What is Life? Defining Life in the Context of Emergent Complexity

Erwin Schrödinger defined life not only as a “self-reproducing” aperiodic crystal of DNA coding for proteins but within the context of living entities increasing their order by dissipating matter/energy gradients to maintain themselves away from equilibirium. Since then most definitions of life have focused on the former. But living cells do more than replicate their DNA. Cells also have membrane barriers across which metabolites must move, via which energy transduction as well as information processing occurs, and within which metabolic transformation occurs. An approach of complex systems dynamics, including nonequilibrium thermodynamics, may provide a more robust approach for defining life than a “naked replicator” at the origin of life. The crucial issue becomes the process of emergence of life from pre-biotic chemistry, concomitant with the emergence of function, information, and semiosis. Living entities can be viewed as bounded, informed autocatalytic cycles feeding off matter/energy gradients, exhibiting agency, capable of growth, reproduction, and evolution. Understanding how life might have emerged should sharpen our definition of what life is.     

Orientation and Navigation in Elasmobranchs: Which Way Forward?

Elasmobranchs possess a multiplicity of mechanisms controlling posture and short distance orientation. Visual–vestibular contributions to posture and locomotion are well documented. So too, are the contributions of vision, olfaction and the octavolateralis senses to short distance orientation, particularly orientation to specific environmental stimuli such as those generated by prey. Less well understood are the mechanisms guiding orientation over longer distances. Anecdotal and systematic observations of behaviour show tidal, daily, repeat long distance, and even seasonal movement patterns. True navigation has not been demonstrated in elasmobranchs and the sensory mechanisms underlying the above movement patterns remain largely speculative. However, they are likely to include responses to water currents, and physical parameters such as temperature, pressure, and the geomagnetic field. Of particular interest in elasmobranchs is that geomagnetic orientation could be mediated directly via a magnetite based sensory system, or indirectly via the electrosensory system. Systematic studies of movement patterns and experimental studies of the underlying mechanisms of orientation are required to gain an increased understanding of orientation and navigation in this intriguing group.     

Diversity in warning coloration: selective paradox or the norm?

Aposematic theory has historically predicted that predators should select for warning signals to converge on a single form, as a result of frequency‐dependent learning. However, widespread variation in warning signals is observed across closely related species, populations and, most problematically for evolutionary biologists, among individuals in the same population. Recent research has yielded an increased awareness of this diversity, challenging the paradigm of signal monomorphy in aposematic animals. Here we provide a comprehensive synthesis of these disparate lines of investigation, identifying within them three broad classes of explanation for variation in aposematic warning signals: genetic mechanisms, differences among predators and predator behaviour, and alternative selection pressures upon the signal. The mechanisms producing warning coloration are also important. Detailed studies of the genetic basis of warning signals in some species, most notably Heliconius butterflies, are beginning to shed light on the genetic architecture facilitating or limiting key processes such as the evolution and maintenance of polymorphisms, hybridisation, and speciation. Work on predator behaviour is changing our perception of the predator community as a single homogenous selective agent, emphasising the dynamic nature of predator–prey interactions. Predator variability in a range of factors (e.g. perceptual abilities, tolerance to chemical defences, and individual motivation), suggests that the role of predators is more complicated than previously appreciated. With complex selection regimes at work, polytypisms and polymorphisms may even occur in Müllerian mimicry systems. Meanwhile, phenotypes are often multifunctional, and thus subject to additional biotic and abiotic selection pressures. Some of these selective pressures, primarily sexual selection and thermoregulation, have received considerable attention, while others, such as disease risk and parental effects, offer promising avenues to explore. As well as reviewing the existing evidence from both empirical studies and theoretical modelling, we highlight hypotheses that could benefit from further investigation in aposematic species. Finally by collating known instances of variation in warning signals, we provide a valuable resource for understanding the taxonomic spread of diversity in aposematic signalling and with which to direct future research. A greater appreciation of the extent of variation in aposematic species, and of the selective pressures and constraints which contribute to this once‐paradoxical phenomenon, yields a new perspective for the field of aposematic signalling.     

Diversity in mimicry: paradox or paradigm?

Visual mimicry is a textbook case of natural selection because it is both intuitively understandable and has repeatedly evolved in a range of organisms: it is the ultimate example of parallel evolution. In many mimetic groups, particularly butterflies, a huge variety of colour patterns has arisen, even in closely related species. There has been much recent controversy over explanations of this variety. Mimicry is today a broad field of evolutionary study; here we discuss the evolution of its diversity in predator-prey systems.     

Levels or Domains of Life?

