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)

First, I offer a short overview on the classical occidental philosophy as propounded by the ancient Greeks and the natural philosophies of the last 2000 years until the dawn of the empiricist logic of science in the twentieth century, which wanted to delimitate classical metaphysics from empirical sciences. In contrast to metaphysical concepts which didn’t reflect on the language with which they tried to explain the whole realm of entities empiricist logic of science initiated the end of metaphysical theories by (...) reflecting on the preconditions for foundation and justification of sentences about objects of investigation, i.e. a coherent definition of language in general, which was not the aim of classical metaphysics. Unexpectedly empiricist logic of science in the linguistic turn failed in the physical and mathematical reductionism of language and its use in communication, as will be discussed below in further detail. Nevertheless, such reflection on language and communication also introduced this vocabulary into biology. Manfred Eigen and bioinformatics, later on biolinguistics, used ‘language’ applied linguistic turn thinking to biology coherent to the logic of science and its formalisable aims. This changed significantly with the birth of biosemiotics and biohermeneutics. At the end of this introduction it will be outlined why and how all these approaches reproduced the deficiencies of the logic of science and why the biocommunicative approach avoids their abstractive fallacies. (shrink)

In searching for life in extraterrestrial space, it is essential to act based on an unequivocal definition of life. In the twentieth century, life was defined as cells that self-replicate, metabolize, and are open for mutations, without which genetic information would remain unchangeable, and evolution would be impossible. Current definitions of life derive from statistical mechanics, physics, and chemistry of the twentieth century in which life is considered to function machine like, ignoring a central role of communication. Recent observations show (...) that context-dependent meaningful communication and network formation (and control) are central to all life forms. Evolutionary relevant new nucleotide sequences now appear to have originated from social agents such as viruses, their parasitic relatives, and related RNA networks, not from errors. By applying the known features of natural languages and communication, a new twenty-first century definition of life can be reached in which communicative interactions are central to all processes of life. A new definition of life must integrate the current empirical knowledge about interactions between cells, viruses, and RNA networks to provide a better explanatory power than the twentieth century narrative. (shrink)

Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (...) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs. (shrink)

Metaphysical theories are often counter-intuitive. But they also often are strongly supported and motivated by intuitions. One way or another, the link between intuitions and metaphysics is a strong and important one, and there is hardly any metaphysical discussion where intuitions do not play a crucial role. In this article, I will be interested in a particular kind of such intuitions, namely those that come, at least partly, from experience. There seems to be a route from experience to metaphysics, and (...) this is the core of my interest here. In order to better understand such ‘arguments from experience’ and the kind of relationship there is between this type of intuitions and metaphysical theories, I shall examine four particular cases where a kind of experience-based intuition seems to motivate or support a metaphysical theory. At the end of the day, I shall argue that this route is a treacherous one, and that in all of the four cases I shall concentrate on, phenomenological considerations are in fact orthogonal to the allegedly ‘corresponding’ metaphysical claims. An anti-realist view of metaphysics will emerge. (shrink)

In this paper, I explore several versions of the bundle theory and the substratum theory and compare them, with the surprising result that it seems to be true that they are equivalent (in a sense of 'equivalent' to be specified). In order to see whether this is correct or not, I go through several steps : first, I examine different versions of the bundle theory with tropes and compare them to the substratum theory with tropes by going through various standard (...) objections and arguing for a tu quoque in all cases. Emphasizing the theoretical role of the substratum and of the relation of compresence, I defend the claim that these views are equivalent for all theoretical purposes. I then examine two different versions of the bundle theory with universals, and show that one of them is, here again, equivalent to the substratum theory with universals, by examining how both views face the famous objection from Identity of Indiscernibles in a completely parallel way. It is only the second, quite extreme and puzzling, version of the bundle theory with universals that is not be equivalent to any other view; and the diagnosis of why this is so will show just how unpalatable the view is. Similarly, only a not-so-palatable version of the substratum theory is genuinely different from the other views; and here again it's precisely what makes it different that makes it less appealing. (shrink)

