In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNAworld. Bacteria and Archaea thus must have lost these complex features secondarily, through (...) ‘streamlining’. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic.We ask what this means and how it might be tested. (shrink)

In this chapter, I shall consider a number of connections between various ideas of the theory of styles of reasoning and the issue of the contingency and inevitability of science. By ‘contingency issue’ it is meant the question as to whether the history of a particular branch of our science could have taken a different route and provided results incompatible with those of our actual science. Apart from Hacking’s recent comments, the discussions on the contingency issue have not involved the (...) notion of style of reasoning. I will fill this gap in the literature by drawing some important implications for the issue of contingency from the theory of styles of reasoning that I have developed so far. I shall address four fundamental questions. First of all, in the next section I shall discuss to which extent the emergence of styles of reasoning at a certain point of history is a contingent circumstance. In the following section I shall ask whether the endurance of styles of reasoning was inevitable by tackling the connected question as to why the styles are long lasting. Afterwards, I shall focus on the growth of knowledge by dealing with questions such as: if a certain style of reasoning continues to be employed and if Q is a ‘live question’, is science bound to converge on a single answer to Q? Finally, on the basis of my previous reflections I shall look into the question of the convergence of science in the long run. The answers to these questions will rely on some basic assumptions of the theory of style of reasoning and imply a picture of the evolution of sciences in which both contingency and inevitability play a key role. (shrink)

The field of language evolution has recently made Gricean pragmatics central to its task, particularly within comparative studies between human and non-human primate communication. The standard model of Gricean communication requires a set of complex cognitive abilities, such as belief attribution and understanding nested higher-order mental states. On this model, non-human primate communication is then of a radically different kind to ours. Moreover, the cognitive demands in the standard view are also too high for human infants, who nevertheless do engage (...) in communication. In this paper I critically assess the standard view and contrast it with an alternative, minimal model of Gricean communication recently advanced by Richard Moore. I then raise two objections to the minimal model. The upshot is that this model is conceptually unstable and fails to constitute a suitable alternative as a middle ground between full-fledged human communication and simpler forms of non-human animal communication. (shrink)

ABSTRACT (ITA) Un’idea emerge, si sviluppa, guadagna consenso, muta, talvolta scompare per poi risorgere. Questo è anche stato il destino dell’idea di evoluzione, il cui lungo cammino viene ricostruito in questo saggio, dai Greci fino ai nostri giorni. A partire dal diciassettesimo secolo questa nozione assume sempre più rilevanza nello studio della natura. In ciascun pensatore l’idea di un’evoluzione delle specie viventi è stata accompagnata da una teoria volta a spiegare le cause e il meccanismo del mutamento. Questo saggio racconta (...) non soltanto la genesi e lo sviluppo dell’idea tout court che la natura in qualche modo si trasformi, ma anche la storia delle teorie che, assumendo come reale questa trasformazione, ne postulano una spiegazione. Particolare attenzione viene data ad alcuni aspetti spesso trascurati che hanno reso possibile il concetto di evoluzione del mondo vivente come la conosciamo adesso, di cui se ne mostra la rilevanza, già a partire dal pensiero greco. -/- ABSTRACT (ENG) An idea emerges, develops, gains consensus, evolves, sometimes disappears and then rises again. This was also the fate of the idea of evolution, whose long journey is reconstructed in this essay, from the Greeks to the present day. Since the seventeenth century, this idea has become more and more relevant in the study of nature. In each thinker the idea of an evolution of living species has been accompanied by a theory aimed at explaining the causes and the mechanism of change. This essay tells not only the genesis and development of the idea that nature somehow transforms itself, but also the history of the theories which, assuming this transformation as real, postulate an explanation. Particular emphasis is given to some often overlooked aspects that made possible the concept of evolution of the living world as we know it now, whose full relevance is shown, starting from Greek thought. Keywords: evolution, natural selection, Charles Darwin, history of ideas, history of science. (shrink)

In this contribution I will retrace the main stages of my research on the objectification problem in quantum mechanics by highlighting some personal memories of my supervisor, the theoretical physicist Giovanni Morchio. The central aim of my MSc thesis was to ask whether the hypothesis of objectification, which is currently added to the formalism, is not, at least in one case, deducible from it and in particular from the dynamics of the temporal evolution. The case study we were looking for (...) had to: 1) represent a situation similar to that in which a macroscopic system such as a measurement apparatus, following interaction with a system, assumes a well-defined state (which or for example represents the fact that the result of a measurement is a particular value), i.e becomes objective 2) represent a fact in nature in which it is not clear whether its explanation can be derived from the formalism of quantum mechanics or whether a hypothesis of objectification is necessary for its explanation. Proving that such a fact can be deduced from the time evolution of quantum mechanics allowed us to conclude that there are cases in which the hypothesis of objectification is superfluous or, in other words, obtainable from the formalism. (shrink)

ABSTRACT (ENG) The recent evolution of the most advanced societies is characterized by the increasing use of hypertext. The latter is an electronic text with hyperlinks to other text that a user can immediately access. The World Wide Web itself is a sort of global hypertext that can be viewed as a network of nodes, represented by individual elements connected through the so-called links. In this paper, I ask myself in what sense reading with new technologies is a different cognitive (...) experience from reading a printed text. In the first part, I examine the conditions that made the emergence of hypertext possible by examining some mutations in human thought. In the second part, I argue that the emergence of hypertext has not only made the reading experience different but has also reshaped the figure of the reader. -/- ABSTRACT (ITA) L’evoluzione recente delle società più avanzate è caratterizzata dall’uso crescente dell’ipertesto. Quest’ultimo è un testo elettronico con riferimenti ad altri documenti, accessibili cliccando su parole chiave. Lo stesso World Wide Web una sorta di ipertesto globale che si può immaginare come una rete di nodi, rappresentati da singoli elementi connessi attraverso i cosiddetti link. In questo articolo ci chiediamo in che senso leggere con le nuove tecnologie sia un’esperienza cognitiva differente rispetto a quella di leggere un testo stampato. Nella prima parte esaminiamo le condizioni che hanno reso possibile l’emergere dell’ipertesto considerando alcune mutazioni in seno al pensiero umano. Nella seconda parte argomentiamo che con l’ipertesto è nata una nuova forma di lettura che ha a sua volta costituito una nuova figura di lettore. (shrink)

