A Tribute to Thomas A. Sebeok

According to the approach developed by Thomas A. Sebeok (1921–2001) and his ‘global semiotics,’ semiosis and life converge. This leads to his cardinal axiom: ‘semiosis is the criterial attribute of life.’ His global approach to sign life presupposes his critique of anthropocentrism and glottocentrism. Global semiotics is open to zoosemiotics, indeed, even more broadly, biosemiotics which extends its gaze to semiosis in the whole living universe to include the realms of macro- and microorganisms. In Sebeok’s conception, the sign science is not only the study of communication in culture, but of communicative behaviour from a biosemiotic perspective.     

Semiotics of Communication: From Semiosis of Nature to Culture

Communication Studies currently undergoes a crisis of paradigms that requires an ontological review that must begin with a debate about the conditions of possibility of every communicational phenomena. In this article we argue that semiosis offers a conceptual framework that allows for the study of communication as qualitative action. Semiosis, or the action of the sign, is here defined as a fundamental process based on perception that models the world of species, creating cognition and culture. At the core of semiosis are dynamic structures that the authors have defined as ‘ontological diagrams’. The first purpose of Semiotics of Communication is to understand how these modeling systems evolve ontologically and phylogenically, producing, in the case of human culture, means of communication ever more varied and technologically advanced.     

A Biosemiotic Approach to the Problem of Structure and Agency

A human being is the simultaneous composite of several different levels of being, from atomic and subatomic to the level of complex social interaction, and these levels are nested within the individual hierarchically (lower levels giving rise to higher levels, etc.). One of the most important and influential approaches developed in the history of science has been that of systems theory and systemic thinking, in which the different levels of the hierarchy, and the interactions between those levels, are considered simultaneously. Although this model provides a comprehensive view of biological being, the transition from one level to the other is not well defined in it. Uexküll and Pauli (Advances: Journal of the Institute for 417 the Advancement of Health 3:158–174, 1986) suggested that semiosis is the translator of the events from one level to the other. From a psychological point of view, a myriad of semiotic events happen inside an individual, and it has been suggested that among other semiotic events, inner speech plays an important role in mediating personal agency. Dialogical theories of the self, Jungian psychology and hypnosis research evidence show that there is a semiotic multiplicity in human agency and consciousness, and that these multiple streams are all converge to a central semiotic singularity. I argue in this paper that by taking a biosemiotic point of view, human ‘agency’ may be defined as the ability of an individual to direct the incoming and internal streams of semioses and the ability to create an integrative and superordinate new stream of semiosis in addition to the upwardly and downwardly component ones, and how such a view might open a new door for research into the concept of human ‘personality’ and ‘agency’.     

Three Types of Semiosis

The existence of different types of semiosis has been recognized, so far, in two ways. It has been pointed out that different semiotic features exist in different taxa and this has led to the distinction between zoosemiosis, phytosemiosis, mycosemiosis, bacterial semiosis and the like. Another type of diversity is due to the existence of different types of signs and has led to the distinction between iconic, indexical and symbolic semiosis. In all these cases, however, semiosis has been defined by the Peirce model, i.e., by the idea that the basic structure is a triad of ‘sign, object and interpretant’, and that interpretation is an essential component of semiosis. This model is undoubtedly applicable to animals, since it was precisely the discovery that animals are capable of interpretation that allowed Thomas Sebeok to conclude that they are also capable of semiosis. Unfortunately, however, it is not clear how far the Peirce model can be extended beyond the animal kingdom, and we already know that we cannot apply it to the cell. The rules of the genetic code have been virtually the same in all living systems and in all environments ever since the origin of life, which clearly shows that they do not depend on interpretation. Luckily, it has been pointed out that semiosis is not necessarily based on interpretation and can be defined exclusively in terms of coding. According to the ‘code model’, a semiotic system is made of signs, meanings and coding rules, all produced by the same codemaker, and in this form it is immediately applicable to the cell. The code model, furthermore, allows us to recognize the existence of many organic codes in living systems, and to divide them into two main types that here are referred to as manufacturing semiosis and signalling semiosis. The genetic code and the splicing codes, for example, take part in processes that actually manufacture biological objects, whereas signal transduction codes and compartment codes organize existing objects into functioning supramolecular structures. The organic codes of single cells appeared in the first three billion years of the history of life and were involved either in manufacturing semiosis or in signalling semiosis. With the origin of animals, however, a third type of semiosis came into being, a type that can be referred to as interpretive semiosis because it became closely involved with interpretation. We realize in this way that the contribution of semiosis to life was far greater than that predicted by the Peirce model, where semiosis is always a means of interpreting the world. Life is essentially about three things: (1) it is about manufacturing objects, (2) it is about organizing objects into functioning systems, and (3) it is about interpreting the world. The idea that these are all semiotic processes, tells us that life depends on semiosis much more deeply and extensively than we thought. We realize in this way that there are three distinct types of semiosis in Nature, and that they gave very different contributions to the origin and the evolution of life.     

