Dialog with black box: using Information Theory to study animal language behaviour

In this review, three main experimental approaches for studying animal language behaviour are compared: (1) direct decoding of animals’ communication, (2) the use of intermediary languages to communicate with animals and (3) application of ideas and methods of the Information Theory for studying quantitative characteristics of animal communication. Each of the three methodological approaches has its specific power and specific limitations. Deciphering animals’ signals reveals a complex picture of natural communication in its evolutionary perspective but only fragmentary because of many methodological barriers, among which low repeatability of standard living situations seems to be a bottleneck. Language-training experiments are of great help for discovering potentials of animal language behaviour but leaves characteristics of their natural communications unclear. The use of the methods of Information Theory is based on measuring the time duration that animals spend on transmitting messages of definite information content and complexity. This approach, although does not reveal the nature of animals’ signals, provides a new dimension for studying important characteristics of natural communication systems, which have not been available before. First of all, this approach enables explorers of animals’ language behaviour to obtain knowledge just about the ability of subjects for transferring meaningful messages. Besides, the important properties of animal communication and intelligence can be evaluated such as the rate of information transmission, the complexity of transferred information and potential flexibility of communication systems.     

Reflexions sur l'usage,en biologie,de la theorie de l'information

For living beings, information is as fundamental as matter or energy. In this paper we show: a) inadequacies of quantitative theories of information, b) how a qualitative analysis leads to a classification of information systems and to a modelling of intercellular communication. From a quantitative point of view, the application in biology of information theories borrowed from communication techniques proved to be disappointing. These theories ignore deliberately the significance of messages, and do not give any definition of information. They refer to quantities, based upon arbitrarily defined probabilistic events. Probability is subjective. The receiver of the message needs to have ‘meta-knowledge’ of the events. The quantity of information depends on language, coding, and arbitrary definition of disorder. The suggested objectivity is fallacious. In common language, the word ‘information’ is synonymous with knowledge of order. Following common sense a message (letters, coded signals, etc.) is information just in case it is interpretable, i.e.if it fits to a previously acquired meaning (the words of an available language, etc.). The consequence is that calculation of quantities in the sense of Shannon can be used for transmissions, but it is itself meaningless (has no significance). In linguistics and semantics, information is composed of a ‘signifier’, a physical medium (letters, coded signals, etc.), and a ‘signified’ or significance. The nature of information is complex. The laws of linguistics and semantics are valid not only at the human, organismic level, but also at the cellular and molecular level. The physiology of sensations gives us many examples for application of a concept of information An electromagnetic wave of 0,7% give us the sensation of a red colour. Sensations have no physical reality. They are purely subjective. At the cellular level communication operates by means of chemical messengers (first messengers), which generally do not penetrate the plasmic membrane. Specific captors operate as transductors: external factors are converted into secondary messengers (cyclic AMP, Ca ion, etc.). Sometimes, electric signals (like depolarization waves) may also play a part in the intercellular communication. Such processes are characterized by changes in a sequence of different molecules carried by a physical signal. What is transmitted is themeaning of the message (significance) which can be memorized by the cell, providing a possible following use. At the molecular level one can find also the processes of linguistic nature. We know that the significance of a word is changed with changing the order of letters (ADD→DAD, etc.). In the same way bases C and U are coding for serine (UCC), leucine (CUC) or proline (CCU). Here, amino-acids express the significance. In spite of the fact that this key-lock mechanism may explain many reactions, the examples prove that other elements are necessary for understanding the information. The living cell is the receiver. The message actualizes only previously learned and memorized significances or actions (trigger effect). Significance is not an emergent property of the shape of the message. It depends on the receiver and the transmitter. A word can have more than one meaning. Similarly, a messenger can order different physiological responses: muscular tension, hormonal secretion, etc.. Thus a chemical messenger is a signal which is identified and interpreted by the receiver, depending upon specific languages and previous learning. These views are in harmony with immunological and Jerne's theory (of idiotypical net). The above mentioned considerations led the author to propose thetheory of data transfer, which takes into account significance. In this theory the quantity of information is the product of the probabilistic recognition of message and the value of significance as determined by its semantic level. (See: Acta biotheoretica vol. 41 No 1/2 June 1993.) The complex nature of information asks to propose a qualitative classification with respect to thematerial support and thesignificance.