Evolutionary aesthetics (EA) investigates the origins and evolution of aesthetic preferences and artistic behaviors, along with the underlying capacities that support these preferences and behaviors. EA is a multidisciplinary approach that intersects various disciplines – e.g. evolutionary psychology, biology, neurosciences, art history, archeology, anthropology, philosophical aesthetics – providing a comprehensive framework for understanding the deep-rooted biological and evolutionary underpinnings of human aesthetic preferences and artistic expressions. Central to EA, in fact, is the exploration of when, how and why aesthetic preferences (...) and artistic behaviors originated in human history, as well as understanding whether these behaviors are evolutionary adaptations, by-products of evolutionary processes, or nonbiological cultural products (Killin 2021; Richards 2022). (shrink)

Après avoir introduit la notion d’espace public dans le contexte de la « théorie générale de la société » avec laquelle Habermas a entrepris une reconstruction de l’évolution des systèmes sociaux et, aussi, de la naissance de la sphère publique au cœur des sociétés bourgeoises et des changements à travers et au-delà des sociétés de masse, cet article se propose d’élaborer un cadre analytique du modèle habermasien de la sphère politique publique, décrivant aujourd’hui sa structure et ses fonctions spécifiques, par (...) rapport à la société civile et au système politique (fonctions de «caisse de résonance », « filtre », « contrôle » et « pression de rationalisation »). Dans un effort pour clarifier le «sens critique» d’un modèle de recherche « normatif » dans son contenu, mais suffisamment « réaliste », Habermas remonte à deux questions essentielles pour des sciences de la communication: a) l’indépendance des médias de masse; et b) les leur effets sur l’auditoire. Ce passage permet de mettre en évidence la « structure » et la « qualité » de la discussion publique. (shrink)

How do scientists navigate between the need to capitalize on their prior knowledge through specialization, and the urge to adapt to evolving research opportunities? Drawing from diverse perspectives on adaptation, this paper proposes an unsupervised Bayesian approach motivated by Optimal Transport of the evolution of scientists' research portfolios in response to transformations in their field. The model relies on $186,162$ scientific abstracts and authorship data to evaluate the influence of intellectual, social, and institutional resources on scientists' trajectories within a cohort (...) of $2\,108$ high-energy physicists between 2000 and 2019. Using Inverse Optimal Transport, the reallocation of research efforts is shown to be shaped by learning costs, thus enhancing the utility of the scientific capital disseminated among scientists. Two dimensions of social capital, namely ``diversity'' and ``power'', have opposite associations with the magnitude of change in scientists' research interests: while ``diversity'' is associated with greater change and expansion of research portfolios, ``power'' is associated with more stable research agendas. Social capital plays a more crucial role in shifts between cognitively distant research areas. More generally, this work suggests new approaches for understanding, measuring and modeling collective adaptation using Optimal Transport. (shrink)

Il libro "Homo Sapiens" (Il Mulino) di Giorgio Manzi propone un viaggio attraverso la storia naturale dell’uomo in quanto specie animale. Questa recensione analizza le strategie di comunicazione della scienza dell'autore individuandone pregi e difetti.

Stephen Jay Gould argued that replaying the ‘tape of life’ would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution—the independent origination of similar biological forms and functions—which many interpret as evidence against Gould’s thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments (...) that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the ‘critique from convergent evolution’ fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life. (shrink)

The modern synthesis in evolutionary biology is taken to be that period in which a consensus developed among biologists about the major causes of evolution, a consensus that informed research in evolutionary biology for at least a half century. As such, it is a particularly fruitful period to consider when reflecting on the meaning and role of chance in evolutionary explanation. Biologists of this period make reference to “chance” and loose cognates of “chance,” such as: “random,” “contingent,” “accidental,” “haphazard,” or (...) “stochastic.” Of course, what an author might mean by “chance” in any specific context varies. -/- In the following, we first offer a historiographical note on the synthesis. Second, we introduce five ways in which synthesis authors spoke about chance. We do not take these to be an exhaustive taxonomy of all possible ways in which chance meaningfully figures in explanations in evolutionary biology. These are simply five common uses of the term by biologists at this period. They will serve to organize our summary of the collected references to chance and the analysis and discussion of the following questions: • What did synthesis authors understand by chance? • How did these authors see chance operating in evolution? • Did their appeals to chance increase or decrease over time during the synthesis? That is, was there a “hardening” of the synthesis, as Gould claimed (1983)? (shrink)

An open question in the semantics of modality is what relations there are among different modal flavours. In this article, we consider the thorny issue of whether ascribing to an agent the obligation to φ implies that it is possible for the agent to φ. Traditionally, this issue has been interpreted as whether ‘ought’ implies ‘can’. But another linguistic interpretation is available as well, namely, whether ‘must’ implies ‘can’ (MIC). We show that ‘must’ does imply ‘can’ via a convergent argument. (...) The first strand of the argument is theoretical: it consists in proving MIC from a well-established theory of modality in natural language, i.e., that proposed by Kratzer. The second strand is empirical: we present novel acceptability judgment studies showing that MIC predicts and explains the linguistic behaviour of native English speakers. (shrink)