Sexual selection for syntax and kin selection for semantics: problems and prospects

The evolution of human language, and the kind of thought the communication of which requires it, raises considerable explanatory challenges. These systems of representation constitute a radical discontinuity in the natural world. Even species closely related to our own appear incapable of either thought or talk with the recursive structure, generalized systematicity, and task-domain neutrality that characterize human talk and the thought it expresses. W. Tecumseh Fitch’s proposal (2004, in press) that human language is descended from a sexually selected, prosodic proto-language that approximated its syntactic complexity, and later acquired semantics thanks to kin selection for its use as a means of pedagogical transmission, has the promise of meeting these explanatory challenges. However, Fitch’s theory raises two problems of its own: (1) according to Boyd and Richerson (1996, Proc. Br. Acad. 88: 77–93), circumstances in which pedagogy is adaptive are inevitably rare in nature, and (2) it is unlikely that our non-discursive precursors had generally systematic, task-domain neutral thoughts to communicate to their offspring. I propose solutions to these problems. Pedagogy would be favored in a population where complex rituals dominated diverse aspects of life. Prosodic proto-language could emerge as the medium of pedagogic transmission. As this medium was used to teach a greater variety of tasks, it would become increasingly general and domain neutral. The presence and importance of such a system of communication in hominid populations could then drive, via Baldwinian mechanisms, the evolution of a kind of ‘thinking for speaking’ (Slobin 1991, Pragmatics 1: 7–25) characterized by recursive structure, generalized systematicity, and task-domain neutrality.     

Semioticians Make Strange Bedfellows! Or, Once Again: “Is Language a Primary Modelling System?”

Like other sciences, biosemiotics also has its time-honoured archive, consisting of writings by those who have been invented and revered as ancestors of the discipline. One such example is Jakob von Uexküll. As to the people who ‘invented’ him, they are either, to paraphrase a French cliché, ‘agents du cosmopolitisme sémiotique’ like Thomas Sebeok, or de jure and de facto progenitor like Thure von Uexküll. In the archive is the special issue of Semiotica 42. 1 (1982) edited by the late Sebeok and introduced by Thure von Uexküll. It is in the opening essay that Thure von UexküIl tries to restore Jakob von Uexküll’s role as a precursor of semiotics by negotiating the Elder with Saussure and the linguistics-oriented ‘semiology’ in his wake. However, semiotic mapping, in the strictly ‘disciplinary’ sense, of Jakob von Uexküll is no easy task because he ‘knew neither Peirce nor Saussure and did not use their terminology’ (Thure von Uexküll 1982,2). Because Thure prefers to call the Elder’s science ‘general semiotics’ (Thure von Uexküll 1982), this paper begins by assessing Thure von Uexküll’s semiotic configuration of Jakob, probe into the force and limits of the linguistic analogy, revisit the already time-honoured debate on the primary and secondary modelling systems, which was made famous by the Moscow-Tartu semioticians in the early 1970s, but severely criticized by Sebeok and his followers. The paper engages Sebeok from several fronts, directed first at his relegation of the Saussurian linguistic model, then at his critique of the Primary Modelling System, and finally at his reservation about evolutionism in light of the current debate on gene/meme co-evolution. Paper presented at the Eighth Annual International Gatherings in Biosemiotics University of the Aegean, Syros, Greece, 23–28 June 2008     