1. The material support may be linear in time (sequential reading, ADN translation)-The material support may be referred to non-temporally (drawings, logos, holograms) (Reading is instantaneous)-The material support may be in circulation, or in stock.
2. The significance may be local (tissues, organs) or general (organisms). Asignificance may be a command to be executed (imperative, conditional order) or knowledge to bememorized. The purpose of significance may be a coding for space (for morphology) or for time (ontogeny, ageing).

Conclusion: Information cannot any longer be regarded as an object. Its nature is complex, at all levels of a living being. At the molecular level to memorize an information by modification of a molecule is comparable with writing words on a diary. The key-lock process does not suppress the question of the interpretation, i.e. relations existing between the shape of a microscopic element as a molecule, and its macroscopic effect, as an antenna or a leg. There are still many unclear points in these relations, e.g. the sweet taste of molecules of tomatine and monelline. The abstract nature of significance which at the human level is concerned to mental processes, is not only a philosophical problem. In fact, there is a hypothesis based on quantum mechanics which allows to consider a physical nature of significance. In any case, the important conclusion is that significance in bio-information must be considered in relation to the message-receiver. The receiver must no longer be considered a passive one. The qualitative classification of information will allow an understanding of circulation of information in organisms and between cells.     

Potential versus actual contribution of vertical transmission to pathogen fitness

Theory predicts that virulent parasites cannot be maintained at high prevalence if they are only vertically transmitted. However, parasites with high rates of vertical transmission that cause severe reduction in host fitness have been reported. Atkinsonella hypoxylon is a fungal pathogen capable of both vertical and horizontal transmission that drastically reduces its host''s fitness. In contrast with theoretical predictions, field and laboratory observations suggested that the primary mechanism of transmission was vertical. Using randomly amplified polymorphic DNA markers, we investigated the effective contribution of vertical and horizontal transmission to the genetic structure of three natural populations of A. hypoxylon. We found high genotypic diversity and low linkage disequilibrium, indicating that most established genotypes are derived from horizontally transmitted, sexual spores. The low contribution of vertical transmission to the parasite''s fitness despite its high potential might be due to lower establishment of cleistogamous seeds (through which vertical transmission occurs) or lower vigour of vertically transmitted fungal genotypes. Low establishment of vertically infected hosts might explain the persistence of virulent parasites with high apparent vertical transmission. Our results suggest that caution must be taken when using the potential for vertical transmission to make predictions about the evolution of parasite virulence.     

Rigorous and extended application of information theory to the afferent visual system of the cat. I. Basic concepts

Information theory is applied to data from microelectrode recordings of the cat's afferent visual system in a manner more general than hitherto usual. It is shown that it is not necessary to know the particular neuronal code for information calculations by taking the signal itself as the symbols. Uncontrollable errors thus can be avoided. It is further shown that by this approach the dynamical behaviour of the system is fully considered for information transfer. Quantities are defined to exhibit the time course of transmitted information.     

The trouble with memes

Memes are hypothetical cultural units passed on by imitation; although nonbiological, they undergo Darwinian selection like genes. Cognitive study of multimodular human minds undermines memetics: unlike in genetic replication, high-fidelity transmission of cultural information is the exception, not the rule. Constant, rapid "mutation" of information during communication generates endlessly varied creations that nevertheless adhere to modular input conditions. The sort of cultural information most susceptible to modular processing is that most readily acquired by children, most easily transmitted across individuals, most apt to survive within a culture, most likely to recur in different cultures, and most disposed to cultural variation and elaboration.     

纠错编码理论在生物信息处理领域的应用

根据生物系统中存在信息传递并且需要高度稳定性的特性,现代通信工程中的纠错编码理论被应用于生物遗传序列的研究和测试系统的设计。该文介绍其分析基础和现有应用并对未来研究展望。     

A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown. Here, we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance. To reduce the environmental factors that might mask genetic factors, the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with a reduced complexity synthetic bacterial community composed of seven strains representing the most abundant phyla in the phyllosphere. From a panel of 55 plant mutants with alterations in the surface structure, cell wall, defense signaling, secondary metabolism, and pathogen recognition, a small number of single host mutations displayed an altered microbiota composition and/or abundance. Host alleles that resulted in the strongest perturbation of the microbiota relative to the wild-type were lacs2 and pec1. These mutants affect cuticle formation and led to changes in community composition and an increased bacterial abundance relative to the wild-type plants, suggesting that different bacteria can benefit from a modified cuticle to different extents. Moreover, we identified ein2, which is involved in ethylene signaling, as a host factor modulating the community''s composition. Finally, we found that different Arabidopsis accessions exhibited different communities, indicating that plant host genetic factors shape the associated microbiota, thus harboring significant potential for the identification of novel plant factors affecting the microbiota of the communities.     