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...) epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

Natural genome editing from a biocommunicative perspective is the competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing integrates both natural editing of genetic code and epigenetic marking that determines genetic reading patterns. As agents that edit genetic code and epigenetically mark genomic structures, viral and subviral agents have been suggested because they may be (...) evolutionarily older than cellular life. This hypothesis that viruses and viral-like agents edit genetic code is developed according to three well investigated examples that represent key evolutionary inventions in which non-lytic viral swarms act symbiotically in a persistent lifestyle within cellular host genomes: origin of eukaryotic nucleus, adaptive immunity, placental mammals. Additionally an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on the genetic code. Most of these RNA agents such as transposons, retroposons and small non-coding RNAs act consortially and are remnants of persistent viral infections that now act as co-opted adaptations in cellular key processes. (shrink)

Biologists are nearing the creation of the first fully synthetic eukaryotic genome. Does this mean that we still soon be able to create genomes that are parts of an existing genetic lineage? If so, it might be possible to bring back extinct species. But do genomes that are synthetically assembled, no matter how similar they are to native genomes, really belong to the genetic lineage on which they were modelled? This article will argue that they are situated within the same (...) genetic lineage. To see why requires closely examining whether material overlap between parents and offspring is a necessary feature of biological reproduction. The processes used to create synthetic genomes shows that these processes are a form of scaffolded reproduction because they use external machinery and take ownership of the material parts used to create synthetic genomes. Closely examining these processes also reveals, surprisingly, that ‘synthetic reproduction’ can take place between entities that don’t participate in the same biological lineages. 1Introduction2The Argument for Lineage-less Genomes3Synthetic Eukaryotic Chromosomes and Material Overlap4Biological Reproduction, Material, and Information5Synthetic Reproductive Processes and Their Implications. (shrink)

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during (...) stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general. (shrink)

Darwinian evolutionary theory has two key terms, variations and biological selection, which finally lead to survival of the fittest variant. With the rise of molecular genetics, variations were explained as results of error replications out of the genetic master templates. For more than half a century, it has been accepted that new genetic information is mostly derived from random error-based events. But the error replication narrative has problems explaining the sudden emergence of new species, new phenotypic traits, and genome innovations (...) as a sudden single event. Meanwhile, it is recognized that errors cannot explain the evolution of genetic information, genetic novelty, and complexity. Now, empirical evidence establishes the crucial role of non-random genetic content editors, such as viruses, diversity generating retroelements, and other RNA networks, to produce new genetic information, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms, and evolutionary transitions. (shrink)

In 1990 the Human Genome Project (HGP) was launched as an important historical marker, a pivotal contribution to the time-old quest for human self-knowledge. However, when in 2001 two major publications heralded its completion, it seemed difficult to make out how the desire for self-knowledge had really been furthered by this endeavor (IHGSC 2001; Venter et al. 2001). In various ways mankind seems to stand out from other organisms as a unique type of living entity, developing a critical perspective on (...) its own behavior and consciously engaged in building a complex society of its own making—and therefore increasingly able to determine the conditions of its own evolution. However, this uniqueness is not easily and .. (shrink)

We examine how insights made in socio-anthropological and evolutionary schools of thought necessitate us to reevaluate the classic philosophical distinction between epistemology and ontology. We adopt an applied evolutionary epistemological stance and demonstrate that both epistemology and ontology evolve. Epistemology is broadened to include all knowledge and information that all life forms evolve, and ontology encompasses all biologically informed realities that life builds. Through processes such as symbiosis and niche construction, organisms acquire and extend information and knowledge into their offspring, (...) onto unrelated organisms, and onto their niches. Life builds biorealities that change over time. Consequently, knowledge and reality are mutable and truth is spatiotemporally bounded. We conclude that the classic distinction between epistemology and ontology has become superfluous and instead, we argue that the evolving knowledge that comes in the form of organisms and their extended niches equals ontological realities. (shrink)

This essay moves along broad lines from molecular biology to evolutionary biology and ecology to theology. Its objectives are to: 1) present some recent scientific findings in the emerging field of epigenetics that indicate that it is “the genome in context,” not genes per se, that are important in biological development and evolution; 2) show that this weakens the gene-centric neo-Darwinist explanation of evolution which, in fact, shares a certain preformationist orientation with intelligent design theory; 3) argue that the evidence (...) against a gene-centric view in no way negates Darwin’s central idea of “descent with modification”; 4) argue that an embrace of the evolutionary story, with all of its contingency and apparent lack of directionality, is not only consistent with Christianity, but actually resonates with the notion of the self-emptying love of God in Jesus Christ; and finally 5) suggest that we are called through an ecological imperative to embrace our evolutionary story, to listen to our “genetic coding,” and to reclaim our grounding as a species in the natural world. Corrigendum (published in later issue of journal): There was an error in the paragraph describing the mode of action of the small temporally-expressed RNAs (stRNAs) lin-4 and let-7 from Caenorhabditis elegans. Instead of reading "These two stRNAs act by binding to the tails of their target messenger RNAs (mRNAs); this results in destruction of the target and an overall drop in the level of production of protein from agouti mRNA" [note that agouti mRNA is not a target of these stRNAs], the sentence should have read, "These two stRNAs act by binding to the tails of target messenger RNAs (mRNAs); this leads to inhibition of translation of the mRNAs into protein and a consequent drop in the levels of the corresponding target protein.". (shrink)

