effects of compounds from herbs on the metabolic activity of mammalian neutrophils.