The Symptom

The symptom (which here refers to both the clinical or ‘objective’ sign, that is, the sign that physicians believe cannot lie, and the patient’s subjective revelation of disorder, which is always considered suspect) has been relegated by a number of semioticians to a category of signs often considered of little consequence, a ‘natural’ sign signaling some specific condition or state within the body whose object stands in a strictly biological and securely determined relationship to the symptom. I believe the symptom, however, is deep, rich, and symbolic in every sense, signifying the misadventures of a body impaled by its perceptual skills and history within its own unique Umwelt or sign-world. Unfortunately, the notion of a sign which reflects biologically coded events alone suggests the body is without the ability to think, learn, and produce a story of unlimited semiosis. This should seem especially problematic to those biosemioticians who find analogic codes of much greater importance than the supposedly digital codes of DNA. I suggest that the disordered and disorderly body and the Umwelt within which it survives offer biosemioticians and those who pursue semiotic models in other disciplines an important opportunity to jointly and more fully explore the experienced world of health and illness, a world in which culture and nature are fully interpenetrated.     

Identification of a major QTL for time of initial vegetative budbreak in apple (<Emphasis Type="Italic">Malus</Emphasis> x <Emphasis Type="Italic">domestica</Emphasis> Borkh.)

In the Western Cape region of South Africa, dormancy release and the onset of growth does not occur normally in apple (Malus x domestica Borkh.) trees during spring due to the mild winter conditions experienced and fluctuations in temperatures experienced during and between winters. In this region, the application of chemicals to induce the release of dormancy forms part of standard orchard management. Increasing awareness of the environmental impact of chemical sprays and global warming has led to the demand for new apple cultivars better adapted to local climatic conditions. We report the construction of framework genetic maps in two F1 crosses using the low chilling cultivar ‘Anna’ as common male parent and the higher chill requiring cultivars ‘Golden Delicious’ and ‘Sharpe’s Early’ as female parents. The maps were constructed using 320 simple sequence repeats, including 116 new markers developed from expressed sequence tags. These maps were used to identify quantitative trait loci (QTL) for time of initial vegetative budbreak (IVB), a dormancy related characteristic. Time of IVB was assessed four times over a 6-year period in ‘Golden Delicious’ x ‘Anna’ seedlings kept in seedling bags under shade in the nursery. The trait was assessed for 3 years on adult full-sib trees derived from a cross between ‘Sharpe’s Early’ and ‘Anna’ as well as for 3 years on replicates of these seedlings obtained by clonal propagation onto rootstocks. A single major QTL for time of IVB was identified on linkage group (LG) 9. This QTL remained consistent in different genetic backgrounds and at different developmental stages. The QTL may co-localize with a QTL for leaf break identified on LG 3 by Conner et al. (1998), a LG that was, after the implementation of transferable microsatellite markers, shown to be homologous to the LG now known to be LG 9 (Kenis and Keulemans 2004). These results contribute towards a better understanding regarding the genetic control of IVB in apple and will also be used to elucidate the genetic basis of other dormancy related traits such as time of initial reproductive budbreak and number of vegetative and reproductive budbreak.     

Linkage maps of the apple ( Malus × domestica Borkh.) cvs ‘Ralls Janet’ and ‘Delicious’ include newly developed EST markers

Two apple genetic linkage maps were constructed using amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), random amplified polymorphic DNAs (RAPDs), and expressed sequence tag (EST)-derived markers in combination with a pseudo-testcross mapping strategy in which the cultivars ‘Ralls Janet’ and ‘Delicious’ were used as the respective seed parents. Mitsubakaido (Malus sieboldii) was used as the pollen parent for each of the segregating F₁ populations. Expressed sequence tag data were obtained from the random sequencing of cDNA libraries constructed from in vitro cultured shoots and maturing fruits of cv ‘Fuji’, which is the offspring of a cross between ‘Ralls Janet’ and ‘Delicious’. In addition, a number of published gene sequences were used to develop markers for mapping. The ‘Ralls Janet’ map consisted of 346 markers (178 AFLPs, 95 RAPDs, 54 SSRs, 18 ESTs, and the S locus) in 17 linkage groups, with a total length of 1082 cM, while that of ‘Delicious’ comprised 300 markers (120 AFLPs, 81 RAPDs, 64 SSRs, 32 ESTs, and the S, Rf, and MdACS-1 loci) on 17 linkage groups spanning 1031 cM. These maps are amenable to comparisons with previously published maps of ‘Fiesta’ and ‘Discovery’ (Liebhard et al., Mol Breed 10:217–241, 2002; Liebhard et al., Theor Appl Genet 106:1497–1508, 2003a) because several of the SSRs (one to three markers per linkage group) were used in all of the maps. Distorted marker segregation was observed in three and two regions of the ‘Ralls Janet’ and ‘Delicious’ maps, respectively. These regions were localized in different parts of the genome from those in previously reported apple linkage maps. This marker distortion may be dependent on the combinations of cultivars used for map construction.     