A summarizing English version on “Theory of Innovation and the Evolution of General Human Capabilities, such as Cognition-based Empathy” is included in the download. Den biologisch modernen Menschentyp charakterisieren sehr allgemeine Fähigkeiten, wie begriffliche Sprache, strategisches Denken und kognitionsgestützte Empathie. Neurobiologisch kann Empathiefähigkeit als eine Verbindung von Repräsentationen von Mitmenschen mit dem je eigenen Gefühlszentren im Gehirn angesehen werden. In Grundzügen ist sie vor vielleicht 100 000 Jahren als Folge von Mutationen der Erbsubstanz DNA entstanden. Für solche genetische Innovationen spielten (...) wohl nicht nur lokale Veränderungen des Genoms eine Rolle, sondern auch seltene größere Umordnungen, besonders neue Zufallskombinationen von Regelbereichen in der DNA. Dies könnte in seltenen Einzelfällen eine Art Weichenstellung für eine neue Richtung der Evolution bewirken, die dann in vielen kleinen Schritten ausgeprägt wurde. Interessant ist die Analogie solcher biologischer mit technischer Innovation: Auch in ihr, Beispiel Dampfschiff, spielt die (seltene) Neukombination von Grundfähigkeiten eine Initialrolle für die Ausbreitung einer Innovation. (shrink)

Better instruments to predict the future evolution of artificial intelligence (AI) are needed, as the destiny of our civilization depends on it. One of the ways to such prediction is the analysis of the convergent drives of any future AI, started by Omohundro. We show that one of the convergent drives of AI is a militarization drive, arising from AI’s need to wage a war against its potential rivals by either physical or software means, or to increase its bargaining power. (...) This militarization trend increases global catastrophic risk or even existential risk during AI takeoff, which includes the use of nuclear weapons against rival AIs, blackmail by the threat of creating a global catastrophe, and the consequences of a war between two AIs. As a result, even benevolent AI may evolve into potentially dangerous military AI. The type and intensity of militarization drive depend on the relative speed of the AI takeoff and the number of potential rivals. We show that AI militarization drive and evolution of national defense will merge, as a superintelligence created in the defense environment will have quicker takeoff speeds, but a distorted value system. We conclude with peaceful alternatives. (shrink)

Change is the fundamental idea of evolution. Explaining the extraordinary biological change we see written in the history of genomes and fossil beds is the primary occupation of the evolutionary biologist. Yet it is a surprising fact that for the majority of evolutionary research, we have rarely studied how evolution typically unfolds in nature, in changing ecological environments, over space and time. While ecology played a major role in the eventual acceptance of the population genetic viewpoint of evolution in the (...) synthetic era (circa 1918-1956), it held a lesser role in the development of evolutionary theory until the 1980s, when we began to systematically study the evolutionary dynamics of natural populations in space and time. As a result, early evolutionary theory was initially constructed in an abstract vacuum that was unrepresentative of evolution in nature. The subtle synthesis between ecology with evolutionary biology (eco-evo synthesis) over the past 40 years has progressed our knowledge of natural selection dynamics as they are found in nature, thus revealing how natural selection varies in strength, direction, form, and, more surprisingly, level of biological organization. Natural selection can no longer be reduced to lower levels of biological organization (i.e., individuals, selfish genes) over shorter timescales but should be expanded to include adaptation at higher levels and over longer timescales. Long-term and/or emergent evolutionary phenomena, such as multilevel selection or evolvability, have thus become tenable concepts within an evolutionary biology that embraces ecology and spatiotemporal change. Evolutionary biology is currently suspended at an intermediate stage of scientific progress that calls for the organization of all the recent knowledge revealed by the eco-evo synthesis into a coherent and unified theoretical framework. This is where philosophers of biology can be of particular use, acting as a bridge between the subdisciplines of biology and inventing new theoretical strategies to organize and accommodate the recent knowledge. Philosophers have recommended transitioning away from outdated philosophies that were originally derived from physics within the philosophical zeitgeist of logical positivism (i.e., monism, reductionism, and monocausation) and toward a distinct philosophy of biology that can capture the natural complexity of multifaceted biological systems within diverse ecosystems—one that embraces the emerging philosophies of pluralism, emergence, and multicausality. Therefore, I see recent advances in ecology, evolutionary biology, and the philosophy of biology as laying the groundwork for another major biological synthesis, what I refer to as the Second Synthesis because, in many respects, it is analogous to the aims and outcomes of the first major biological synthesis (but is notably distinct from the inorganic and contrived progressive movement known as the extended evolutionary synthesis). With the general development of a distinctive philosophy of science, biology has rightfully emerged as an autonomous science. Thus, while the first synthesis legitimized biology, the Second Synthesis autonomized biology and afforded biology its own philosophy, allowing biology to finally realize its full scientific potential. (shrink)

What might be the fundamental psychology of intelligence naturally selected in biological evolution to minimize, prevent, and cure social and personal issues like war, crime, commit suicide, homicide, theft, drug addictions, and so on? How to achieve a higher level of well-being? I found a primary cognitive limiting factor called mind viruses (MV)(more than 3000) which regresses intelligence and well-being and makes the grand delusion: remedies are healthy mind viruses(HMV)(3000). Here, I show the disclosed core of early Buddhist teachings (on (...) learning, training the mind, and behavior on the 8-fold psychological course psychologically 'program' for better (intelligent) decisions. A theoretical 3D graph might represent the state of evolution of intelligence, nature, nurture, X-ultra quantum unique consciousness particle (X-UQUPC), and psychological well-being with the psychological time of a person. To this hypothesis, if the afterlife occurs, the natural selection of vacant zygote/early embryo neurons of the next life and their quality might depend on the finally evolved X-ultra quantum genomic particle of consciousness (X-UQGPC). Therefore, the quality, including the species of the new life and its nurture in the universe/s, depends on the quality of the finally evolved X-UQGPC. Such natural selection of a new nurturing environment for future (promising)life might be uncertain and, therefore, a high risk of finding a life-consciousness in great nature and nurture. However, there may be more mysterious issues to be solved in future research; therefore, the article might not discuss a theory of everything on the central theme. -/- . (shrink)

Neo-Darwinism is simply incorrect and it is an indictment of modern biology that the Theory of Evolution has not been updated in the light of research that can easily be conducted by anyone with a programmable computer.

