A new formal perspective on ‘Cambrian explosions’

The ‘Cambrian explosion’ 500 Myr ago saw a relatively sudden proliferation of organism Bauplan and ecosystem niche structure that continues to haunt evolutionary biology. Here, adapting standard methods from information theory and statistical mechanics, we model the phenomenon as a noise-driven phase transition, in the context of deep-time relaxation of current path-dependent evolutionary constraints. The result is analogous to recent suggestions that multiple ‘explosions’ of increasing complexity in the genetic code were driven by rising intensities of available metabolic free energy. In the absence of severe path-dependent lock-in, ‘Cambrian explosions’ are standard features of blind evolutionary process, representing outliers in the ongoing routine of evolutionary punctuated equilibrium.     

What Does it Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics

This paper presents a critical analysis of code-semiotics, which we see as the latest attempt to create paradigmatic foundation for solving the question of the emergence of life and consciousness. We view code semiotics as a an attempt to revise the empirical scientific Darwinian paradigm, and to go beyond the complex systems, emergence, self-organization, and informational paradigms, and also the selfish gene theory of Dawkins and the Peircean pragmaticist semiotic theory built on the simultaneous types of evolution. As such it is a new and bold attempt to use semiotics to solve the problems created by the evolutionary paradigm’s commitment to produce a theory of how to connect the two sides of the Cartesian dualistic view of physical reality and consciousness in a consistent way.     

Leo Semenovich Berg and the biology of Acipenseriformes: a dedication

This volume is dedicated to the memory of Leo Semenovich Berg (1876–1950), a Russian ichthyologist and geographer. In the foreword to the English translation of Berg's remarkable treatise, Nomogenesis or evolution according to law, Theodosius Dobzhansky wrote: Berg was one of the outstanding intellects among Russian scientists. The breadth of his interests and the depth as well as the amplitude of his scholarship were remarkable. He had the reputation of being a walking library, because of the amount of information he could produce from his memory (Dobzhansky 1969, p. xi). Berg was prolific, publishing 217 papers and monographs on ichthyology, 30 papers on general zoology and biology, 20 papers on paleontology, 32 papers on zoogeoégraphy, 320 papers and monographs on geography, geology, and ethnography, as well as 290 biographies, obituaries, and popular articles (Berg 1955, Sokolov 1955).     

The evolution of senescence in multi-component systems

Actuarial senescence is characterized by an increase in mortality rate with increasing chronological age. The reliability theory of senescence proposes that organisms’ vital functions can be modelled as a suite of damageable, irreplaceable elements (typically genes or their products) that protect their bearer from condition-dependent death so long as at least one of the elements remains intact. Current incarnations of the reliability theory of senescence are continuous-time models with no explicit evolutionary component. Here, we use elementary probability theory and evolutionary dynamics analysis to derive a discrete-time version of the reliability theory of senescence. We include three variations on this theme: the ‘Series’ model in which damage to any of n elements results in death, the ‘Parallel’ model, in which damage accumulates in random order and damage to all n elements results in death, and the ‘Cascade’ (multi-stage) model, which is like the Parallel model, except the irreparable damage necessarily follows a strict sequence. For simplicity, we refer to the state of having multiple elements as ‘redundancy’, but this does not imply that the elements are necessarily identical. We show that redundancy leads to actuarial senescence in the Parallel and Cascade models but not in the Series model. We further demonstrate that in the Parallel and Cascade models, lifetime reproductive output (a potential proxy for fitness in populations with discrete generations) is a positive but decelerating function of redundancy. The positive nature of the fitness function leads to the prediction that redundancy and senescence should evolve from non-redundant, non-senescing ancestral populations; however, the deceleration of the fitness function leads to the prediction that this evolution towards increased redundancy will eventually be limited by mutation-selection balance. Using evolutionary dynamics analysis involving the discrete-generation quasispecies equation, we confirm these two predictions. Finally, we show that a population's equilibrium redundancy is sensitive to the environmental conditions that prevailed during its evolution, such as the rate of extrinsic mortality.     