The main task of this paper is to understand if and how static images like photographs can represent and/or depict temporal extension (duration). In order to do this, a detour will be necessary to understand some features of the nature of photographic representation and depiction in general. This important detour will enable us to see that photographs (can) have a narrative content, and that the skilled photographer can 'tell a story' in a very clear sense, as well as control and (...) guide the attention of the spectator of the photograph. The understanding and defence of this claim is a secondary aim of this paper, and it will then allow us to provide a good treatment of the particular case of photographic representation and depiction of temporal extension. (shrink)

Přehledová studie sleduje a analyzuje proměny pojmu sociální inovace. Na základě silné společenské poptávky se z původně dílčí, teoreticky nediskutované a nefixované kategorie stává kategorie obecná. Pokrývá širokou oblast nemateriálních inovací a zároveň se profiluje jako aktivita normativní a intencionální, zaměřená na obecně uznávané sociální cíle. Co do ideově-hodnotových orientací současných koncepcí sociálních inovací studie identifikuje kromě mainstreamu, který zůstává u otevřených hodnotových charakteristik, ještě směr emancipačně-mobilizační a sociálně-tržně odpovědný. V epistemologické rovině se teoretici sociálních inovací hlásí především k praktickému (...) experimentování, pragmatismu, teorii komplexnosti a principům transdisciplinarity. (shrink)

Metaphysical theories heavily rely on the use of primitives to which they typically appeal. I will start by examining and evaluating some traditional well-known theories and I will discuss the role of primitives in metaphysical theories in general. I will then turn to a discussion of claims of between theories that, I think, depend on equivalences of primitives, and I will explore the nature of primitives. I will then claim that almost all explanatory power of metaphysical theories comes from their (...) primitives, and so I will turn to scrutinize the notion of "power" and "explanatory". (shrink)

In this article, I want to understand the nature of aesthetic experiences of landscapes. I offer an understanding of aesthetic appreciation of landscapes based on a notion of a landscape where landscapes are perspectival observer-dependent entities, where the 'creator' of the landscape necessarily happens to be the same person as the spectator, and where her scientific (and other) knowledge and beliefs matter for the appreciation to be complete. I explore the idea that appreciating a landscape in this sense has quite (...) a lot in common with taking and appreciating a photograph. On our way, we will see how imagination plays a crucial role in the story. (shrink)

Abstract: There are two traditionally rival views about the nature of time: substantivalism that takes time to be a substance that exists independently of events located in it, and relationism that takes time to be constructed out of events. In this paper, first, I want to make some progress with respect to the debate between these two views, and I do this mainly by examining the strategies they use to face the possibilities of ‘empty time’ and ‘time without change’. As (...) we shall see, the two allegedly very different rival views are much less different than has been thought: their structure is extremely similar, their strategies are extremely similar, and they can both face the possibilities of ‘empty time’ and ‘time without change’ in the same way. Thus, I argue in favour of a certain kind of equivalence between the two views; I discuss a Strong and a Weak version of this claim; and I provide reasons for endorsing the former. I also discuss the parallel between this pair of views about the nature of time and another analogous pair of views: the bundle theory and the substratum theory about the nature of material objects, with respect to the problem with Identity of Indiscernibles. (shrink)

Although molecular biology, genetics, and related special disciplines represent a large amount of empirical data, a practical method for the evaluation and overview of current knowledge is far from being realized. The main concepts and narratives in these fields have remained nearly the same for decades and the more recent empirical data concerning the role of noncoding RNAs and persistent viruses and their defectives do not fit into this scenario. A more innovative approach such as applied biocommunication theory could translate (...) empirical data into a coherent perspective on the functions within and between biological organisms and arguably lead to a sustainable integrative biology. (shrink)

The claim that the having of aesthetic properties supervenes on the having of non-aesthetic properties has been widely discussed and, in various ways, defended. In this paper, I will show that even if it is sometimes true that a supervenience relation holds between aesthetic properties and the 'subvenient' non-aesthetic ones, it is not the interesting relation in the neighbourhood. As we shall see, a richer, asymmetric and irreflexive relation is required, and I shall defend the claim that the more-and-more-popular relation (...) of grounding does a much better job than supervenience. (shrink)