Denis Walsh has written a striking new defense in this journal of the statisticalist (i.e., noncausalist) position regarding the forces of evolution. I defend the causalist view against his new objections. I argue that the heart of the issue lies in the nature of nonadditive causation. Detailed consideration of that turns out to defuse Walsh’s ‘description‐dependence’ critique of causalism. Nevertheless, the critique does suggest a basis for reconciliation between the two competing views. *Received December 2009; revised December 2009. †To contact (...) the author, please write to: Department of Philosophy, 599 Lucas Hall, One University Boulevard, University of Missouri, St. Louis, MO 63121; e‐mail: [email protected]. (shrink)

In “Milvian Bridges in Science, Religion, and Theology: Debunking Arguments and Cultural Evolution,” Lari Launonen and Aku Visala engage with an EDA against religious belief that appeals to cultural rather than biological evolution. According to this EDA, religious beliefs are unjustified, not because they are generated by biologically shaped cognitive processes that are unreliable as far as those beliefs are concerned but because they are generated by cultural processes that select for those beliefs for their ability to produce prosocial behavior (...) rather than for their truth sensitivity. Scientific beliefs, by contrast, are truth-sensitive because their cultural fitness depends on their power to produce accurate predictions. Their truth sensitivity explains the great amount of convergence on them that exists across cultures. In response to the EDA in question, Launonen and Visala argue that the difference between science and religion is actually more a matter of degree than a matter of kind, that there is considerable cross-cultural convergence on theistic and Christian beliefs, and that folk Christian beliefs, just as folk scientific ones, are truth-sensitive to the extent that they are constrained by expert beliefs. (shrink)

Behavioural flexibility is often treated as the gold standard of evidence for more sophisticated or complex forms of animal cognition, such as planning, metacognition and mindreading. However, the evidential link between behavioural flexibility and complex cognition has not been explicitly or systematically defended. Such a defence is particularly pressing because observed flexible behaviours can frequently be explained by putatively simpler cognitive mechanisms. This leaves complex cognition hypotheses open to ‘deflationary’ challenges that are accorded greater evidential weight precisely because they offer (...) putatively simpler explanations of equal explanatory power. This paper challenges the blanket preference for simpler explanations, and shows that once this preference is dispensed with, and the full spectrum of evidence—including evolutionary, ecological and phylogenetic data—is accorded its proper weight, an argument in support of the prevailing assumption that behavioural flexibility can serve as evidence for complex cognitive mechanisms may begin to take shape. An adaptive model of cognitive-behavioural evolution is proposed, according to which the existence of convergent trait–environment clusters in phylogenetically disparate lineages may serve as evidence for the same trait–environment clusters in other lineages. This, in turn, could permit inferences of cognitive complexity in cases of experimental underdetermination, thereby placing the common view that behavioural flexibility can serve as evidence for complex cognition on firmer grounds. (shrink)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

A holobiont is a composite organism consisting of a host together with its microbiome, such as a coral with its zooxanthellae. To explain the often intimate integration between hosts and their microbiomes, some investigators contend that selection operates on holobionts as a unit and view the microbiome’s genes as extending the host’s nuclear genome to jointly comprise a hologenome. Because vertical transmission of microbiomes is uncommon, other investigators contend that holobiont selection cannot be effective because a holobiont’s microbiome is an (...) acquired condition rather than an inherited trait. This disagreement invites a simple mathematical model to see how holobiont selection might operate and to assess its plausibility as an evolutionary force. This paper presents two variants of such a model. In one variant, juvenile hosts obtain microbiomes from their parents (vertical transmission). In the other variant, microbiomes of juvenile hosts are assembled from source pools containing the combined microbiomes of all parents (horizontal transmission). According to both variants, holobiont selection indeed causes evolutionary change in holobiont traits. Therefore, holobiont selection is plausibly an effective evolutionary force with either mode of microbiome transmission. The modeling employs two distinct concepts of inheritance, depending on the mode of microbiome transmission: collective inheritance whereby juveniles inherit a sample of the collected genomes from all parents, as contrasted with lineal inheritance whereby juveniles inherit the genomes from only their own parents. A distinction between collective and lineal inheritance also features in theories of multilevel selection. (shrink)

Evolutionary, ecological and ethical studies are, at the same time, specific scientific disciplines and, from an historical point of view, structurally linked domains of research. In a context of environmental crisis, the need is increasingly emerging for a connecting epistemological framework able to express a common or convergent tendency of thought and practice aimed at building, among other things, an environmental policy management respectful of the planet’s biodiversity and its evolutionary potential.