A theoretical approach to the large-scale evolution of multicellularity and cell differentiation

In contrast to Darwinian evolution in which organisms have been selected by the instantaneous judgment of advantage or disadvantage for a mutated gene, the large-scale evolution of multicellular organisms by drastic changes in their genomes to produce new genes is theoretically formulated on the basis of the new concept of ‘biological activity’. The ‘biological activity’ of an organism is a macroscopic quantity determined by its whole genome and the environment, consisting of three terms; the energy acquired from the outside, the energy stored in the form of bio-molecules, and the systematization of multicellularity as well as of organizing genes and their products. The acquired energy minus stored energy is lost as heat, and the entropy production by the heat must compensate for the entropy reduction owing to the systematization in the organism. Under the boundary determined by this thermodynamic law, the organisms, which experienced gene duplication to produce new genes for multicellularity and cell differentiation, first decline to be minor members in a population by the increase in the energy to be stored and by the advanced systematization of cell differentiation. If the acquired energy is raised by the cooperative action of newly differentiated cells with the pre-existing types of cells, however, the ‘biological activity’ of this new style of organism can be recovered. The new style of organism generated through this evolutionary process does not necessarily expel the old style of organism to extinction but can coexist by choosing different material and energy resources. Moreover, this theory of large-scale evolution not only explains the punctuated mode of evolution indicated by paleontology but also reproduces the divergence of body plans observed in Triploblastica and Tracheophyta.     

Evolutionary Change and Epistemology

This paper is concerned with the debate in evolutionary epistemology about the nature of the evolutionary process at work in the development of science: whether it is Darwinian or Lamarckian. It is claimed that if we are to make progress through the many arguments that have grown up around this issue, we must return to an examination of the concepts of change and evolution, and examine the basic kinds of mechanism capable of bringing evolution about. This examination results in two kinds of processes being identified, dubbed direct and indirect, and these are claimed to exhaust all possibilities. These ideas are then applied to a selection of the debates within evolutionary epistemology. It is shown that while arguments about the pattern and rate of evolutionary change are necessarily inconclusive, those concerning the origin of novel variations and the mode of inheritance can be resolved by means of the distinctions made here. It is claimed that the process of selection in the evolution of science can also be clarified. The conclusion is that the main process producing the evolution of science is a direct or Lamarckian one although, if realism is correct, an indirect or Darwinian process plays a vital role.     

Comparative social cognition: what can dogs teach us?

Research in comparative social cognition addresses how challenges of social living have formed the cognitive structures that control behaviours involved in communication, social learning and social understanding. In contrast to the traditional psychological approach, recent investigations take both evolutionary and functional questions into account, but the main emphasis is still on the mechanisms of behaviour. Although in traditional research ‘comparative’ meant mainly comparisons between humans and other primates, ethological influences have led to a broadening of the spectrum of species under study. In this review, we evaluated how the study of dogs broadens our understanding of comparative social cognition. In the early days of ethology, dogs enjoyed considerable interest from ethologists, but during the last 20 years, dogs have rarely been studied by ethological methods. Through a complex evolutionary process, dogs became adapted for living in human society; therefore, the human environment and social setting now represents a natural ecological niche for this species. We have evidence that dogs have been selected for adaptations to human social life, and that these adaptations have led to marked changes in their communicative, social, cooperative and attachment behaviours towards humans. Until now, the study of dogs was hindered by the view that they represent an ‘artificial’ species, but by accepting that dogs are adapted to their niche, as are other ‘natural’ species, comparative investigations can be put into new light.     

Instinct in the '50s: the British reception of Konrad Lorenz's theory of instinctive behavior<Superscript>*</Superscript>

At the beginning of the 1950s most students of animal behavior in Britain saw the instinct concept developed by Konrad Lorenz in the 1930s as the central theoretical construct of the new ethology. In the mid 1950s J.B.S. Haldane made substantial efforts to undermine Lorenz's status as the founder of the new discipline, challenging his priority on key ethological concepts. Haldane was also critical of Lorenz's sharp distinction between instinctive and learnt behavior. This was inconsistent with Haldane's account of the evolution of language, and, according to Haldane, inconsistent with elementary genetics. British attitudes to the instinct concept changed dramatically in the wake of Daniel S. Lehraman's 1953 critique of Lorenz, and by the 1960s Lorenz drew a clear distinction between his own views and those of the English-speaking ethologists. The inconsistencies between Lorenz's ideas and the trends in contemporary evolutionary genetics that are reflected in Haldane's critiques may help to explain why the Lorenzian instinct concept was unable to maintain itself in Britian.     