In this paper, I explore the nature of photographs by comparing them to hand-made paintings, as well as by comparing traditional film photography with digital photography, and I concentrate on the question of realism. Several different notions can be distinguished here. Are photographs such that they depict the world in a 'realist' or a 'factive' way ? Do they show us the world as it is with accuracy and reliability other types of pictures don't posses ? Do they allow us, (...) as some have suggested, to literally see the world through them ? Below, I will distinguish three kinds of realism about photographs, reject two, and partly endorse one. Indeed, the label "realism", when concerning photographs, can stand for a variety of very different claims. The first (and quite obvious) distinction to start with concerns what the realist thesis is about : the claim that somehow photographs are more accurate or more reliable or that they somehow depict the world better than hand-made pictures can be a claim about the photographic image itself or alternatively a claim about the way in which photographs are produced. In the former case, realism is a thesis about how photographs look and what sort of information they contain, while in the latter case realism is a claim about the process of production of photographs. It is the latter claim that is the most discussed in the philosophical literature about photography. I will concentrate on this type of realism, of which I shall examine two varieties. (shrink)

Several metaphysical debates have typically been modeled as oppositions between a relationist approach and a substantivalist approach. Such debates include the Bundle Theory and the Substratum Theory about ordinary material objects, the Bundle (Humean) Theory and the Substance (Cartesian) Theory of the Self, and Relationism and Substantivalism about time. In all three debates, the substantivalist side typically insists that in order to provide a good treatment of the subject-matter of the theory (time, Self, material objects), it is necessary to postulate (...) the existence of a certain kind of substance, while the other side, the relationist one, characteristically feels that this is an unnecessary expense and that one can get the job done in an ontologically cheaper way just with inter-related properties or events. In this paper I shall defend the view that there is much less of a disagreement between relational ontologies and substantival ontologies than it is usually thought. I believe that, when carefully examined, the two sides of the debate are not that different from each other, in all three cases of pairs of views mentioned above. As we will see, both the relational side and the substantival side work in the same way, suffer from and answer the same objections, and are structurally extremely similar. It will be an important question – one that I shall discuss in detail, and that is indeed the main point of interest for me in this paper – whether this means that the two sides of the debate are somehow 'equivalent' or not, and what 'equivalent' could mean. (shrink)

All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it (...) could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA-networks andRNA-communication can interconnect these levels.With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact. (shrink)

In this paper, I examine various theories of persistence through time under presentism. In Part I, I argue that both perdurantist views (namely, the worm view and the stage view) suffer, in combination with presentism, from serious difficulties and should be rejected. In Part II, I discuss the presentist endurantist view, to see that it does avoid the difficulties of the perdurantist views, and consequently that it does work, but at a price that some may consider as being very high: (...) its ontological commitments to platonic universals and to the substratum theory, that as we shall see follow from the combination of endurantism with presentism, will perhaps not be to everyone's taste. (shrink)

Abstract The quasispecies theory is a helpful concept in the explanation of RNA virus evolution and behaviour, with a relevant impact on methods used to fight viral diseases. It has undergone some adaptations to integrate new empirical data, especially the non-deterministic nature of mutagenesis, and the variety of behavioural motifs in cooperation, competition, communication, innovation, integration, and exaptation. Also, the consortial structure of quasispecies with complementary roles of memory genomes of minority populations better fits the empirical data than did the (...) original concept of a master sequence and its mutant spectra. The high productivity of quasispecies variants generates unique sequences that never existed before and will never exist again. In the present essay, we underline that such sequences represent really new ontological entities, not just error copies of previous ones. Their primary unique property, the incredible variant production, is suggested here as quasispecies productivity, which replaces the error-replication narrative to better fit into a new relationship between mankind and living nature in the twenty-first century. (shrink)

In this article, I am interested in dual-aspect monism as a solution to the mind-body problem. This view is not new, but it is somewhat under-represented in the contemporary debate, and I would like to help it make its way. Dual-aspect monism is a parsimonious, elegant and simple view. It avoids problems with “mental causation”. It naturally explains how and why mental states are correlated with physical states while avoiding any mysteries concerning the nature of this relation. It fits well (...) with our ordinary picture of the world, as well as with the scientific picture. It gives its rightful place to the phenomenal, qualitative, subjective character of experience, instead of reducing it or eliminating it. It does not unnecessarily multiply ontological categories. It can come in many versions, and is compatible with other interesting views, such as panpsychism. (shrink)