This paper considers clinical psychoanalysis together with developmental psychology (particularly attachment theory), evolution, and neuroscience in the context a Bayesian account of confirmation and disconfrimation. -/- In it I argue that these converging sources of support indicate that the combination of relatively low predictive power and broad explanatory scope that characterise the theories of both Freud and Darwin suggest that Freud's theory, like Darwin's, may strike deeply into natural phenomena. -/- The same argument, however, suggests that conclusive confirmation for Freudian (...) hypotheses, as in the case of Darwin's, will come from outside the original domain of explanation sketched out by Freud. As in Darwin's case conclusive confirmation came from understanding the physical mechanisms or reproduction, in Freud's case it will come from understanding the neural mechanisms that realise the phenomena described in psychoanalysis. (shrink)

A network of gene regulation organized in a hierarchical and combinatorial manner is crucially involved in the development of the neural network, and has to be considered one of the main substrates of genetic change in its evolution. Though qualitative features may emerge by way of the accumulation of rather unspecific quantitative changes, it is reasonable to assume that at least in some cases specific combinations of regulatory parts of the genome initiated new directions of evolution, leading to novel capabilities (...) of the brain. These notions are applied, in this paper, to the evolution of the capability of cognition-based human empa­thy. It is suggested that it has evolved as a secondary effect of the evolution of strategic thought. Development of strategies depends on abstract representations of one’s own pos­sible future states in one’s own brain to allow assessment of their emotional desirability, but also on the representation and emotional evaluation of possible states of others, allowing anticipation of their behaviour. This is best achieved if representations of others are con­nected to one’s own emotional centres in a manner similar to self-representations. For this reason, the evolution of the human brain is assumed to have established representations with such linkages. No group selection is involved, because the quality of strategic thought affects the fitness of the individual. A secondary effect of this linkage is that both the actual states and the future perspectives of others elicit vicarious emotions, which may contribute to the motivations of altruistic behaviour. (shrink)

Our intuition tells us that there is a general trend in the evolution of nature, a trend towards greater complexity. However, there are several definitions of complexity and hence it is difficult to argue for or against the validity of this intuition. Christoph Adami has recently introduced a novel measure called physical complexity that assigns low complexity to both ordered and random systems and high complexity to those in between. Physical complexity measures the amount of information that an organism stores (...) in its genome about the environment in which it evolves. The theory of physical complexity predicts that evolution increases the amount of ‘knowledge’ an organism accumulates about its niche. It might be fruitful to generalize Adami’s concept of complexity to the entire evolution (including the evolution of man). Physical complexity fits nicely into the philosophical framework of cognitive biology which considers biological evolution as a progressing process of accumulation of knowledge (as a gradual increase of epistemic complexity). According to this paradigm, evolution is a cognitive ‘ratchet’ that pushes the organisms unidirectionally towards higher complexity. Dynamic environment continually creates problems to be solved. To survive in the environment means to solve the problem, and the solution is an embodied knowledge. Cognitive biology (as well as the theory of physical complexity) uses the concepts of information and entropy and views the evolution from both the information-theoretical and thermodynamical perspective. Concerning humans as conscious beings, it seems necessary to postulate an emergence of a new kind of knowledge - a self-aware and self-referential knowledge. Appearence of selfreflection in evolution indicates that the human brain reached a new qualitative level in the epistemic complexity. (shrink)

As eugenics is defined, it is very difficult to make a clear distinction between science (medicine, genetic engineering) and eugenics as a included field. And to set a line over which genetic engineering should not go further, according to moral, legal and religious norms. If we accept the help of genetics in finding ways to fight cancer, diabetes, or HIV, we also accept positive eugenics as they are defined now. And if we accept genetic screening, and interventions on the unborn (...) baby, or abortion, we also implicitly accept negative eugenics. In addition, at government level, although eugenics are officially denied, it has been legalized in many countries until recently, and is still accepted and legalized, albeit in subtle forms, even these days. The section Introduction defines the term and classification modes. The section History of Eugenics follows eugenics from the ancient period, the introduction of eugenics by Francis Galton, the practice of eugenics as a state policy in various countries, and the present eugenics (liberal eugenics). I then analyze various issues raised by the Ethics of Liberal Eugenics, and I have developed a special section for the Future of Eugenics, focusing on the human genome project. Finally, in the Conclusions, I express my personal views on the current practice of eugenics. -/- CONTENTS: -/- Abstract Introduction New Eugenics The Future of Eugenics Conclusions Bibliography -/- DOI: 10.13140/RG.2.2.28662.45120. (shrink)

The neo-Darwinian theory of genetic random mutation and Natural Selection, does nothing to explain speciation. Thus, what has been called "natural selection" has come under much scrutiny and critique in recent times. The problem is that natural selection requires the existence of a stable array of species from which selection can be made. So natural selection does not perform the speciation, only the selection after speciation has occurred. The activity of creating new species must therefore lie in the random mutations (...) of the genome. But this raises the problem that such mutations are generally always fatal to the organism, plus a whole host of other problems that modern advances in molecular biology have revealed about the detailed mechanisms occurring in DNA replication processes, including such things as intrinsic error correcting mechanisms during DNA transcription. Thus a theory of how species arise (speciation) does not currently exist in biology. The Vedantic/Bhagavat paradigm rejects the objectivist theory of evolution as not only wrong but an impediment to the actual scientific comprehension of Nature. The Vedantic conception of Life is a fully differentiated/determinate one that displays its variety in and as an dynamic organic whole. The crucial element of interdependence that is missing in modern theories of insular organism life is fully embraced in what we may call the Post-Darwinian, post-reductionist, post-modern conception of Life the Vedantic/Bhagavat conception offers. (shrink)

In this paper, I trace the three-fold essence of “return”—a generating trope of identity and difference, through which formal aspects of the theory of relativity, the movement of language and emergence in evolution might converge. The trope of return is contrasted with the more common two-fold structure of relatedness underwriting differential calculus, propositional semantics and reductionism, which privileges space over time, identity over difference, self over creation.