Factors Affecting Geographic Variation in Echolocation Calls of the Endemic Myotis davidii in China

The sensory drive hypothesis of speciation predicts that divergence in communication systems will occur when environments differ and that this sensory divergence can ultimately promote speciation. The factors affecting geographic evolution in acoustic signals remain poorly understood, especially in the contexts of high gene flow. This study investigated variation patterns in peak frequency emitted by the Chinese endemic Myotis davidii on a broad geographic scale by evaluating the relative importance of morphological, environmental, geographic, and genetic variables. Significant variation in peak frequency was observed among regions, but peak frequencies among populations within region had some percentage of similarity. Differences in peak frequency were not associated with morphological difference, genetic structure, and geographic distance among regions, which suggested that peak frequency divergences in M. davidii were not the primary driver of regions' isolation in a context of weak gene flow. Within the Middle East Plain (MEP), one of the regions delineated in this study, peak frequency differences of M. davidii were not significantly correlated with genetic distance and geographic distance among populations, suggesting that peak frequency was not be subject to cultural drift within MEP. Our results provide evidence that geographic variation in echolocation call design may evolve as a consequence of local adaptation to climate conditions.     

Revisiting intracellular calcium signaling semantics

Cells use intracellular free calcium concentration changes for signaling. Signal encoding occurs through both spatial and temporal modulation of the free calcium concentration. The encoded message is detected by an ensemble of intracellular sensors forming the family of calcium-binding proteins (CaBPs) which must faithfully translate the message using a new syntax that is recognized by the cell. The cell is home to a significant although limited number of genes coding for proteins involved in the signal encoding and decoding processes. In a cell, only a subset of this ensemble of genes is expressed, leading to a genetic regulation of the calcium signal pathways. Calmodulin (CaM), the most ubiquitous expressed intracellular calcium-binding protein, plays a major role in calcium signal translation. Similar to a hub, it is central to a large and finely tuned network, receiving information, integrating it and dispatching the cognate response. In this review, we examine the different steps starting with an external stimulus up to a cellular response, with special emphasis on CaM and the mechanism by which it decodes calcium signals and translates it into exquisitely coordinated cellular events. By this means, we will revisit the calcium signaling semantics, hoping that we will ease communication between scientists dealing with calcium signals in different biological systems and different domains.     

Mononuclear-cell-derived microparticles attenuate endothelial inflammation by transfer of miR-142-3p in a CD39 dependent manner

Plasma microparticles (MP) bear functional active ectonucleotidases of the CD39 family with implications in vascular inflammation. MP appear to be able to fuse with cells and transfer genetic information. Here, we tested whether levels of different immunomodulatory microRNAs (miRs) in plasma MP are modulated by CD39 after experimental hepatectomy. We further investigated whether horizontal transfer of miR-142-3p between mononuclear (MNC) and endothelial cells via MP is regulated by purinergic signaling. Partial hepatectomy was performed in C57BL/6 wild type and Cd39 null mice. MP were collected via ultracentrifugation. MNC were stimulated with nucleotides and nucleosides, in vitro, and tested for miR-142-3p levels. Fusion of MNC-derived MP and endothelial cells with subsequent transfer of miR-142-3p was imaged by flow cytometry and confocal microscopy. Endothelial inflammation and apoptosis were quantified after transfection with miR-142-3p. Significantly lower miR-142-3p levels were observed in plasma MP of Cd39 null mice after partial hepatectomy, when compared to C57BL/6 wild types (p?<?0.05). In contrast to extracellular nucleotides, anti-inflammatory adenosine significantly increased miR-142-3p levels in MNC-derived MP, in vitro (p?<?0.05). MNC-derived MP are able to transfer miR-142-3p to endothelial cells by fusion. Transfection of endothelial cells with miR-142-3p decreased TNF-α levels (p?<?0.05) and endothelial apoptosis (p?<?0.05). MiR-142-3p levels in MNC-derived MP are modulated by nucleoside signaling and might reflect compensatory responses in vascular inflammation. Our data suggest the transfer of genetic information via shed MP as a putative mechanism of intercellular communication—with implications in organ regeneration.     

