The Forbidden Signs

While the field of semiotics has been active since it was started by Peirce, it appears like the last decade has been especially productive with a number of important new concepts being developed within the biosemiotics community. The novel concept of the Semiotic scaffold by Hoffmeyer is an important addition that offers insight into the hardware requirements for bio-semiosis. As any type of semiosis must be dependent upon Semiotic scaffolds, I recently argued that the process of semiosis has to be divided into two separate processes of sign establishment and sign interpretation, and that misalignment between the two processes result in faulty sign interpretation and over-signification. Such faulty signs were forbidden in the sign classification system of Peirce, so I defined them as forbidden signs. Here I present an analysis of the forbidden sign categories with examples from Occult semiotics. I also show that biological semiosis offers examples of forbidden signs, where the faulty interpretation of signs may lead to decimation of whole evolutionary lines of organisms. A new concept of Evolutionary memory which is applicable to both human and biological semiosis is explained as the combination of two processes; one leading to diversity generation within semiotic scaffolds followed by a second process of decimation of faulty signs during selection in specific learning environments. The analysis suggests that forbidden signs are always used as early stages in the iterative sign establishment process during semiosis.     

The Great Chain of Semiosis. Investigating the Steps in the Evolution of Semiotic Competence

Based on the conception of life and semiosis as co-extensive an attempt is given to classify cognitive and communicative potentials of species according to the plasticity and articulatory sophistication they exhibit. A clear distinction is drawn between semiosis and perception, where perception is seen as a high-level activity, an integrated product of a multitude of semiotic interactions inside or between bodies. Previous attempts at finding progressive trends in evolution that might justify a scaling of species from primitive to advanced levels have not met with much success, but when evolution is considered in the light of semiosis such a scaling immediately catches the eye. The main purpose of this paper is to suggest a scaling of this progression in semiotic freedom into a series of distinct steps. The elleven steps suggested are: 1) molecular recognition, 2) prokaryote-eukaryote transformation (privatization of the genome), 3) division of labor in multicellular organisms (endosemiosis), 4) from irritability to phenotypic plasticity, 5) sense perception, 6) behavioral choice, 7) active information gathering, 8) collaboration, deception, 9) learning and social intelligence, 10) sentience, 11) consciousness. In light of this, the paper finally discusses the conceptual framework for biosemiotic evolution. The evolution of biosemiotic capabilities does not take the form of an ongoing composition of simple signs (icons, indices, signals, etc.) into composite wholes. Rather, it takes the shape of the increasing subdivision and control of a primitive, holophrastic perception-action circuit already committed to “proto-propositions” (dicisigns) reliably guiding action already in the most primitive species.     

Just How Emergent is the Emergence of Semiosis?

Studying the origin of semiosis is a task obscured by terminological and metaphysical issues which create an ambiguous set of definitions for biosemiotics when referring to the concept of emergence. The question is, how emergent can semiosis be? And what are the conditions for semiosis to be an emergent of a certain type? This paper will attempt to briefly deal with the general terminology of emergence from a philosophical point of view and will discuss the characterization of semiosis as an emergent phenomenon based on the distinctions made by Bedau, Kim and Chalmers. Accordingly, we will consider the possibility of strong and weak emergence in an attempt to bring some clarity to what it means for something in biosemiotics to be an emergent and how the philosophical concepts play out when applied to biosemiotic research. In inquiring into the metaphysical status of semiosis, we change our semiotic theories to correspond to the assumptions contained in the elementary objects of our theories. This being the case, the way semiosis–the constitutive element that it is for semiotics–is taken to be with regards to its possible ontology, will conduct to different research objects for the long-term investigation of its origins and necessary conditions.     

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.     

