The largest proportion of microRNAs in humans (ca. 40–50%) originated in the phylogenetic grouping defined as primates. The dynamic evolution of this family of non‐coding RNA is further demonstrated by the presence of microRNA unique to the human species. Investigations into the role of microRNA in cancer have until recently mainly focused on the more ancient members of this RNA family that are widely conserved in the animal kingdom. As I describe in this review the evolutionary young (...) lineage and species‐specific microRNA could be important contributors to cancers, especially in particular organs in primates compared to more distantly‐related research models. Elucidating the biological significance of primate and human‐specific microRNA in cancer could have important implications for cancer research and the use of non‐primate animal models. (shrink)

This paper is devoted to an examination of the discovery, characterization, and analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating the importance of exploratory experimentation in current (post-genomic) molecular biology. The material on microRNAs is important in its own right: it provides important insight into the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate the importance (...) of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only important for philosophy of science, but also of practical importance for the evaluation of grant proposals, although the elaboration of this latter claim must be left for another occasion. (shrink)

MicroRNAs are non‐coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts decisively to (...) improve the accuracy of miRNAome annotations. We encourage genome annotation teams to do it right or not at all. (shrink)

One of the most interesting challenges facing paleobiologists is explaining the Cambrian explosion, the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years. We propose that because phenotypic variation decreases through geologic time, because microRNAs (miRNAs) increase genic precision, by turning an imprecise number of mRNA transcripts into a more precise number of protein molecules, and because miRNAs are continuously being added to metazoan genomes (...) through geologic time, miRNAs might be instrumental in the canalization of development. Further, miRNAs ultimately allow for natural selection to elaborate morphological complexity, because by reducing gene expression variability, miRNAs increase heritability, allowing selection to change characters more effectively. Hence, miRNAs might play an important role in shaping metazoan macroevolution, and might be part of the solution to the Cambrian conundrum. (shrink)

Short (“seed”) or extended base pairing between microRNAs (miRNAs) and their target RNAs enables post‐transcriptional silencing in many organisms. These interactions allow the computational prediction of potential targets. In model organisms, predicted targets are frequently validated experimentally; hence meaningful miRNA‐regulated processes are reported. However, in non‐models, these reports mostly rely on computational prediction alone. Many times, further bioinformatic analyses such as Gene Ontology (GO) enrichment are based on these in silico projections. Here such approaches are reviewed, their caveats are highlighted (...) and the ease of picking false targets from predicted lists is demonstrated. Discoveries that shed new light on how miRNAs evolved to regulate targets in various phyletic groups are discussed, in addition to the pitfalls of target identification in non‐model organisms. The goal is to prevent the misuse of bioinformatic tools, as they cannot bypass the biological understanding of miRNA–target regulation. (shrink)

In this paper, we hypothesize that X chromosome-associated mechanisms, which affect X-linked genes and are behind the immunological advantage of females, may also affect X-linked microRNAs. The human X chromosome contains 10% of all microRNAs detected so far in the human genome. Although the role of most of them has not yet been described, several X chromosome-located microRNAs have important functions in immunity and cancer. We therefore provide a detailed map of all described microRNAs located on human and mouse X (...) chromosomes, and highlight the ones involved in immune functions and oncogenesis. The unique mode of inheritance of the X chromosome is ultimately the cause of the immune disadvantage of males and the enhanced survival of females following immunological challenges. How these aspects influence X-linked microRNAs will be a challenge for researchers in the coming years, not only from an evolutionary point of view, but also from the perspective of disease etiology. (shrink)

The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re‐evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective miRNA (...) genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery. (shrink)

Phenotypic divergence among animal species may be due in part to species‐specific (SS) regulation of gene expression by small, non‐coding regulatory RNAs termed “microRNAs”. This phenomenon can be modulated by several variables. First, microRNA genes vary by their level of conservation, many of them being SS, or unique to a particular evolutionary lineage. Second, microRNA expression levels vary spatially and temporally in different species. Lastly, while microRNAs bind the 3′UTR of target genes in order to silence their expression, (...) the binding sites themselves are often non‐conserved. The variability of the miRNA‐target paradigm between different species is thus multifactorial, and this paradigm has only just started to gain attention from researchers in various fields. Here we present and discuss recent findings regarding the characteristics and implications of SS microRNA regulation. (shrink)