Manfred Eigen employs the terms language and communication to explain key recombination processes of DNA as well as to explain the self-organization of human language and communication: Life processes as well as language and communication processes are governed by the logic of a molecular syntax, which is the exact depiction of a principally formalizable reality. The author of the present contribution demonstrates that this view of Manfred Eigen’s cannot be sufficiently substantiated and that it must be supplemented by an approach (...) based on linguistic pragmatics. (shrink)

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language.However, the basics of scientific knowledge changed dramatically within the second half (...) of the 20th century.Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life. (shrink)

Depiction and imagination are intimately linked. In this article, I discuss the role imagination (as well as inference and knowledge/belief) plays in depiction, with a focus on photographic depiction. I partly embrace a broadly Waltonian view, but not always, and not always for Walton's own reasons. In Walton's view, imagination plays a crucial role in depiction. I consider the objection to his view that not all cases of depiction involve imagination – for instance, documentary photographs. From this discussion, two points (...) will emerge: first, we will see that it is an unnecessary mistake to insist too heavily on the fact that photographs are produced in a mechanical way (as opposed to, say, paintings), and second, we will see that the notion of "imagining-seeing", as it is articulated by Walton, is perhaps too strong and does not entirely do justice to the external character of the role imagination plays here. Focusing mainly on photographs, I then illustrate the view I want to advocate by a series of different cases, where the nature of the role that imagination, knowledge/belief, and inference play in depiction will become apparent. (shrink)

There are three main traditional accounts of vagueness : one takes it as a genuinely metaphysical phenomenon, one takes it as a phenomenon of ignorance, and one takes it as a linguistic or conceptual phenomenon. In this paper I first very briefly present these views, especially the epistemicist and supervaluationist strategies, and shortly point to some well-known problems that the views carry. I then examine a 'statistical epistemicist' account of vagueness that is designed to avoid precisely these problems – it (...) will be a view that provides an account of the phenomenon of vagueness as coming from our linguistic practices, while insisting that meaning supervenes on use, and that our use of vague terms does yield sharp and precise meanings, which we ignore, thus allowing bivalence to hold. (shrink)

This book assembles recent research on memory and learning in plants. Organisms that share a capability to store information about experiences in the past have an actively generated background resource on which they can compare and evaluate coming experiences in order to react faster or even better. This is an essential tool for all adaptation purposes. Such memory/learning skills can be found from bacteria up to fungi, animals and plants, although until recently it had been mentioned only as capabilities of (...) higher animals. With the rise of epigenetics the context dependent marking of experiences on the genetic level is an essential perspective to understand memory and learning in organisms. -/- Plants are highly sensitive organisms that actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate information and then modify their behavior accordingly. -/- The book will guide scientists in further investigations on these skills of plant behavior and on how plants mediate signaling processes between themselves and the environment in memory and learning processes. (shrink)

This article is concerned with the alleged incompatibility between presentism and specious present theories of temporal experience. According to presentism, the present time is instantaneous (or, near-instantaneous), while according to specious present theories, the specious present is temporally extended—therefore, it seems that there is no room in reality for the whole of a specious present, if presentism is true. It seems then that one of the two claims—presentism or the specious present theory—has to go. I shall argue that this kind (...) of worries is mislead. Once we understand properly how our phenomenal experience as of passage and as of change, such as it is understood by specious present theorists, comes into being, the apparent phenomenologico-metaphysical conflict will disappear. In short, the mistake here is to presuppose that there is a link between phenomenology and metaphysics stronger than it actually is. Presentism is a metaphysical theory about what exists. Specious presentism is a phenomenological theory about how things appear to us in experience. As we will see, the two claims are not in conflict, and are in fact entirely orthogonal. (shrink)