The evolutionary origins and ecological context of tool use in New Caledonian crows

New Caledonian (NC) crows Corvus moneduloides are the most prolific avian tool users. In the wild, they use at least three distinct tool types to extract invertebrate prey from deadwood and vegetation, with some of their tools requiring complex manufacture, modification and/or deployment. Experiments with captive-bred, hand-raised NC crows have demonstrated that the species has a strong genetic predisposition for basic tool use and manufacture, suggesting that this behaviour is an evolved adaptation. This view is supported by recent stable-isotope analyses of the diets of wild crows, which revealed that tool use provides access to highly profitable hidden prey, with preliminary data indicating that parents preferentially feed their offspring with tool-derived food. Building on this work, our review examines the possible evolutionary origins of these birds’ remarkable tool-use behaviour. Whilst robust comparative analyses are impossible, given the phylogenetic rarity of animal tool use, our examination of a wide range of circumstantial evidence enables a first attempt at reconstructing a plausible evolutionary scenario. We suggest that a common ancestor of NC crows, originating from a (probably) non-tool-using South-East Asian or Australasian crow population, colonised New Caledonia after its last emersion several million years ago. The presence of profitable but out-of-reach food, in combination with a lack of direct competition for these resources, resulted in a vacant woodpecker-like niche. Crows may have possessed certain behavioural and/or morphological features upon their arrival that predisposed them to express tool-use rather than specialised prey-excavation behaviour, although it is possible that woodpecker-like foraging preceded tool use. Low levels of predation risk may have further facilitated tool-use behaviour, by allowing greater expenditure of time and energy on object interaction and exploration, as well as the evolution of a ‘slow’ life-history, in which prolonged juvenile development enables acquisition of complex behaviours. Intriguingly, humans may well have influenced the evolution of at least some of the species’ tool-oriented behaviours, via their possible introduction of candlenut trees together with the beetle larvae that infest them. Research on NC crows’ tool-use behaviour in its full ecological context is still in its infancy, and we expect that, as more evidence accumulates, some of our assumptions and predictions will be proved wrong. However, it is clear from our analysis of existing work, and the development of some original ideas, that the unusual evolutionary trajectory of NC crows is probably the consequence of an intricate constellation of interplaying factors.     

Not my brother's keeper: A thought experiment for Hamilton's rule

The now popular ‘selfish gene’ view defines evolutionary fitness at the gene level - in terms of the number of gene copies residing in future generations (or propelled from previous generations). Yet, most current biology textbooks still apply the concept of fitness to the individual, where it is defined more traditionally as the number of descendants residing in future generations. The existing literature remains ambiguous regarding whether one of these concepts is more meaningful than the other, or whether they both represent legitimate, functional definitions of fitness. In support of the latter view, I present a composite perspective that recognizes the gene as evolutionarily ‘selfish’, but also the individual as a ‘selfish vehicle’ for resident genes. Hamilton's rule explains, based on genetic relatedness, why natural selection has favoured behaviours that compel individuals (as ‘donors’ of help) to act for the good of copies of their genes residing in close kin (‘recipients’). I propose however, that natural selection should particularly favour helping behaviours directed at those recipient kin who have the highest relative probability of being the vehicle for a remarkably adaptive newly mutant gene, weighted by the proportion of genes shared with the donor. According to this ‘adaptive-genetic-novelty-rescue’ (AGNR) hypothesis, these favoured vehicles for shared gene copies are more likely to involve direct descendants (e.g. offspring) than other close kin from one's collateral lineage (e.g. siblings), even when the donor (e.g. a father) shares fewer genes with an offspring (e.g. a son) than with a sibling (e.g. a brother).     

Changing conceptions of species

Species are thought by many to be important units of evolution. In this paper, I argue against that view. My argument is based on an examination of the role of species in the synthetic theory of evolution. I argue that if one adopts a gradualist view of evolution, one cannot make sense of the claim that species are units in the minimal sense needed to claim that they are units of evolution, namely, that they exist as discrete entities over time. My second argument is directed against an appeal to Eldredge and Gould's theory of punctuated equilibria to support the claim that species are units of evolution. If one adopts their view, it may be possible to identify discrete temporal entities that can plausibly be termed species, but there is no reason to claim that those entities are units of evolution. Thus, on two plausible interpretations of the role of natural selection in the process of evolution, species are of no special importance. I then consider some of the reasons why species have been thought to be important evolutionary units by many contemporary evolutionary biologists. Finally, I discuss briefly the implications of this conclusion for evolutionary biology.     