Introduction to complexity and complex systems -- Introduction to large linear systems -- Introduction to biochemical oscillators and nonlinear biochemical systems -- Modularity, redundancy, degeneracy, pleiotropy and robustness in complex biological systems -- The evolution of biological complexity; invertebrate immune systems -- Irreducible and specified complexity in living systems -- The complex adaptive and innate human immune systems -- Complexity in quasispecies : microRNAs -- Introduction to complexity in economic systems -- Complexity in quasispecies : micrornas -- Dealing with (...) complexity. (shrink)

Theories of music evolution rely on our understanding of what music is. Here, I argue that music is best conceptualized as an interactive technology, and propose a coevolutionary framework for its emergence. I present two basic models of attachment formation through behavioral alignment applicable to all forms of affiliative interaction and argue that the most critical distinguishing feature of music is entrained temporal coordination. Music's unique interactive strategy invites active participation and allows interactions to last longer, include more participants, (...) and unify emotional states more effectively. Regarding its evolution, I propose that music, like language, evolved in a process of collective invention followed by genetic accommodation. I provide an outline of the initial evolutionary process which led to the emergence of music, centered on four key features: technology, shared intentionality, extended kinship, and multilevel society. Implications of this framework on music evolution, psychology, cross-species and cross-cultural research are discussed. (shrink)

This paper delves into the character concept as applied to reproduction. Our argument is that the prevailing functional-adaptationist perspective falls short in explaining the evolution of reproductive traits, and we propose an alternative organismal-relational approach that incorporates the developmental and interactive aspects of reproduction. To begin, we define the functional individuation of reproductive traits as evolutionary strategies aimed at enhancing fitness, and we demonstrate how this perspective influences the classification of reproductive characters and modes, the comprehension of shared traits (...) as resulting from conflicts of evolutionary interest between individuals, and the explanation of reproductive diversity. After outlining the shortcomings of this framework, we introduce an organismal-relational approach grounded in evolutionary developmental studies of reproduction. This view provides a revised classification for reproductive characters and modes and offers a new understanding of interorganismal traits that takes into account their inherently relational nature. Lastly, we present the research agenda that emerges from this approach, which addresses the core explanatory gaps left by the adaptationist perspective, including the explanation of reproductive homologies and homoplasies, the developmental constraints associated with the evolution of reproductive modes, and the evolvability of reproductive characters. (shrink)

One of the major developments in cancer research in recent years has been the construction of models that treat cancer as a cellular population subject to natural selection. We expand on this idea, drawing upon multilevel selection theory. Cancer is best understood in our view from a multilevel perspective, as both a by-product of selection at other levels of organization, and as subject to selection at several levels of organization. Cancer is a by-product in two senses. First, cancer cells co-opt (...) signaling pathways that are otherwise adaptive at the organismic level. Second, cancer is also a by-product of features distinctive to the metazoan lineage: cellular plasticity and modularity. Applying the multilevel perspective in this way permits one to explain transitions in complexity and individuality in cancer progression. Our argument is a reply to Germain’s scepticism towards the explanatory relevance of natural selection for cancer. The extent to which cancer fulfills the conditions for being a paradigmatic Darwinian population depends on the scale of analysis, and the details of the purported selective scenario. Taking a multilevel perspective clarifies some of the complexities surrounding how to best understand the relevance of evolutionary thinking in cancer progression. (shrink)

Recent studies on neural pathways in a broad spectrum of vertebrates suggest that, in addition to migration and an increase in the number of certain select neurons, a significant aspect of neural evolution is a “parcellation” (segregation-isolation) process that involves the loss of selected connections by the new aggregates. A similar process occurs during ontogenetic development. These findings suggest that in many neuronal systems axons do not invade unknown territories during evolutionary or ontogenetic development but follow in their ancestors' (...) paths to their ancestral targets; if the connection is later lost, it reflects the specialization of the circuitry.The pattern of interspecific variability suggests (1) that overlap of circuits is a more common feature in primitive (generalized) than in specialized brain organizations and (2) that most projections, such as the retinal, thalamotelencephalic, corticotectal, and tectal efferent ones, were bilateral in the primitive condition. Specialization of these systems in some vertebrate groups has involved the selective loss of connections, resulting in greater isolation of functions. The parcellation process may also play an important role in cell diversification.The parcellation process as described here is thought to be one of several underlying mechanisms of evolutionary and ontogenetic differentiation. (shrink)

What can microbiology teach us about cultural evolution? Philosopher of Biology, Jonathan Birch, discusses “horizontal transmission”.