Autopoiesis and Interpretive Semiosis

Translation has long been viewed as ‘code-switching’ either within or between languages. Hence, most translation discussions center on its linguistic and cultural aspects. However, the fundamental mechanism of ‘translation as interpretative semiosis’ has yet to be studied with appropriate rigor. Susan Petrilli (2008) has identified ‘iconicity’ as the key that enables translative semiosis. Nevertheless, as her model is restricted to a discussion of literary translation activity in verbal sign systems, a fundamental mechanism to explain translation as interpretative semiosis is still needed. By analyzing the interactions between the source sign (the translated) and the target sign (the translatant) in the translating process, it can be discerned that Humberto Maturana’s notion of autopoiesis may provide some crucial insights into translative semiosis. By identifying the autopoietic nature of translation, that is, the interlocked structural coupling between the Translated and Translatant, translation is no longer the ‘one-to-one-correspondence’ between sign systems, but rather a recursive process of interpretation—an interpretive semiosis. Moreover, it is by this autopoietic, self-productive mechanism of translation that I would suggest translation becomes a recursive generation of new inter-connections between semiotics systems.     

A novel plant protein-disulfide isomerase involved in the oxidative folding of cystine knot defense proteins

We have isolated a protein-disulfide isomerase (PDI) from Oldenlandia affinis (OaPDI), a coffee family (Rubiaceae) plant that accumulates knotted circular proteins called cyclotides. The novel plant PDI appears to be involved in the biosynthesis of cyclotides, since it co-expresses and interacts with the cyclotide precursor protein Oak1. OaPDI exhibits similar isomerase activity but greater chaperone activity than human PDI. Since domain c of OaPDI is predicted to have a neutral pI, we conclude that this domain does not have to be acidic in nature for PDI to be a functional chaperone. Its redox potential of -157 +/- 4 mV supports a role as a functional oxidoreductase in the plant. The mechanism of enzyme-assisted folding of plant cyclotides was investigated by comparing the folding of kalata B1 derivatives in the presence and absence of OaPDI. OaPDI dramatically enhanced the correct oxidative folding of kalata B1 at physiological pH. A detailed investigation of folding intermediates suggested that disulfide isomerization is an important role of the new plant PDI and is an essential step in the production of insecticidal cyclotides. The nucleotide sequence(s) reported in this paper have been submitted to the GenBank/EBI Data Bank with accession number(s) 911777.     

The priming of periodical cicada life cycles

Periodical cicadas in the genus Magicicada have unusually long life cycles for insects, with periodicities of either 13 or 17 years. Biologists have explained the evolution of these prime number period lengths in terms of resource limitation, enemy avoidance, hybridization and climate change. Here, I question two aspects of these explanations: that the origin of the life cycles was associated with Pleistocene ice age events, and that they evolved from shorter life cycles through the lengthening of nymphal stages in annual increments. Instead, I suggest that these life cycles evolved earlier than the Pleistocene and involved an abrupt transition from a nine-year to a 13-year life cycle, driven, in part, by interspecific competition.     

Plant mitochondria actively import DNA via the permeability transition pore complex

Plant mitochondria are remarkable with respect to their content in foreign, alien and plasmid-like DNA, raising the question of the transfer of this information into the organelles. We demonstrate the existence of an active, transmembrane potential-dependent mechanism of DNA uptake into plant mitochondria. The process is restricted to double-strand DNA, but has no obvious sequence specificity. It is most efficient with linear fragments up to a few kilobase pairs. When containing appropriate information, imported sequences are transcribed within the organelles. The uptake likely involves the voltage-dependent anion channel and the adenine nucleotide translocator, i.e. the core components of the mitochondrial permeability transition pore complex in animal cells, but it does not rely on known mitochondrial membrane permeabilization processes. We conclude that DNA import into plant mitochondria might represent a physiological phenomenon with some functional relevance.     

