A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains

The cellular theory on the nature of life has been one of the first major advancements in biology. Viruses, however, are the most abundant life forms, and their exclusion from mainstream biology and the Tree of Life (TOL) is a major paradox in biology. This article presents a broad, unifying scenario on the origin and evolution of cellular and viral domains that challenges the conventional views about the history of life and supports a TOL that includes viruses. Co-evolution of viruses and their host cells has led to some of the most remarkable developments and transitions in the evolution of life, including the origin of non-coding DNA as a genomic protective device against viral insertion damage. However, one of the major fundamental evolutionary developments driven by viruses was probably the origin of cellular domains - Bacteria, Archaea and Eukarya - from the Last Universal Common Ancestor (LUCA) lineage, by evolving anti-fusion mechanisms. Consistent with a novel fusion/fission model for the population mode of evolution of LUCA, this paper presents a “cell-like world” model for the origin of life. According to this model the evolution of coupled replication, transcription and translation system (RT&T) occurred within non-living cell-like compartments (CCs). In this model, the ancestral ribosome originated as template-based RNA synthesizing machinery. The origin of the cellular genome as a centralized unit for storage and replication of genetic information within the CCs facilitated the evolution of the ancestral ribosome into a powerful translation machinery - the modern ribosome. After several hundred millions of years of providing an enclosed environment and fusion/fission based exchanges necessary for the population mode of evolution of the basic metabolism and the RT&T, the CCs evolved into the first living entities on earth - the LUCA lineage. The paper concludes with a proposal for a TOL that integrates the co-evolution of cellular and viral domains. This is one of a series of three articles that present a unifying scenario on the origin and evolution of viral and cellular domains, including the origin of life, which has significant t bio-medical implications and could lead to a significant paradigm shift in biology

Innovation as a Nonlinear Process, the Scientometric Perspective, and the Specification of an "Innovation Opportunities Explorer"

The process of innovation follows non-linear patterns across the domains of science, technology, and the economy. Novel bibliometric mapping techniques can be used to investigate and represent distinctive, but complementary perspectives on the innovation process (e.g., "demand" and "supply") as well as the interactions among these perspectives. The perspectives can be represented as "continents" of data related to varying extents over time. For example, the different branches of Medical Subject Headings (MeSH) in the Medline database provide sources of such perspectives (e.g., "Diseases" versus "Drugs and Chemicals"). The multiple-perspective approach enables us to reconstruct facets of the dynamics of innovation, in terms of selection mechanisms shaping localizable trajectories and/or resulting in more globalized regimes. By expanding the data with patents and scholarly publications, we demonstrate the use of this multi-perspective approach in the case of RNA Interference (RNAi). The possibility to develop an "Innovation Opportunities Explorer" is specified.Comment: Technology Analysis and Strategic Management (forthcoming in 2013

A canonical theory of dynamic decision-making

Decision-making behavior is studied in many very different fields, from medicine and eco- nomics to psychology and neuroscience, with major contributions from mathematics and statistics, computer science, AI, and other technical disciplines. However the conceptual- ization of what decision-making is and methods for studying it vary greatly and this has resulted in fragmentation of the field. A theory that can accommodate various perspectives may facilitate interdisciplinary working. We present such a theory in which decision-making is articulated as a set of canonical functions that are sufficiently general to accommodate diverse viewpoints, yet sufficiently precise that they can be instantiated in different ways for specific theoretical or practical purposes. The canons cover the whole decision cycle, from the framing of a decision based on the goals, beliefs, and background knowledge of the decision-maker to the formulation of decision options, establishing preferences over them, and making commitments. Commitments can lead to the initiation of new decisions and any step in the cycle can incorporate reasoning about previous decisions and the rationales for them, and lead to revising or abandoning existing commitments. The theory situates decision-making with respect to other high-level cognitive capabilities like problem solving, planning, and collaborative decision-making. The canonical approach is assessed in three domains: cognitive and neuropsychology, artificial intelligence, and decision engineering