A crucially important part of the biosphere – the virosphere – is too often overlooked. Inclusion of the virosphere into the global picture of protein structure space reveals that 63 protein domain superfamilies in viruses do not have any structural and evolutionary relatives in modern cellular organisms. More than half of these have functions which are not virus‐specific and thus might be a source of new folds and functions for cellular life. The number of viruses on the planet exceeds that (...) of cells by an order of magnitude and viruses evolve up to six orders of magnitude faster. As a result, cellular species are subject to a constitutive ‘flow‐through’ of new viral genetic material. Due to this and the relaxed evolutionary constraints in viruses, the transfer of domains between host‐to‐virus could be a mechanism for accelerated protein evolution. The virosphere could be an engine for the genesis of protein structures, and may even have been so before the last universal common ancestor of cellular life. (shrink)

Decision making is a fundamental aspect of cognition that lies at the heart of theories about behaviour, learning, and mental processing. It spans multiple levels of complexity, from high-level planning to low-level movement control and perceptual recognition. Tracking the evolutionary trajectory of this elementary cognitive process can illuminate the foundations of behaviour and brain functions. This paper highlights a previously understudied defining feature of decision mechanisms: the ways in which mutual exclusion between alternatives is achieved. We argue that any decision (...) is defined by a set of mutually exclusive alternatives, and this exclusivity – rather than the specific identity of the alternatives – requires specialized mechanisms. We demonstrate how the physical body of simple decision-making entities can serve as such a mechanism, and that the detachment of these mechanisms from bodily and environmental constraints enabled complex decision-making. Furthermore, while many theories emphasize how the evolution of neural circuits enhanced integration and control through associative structures, we propose that the evolution of mutual exclusion requires non-associative constructions. We conclude that understanding the evolution of these mechanisms is crucial for studying cognitive evolution, and we propose a potential evolutionary trajectory. (shrink)

Well before patient-centered or patient-controlled research became trendy, and earlier than calls to preferentially refer to research subjects as participants, Bob Veatch wrote “The Patient as Partner” Veatch presciently argued that research patients should not be thought of as passive subjects nor material from which to obtain data, but rather as partners in discovery. In this manuscript, I will explore Veatch’s conception of patient as partner in research and how that idea has evolved and been implemented over time and consider (...) some of the remaining challenges. Complexities of patient partnership include: clarifying the types of research in which patient partnership is most appropriate, recognizing the various possible levels of patient engagement in each case, avoiding tokenism and striving for respectful partnership, and keeping in mind the appropriate implementation of protections and safeguards. Bob Veatch would be pleased with the progress that has been made in creating research partnerships with patients, while also undoubtedly pushing us to continue to do better. (shrink)

Why have theories of evolution become now a matter of concern for critically rethinking sex and sexual difference? Why after years of deconstructing the ontologies of sex rooted in biological discourses and metaphysics of identity has critical thought turned to biology, physics, and mathematics? One way to tackle this new turn toward scientific thought may be derived from the reaction against an overused method of textual critique, which has come short of engaging with the reality of matter. If sexuality (...) and sex are material forms of irreducible difference, then one needs a window into the material processes that lead to such forms. (shrink)

The climate of epistemological opinion is rapidly changing in the direction of an increasing concern with the substantive results of the empirical sciences of man, such as psychology and biology. This change is of a comparatively recent date: as late as in 1964, Chauncey Wright’s seminal speculations on the biology of knowledge-processes were shrugged off by one commentator as “nineteenth-century impedimenta and paraphernalia”. Today, such a judgment seems strangely out of date. Our knowledge of man as an animal has been (...) broadened and deepened, both by the dramatic advances of molecular biology and by the recent appearance of the ‘sociobiology’ represented by Edward O. Wilson. To the philosopher, the question inevitably arises of how far this knowledge extends and, in particular, to what extent it can account for peculiarly human intellectual phenomena, such as the growth of scientific knowledge. The study of man as an animal and the study of man as a knower can no longer be simply assumed to be two distinct and separate departments of thought. (shrink)