Diversity of biological rhythm and food web stability

How ecosystem biodiversity is maintained remains a persistent question in the field of ecology. Here, I present a new coexistence theory, i.e. diversity of biological rhythm. Circadian, circalunar and circannual rhythms, which control short- and long-term activities, are identified as universal phenomena in organisms. Analysis of a theoretical food web with diel, monthly and annual cycles in foraging activity for each organism shows that diverse biological cycles play key roles in maintaining complex communities. Each biological rhythm does not have a strong stabilizing effect independently but enhances community persistence when combined with other rhythms. Biological rhythms also mitigate inherent destabilization tendencies caused by food web complexity. Temporal weak interactions due to hybridity of multiple activity cycles play a key role toward coexistence. Polyrhythmic changes in biological activities in response to the Earth''s rotation may be a key factor in maintaining biological communities.     

Progress in understanding the role of microtubules in plant cells

Microtubules have long been known to play a key role in plant cell morphogenesis, but just how they fulfill this function is unclear. Transverse microtubules have been thought to constrain the movement of cellulose synthase complexes in order to generate transverse microfibrils that are essential for elongation growth. Surprisingly, some recent studies demonstrate that organized cortical microtubules are not essential for maintaining or re-establishing transversely oriented cellulose microfibrils in expanding cells. At the same time, however, there is strong evidence that microtubules are intimately associated with cellulose synthesis activity, especially during secondary wall deposition. These apparently conflicting results provide important clues as to what microtubules do at the interface between the cell and its wall. I hypothesize that cellulose microfibril length is an important parameter of wall mechanics and suggest ways in which microtubule organization may influence microfibril length. This concept is in line with current evidence that links cellulose synthesis levels and microfibril orientation. Furthermore, in light of new evidence showing that a wide variety of proteins bind to microtubules, I raise the broader question of whether a major function of plant microtubules is in modulating signaling pathways as plants respond to sensory inputs from the environment.     

Spontaneous urban vegetation as an indicator of soil functionality and ecosystem services

Questions

Our study focused on spontaneous vegetation in urban greenspaces in a Mediterranean city with the aim of relating plant community properties with ecological services along soil disturbance gradients. We asked which plant communities have the greatest plant biodiversity and soil carbon storage and the best-performing nutrient cycles and water regulation.

Location

Madrid City (Central Spain).

Methods

We studied four types of plant communities following soil disturbance gradients: vegetation on trampled soils, roadside vegetation, annual grasslands and perennial forbs. Regarding vegetation, we studied plant composition and productivity, plant diversity, plant growth forms and functional groups. Regarding soils, we determined soil organic carbon (TOC), available nutrients, the activity of seven enzymes relating to the main macronutrient cycles, and physical properties such as bulk density (BD) and soil water-holding capacity (WHC). We used one-way ANOVA to determine the influence of the plant community type on both soil and vegetation variables. Canonical correspondence analysis was performed to interpret the relationships between plant species assemblages with environmental gradients.

Results

Perennial forbs showed greater biomass and developed on soils with the greatest TOC and available phosphorus. Annual grasslands displayed the highest plant diversity. Roadside vegetation developed on soils with higher phenoloxidase activity when compared to vegetation on trampled soils and annual grasslands. Vegetation on trampled soils developed on soils with lower WHC, lower beta-glucosidase, arylamidase and phosphatase activities and higher BD when compared to perennial forbs. Plant community distribution followed gradients most significantly associated with soil organic matter content, soil compaction and nutrient cycling performance.

Conclusions

We conclude that plant communities are good indicators of ecosystem function and services which are unevenly distributed throughout urban habitats. The management in Mediterranean unmaintained urban greenspaces should be aimed at avoiding soil compaction to promote biodiversity, carbon storage and water regulation.     

The System of Interpretance, Naturalizing Meaning as Finality

A materialist construction of semiosis requires system embodiment at particular locales, in order to function as systems of interpretance. I propose that we can use a systemic model of scientific measurement to construct a systems view of semiosis. I further suggest that the categories required to understand that process can be used as templates when generalizing to biosemiosis and beyond. The viewpoint I advance here is that of natural philosophy—which, once granted, incurs no principled block to further generalization all the way to pansemiotics—nearer to Peirce’s own very general perspective. This project requires a hylozooic framework, which I present in the form of a specification hierarchy, whereby physical dynamics subsume all other transactions at more highly developed integrative levels. The upshot of the paper is a proposal that meanings can be assimilated most generally to final causes.     