Eco/logical R/evolution, is the story of mankind, told with words of a great and wonderful subjective odyssey, the never-ending quest; for objective truths and collective Eudaimonia. The author raises the issues; of political weakness and widespread confusion, about logical analytical errors, of which we find many of in Old Marxist Ideology. As a conscious effort, is thus made, to expel the mental subjugation of Platonic Idealism, away from the clenches Aristotelian Realism, and its bastard offspring; Old Historical Materialism. The book (...) identifies, in the works of Darwin and Marx, a wide range of worrying philosophical incompatibilities, such that are clearly found; in their respective theories and research methodologies. -/- We hereby propose; that a New Marxist Philosophy of Science, stands a probable chance; at unifying the Natural and Social Sciences. As the convergence of truths is manifest, thus, it is mapped out in detail by the author, out of necessity. It invokes, a Marxist Metaphysical Identity, for the sole purpose off; presenting a teleological framework, for New Marxist Theory. -/- NOTE: Reader must look up each word in a dictionary, which they see on both sides of the "/" when found in the middle of a word. (shrink)

Information Theory, Evolution and The Origin ofLife: The Origin and Evolution of Life as a Digital Message: How Life Resembles a Computer, Second Edition. Hu- bert P. Yockey, 2005, Cambridge University Press, Cambridge: 400 pages, index; hardcover, US $60.00; ISBN: 0-521-80293-8. The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is much (...) larger than the information content of these laws. Yockey in his previous book (1992, 335) In this new book, Information Theory, Evolution and The Origin ofLife, Hubert Yockey points out that the digital, segregated, and linear character of the genetic information system has a fundamental significance. If inheritance would blend and not segregate, Darwinian evolution would not occur. If inheritance would be analog, instead of digital, evolution would be also impossible, because it would be impossible to remove the effect of noise. In this way, life is guided by information, and so information is a central concept in molecular biology. The author presents a picture of how the main concepts of the genetic code were developed. He was able to show that despite Francis Crick's belief that the Central Dogma is only a hypothesis, the Central Dogma of Francis Crick is a mathematical consequence of the redundant nature of the genetic code. The redundancy arises from the fact that the DNA and mRNA alphabet is formed by triplets of 4 nucleotides, and so the number of letters (triplets) is 64, whereas the proteome alphabet has only 20 letters (20 amino acids), and so the translation from the larger alphabet to the smaller one is necessarily redundant. Except for Tryptohan and Methionine, all amino acids are coded by more than one triplet, therefore, it is undecidable which source code letter was actually sent from mRNA. This proof has a corollary telling that there are no such mathematical constraints for protein-protein communication. With this clarification, Yockey contributes to diminishing the widespread confusion related to such a central concept like the Central Dogma. Thus the Central Dogma prohibits the origin of life "proteins first." Proteins can not be generated by "self-organization." Understanding this property of the Central Dogma will have a serious impact on research on the origin of life. (shrink)

This is a wonderful book that ambitiously and impressively brings to convergence two parallel, perennial lines of inquiry in Hume’s scholarship. One is the classic Kemp Smith question concerning the relation between Hume’s naturalism and skepticism. The other is about the relation of the first Enquiry to book 1 of the Treatise. Qu observes that the Treatise is most distinctively naturalist or descriptive, while the Enquiry is decidedly normative. His approach is to examine the two questions through a single (...) lens by inquiring into the nature and causes of Hume’s epistemological evolution.Any evolutionary account must identify what evolutionary biologists refer to as the “transitional form.” For Qu, this is part 4 of... (shrink)

A new trend in deep learning, represented by Mutual Information Neural Estimation (MINE) and Information Noise Contrast Estimation (InfoNCE), is emerging. In this trend, similarity functions and Estimated Mutual Information (EMI) are used as learning and objective functions. Coincidentally, EMI is essentially the same as Semantic Mutual Information (SeMI) proposed by the author 30 years ago. This paper first reviews the evolutionary histories of semantic information measures and learning functions. Then, it briefly introduces the author’s semantic information G theory with (...) the rate-fidelity function R(G) (G denotes SeMI, and R(G) extends R(D)) and its applications to multi-label learning, the maximum Mutual Information (MI) classification, and mixture models. Then it discusses how we should understand the relationship between SeMI and Shannon’s MI, two generalized entropies (fuzzy entropy and coverage entropy), Autoencoders, Gibbs distributions, and partition functions from the perspective of the R(G) function or the G theory. An important conclusion is that mixture models and Restricted Boltzmann Machines converge because SeMI is maximized, and Shannon’s MI is minimized, making information efficiency G/R close to 1. A potential opportunity is to simplify deep learning by using Gaussian channel mixture models for pre-training deep neural networks’ latent layers without considering gradients. It also discusses how the SeMI measure is used as the reward function (reflecting purposiveness) for reinforcement learning. The G theory helps interpret deep learning but is far from enough. Combining semantic information theory and deep learning will accelerate their development. (shrink)

This analysis summarizes conclusions on an evolutionary model for the origin of moral and religious capacities in the genus Homo. The authors’ published model (2020, Routledge) is now extended to the emergence of nascent theological thinking, augmenting the previous line of theory based on genomics, cognitive science, neuroscience, paleoneurology, cognitive archaeology, ethnography, and modern social science. This analysis concludes that findings support the earliest theological thinking in Homo sapiens, but not in an earlier species, Homo erectus, and clarifies why and (...) when it likely began. Types of anatomy, behavior, neurology, and cognition are presented that support tendencies to frame a structure of religious principles and a set of supernatural figures that early humans would consider right, just, exemplary, and even sacred. Stages of emergent physical, behavioral, and cognitive features are presented in tables. While based on published research results in the sciences, the model is presented here with anticipation of future testing. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This (...) review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