The mammalian placenta exhibits elevated expression of endogenous retroviruses (ERVs), but the evolutionary significance of this feature remains unclear. I propose that ERV‐mediated regulatory evolution was, and continues to be, an important mechanism underlying the evolution of placental development. Many recent studies have focused on the co‐option of ERV‐derived genes for specific functional adaptations in the placenta. However, the co‐option of ERV‐derived regulatory elements could potentially lead to the incorporation of entire gene regulatory networks, which, I argue, would (...) facilitate relatively rapid developmental evolution of the placenta. I suggest a model in which an ancient retroviral infection led to the establishment of the ancestral placental developmental gene network through the co‐option of ERV‐derived regulatory elements. Consequently, placental development would require elevated tolerance to ERV activity. This in turn would expose a continuous stream of novel ERV mutations that may have catalyzed the developmental diversification of the mammalian placenta. (shrink)

Anthropological inquiry suggests that all societies classify animals and plants in similar ways. Paradoxically, in the same cultures that have seen large advances in biological science, citizenry's practical knowledge of nature has dramatically diminished. Here we describe historical, cross-cultural and developmental research on how people ordinarily conceptualize organic nature, concentrating on cognitive consequences associated with knowledge devolution. We show that results on psychological studies of categorization and reasoning from “standard populations” fail to generalize to humanity at large. Usual populations have (...) impoverished experience with nature, which yields misleading results about knowledge acquisition and the ontogenetic relationship between folkbiology and folkpsychology. We also show that groups living in the same habitat can manifest strikingly distinct behaviors, cognitions and social relations relative to it. This has novel implications for environmental decision making and management, including commons problems. (shrink)

The Homo naledi discovery introduced questions that had not been previously posed regarding fossil finds. This is because, apart from their fascinating physiology, they seemingly deliberately disposed of their dead in a ritualised way. Although this theory may still be disproved in future, the present article provisionally accepts it. This evokes religious questions because it suggests the possibility of causal thinking, wilful and cooperative behaviour, and the possibility that this behaviour entails traces of proto-religious ideas. This poses the challenge to (...) develop a hominin hermeneutics that endeavours to reconstruct the possible motivation behind this action. The relatively larger brain with its enlarged Broca's area suggests the possibility of a sophisticated communication system and an enhanced way of dealing with emotion. We know that almost all life forms have some form of awareness and that more sophisticated degrees of consciousness may be present in the higher primates. Various 'clues' are investigated to try and understand the H. naledi phenomenon: lessons from chimpanzee studies, the implications of tool making for hominin development, the possibility of a proto-language and the role symbol formation may have played. The H. naledi case also indicates on a theological level that religion is natural. Some attention is given to this thesis. Biological and environmental factors come into play to illuminate biological factors like emotion and higher cognition without which religion would not be possible. Sophisticated cognition is coloured by affect and this makes some form of reflection on the fate of loved ones who have died a strong possibility. (shrink)

Conspicuous consumption associated with status reinforcement behavior can be explained in terms of costly signaling, or strategic handicap theory, first articulated by Zahavi and later formalized by Grafen. A theory is introduced which suggests that the evolutionary raison d’être of status reinforcement behavior lies not only in its effects on lifetime reproductive success, but in its positive effects on the probability of survival through infrequent, unpredictable demographic bottlenecks. Under some circumstances, such “wasteful” displays may take the form of displays of (...) altruistic behavior and generosity on the part of high status individuals, in that is signals the ability to bear the short-term costs of being generous or “cooperative,” while at the same time reinforcing the long-term benefits of higher status. (shrink)

Cognitive Science, Volume 46, Issue 4, April 2022.

In his recent book, The Human Factor, Philip Hefner proposes to deepen theological understanding of the natural world and the place of humans within it. He describes humans as products of converging streams of genes and culture, and as possessors of freedom that requires them to be “created cocreators.” In accordance with the requirements of “the way things really are” (God), humans are to become divine agents in enlarging the realm of freedom in the world through self‐sacrificing altruism. While Hefner's (...) insights are admirable, his work could be viewed, in part, as a covert expression of nineteenth century liberal beliefs in progress. In fact, human culture and freedom are more ambiguous products of both good and evil, and hence we must take more cognizance of the pervasiveness of what theology has termed sin. (shrink)

We advocate for an integrative long-term perspective on time, noting that culture changes on timescales amenable to behavioral genetic study with appropriate design and modeling extensions. We note the need for replications of behavioral genetic studies to examine model invariance across long-term timescales, which would afford examination of specified as well as unspecified cultural moderators of behavioral genetic effects.