Examination of subunit interaction in human ADH: carboxymethylation of the heterodimer beta 2 gamma 1.

Conflicting results have been obtained on whether the subunits of the human dimeric enzyme alcohol dehydrogenase interact kinetically. To examine this question, chemical modification by iodoacetate was used to selectively inactivate the beta 2 subunit of the heterodimeric isozyme beta 2 gamma 1. Subsequent studies of the modified beta 2 gamma 1 which, presumably, has only one functional active site per dimeric molecule, indicate that it is still active. Moreover, the properties of this hybrid are similar to those of the unmodified subunit. From these results, it is fair to conclude that the individual subunits of alcohol dehydrogenase contribute to the activity of the dimeric isozymes in an independent manner.     

Subliminal instrumental conditioning demonstrated in the human brain

How the brain uses success and failure to optimize future decisions is a long-standing question in neuroscience. One computational solution involves updating the values of context-action associations in proportion to a reward prediction error. Previous evidence suggests that such computations are expressed in the striatum and, as they are cognitively impenetrable, represent an unconscious learning mechanism. Here, we formally test this by studying instrumental conditioning in a situation where we masked contextual cues, such that they were not consciously perceived. Behavioral data showed that subjects nonetheless developed a significant propensity to choose cues associated with monetary rewards relative to punishments. Functional neuroimaging revealed that during conditioning cue values and prediction errors, generated from a computational model, both correlated with activity in ventral striatum. We conclude that, even without conscious processing of contextual cues, our brain can learn their reward value and use them to provide a bias on decision making.     

Differential effects of static and cyclic stretching during elastase digestion on the mechanical properties of extracellular matrices.

Enzyme activity plays an essential role in many physiological processes and diseases such as pulmonary emphysema. While the lung is constantly exposed to cyclic stretching, the effects of stretch on the mechanical properties of the extracellular matrix (ECM) during digestion have not been determined. We measured the mechanical and failure properties of elastin-rich ECM sheets loaded with static or cyclic uniaxial stretch (40% peak strain) during elastase digestion. Quasistatic stress-strain measurements were taken during 30 min of digestion. The incremental stiffness of the sheets decreased exponentially with time during digestion. However, digestion in the presence of static stretch resulted in an accelerated stiffness decrease, with a time constant that was nearly 3 x smaller (7.1 min) than during digestion alone (18.4 min). These results were supported by simulations that used a nonlinear spring network model. The reduction in stiffness was larger during static than cyclic stretch, and the latter also depended on the frequency. Stretching at 20 cycles/min decreased stiffness less than stretching at 5 cycles/min, suggesting a rate-dependent coupling between mechanical forces and enzyme activity. Furthermore, pure digestion reduced the failure stress of the sheets from 88 +/- 21 kPa in control to 29 +/- 15 kPa (P < 0.05), while static and cyclic stretch resulted in a failure stress of 7 +/- 5 kPa (P < 0.05). We conclude that not only the presence but the dynamic nature of mechanical forces have a significant impact on enzyme activity, hence the deterioration of the functional properties of the ECM during exposure to enzymes.     

Locomotor activity and body temperature rhythms in the Mahali mole-rat (C. h. mahali): The effect of light and ambient temperature variations

African mole-rats (family: Bathyergidae) are strictly subterranean mammals that reside in extensive networks of underground tunnels. They are rarely, if ever, exposed to light and experience muted temperature ranges. Despite these constant conditions, the presence of a functional circadian clock capable of entraining to external light cues has been reported for a number of species. In this study, we examine a social mole-rat species, Cryptomys hottentotus mahali, to determine if it possesses a functional circadian clock that is capable of perceiving light and ambient temperature cycles, and can integrate these cues into circadian rhythms of locomotor activity and core body temperature. Eight male and eight female, non-reproductive individuals were subjected to six cycles of varying light and temperature regimes. The majority of the individuals displayed daily rhythms of locomotor activity and body temperature that are synchronised to the external light and temperature cycles. Furthermore, endogenous rhythms of both locomotor activity and core body temperature were displayed under constant conditions. Thus, we can conclude that C. h. mahali possesses a functional circadian clock that can integrate external light and temperature cues into circadian rhythms of locomotor activity and core-body temperature.     