[This paper is written in Czech language.] The aim of the article is to re-evaluate the still-surviving anthropological trope which, in reaction to an inquiry into the essence of man, compares humans with animals and points to culture as the means by which humans complete their “deficient” nature. This motif contrasting humans with animals has been extended by A. Gehlen who characterises humans as “beings of deficiencies”. In his view, the morphological-instinctive insufficiency of the human being must be stabilised by (...) cultural institutions, i.e. complexes of habitual actions. Merleau-Ponty, however, demonstrates that bodily beings always relate to their environment in an indirect way, on the basis of certain “standards” and “norms” of interaction, which exist by way of institution. The anthropological trope confronting humans and animals thus cannot produce, as in Gehlen, a contrast between an allegedly “direct” relationship to the world in animals, and a supposedly “indirect” relationship to the world in humans. It can be meaningfully retained only if it is interpreted in a Merleau-Pontyan way, that is, as an invitation to understand the transformation of the norms of indirect interaction with the world found in animals into those found in people, that is, if viewed as a comparison of their respective institutions. (shrink)

For the metaphysician, photographs are very puzzling entities indeed. And even from the non-philosopher's intuitive point of view, it is not that clear what sort of thing a photograph is. Typically, if a client wants to purchase a photograph, she can mean very different things by 'buying a photograph' : she can mean to buy a print or a number of prints, or she can mean to buy a negative (when traditional film photographs are concerned) or a file (when digital (...) photography is concerned), or she can mean to buy a right to use a photograph a precisely determined number of times in a number of brochures or on a website, and so on. When facing a new client, I always, without exception, face the problem of explaining to her what it is that she is actually buying – and it is not always clear that she is ever buying a photograph. As a metaphysician, I face a much more difficult challenge : find out to what ontological category photographs belong to. Are they concrete spatio-temporal entities like prints, are they universals since there can be many 'prints-instances' of a same photograph, are they sets or aggregates of prints, or something even different ? This is the task that I wish to undertake in this paper : examine all plausible metaphysical categories to which photographs could belong to, and see which one is the fittest. As we shall see, in this 'survival for the fittest' competition between traditional metaphysical categories, there will be no real winner : several categories will reveal themselves to be enlightening and useful when describing features of what photographs are, but none will prove to be entirely satisfactory. Photographs, it seems, are a sort of borderline entities that share some but not all aspects of several traditional metaphysical categories. Is it then justified to postulate a new ontological category to which photographs would properly belong ? On mainly methodological grounds, I shall argue that it is not, and I will suggest a different way out of this metaphysician's trouble by defending a nihilism about photographs. To put it bluntly, I will defend the claim that photographs do not exist – but I will also argue that this is not a very revisionary or anti-commonsensical claim. (shrink)

In this article, I am interested in four versions of what is often referred to as "the Humphrey objection". This objection was initially raised by Kripke against Lewis's modal counterpart theory, so this is where I will start the discussion. As we will see, there is a perfectly good answer to the objection. I will then examine other places where a similar objection can be raised: it can arise in the case of temporal counterpart theory (in fact, it can arise (...) in the case of all kinds of counterpart theories, independently on modal realism), and a very similar worry can also arise against modal realism itself or against an ersatzist theory of possible worlds itself. For similar reasons, in similar situations, a similar objection will arise. What is interesting is that it is not the case that a similar response can be given in all of these similar cases. So, in the end, we will see what dissimilarities there are and how and why they are relevant. In particular, we will see the differences there are between alethic modalities and temporal modalities. In the case of alethic modalities (metaphysical necessity and possibility), the objection can be answered by appealing to the notion of representation, while this does not work very well in the case of temporal modalities. (shrink)

Does mere passage of time have causal powers ? Are properties like "being n days past" causally efficient ? A pervasive intuition among metaphysicians seems to be that they don't. Events and/or objects change, and they cause or are caused by other events and/or objects; but one does not see how just the mere passage of time could cause any difference in the world. In this paper, I shall discuss a case where it seems that mere passage of time does (...) have causal powers : Sydney Shoemaker's (1969) possible world where temporal vacua (allegedly) take place. I shall argue that Shoemaker's thought-experiment doesn't really aim at teaching us that there can be time without change, but rather that if such a scenario is plausible at all (as I think it is) it provides us with good reasons to think that mere passage of time can be directly causally efficient. (shrink)