��The Climax of Reconciliation��: Transgression, Apology, Forgiveness and the Body in Conflict Resolution

According to Charles Hauss, “[i]n the last few years, reconciliation has become one of the ‘hottest’ topics in the increasingly ‘hot’ field of conflict resolution” (2003, ?1). However, despite the apparent interest in this “hot” academic topic (which is becoming increasingly warm in Canada as our own Truth and Reconciliation Commission commences), reconciliation studies have been dominated by Truth-based approaches. The restrictions of these approaches, which emphasize objectivity and rationality, often elide the body and the primacy of emotions in the reparative process. This essay begins a conversation on the role of the body and emotion in the study of reconciliation by engaging the work being done in the social sciences with contemporary trends in critical theory and literature. I argue that by looking at the fundamental role the body plays on the “road to reconciliation” we can devise a more vital approach to conflict resolution and the various processes that make it up.     

Delectable Creatures and the Fundamental Reality of Metaphor: Biosemiotics and Animal Mind

This article argues that organisms, defined by a semi-permeable membrane or skin separating organism from environment, are (must be) semiotically alert responders to environments (both Innenwelt and Umwelt). As organisms and environments complexify over time, so, necessarily, does semiotic responsiveness, or ‘semiotic freedom’. In complex environments, semiotic responsiveness necessitates increasing plasticity of discernment, or discrimination. Such judgements, in other words, involve interpretations. The latter, in effect, consist of translations of a range of sign relations which, like metaphor, are based on transfers (carryings over) of meanings or expressions from one semiotic ‘site’ to another. The article argues that what humans describe as ‘metaphor’ (and believe is something which only pertains to human speech and mind and, in essence, is ‘not real’) is, in fact, fundamental to all semiotic and biosemiotic sign processes in all living things. The article first argues that metaphor and mind are immanent in all life, and are evolutionary, and, thus, that animals certainly do have minds. Following Heidegger and then Agamben, the article continues by asking about the place of animal mind in humans, and concludes that, as a kind of ‘night science’, ‘humananimal’ mind is central to the semiotics of Peircean abduction.     

Rapid shoot regeneration in industrial ‘high starch’ sweetpotato (<Emphasis Type="Italic">Ipomoea batatas</Emphasis> L.) genotypes

Sweetpotato (Ipomoea batatas L.) is an important crop in North Carolina with annual production of 0.33 million tons, accounting for 37% of total US supply (USDA, Louisiana Farm Reporter 8(12), August 2008). To target industrial use, novel high-starch industrial-type varieties that contain more than 30% dry matter were developed by conventional breeding methods. In vitro cultures from selected genotypes were established using meristem culture. To establish regeneration procedures that could be coupled with transformation experiments, conditions for the induction of rapid shoot-organogenesis in leaf explants were compared using varying concentrations of the auxins ‘NAA’, ‘IAA’, ‘2,4-D’, and ‘4-FA’ either alone or in combination with zeatin riboside. Regeneration efficiencies, defined as the number of explants developing shoots out of the total number tested, were as high as 57% for the best genotypes, with a significant genotype-dependent response observed in all the hormone regimes evaluated. In all treatments, shoot regeneration was observed within 2 months. Our results led to the establishment of optimized in vitro regeneration procedures for the novel high-starch sweetpotato (SP) genotypes ‘DM01-158’, ‘FTA94’, ‘FT489’, and ‘PDM P4’ that are rapid and reliable.     