White-faced capuchin monkeys show triadic awareness in their choice of allies

The social intelligence hypothesis, which holds that social challenges have selected for increased intelligence and social skills, has been supported by evidence that, in catarrhine primates, individuals know about the characteristics of groupmates' social relationships. Evidence for such ‘triadic awareness’ has not been sought for platyrrhine primates, although two platyrrhine genera, capuchins, Cebus, and squirrel monkeys, Saimiri, are among the most highly encephalized primates. We examined patterns of coalitionary recruitment in wild white-faced capuchins, C. capucinus. Analyses have shown that more dominant individuals are more likely to join aggressive coalitions than low-rankers, and that individuals preferentially support those with whom they have stronger affiliative relationships. Data from 110 fights, analysed using simulation techniques that produced distributions of results expected under null hypotheses, revealed that contestants preferentially solicited prospective coalition partners that (1) were dominant to their opponents, and (2) had better social relationships (higher ratios of affiliative/cooperative interactions to agonistic interactions) with themselves than with their opponents. Further analyses showed that soliciting dominant partners could be explained by either of two simpler rules, ‘Solicit an ally that outranks yourself’ or ‘Solicit the highest-ranking available individual’. However, soliciting partners with better social relationships appears to indicate triadic awareness, because subjects did not preferentially solicit the nearby individual with whom they shared the highest-quality social relationship. Effects of relative relationship quality on coalition solicitation decisions were independent of effects of dominance rank.     

Thermodynamics and the conceptual structure of evolutionary theory

Thermodynamics and evolutionary theory have spent most of their shared history in adversarial relationship to one another. The point of this paper is to consider some qualitative ways in which thermodynamics can enrich both the theory and epistemology of evolution. The "autonomy of biology" posture in evolutionary theory hangs on the supposed uniqueness of why-questions in biology. With this posture, and with the general obstruction of constructive dialogue between evolution and the physical sciences it fosters, come the perennial accusations that Darwinism deals in adaptational teleology but not mechanisms. Thermodynamics provides for a two-tiered hierarchy of causation in nature in which the why-question is rendered not only legitimate materialistically, but essential to understanding the evolutionary process in its totality--from the emergence of life to the branching of lineages in speciation.     

MENT: Methylation and expression database of normal and tumor tissues

Integrated analysis of DNA methylation and gene expression can reveal specific epigenetic patterns that are important during carcinogenesis. We built an integrated database of DNA methylation and gene expression termed MENT (Methylation and Expression database of Normal and Tumor tissues) to provide researchers information on both DNA methylation and gene expression in diverse cancers. It contains integrated data of DNA methylation, gene expression, correlation of DNA methylation and gene expression in paired samples, and clinicopathological conditions gathered from the GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas). A user-friendly interface allows users to search for differential DNA methylation by either ‘gene search’ or ‘dataset search’. The ‘gene search’ returns which conditions are differentially methylated in a gene of interest, while ‘dataset search’ returns which genes are differentially methylated in a condition of interest based on filtering options such as direction, DM (differential methylation value), and p-value. MENT is the first database which provides both DNA methylation and gene expression information in diverse normal and tumor tissues. Its user-friendly interface allows users to easily search and view both DNA methylation and gene expression patterns. MENT is freely available at http://mgrc.kribb.re.kr:8080/MENT/.     

Functional divergence in protein (family) sequence evolution

As widely used today to infer function, the homology search is based on the neutral theory that sites of greatest functional significance are under the strongest selective constraints as well as lowest evolutionary rates, and vice versa. Therefore, site-specific rate changes (or altered selective constraints) are related to functional divergence during protein (family) evolution. In this paper, we review our recent work about this issue. We show a great deal of functional information can be obtained from the evolutionary perspective, which can in turn be used to facilitate high throughput functional assays. The emergence of evolutionary functional genomics is also indicated. The related software DIVERGE can be obtained form http://xgu1.zool.iastate.edu.     