Eliminativism about macroscopic material objects claims that we do not need to include tables in our ontology, and that any job – practical or theoretical – they have to do can be done by 'atoms arranged tablewise'. This way of introducing eliminativism faces the worry that if there are no 'atoms', that is, if there are no simples and the world is 'gunky', there are no suitable entities to be 'arranged tablewise'. In this article, I discuss various strategies the eliminativist (...) can have to face this objection, and I conclude by showing that the objection is actually misdirected and does not threaten eliminativism at all. (shrink)

Organisms actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between “self” and “non-self.” Current empirical data on all domains of life indicate that unicellular organisms such as bacteria, archaea, giant viruses, and protozoa as well as multicellular organisms such as animals, fungi, and plants coordinate and organize their essential life functions (...) through signaling processes. Signaling allows for real life coordination and organization and is a communicative action in which speciesspecific behavioral patterns and sign repertoires are used. Cells, tissues, organs, and organisms that communicate share several key levels that are essential to all life forms and which serve as a uniform tool for investigating biocommunication. (shrink)

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural (...) laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer sciencebased formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language. (shrink)

The recent debate in metaontology gave rise to several types of (more or less classical) answers to questions about "equivalences" between metaphysical theories and to the question whether metaphysical disputes are substantive or merely verbal (i.e. various versions of realism, strong anti-realism, moderate anti-realism, or epistemicism). In this paper, I want to do two things. First, I shall have a close look at one metaphysical debate that has been the target and center of interest of many meta-metaphysicians, namely the problem (...) of how material objects persist through time : the endurantism vs. perdurantism controversy. It has been argued that this debate is a good example of a merely verbal one, where two allegedly competing views are in fact translatable one into each other – they end up, contrary to appearances, to be equivalent. In my closer look at this debate, I will conclude that this is correct, but only to some extent, and that there does remain room for substantive disagreement. The second thing that I wish to achieve in this paper, and that I hope will stem from my considerations about the persistence debate, is to defend a metaontological view that emphasizes that when asking the question "Are metaphysical debates substantive or verbal?" the correct answer is "It depends." Some debates are substantive, some debates are merely verbal, sometimes it is true that a problem or a question can be formulated in equally good frameworks where there is no fact of the matter as to which one is correct or where we just cannot know it. Furthermore, importantly, as my examination of the persistence debate will show, there is room for the view that a debate is largely merely verbal but not entirely and that some parts of it are substantive, and decidable by philosophical methods. It is possible, and it is the case with respect to the persistence debate, that inside a debate some points are merely verbal while other are places of substantive disagreement. A moral of this is that, at the end of the day, the best way to do meta-metaphysics is to do first-level metaphysics. (shrink)

Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures (...) in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses. (shrink)

When I say that I am a lot of things, I mean it literally and metaphysically speaking. The Self, or so I shall argue, is a plurality (notwithstanding the fact that ordinary language takes "the Self" to be a singular term – but, after all, language is only language). It is not a substance or a substratum, and it is not a collection or a bundle. The view I wish to advocate for is a kind of reductionism, in line with (...) some – but not all – broadly Humean ideas. In short, I will defend the view there are the experiences and mental states we have, and that's it: no additional substances, and no bundles. This does not mean, however, that there is no Self – the Self simply is the experiences. I will try to articulate and defend this view by showing that it can accommodate what I take to be the three main desiderata for any theory of the Self to satisfy: first, that the Self is the subject of experience (a subject of mental states, in general); second, that there is a unity to the Self in the sense that our (conscious, phenomenal) experience is at least partly continuous or 'stream-like'; and third, that we do not die when we go to sleep or when we otherwise don't have any (conscious, phenomenal) experiences. (shrink)