Moral naturalism is the view that moral properties exist in a manner that fits with our scientific worldview. Might empirical discoveries about the genealogy of moral judgments (that, for example, they issue from an evolved psychological faculty) serve to undermine moral naturalism? One way of undermining moral naturalism is to show that moral properties do not exist at all. The possibility of genealogical considerations supporting this conclusion is examined and found to be weak. Alternatively, might empirical discoveries about the genealogy (...) of moral judgments serve to vindicate some form of moral naturalism? This possibility is also explored and found to be unconvincing. (shrink)

I propose in this essay to briefly describe some of the main current stakeholders who issue guidance on the ethics of human subjects research. This will be preceded by a very brief historical introduction.Prior to World War II, as far as I have been able to ascertain, there were no international efforts to regulate human experimentation. National activities were few and far between. One exception was a Directive on Human Experimentation issued in December 1900 by the then Prussian Minister of (...) Religious, Educational and Medical Mairs. This was followed by a Circular on innovative therapy and scientific experimentation promulgated by the then Reich Minister of the Interior in February 1931. Just over five years later, in April 1936, the Bureau of the Medico-Scientific Council of the People’s Commissariat for Health of the Russian Socialist Federated Soviet Republic, the main constituent Republic of the then Union of Soviet Socialist Republics, issued an Advisory Resolution on the procedures for testing new medicinal substances and methods which may present a hazard for the health and life of patients. (shrink)

The text is a plausible presentation and critical review of the main work ofTheodosius Dobzhansky: “Evolution of Humanity”. It tries to show and proves thatDobzhansky tries and largely succeeds in offering a different, let’s say, dialectical interpretationof the biological evolution of humanity, i.e., the stages and differences inthe evolution of the human species and race. Following in the footsteps of, but also incontrast to, traditional Darwinism and some similar evolutionary theories, Dobzhanskyinsists on the claim that evolution, (...) primarily biological, is not over, but that it is stillgoing on, despite human, i.e., a cultural intervention, namely simultaneous and together/conjunctive with it, which seeks to influence and change the directions of the existingnatural flows and processes. During the multi-millennium history, biology and culturebecame interdependent and interfering, with which man (woman and man) with hisappearance asserted himself as the main and most responsible factor/agent of the fateof the human race and the survival of the human community/human species, namelysurvival of oneself, but also of the totality and entirety of the planetary biodiversity, asa necessary prerequisite for one’s own survival and existence.In his research on the evolution of humanity, Dobzhansky starts from the inspiringviews of some famous predecessors, such as Pierre Teilhard De Chardin, but wecan argue that Dobzhansky influenced many of his contemporaries, including NoamChomsky, especially when it comes to linguistic research on the genesis and emergenceof human language, and the influence of transformative-generative grammar on thedevelopment of the human mind, i.e., on the development of the human brain.At the same time, we can state that Dobzhansky’s research and insights correspondand coincide with the research and ethical attitudes of some modern bioethicists,philosophers of biology and culturologists, as well as with the attitudes of manylike-minded people and followers. (shrink)

Abstract This paper argues that a genuine engagement of Christianity with evolution needs to include a discussion of Christology. Further, it develops a particular approach to Christology through a theo-dramatic account of incarnation. The somewhat static post-Chalcedon theological categories of divine and human natures are hard to square with contemporary evolutionary accounts of human origins. Once the divine Logos is portrayed in the active categories of Wisdom it becomes easier to envisage divine and creaturely wisdom coexisting in the person (...) of Christ. I argue, in particular, that a focus on God's agency through a modified version of Hans Urs von Balthasar's account of theo-drama invites participation and affirms human agency in a way that grand narratives do not. More particularly, drawing on examples from hominid evolution, contemporary discussion of paleontology and cooperative evolutionary theories, I suggest that the most convincing accounts of evolutionary biology fit into this theo-dramatic account more readily than alternatives. As such, in the spirit of Robert Boyle, this paper deliberately blurs the categories of revealed and natural theology by arguing that we can make sense of the former through concentration on the latter. (shrink)

Glowacki's work meshes well with our view of human nature as having evolved to use culture to improve survival and reproduction. Peace is a cultural achievement, requiring advances in social organization and control, including leaders who can implement policies to benefit the group, third-party mediation, and intergroup cooperation. Cultural advances shift intergroup interactions from negative-sum (war) to positive-sum (trade).