Characterization of chloroplast microsatellite loci from whole chloroplast genome of Camellia taliensis and their utilization for evaluating genetic diversity of Camellia reticulata (Theaceae)

This study characterized chloroplast microsatellite markers for Camellia reticulata, a famous ornamental and edible economic tree species only distributed in Southwestern China. Thirty-two chloroplast microsatellite markers were originally annotated in the whole chloroplast genome of Camellia taliensis, ten polymorphic microsatellite markers were tested in 96 individuals from four natural populations of C. reticulata. Alleles numbered from two to four, and average value of Shannon's Information index, Nei's gene diversity, total genetic diversity, genetic diversity within populations, gene differentiation coefficient and gene flow index were 0.408, 0.225, 0.217, 0.102, 0.530 and 0.443, respectively. Our results showed high genetic differentiation and limited gene flow among the studied populations, which may be explained by recent fragmentation of the remnant populations due to human destruction and disturbance of natural habitats of the species. The identified cpSSR markers will be useful for the future studies on population genetics, conservation biology and phylogeography of C. reticulata.     

How do king penguins (Aptenodytes patagonicus apply the mathematical theory of information to communicate in windy conditions?

In the king penguin (Aptenodytes patagonicus), both pair members alternate in incubating and rearing their chick. Mates can recognize each other among thousands of other birds in the hubbub of the colony using only acoustic signalling: the display call. Large penguin colonies are found on sub-Antarctic islands where strong winds blow throughout the year. We have shown by experiments under natural conditions that the level of background noise increases in windy conditions and thus leads to a diminution of the signal-to-noise ratio. Moreover the emergence level of the signal revealed by entropy calculation is statistically weaker in windy conditions. To achieve breeding success, birds must continue communicating in spite of the significant decrease in the total amount of information that can be transmitted in windy situations. For the first time, to our knowledge, we have shown that a bird species takes into account the constraints imposed by wind on their acoustic communication. In windy conditions, birds try to maintain the efficiency of communication by increasing both the number of calls emitted and the number of syllables per call. This result conforms with predictions from the mathematical theory of communication: increased redundancy in a signal improves the probability of receiving a message in a noisy channel.     

Public Response to Official Information on Cancer and Cancer Clusters

Official information about cancer and cancer clusters from state health departments clashes with lay views. A few studies have covered site-specific communication by telephone and public meetings, and hypothetical messages, but not generic information actually provided. Public response to such information was probed with a random survey of New Jersey households (n = 327), part of a quasi-experiment contrasting the agency's cognitive message and an alternative message adding procedural and affective information. Respondents rated both information types as understandable, helpful, and trustworthy, particularly among those trusting the agency, agreeing with officials’ views of facts, and with low concern about local clusters. Anxiety about cancer, aversion to uncertainty, cancer experience, and familiarity with clusters or the agency did not affect responses. Agreeing with officially defined facts (knowledge) was associated with trust in the agency and concern about clusters, but scepticism about expert knowledge. Information exposure increased trust, belief in expert knowledge (except on whether cancers cluster), and (some) factual knowledge, but also increased self-reported concern among those already concerned. These findings suggest that, absent specific learning, people believe scientific information is understandable, helpful, and trustworthy when they already trust experts and institutions; people with prior distrust offer less positive evaluations.     

Obscurantist Holism Versus Clear-Cut Analysis: Will Anthropology Obviate the Biology-Culture Divide?

Although holism has long been a central theme in anthropology, current perception is that anthropological discourse is being pulled apart along its biology-culture seams. Despite reservations among sociocultural theorists, Darwinism remains the only body of theory that purports to link sub-disciplines of anthropology. The importance of holism in anthropology is reconciled here with disciplinary fragmentation and evolutionary theory. While Darwinism appears to provide interdisciplinary theoretical ties, it cannot successfully relate sub-disciplines of anthropology because this theory itself relies on a preformationist divide between inherited and acquired characteristics. Increasingly subtle language of genetic information and constraints does not ameliorate this problem. Research potential for the ecological constraints model in biological anthropology is discussed. Developmental systems theory (DST) is advocated as a tool for working toward a holistic anthropology [Susan Oyama, Paul Griffiths, and Russell Gray, ``Introduction: What is Developmental Systems Theory?,'' in Susan Oyama, Paul Griffiths, and Russell Gray, eds., Cycles of Contingency: Developmental Systems and Evolution (Cambridge, MA: MIT Press, 2001), 1–11].