At a first glance, and even at a second one, it seems that if time is linear the threat of determinism is more severe than if time is branching, since in the latter case the future is open in a way it is not in the former one where, so to speak, there exists only one branch – one future. In this paper, I want to give a 'third glance' at this claim. I acknowledge that such a claim is intuitive (...) (this is the first glance) and that it is also meaningfully and interestingly defended in recent literature where branching time is either said to imply indeterminism or at least to be compatible with it. To try to make my third glance as precise and as fleshed out as possible, I shall first concentrate on what 'branching' is or could be, and I shall discuss various versions and interpretations of this view. I shall then (more quickly) turn my attention to what determinism is or could be, and I will distinguish three (well-known) kinds of it – focusing mainly on 'metaphysical determinism'. Having these tools in hand, I will then ask (and answer) the question whether branching time helps with avoiding determinism or not. As we shall see, it is incorrect to think that under the branching hypothesis the threat of determinism is any smaller – rather, I will argue that if one has reasons to think that determinism is true, branching will not help, and that the issue of branching versus linear time is then actually neutral with respect to the question whether determinism or indeterminism is true. (shrink)

This contribution demonstrates that the development and growth of plants depends on the success of complex communication processes. These communication processes are primarily sign-mediated interactions and are not simply an mechanical exchange of ‘information’, as that term has come to be understood (or misunderstood) in science. Rather, such interactions as I will be describing here involve the active coordination and organisation of a great variety of different behavioural patterns — all of which must be mediated by signs. Thus proposed, a (...) biosemiotics of plant communication investigates communicationprocesses both within and among the cells, tissues, and organs of plants as sign-mediated interactions which follow (1) combinatorial (syntactic), (2) context-sensitive (pragmatic) and (3) content-specific (semantic) levels of rules. As will be seen in the cases under investigation, the context of interactionsin which a plant organism is interwoven determines the content arrangement of its response behaviour. And as exemplified by the multiply semiotic roles playedby the plant hormone auxin that I will discuss below, this means that a molecule type of identical chemical structure may function in the instantiation of differentmeanings (semantics) that are determined by the different contexts (pragmatics) in which this sign is used. (shrink)

If ordinary particulars are bundles of properties, and if properties are said to be universals, then three well-known objections arise : no particular can change, all particulars have all of their properties essentially (even the most insignificant ones), and there cannot be two numerically distinct but qualitatively indiscernible particulars. In this paper, I try to make a little headway on these issues and see how the objections can be met, if one accepts a certain view about persistence through time and (...) across possible worlds – namely, four-dimensionalism and its modal analogue. The paper is especially devoted to the second and third of the three objections. (shrink)

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and non-coding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a re-examination. In (...) this review we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioural motifs of cooperative RNA consortia. In addition to molecular biological perspectives this may lead to a better understanding of genetic code evolution and dynamics. (shrink)

Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of (...) viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing. (shrink)

Is there an entity such that it can be in two places at the same time ? According to one traditional view, properties can, since they are immanent universals. But what about objects such as a person or a table ? Common sense seems to say that, unlike properties, objects are not multiply locatable. In this paper, I will argue first of all that endurantism entails a consequence that is quite bizarre, namely, that objects are universals, while properties are particulars. (...) I then conclude by examining and rejecting two theories according to which objects can wholly be in two places at the same time. (shrink)

Finding an adequate definition of "life" has proven to be a tricky affair. In this article, I discuss the idea that nothing is really alive: we only say so. I shall argue that 'being alive' is not a genuine property of things, and that it only reflects the way we think and talk about things. An eliminativist strategy will then allow us to free ourselves from the burden of having to find a definition of life, and will allow us to (...) focus on the genuinely interesting properties of living (and non-living) entities. (shrink)

The concepts of the origin of the genetic code and the definitions of life changed dramatically after the RNA world hypothesis. Main narratives in molecular biology and genetics such as the “central dogma,” “one gene one protein” and “non-coding DNA is junk” were falsified meanwhile. RNA moved from the transition intermediate molecule into centre stage. Additionally the abundance of empirical data concerning nonrandom genetic change operators such as the variety of mobile genetic elements, persistent viruses and defectives do not fit (...) with the dominant narrative of error replication events (mutations) as being the main driving forces creating genetic novelty and diversity. The reductionistic and mechanistic views on physico-chemical properties of the genetic code are no longer convincing as appropriate descriptions of the abundance of non-random genetic content operators which are active in natural genetic engineering and natural genome editing. (shrink)