Building momentum for systems and synthetic biology in India

Biological systems are inherently noisy. Predicting the outcome of a perturbation is extremely challenging. Traditional reductionist approach of describing properties of parts, vis-a-vis higher level behaviour has led to enormous understanding of fundamental molecular level biology. This approach typically consists of converting genes into junk (knock-down) and garbage (knock-out) and observe how a system responds. To enable broader understanding of biological dynamics, an integrated computational and experimental strategy was formally proposed in mid 1990s leading to the re-emergence of Systems Biology. However, soon it became clear that natural systems were far more complex than expected. A new strategy to address biological complexity was proposed at MIT (Massachusetts Institute of Technology) in June 2004, when the first meeting of synthetic biology was held. Though the term ‘synthetic biology’ was proposed during 1970s (Szybalski in Control of gene expression, Plenum Press, New York, 1974), the usage of the original concept found an experimental proof in 2000 with the demonstration of a three-gene circuit called repressilator (Elowitz and Leibler in Nature, 403:335–338, 2000). This encouraged people to think of forward engineering biology from a set of well described parts.     

A role for anions in ATP synthesis and its molecular mechanistic interpretation

ATP, the ‘universal biological energy currency’, is synthesized by utilizing energy either from oxidation of fuels or from light, via the process of oxidative and photo-phosphorylation respectively. The process is mediated by the enzyme F₁F₀-ATP synthase, using the free energy of ion gradients in the final energy catalyzing step, i.e., the synthesis of ATP from ADP and inorganic phosphate (P_i). The details of the molecular mechanism of ATP synthesis are among the most important fundamental issues in biology and hence need to be properly understood. In this work, a role for anions in making ATP has been found. New experimental data has been reported on the inhibition of ATP synthesis at nanomolar concentrations by the potent, specific anion channel blockers 4,4′-diisothiocyanostilbene-2, 2′-disulphonic acid (DIDS) and tributyltin chloride (TBTCl). Based on these inhibition studies, attention has been drawn to anion translocation (in addition to proton translocation) as a requirement for ATP synthesis. The type of inhibition has been quantified and an overall kinetic scheme for mixed inhibition that explains the data has been evolved. The experimental data and the type of inhibition found have been interpreted in the light of the torsional mechanism of energy transduction and ATP synthesis (Nath J Bioenerg Biomembr 42:293–300, 2010a; J Bioenerg Biomembr 42:301–309, 2010b). This detailed and unified mechanism resolves long-standing problems and inconsistencies in the first theories (Slater Nature 172:975–978, 1953; Williams J Theor Biol 1:1–17, 1961; Mitchell Nature 191:144–148, 1961; Mitchell Biol Rev 41:445–502, 1966), makes several novel predictions that are experimentally verifiable (Nath Biophys J 90:8–21, 2006a; Process Biochem 41:2218–2235, 2006b), and provides us with a new and fruitful paradigm in bioenergetics. The interpretation presented here provides intelligent answers to the unexplained existing results in the literature. It is shown that mechanistic interpretation of the experimental data requires substantial addition to available conceptual foundations such that present concepts, theories, and mechanisms must be revised.     

Comparison of the developmental stages of some European allocreadiid trematode species and a clarification of their life-cycles based on ITS2 and 28S sequences

Genetic data were used to examine the diversity in some allocreadiid trematodes. Nuclear ribosomal DNA (ITS2 and partial sequences of 5.8S and 28S) was sampled from sexual adult and ‘larval’ stages. From these and previous reference datasets phylogenetic trees were constructed. The results uncovered genetically distinct lineages within Bunodera luciopercae (Müller, 1776), suggesting that the two Palaearctic subspecies, B. l. luciopercae and B. l. acerinae Roitman & Sokolov, 1999, and Nearctic B. luciopercae from Perca flavescens may represent distinct species with a restricted host-specificity. Identical rDNA was revealed for the sexual adult of B. l. acerinae and ‘larval’ B. luciopercae described by Wiśniewski (1958). An unexpected match between the rDNA sequences of adult B. l. luciopercae and ‘larval’ Allocreadium isoporum (sensu Wiśniewski, 1958) was also detected. The adult A. isoporum (Looss, 1894) differs significantly from the ‘larval’ A. isoporum, the level of rDNA sequence divergence between them (8.6 % for 5.8S-ITS2-28S sequences and 6.26% for 28S) being consistent with the level expected for intergeneric variation. These results revealed the possible existence of a cryptic species complex within the nominal species B. luciopercae and a clear need for reconsideration of some of the accepted, but largely untested, tenets regarding allocreadiid life-cycles.     