In the case of living beings – the very concept of “level” of organization becomes obscure: it suggests a value-based assessment, assigning notions like “lower” and “higher” with rather vague criteria for constructing the ladder of perfection, complexity, importance, etc. We prefer therefore the term “domain”, entities ranking equal. Domains may represent natural entities as well as purely human constructs developed in order to gain understanding of some facets of living things; living, evolved beings (e.g. viviparous animals, eukaryotic cells, etc.) as well as those abstract constructs, such as genotype and ‘niche’ which have been developed in the search for better understanding of such living things. Delimitation of such domains is sometimes a question of the dexterity of the researcher, and sometimes draws from the tradition in a given field. Such domains are not completely (canonically) translatable to each other. Rather, they interact by a process that we call here reciprocal formation. Life (including the biosphere and human cultures which are emergent within the frame of the biosphere) is unique among multi-domain systems. In contrast to purely physical systems, life is a semiotic system driven by the historical experience of lineages, interpreted and re-interpreted by the incessant turnover of both individuals and their communities. This paper provides cases of domain interrelations, and addresses two questions: (1) How do new qualities of inter-domain interaction emerge historically? (2) How do new domains (ways of understanding the world) emerge in evolution. Two approaches, physical and biosemiotic, are discussed as we seek to get a better understanding of the overarching tasks.     

Calcium: Just Another Regulator in the Machinery of Life?

*BACKGROUND: Current hypotheses imply that stimulus-response systems in plants are networks of signal transduction pathways. It is usually assumed that these pathways connect receptors with effectors via chains of molecular events. Diverse intermediate signalling components (transducers) participate in these processes. However, many cellular transducers respond to several stimuli. Hence, there are no discrete chains but rather pathways that interconnect network-modules of different command structure. In particular, the cytosolic free Ca2+ concentration ([Ca2+](cyt)) is thought to perform many different tasks in a wide range of cellular events. However, this range of putative functions is so wide that it is often questioned how Ca2+ can comply with the definition of a second messenger. *THE Ca2+ SIGNATURE HYPOTHESIS: Some authors have suggested the concept of a specific signature of the ([Ca2+](cyt)) response. This implies that characteristics of the time course of changes in ([Ca2+](cyt)) and their localized sites of appearance in cells are used by the plant to identify the type and intensity of the stimulus. This hypothesis has triggered many investigations, which have yielded contradictory results. * THE CURRENT PICTURE: Much evidence suggests that the functions of calcium can be grouped into three classes: Ca2+ as a protective agent, Ca2+ as a chemical switch and Ca2+ as a 'digital' information carrier. Examples of the first two classes are presented here. The third is more controversial; while some investigations seem to support this idea, others call the Ca2+ signature hypothesis into question. Further investigations are needed to shed more light on Ca(2+)-driven signalling cascades.     

Diversity in the immune system: “Preconceived ideas” or ideas preconceived?

Two concepts of the evolution and regulation of expression of the combining site repertoire of the immune system, are compared. One view is based on the Associative Recognition Theory as formulated by the author and the other is based on the Idiotype Network Idea as conceived by Jerne. The two concepts are analyzed from the point of view of their logic, internal consistency and factual support.     

Light Perception in Two Strictly Subterranean Rodents: Life in the Dark or Blue?

Background

The African mole-rats (Bathyergidae, Rodentia) are strictly subterranean, congenitally microphthalmic rodents that are hardly ever exposed to environmental light. Because of the lack of an overt behavioural reaction to light, they have long been considered to be blind. However, recent anatomical studies have suggested retention of basic visual capabilities. In this study, we employed behavioural tests to find out if two mole-rat species are able to discriminate between light and dark, if they are able to discriminate colours and, finally, if the presence of light in burrows provokes plugging behaviour, which is assumed to have a primarily anti-predatory function.

Methodology/Principal Finding

We used a binary choice test to show that the silvery mole-rat Heliophobius argenteocinereus and the giant mole-rat Fukomys mechowii exhibit a clear photoavoidance response to full-spectrum (“white”), blue and green-yellow light, but no significant reaction to ultraviolet or red light during nest building. The mole-rats thus retain dark/light discrimination capabilities and a capacity to perceive short to medium-wavelength light in the photopic range of intensities. These findings further suggest that the mole-rat S opsin has its absorption maximum in the violet/blue part of the spectrum. The assay did not yield conclusive evidence regarding colour discrimination. To test the putative role of vision in bathyergid anti-predatory behaviour, we examined the reaction of mole-rats to the incidence of light in an artificial burrow system. The presence of light in the burrow effectively induced plugging of the illuminated tunnel.