Semiotic Mechanisms Underlying Niche Construction

The explanatory value of niche construction can be strengthened by firm footing in semiotic theory. Anthropologists have a unique perspective on the integration of such diverse approaches to human action and evolutionary processes. Here, we seek to open a dialogue between anthropology and biosemiotics. The overarching aim of this paper is to demonstrate that niche construction, including the underlying mechanism of reciprocal causation, is a semiotic process relating to biological development (sensu stricto) as well as cognitive development and cultural change. In making this argument we emphasize the semiotic mechanisms underlying the niche concept. We argue that the “niche” in ecology and evolutionary biology can be consistent with the Umwelt of Jakob von Uexkull. Following John Deely we therefore suggest that investigations into the organism—environment interface constituting niche construction should emphasize the semiotic basis of experience. Peircean signs are pervasive and allow for flexible interpretations of phenomena in relation to the perceptual and cognitive capacities of the behaving organism, which is particularly pertinent for understanding the relation of proximate/ultimate selective forces as co-productive (i.e., reciprocal). Additionally, theoretical work by Kinji Imanishi on the evolution of daily life and Gregory Bateson’s relational view of evolution both support the linkage between proximate and ultimate evolutionary processes of causation necessitated by the niche construction perspective. We will then apply this theoretical framework to two specific examples: 1) hominin evolution, including uniquely human cultural behaviors with niche constructive implications; and 2) the multispecies and anthropocentric niche of human-dog coevolution from which complex cognitive capacities and semiotic relationships emerged. The intended outcome of this paper is the establishment of concrete semiotic mechanisms and theory underlying niche constructive behavior which can then be applied to a broad spectrum of organisms to contextualize the reciprocal relation between proximate and ultimate drivers of behavior.     

Triadic (ecological, neural, cognitive) niche construction: a scenario of human brain evolution extrapolating tool use and language from the control of reaching actions

Hominin evolution has involved a continuous process of addition of new kinds of cognitive capacity, including those relating to manufacture and use of tools and to the establishment of linguistic faculties. The dramatic expansion of the brain that accompanied additions of new functional areas would have supported such continuous evolution. Extended brain functions would have driven rapid and drastic changes in the hominin ecological niche, which in turn demanded further brain resources to adapt to it. In this way, humans have constructed a novel niche in each of the ecological, cognitive and neural domains, whose interactions accelerated their individual evolution through a process of triadic niche construction. Human higher cognitive activity can therefore be viewed holistically as one component in a terrestrial ecosystem. The brain's functional characteristics seem to play a key role in this triadic interaction. We advance a speculative argument about the origins of its neurobiological mechanisms, as an extension (with wider scope) of the evolutionary principles of adaptive function in the animal nervous system. The brain mechanisms that subserve tool use may bridge the gap between gesture and language--the site of such integration seems to be the parietal and extending opercular cortices.     

On evolution of the photosynthetic pigments

Some considerations on the origin of the photosynthetic pigment apparatus in the period of transition of organisms from heterotrophic to phototrophic mode of life and further evolution of this apparatus are given in this paper.Some ideas about interrelation between major and auxiliary pigments and about different forms of the pigments in vivo are discussed from an evolutionary point of view.Special Symposium on Photochemistry and the Origins of Life, Sixth International Congress on Photobiology, Bochum, Germany.     

Acoustic signals of baby black caimans

In spite of the importance of crocodilian vocalizations for the understanding of the evolution of sound communication in Archosauria and due to the small number of experimental investigations, information concerning the vocal world of crocodilians is limited. By studying black caimans Melanosuchus niger in their natural habitat, here we supply the experimental evidence that juvenile crocodilians can use a graded sound system in order to elicit adapted behavioral responses from their mother and siblings. By analyzing the acoustic structure of calls emitted in two different situations (‘undisturbed context’, during which spontaneous calls of juvenile caimans were recorded without perturbing the group, and a simulated ‘predator attack’, during which calls were recorded while shaking juveniles) and by testing their biological relevance through playback experiments, we reveal the existence of two functionally different types of juvenile calls that produce a different response from the mother and other siblings. Young black caimans can thus modulate the structure of their vocalizations along an acoustic continuum as a function of the emission context. Playback experiments show that both mother and juveniles discriminate between these ‘distress’ and ‘contact’ calls. Acoustic communication is thus an important component mediating relationships within family groups in caimans as it is in birds, their archosaurian relatives. Although probably limited, the vocal repertoire of young crocodilians is capable of transmitting the information necessary for allowing siblings and mother to modulate their behavior.