The Origin and Evolution of Viruses as Molecular Organisms

Viruses are the most abundant life forms and the repertoire of viral genes is greater than that of cellular genes. It is also evident that viruses have played a major role in driving cellular evolution, and yet, viruses are not part of mainstream biology, nor are they included in the Tree of Life. A reason for this major paradox in biology is the misleading dogma of viruses as viral particles and their enigmatic evolutionary origin. This article presents an alternative view about the nature of viruses based on their properties during the intracellular stage of their life cycle, when viruses express features comparable to those of many parasitic cellular species. Supporting this view about the nature of viruses is a novel hypothetical evolutionary model for their origin from parasitic cellular species that fused with their host cells. By losing their membrane and cellular structure within the host cell, these new types of parasitic species gained full access to precursors for the synthesis of their specific molecules and to the host’s information processing machineries, such as translation, which created unique parasitic and evolutionary opportunities. To identify viruses during their intracellular stage of their life cycle, in which their specific molecules are free or dispersed within the host cell, this paper introduces the concept of “molecular structure” and labels viruses as “molecular organisms.” Among the extant viruses, the life cycle of poxviruses and other complex viruses that fuse with their host cells provides compelling evidence for the fusion model. One of the most remarkable implications of fusion model is that new viral lineages originated from parasitic cellular species throughout the history of life, and that this process might still be active. Surprisingly, it appears that several parasitic cellular species are currently evolving into molecular organisms. More remarkably though, according to this model, several parasites that are currently classified as cellular organisms are in fact genuine molecular organisms. The current evidence for the fusion hypothesis is strong and it is fully testable using both experimental and phylogenetic approaches. The academic and research implications of this model, which supports the inclusion of viruses in the Tree of Life, are highly significant. Some of these implications are discussed in more detail in two other articles of this series, which presents a unifying model for the origin and evolution of cellular and viral domains, including the origin of life

Mission drift in qualitative research, or moving toward a systematic review of qualitative studies, moving back to a more systematic narrative review

The paper argues that the systematic review of qualitative research is best served by reliance upon qualitative methods themselves. A case is made for strengthening the narrative literature review and using narrative itself as a method of review. A technique is proposed that builds upon recent developments in qualitative systematic review by the use of a narrative inductive method of analysis. The essence of qualitative work is described. The natural ability for issues of ethnicity and diversity to be investigated through a qualitative approach is elaborated. Recent developments in systematic review are delineated, including the Delphi and Signal and Noise techniques, inclusion of grey literature, scoping studies and meta-ethnography. A narrative inductive interpretive method to review qualitative research is proposed, using reflective teams to analyse documents. Narrative is suggested as a knowledge-generating method and its underlying hermeneutic approach is defended as providing validity and theoretical structure. Finally, qualities that distinguish qualitative research from more quantitative investigations are delineated. Starting points for reflecting on qualitative studies and their usefulness are listed. Key words: Qualitative Systematic Review, Evidence-Based Policy, Grey Literature, Scoping Studies, Delphi, ‘Signal and Noise’, Meta-ethnography, Narrative Review, Narrative Method, and Reflective Teams

Facial expression of pain: an evolutionary account.

This paper proposes that human expression of pain in the presence or absence of caregivers, and the detection of pain by observers, arises from evolved propensities. The function of pain is to demand attention and prioritise escape, recovery, and healing; where others can help achieve these goals, effective communication of pain is required. Evidence is reviewed of a distinct and specific facial expression of pain from infancy to old age, consistent across stimuli, and recognizable as pain by observers. Voluntary control over amplitude is incomplete, and observers can better detect pain that the individual attempts to suppress rather than amplify or simulate. In many clinical and experimental settings, the facial expression of pain is incorporated with verbal and nonverbal vocal activity, posture, and movement in an overall category of pain behaviour. This is assumed by clinicians to be under operant control of social contingencies such as sympathy, caregiving, and practical help; thus, strong facial expression is presumed to constitute and attempt to manipulate these contingencies by amplification of the normal expression. Operant formulations support skepticism about the presence or extent of pain, judgments of malingering, and sometimes the withholding of caregiving and help. To the extent that pain expression is influenced by environmental contingencies, however, "amplification" could equally plausibly constitute the release of suppression according to evolved contingent propensities that guide behaviour. Pain has been largely neglected in the evolutionary literature and the literature on expression of emotion, but an evolutionary account can generate improved assessment of pain and reactions to it

Computational scientific discovery in psychology

Scientific discovery is a driving force for progress, involving creative problem-solving processes to further our understanding of the world. Historically, the process of scientific discovery has been intensive and time-consuming; however, advances in computational power and algorithms have provided an efficient route to make new discoveries. Complex tools using artificial intelligence (AI) can efficiently analyse data as well as generate new hypotheses and theories. Along with AI becoming increasingly prevalent in our daily lives and the services we access, its application to different scientific domains is becoming more widespread. For example, AI has been used for early detection of medical conditions, identifying treatments and vaccines (e.g., against COVID-19), and predicting protein structure. The application of AI in psychological science has started to become popular. AI can assist in new discoveries both as a tool that allows more freedom to scientists to generate new theories, and by making creative discoveries autonomously. Conversely, psychological concepts such as heuristics have refined and improved artificial systems. With such powerful systems, however, there are key ethical and practical issues to consider. This review addresses the current and future directions of computational scientific discovery generally and its applications in psychological science more specifically