Conclusion/Significance

Our findings suggest that the photopic vision is conserved and that low acuity residual vision plays an important role in predator avoidance and tunnel maintenance in the African mole-rats.     

An epidemic of depression or the medicalization of distress?

The syndrome of major depression is widely regarded as a specific mental illness that has increased to the point where it will be second in the International Burden of Disease ranking by 2020. This article examines the assumption that major depression is a specific illness, that it is rapidly increasing, and that a medical response is justified. I argue that major depression is not a natural entity and does not identify a homogenous group of patients. The apparent increase in major depression results from: confusing those who are ill with those who share their symptoms; the surveying of symptoms out of context; the benefits that accrue from such a diagnosis to drug companies, researchers, and clinicians; and changing social constructions around sadness and distress. Standardized medical treatment of all these individuals is neither possible nor desirable. The major depression category should be replaced by a clinical staging strategy that acknowledges the continuous distribution of depressive symptoms. Trials that test social and lifestyle treatments as well as drugs and cognitive behavioral therapy across different levels of severity, chronicity, and symptom patterns might lead to the development of a coherent evidence-based stepped treatment model.     

Diversity in the circumsporozoite protein of Plasmodium vivax: Does it matter?

Since the gene encoding the malarial circumsporozoite surface protein was characterized a decade ago, the corresponding protein has been considered an important vaccine candidate. Victoria Mann, Michael Good and Allan Saul here discuss molecular variation in the circumsporozoite surface protein of Plasmodium vivax in this context. There is still doubt about the degree and importance of polymorphisms in non-repetitive regions of the molecule. The degree of polymorphisms and data on naturally occurring protective responses suggests there has been minimal immunological pressure; the authors contend that antigenic diversity is unlikely to be a major factor in the use of this antigen as a vaccine for P. vivax.     

Synthesis of life in the lab? Defining a protoliving system

The synthesis of a living system in the lab has been judged by a number of critics as partly attained by the proteinoid microsphere because of its primitive properties of metabolism, growth, and reproduction. These same critics, however, judge the organism as not alive, or as being 50 to 75 percent alive (Baltscheffsky and Jurka, 1984), owing to the absence of a nucleic acid genetic coding mechanism. The experiments in retracing evolution suggest, however, that the self-sequencing of amino acids was the evolutionary precursor of modern nucleic acid templating; the genetic memory is the molecule. The proteinoid microsphere is not a modern living system, but does represent at least a protoliving system (Fox and Dose, 1972). Berra (1990, p. 75) has commented on other difficulties in defining a protoliving system. In Berra's opinion, metabolism, reproduction, responsiveness to stimuli, and cellularity constitute or describe aliveness. These properties characterize proteinoid microspheres. A number of experiments demonstrate that amino acids in aminoacyl adenylates yield specific products, whereas nucleotides are without effect. For this and related reasons, especially the demonstrated self-sequencing of amino acids when they are warmed, resultant bio-functional properties of self-assembled microstructures, and demonstrated self-sequencing of amino acids in modern systems, the results appear to bridge from the chemical era to the biological period. All the above emerges from a departure in style of research (Young, 1984; Pauling and Zuckerkandl, 1972). The latter authors said, "It appears likely that biogenesis is the passage from a 'non-living system' existing in a large number of states to a 'living' system also existing in a large number of states."(ABSTRACT TRUNCATED AT 250 WORDS)     

Epistasis: Obstacle or Advantage for Mapping Complex Traits?

Identification of genetic loci in complex traits has focused largely on one-dimensional genome scans to search for associations between single markers and the phenotype. There is mounting evidence that locus interactions, or epistasis, are a crucial component of the genetic architecture of biologically relevant traits. However, epistasis is often viewed as a nuisance factor that reduces power for locus detection. Counter to expectations, recent work shows that fitting full models, instead of testing marker main effect and interaction components separately, in exhaustive multi-locus genome scans can have higher power to detect loci when epistasis is present than single-locus scans, and improvement that comes despite a much larger multiple testing alpha-adjustment in such searches. We demonstrate, both theoretically and via simulation, that the expected power to detect loci when fitting full models is often larger when these loci act epistatically than when they act additively. Additionally, we show that the power for single locus detection may be improved in cases of epistasis compared to the additive model. Our exploration of a two step model selection procedure shows that identifying the true model is difficult. However, this difficulty is certainly not exacerbated by the presence of epistasis, on the contrary, in some cases the presence of epistasis can aid in model selection. The impact of allele frequencies on both power and model selection is dramatic.