Abstract - Evolutionary, ecological and ethical studies are, at the same time, specific scientific disciplines and, from an historical point of view, structurally linked domains of research. In a context of environmental crisis, the need is increasingly emerging for a connecting epistemological framework able to express a common or convergent tendency of thought and practice aimed at building, among other things, an environmental policy management respectful of the planet’s biodiversity and its evolutionary potential. -/- Evolutionary biology, ecology and ethics: at (...) first glance, three different objects of research, three different worldviews and three different scientific communities. In reality, there are both structural and historical links between these disciplines. First, some topics are obviously common across the board. Second, the emerging need for environmental policy management has gradually but radically changed the relationship between these disciplines. Over the last decades in particular, there has emerged a need for an interconnecting meta-paradigm that integrates more strictly evolutionary studies, biodiversity studies and the ethical frameworks that are most appropriate for allowing a lasting co-evolution between natural and social systems. Today such a need is more than a mere luxury, it is an epistemological and practical necessity. -/- In short, the authors of this volume address some of the foundational themes that interconnect evolutionary studies, ecology and ethics. Here they have chosen to analyze a topic using one of these specific disciplines as a kind of epistemological platform with specific links to topics from one or both of the remaining disciplines. Michael Ruse’s chapter, for instance, elucidates some of the structural links between Darwinismand ethics. Ruse analyzes the Evolutionism vs. Creationism debate, emphasizing the risks run by scientists when they ideologize the scientific content of their studies. In the case of the contributions of Jean Gayon and Jean-Marc Drouin, which respectively deal with the disciplines of evolutionary biology and ecology, some central connections have been developed between these two disciplines, while reserving the option to consider in detail their topic in order to discover essential features ormeanings. Gayon analyzes the multilayered meanings of “chance” in evolutionary studies and the methodological implications that accompany such disparatemeanings. Froma similar analytical perspective, Drouin’s contribution focuses on the identification and critical evaluation of the different conceptions of time in ecology. Chance and time, factors of evolution in species and ecological systems, play a very important function in both disciplines, and these chapters help to capture their polysemous structure and development. Bryan Norton’s chapter, on adaptive environmental management, is set within an epistemological context where the Darwinian paradigm, ecological knowledge and ethical frameworks meet to give rise to practical, conservationist policies. In his contribution, Patrick Blandin pleads for the necessity of an eco-evolutionary ethics capable of fully encompassing humanity’s responsibility in the future determination of the biosphere’s evolutionary paths. Our value systems must recognize the predominant place that humanity has taken in the evolutionary history of the planet, and integrate the ethical ramifications of scientific advances in evolutionary and ecological studies. The chapter by J. Baird Callicott introduces us to a metaphorical ecological reversion with direct consequences for our moral conduct. If ecology showed that ecosystems are not organisms, recognizing organisms as a kind of ecosystem could be the basis for a new post-modern ecological ethics that lays the foundation for a better moral integration of humans with the environment. The contributions of Robin Attfield and Tom Regan delve into some of the classical issues in environmental ethics, situating them within a broader ecological and evolutionary context. Attfield’s chapter tackles the confrontation between individualistic and ecologically holistic perspectives, their different approaches to the issue of intrinsic value, and their tangled relation to monism and pluralism. Regan’s contribution ponders the criteria that allow individual beings, human and non-human, to own moral rights, the role of the struggle for existence in the relationship between species, and the logical difficulties involved in attributing intrinsic value to collective entities (species, ecosystems). Catherine Larrère’s chapter discusses the opposition between two environmental and ethical worldviews with very different philosophical centers of gravity: nature and technology. These opposing perspectives have direct consequences not only for the perception of the problems at hand and for what entities are deemed morally significant, but also for the proposed solutions. -/- To set out some foundational events in the history of evolutionary biology, ecology and environmental ethics is a first necessary step towards a clarification of their major epistemological orientations. On the basis of this inevitably nonexhaustive history, it will be possible to better position the work of the different contributors, and to build a meta-paradigm, i.e. a connecting epistemological framework resulting from one common or convergent tendency of thought and practice shared by different disciplines. (shrink)

Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic (...) plasticity, macroevolutionary studies of integration, and statistical and conceptual issues in the study of the evolution of complex phenotypes. I then conclude with a brief discussion of what I see as the major future directions of research on phenotypic integration and how they relate to our more general quest for the understanding of phenotypic evolution within the neo-Darwinian framework. I suggest that studying integration provides a particularly stimulating and truly interdisciplinary convergence of researchers from fields as disparate as molecular genetics, developmental biology, evolutionary ecology, palaeontology and even philosophy of science. (shrink)

Darwinism, especially in the form of the Modern Synthesis, has become one of the most influential theories in the worldwide scientific community. However, due to its often dogmatic interpretation, it is more and more orthodoxical. An increasing number of scientists have come to criticise Darwinism and go beyond it with a systemic approach and an expanded vision of the evolutionary process. As a matter of fact, the discovery of natural genetic engineering mechanisms shows that living cells are able to rewrite (...) their own genetic material at the genomic level, thus leading to evolutionary innovations. This teleological standpoint triggers a paradigm shift that could turn out to be a genuine scientific revolution. (shrink)

Alternative splicing allows for the production of many gene products from a single coding sequence. I introduce the concept of alternative splicing via some examples. I then discuss some current hypotheses about the explanatory role of alternative splicing, including the claim that splicing is a significant contributor to the difference in complexity between the human genome and proteosome. Hypotheses such as these bring into question our working concepts of the gene. I examine several gene concepts introduced to cope with processes (...) such as alternative splicing. Next I introduce some hypotheses about the evolution of mechanisms alternative splicing in higher organisms. I conclude that attention to alternative splicing reveals that we adopt an attitude that developmental theorizing must inform evolutionary theorizing and vice versa. (shrink)