Inflammation,Aging, and Cancer: Tumoricidal Versus Tumorigenesis of Immunity

Acute inflammation is a highly regulated defense mechanism of immune system possessing two well-balanced and biologically opposing arms termed apoptosis (‘Yin’) and wound healing (‘Yang’) processes. Unresolved or chronic inflammation (oxidative stress) is perhaps the loss of balance between ‘Yin’ and ‘Yang’ that would induce co-expression of exaggerated or ‘mismatched’ apoptotic and wound healing factors in the microenvironment of tissues (‘immune meltdown’). Unresolved inflammation could initiate the genesis of many age-associated chronic illnesses such as autoimmune and neurodegenerative diseases or tumors/cancers. In this perspective ‘birds’ eye’ view of major interrelated co-morbidity risk factors that participate in biological shifts of growth-arresting (‘tumoricidal’) or growth-promoting (‘tumorigenic’) properties of immune cells and the genesis of chronic inflammatory diseases and cancer will be discussed. Persistent inflammation is perhaps a common denominator in the genesis of nearly all age-associated health problems or cancer. Future challenging opportunities for diagnosis, prevention, and/or therapy of chronic illnesses will require an integrated understanding and identification of developmental phases of inflammation-induced immune dysfunction and age-associated hormonal and physiological readjustments of organ systems. Designing suitable cohort studies to establish the oxido-redox status of adults may prove to be an effective strategy in assessing individual’s health toward developing personal medicine for healthy aging.     

A chimeric <Emphasis Type="Italic">Rfo</Emphasis> gene generated by intergenic recombination cosegregates with the fertility restorer phenotype for cytoplasmic male sterility in radish

In this work, we have identified a chimeric pentatricopeptide repeat (PPR)-encoding gene cosegregating with the fertility restorer phenotype for cytoplasmic male sterility (CMS) in radish. We have constructed a CMS-Rf system consisting of sterile line ‘9802A2’, maintainer line ‘9802B2’ and restorer line ‘2007H’. F₂ segregating population analysis indicated that male fertility is restored by a single dominant gene in the CMS-Rf system described above. A PPR gene named Rfoc was found in the restorer line ‘2007H’. It cosegregated with the fertility restorer in the F₂ segregating population which is composed of 613 fertile plants and 187 sterile plants. The Rfoc gene encodes a predicted protein 687 amino acids in length, comprising 16 PPR domains and with a putative mitochondrial targeting signal. Sequence alignment showed that recombination between the 5′ region of Rfob (EU163282) and the 3′ region of PPR24 (AY285675) resulted in Rfoc, indicating a recent unequal crossing-over event between Rfo and PPR24 loci at a distance of 5.5 kb. The sterile line ‘9802A2’ contains the rfob gene. In the F₂ population, Rfoc and rfob were observed to fit a segregation ratio 1:2:1 showing that Rfoc was allelic to Rfo. Previously we have reported that a fertile line ‘2006H’, which carries the recessive rfob gene, is able to restore the male fertility of CMS line ‘9802A1’ (Wang et al. in Theor Appl Genet 117:313–320, 2008). However, here when conducting a cross between the fertile line ‘2006H’ and CMS line ‘9802A2, the resulting plants were male sterile, which shows that sterile line ‘9802A2’ possesses a different nuclear background compared to ‘9802A1’. Based on these results, the genetic model of fertility restoration for radish CMS is also discussed.     

Assessing freshwater use impacts in LCA,part 2: case study of broccoli production in the UK and Spain

Background, aim and scope  

Milà i Canals et al. (Int J Life Cycle Ass 14(1):28-42, 2009) referred to as ‘Part 1’ in this paper) showed that impacts associated with use of freshwater must be treated more rigorously than is usual in life cycle assessment (LCA), going beyond the conventional consideration only of ‘blue’ water (i.e. irrigation and other abstractions), and suggested an operational method to include the impacts on freshwater ecosystems (freshwater ecosystem impact) and abiotic resource depletion (freshwater depletion). The inclusion of water-related impacts in LCA is of paramount importance, particularly for agricultural systems due to their large water consumption worldwide. A case study of UK consumption of broccoli grown in the UK and Spain is presented here to illustrate the method suggested in Part 1.