Neuroeconomics

This paper introduces an emerging transdisciplinary field known as neuroeconomics. Neuroeconomics uses neuroscientific measurement techniques to investigate how decisions are made. First, I present a basic overview of neuroanatomy and explain how brain activity is measured. I then survey findings from the neuroeconomics literature on acquiring rewards and avoiding losses, learning, choice under risk and ambiguity, delay of gratification, the role of emotions in decision-making, strategic decisions and social decisions. I conclude by identifying new directions that neuroeconomics is taking, including applications to public policy and law.     

Functional–structural models optimize the placement of foliage units for multiple whole-canopy functions

I present examples of plant functional–structural models (FSMs) that are used to evaluate how foliage units affect whole-canopy functions, and I show that multi-criteria optimization is an effective tool for these models. FSMs produce plant structures through the repeated application of a set of rules for the placement of foliage units. The models are blind (rules are the same regardless of dynamic simulation conditions), sighted (rules change with interference from other foliage units) or self-regulatory (rules change depending on the conditions of the simulation, i.e., internal conditions). In the examples presented, the models are used to optimize plant morphology for one or more measures of plant performance; these measures include movement of materials and associated hydraulic functions, foliage display, light interception and net carbon, mechanical support and stability, and reproductive success. It is consistently found that no morphology is optimal for any single measure of plant performance, and the rules for plant development are not stationary in space and time. In multi-criteria optimization, alternative morphologies are compared against multiple measures of plant performance; these are optimized simultaneously using Pareto optimality, which yields the set of mutually co-dominant solutions not dominated by any other solution. Two solutions are considered to be mutually co-dominant if improvement with respect to one criterion is at the expense of another criterion. I conclude that multi-criteria optimization is an essential tool for the use of FSMs to relate processes at the foliage level to whole-canopy function and to explain the structural diversity of old-growth forests.     

Cyclic electron flow around photosystem I in C(3) plants. In vivo control by the redox state of chloroplasts and involvement of the NADH-dehydrogenase complex

Cyclic electron flow around photosystem (PS) I has been widely described in vitro in chloroplasts or thylakoids isolated from C(3) plant leaves, but its occurrence in vivo is still a matter of debate. Photoacoustic spectroscopy and kinetic spectrophotometry were used to analyze cyclic PS I activity in tobacco (Nicotiana tabacum cv Petit Havana) leaf discs illuminated with far-red light. Only a very weak activity was measured in air with both techniques. When leaf discs were placed in anaerobiosis, a high and rapid cyclic PS I activity was measured. The maximal energy storage in far-red light increased to 30% to 50%, and the half-time of the P(700) re-reduction in the dark decreased to around 400 ms; these values are comparable with those measured in cyanobacteria and C(4) plant leaves in aerobiosis. The stimulatory effect of anaerobiosis was mimicked by infiltrating leaves with inhibitors of mitochondrial respiration or of the chlororespiratory oxidase, therefore, showing that changes in the redox state of intersystem electron carriers tightly control the rate of PS I-driven cyclic electron flow in vivo. Measurements of energy storage at different modulation frequencies of far-red light showed that anaerobiosis-induced cyclic PS I activity in leaves of a tobacco mutant deficient in the plastid Ndh complex was kinetically different from that of the wild type, the cycle being slower in the former leaves. We conclude that the Ndh complex is required for rapid electron cycling around PS I.