The expansion of information in ecological systems: Emergence as a quantifiable state

Although the term ‘emergence’ has received wide attention in the literature, most of this attention has been focused on epistemological discussions about the nature of what might be considered emergent behavior in self-organizing systems. For the concept of emergence to have any great utility for biologists, it must (1) be perceptible as a physical, quantitative property rather than just a philosophical one; (2) have a quantitative definition applicable to all levels of biological organization; and (3) be an essential component of biological system performance or evolution. Using an independent, cellular population model (running in the StarLogo system), we have developed a mutual information calculation to measure the information expansion when considering the interactions between a population of herbivores and an environment in comparison to the interactions between the individual herbivores and that environment. In self-organizing biological systems, the collective action of massively parallel units generates a greater potential complexity in the information processing capacity of the ‘whole’ system relative to the ‘individual’ parts, and as such, there is a demonstrable increase in mutual information content. From this perspective, we consider emergence to exist as a simple information expansion that is a default behavior of any system with multiple, component parts governed by a simple, probabilistic rule set. It is not a first principle of self-organizing biological systems, but rather a collective behavior that can be quantitatively described in practical terms for experimental biologists. With a quantitative formulation, the concept of emergence may become a useful information statistic in assessing the structure of biological systems.     

Epidemiology of organic solvents and connective tissue disease

Case reports suggest that solvents are associated with various connective tissue diseases (systemic sclerosis, scleroderma, undifferentiated connective tissue disease, systemic lupus erythematosis, and rheumatoid arthritis), particularly systemic sclerosis. A small number of epidemiological studies have shown statistically significant but weak associations between solvent exposure, systemic sclerosis, and undifferentiated connective tissue disease. However, the interpretation of these positive findings is tempered by a lack of replication, an inability to specify which solvents convey risk, and an absence of increasing risk with increasing exposure. Existing studies, on aggregate, do not show conclusively that solvents (either as a group of chemicals or individual chemicals) are causally associated with any connective tissue disease. Further investigations should be carried out to replicate the positive existing findings and to specify the solvents and circumstances of exposure that carry risk.     

Epidemiology of organic solvents and connective tissue disease

Case reports suggest that solvents are associated with various connective tissue diseases (systemic sclerosis, scleroderma, undifferentiated connective tissue disease, systemic lupus erythematosis, and rheumatoid arthritis), particularly systemic sclerosis. A small number of epidemiological studies have shown statistically significant but weak associations between solvent exposure, systemic sclerosis, and undifferentiated connective tissue disease. However, the interpretation of these positive findings is tempered by a lack of replication, an inability to specify which solvents convey risk, and an absence of increasing risk with increasing exposure. Existing studies, on aggregate, do not show conclusively that solvents (either as a group of chemicals or individual chemicals) are causally associated with any connective tissue disease. Further investigations should be carried out to replicate the positive existing findings and to specify the solvents and circumstances of exposure that carry risk.     

From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0

This paper presents Integrated Information Theory (IIT) of consciousness 3.0, which incorporates several advances over previous formulations. IIT starts from phenomenological axioms: information says that each experience is specific – it is what it is by how it differs from alternative experiences; integration says that it is unified – irreducible to non-interdependent components; exclusion says that it has unique borders and a particular spatio-temporal grain. These axioms are formalized into postulates that prescribe how physical mechanisms, such as neurons or logic gates, must be configured to generate experience (phenomenology). The postulates are used to define intrinsic information as “differences that make a difference” within a system, and integrated information as information specified by a whole that cannot be reduced to that specified by its parts. By applying the postulates both at the level of individual mechanisms and at the level of systems of mechanisms, IIT arrives at an identity: an experience is a maximally irreducible conceptual structure (MICS, a constellation of concepts in qualia space), and the set of elements that generates it constitutes a complex. According to IIT, a MICS specifies the quality of an experience and integrated information Φ^Max its quantity. From the theory follow several results, including: a system of mechanisms may condense into a major complex and non-overlapping minor complexes; the concepts that specify the quality of an experience are always about the complex itself and relate only indirectly to the external environment; anatomical connectivity influences complexes and associated MICS; a complex can generate a MICS even if its elements are inactive; simple systems can be minimally conscious; complicated systems can be unconscious; there can be true “zombies” – unconscious feed-forward systems that are functionally equivalent to conscious complexes.     

Theoretical requirements for the interpretation of signals of intramuscular tension

A model of a simple hinge joint is developed which allows the expression of intramuscular tension in terms of the angle at the joint and an applied force. A particular intramuscular tension does not specify uniquely the size of the force applied to a limb. For the nervous system to use signals of intramuscular tension from the agonist muscle to specify the applied force it requires information about (i) the angle at the joint, (ii) the angle between the line of applied force and the line of muscular contraction, and (iii) the relation between the axis of joint rotation and gravity.Sensory information about intramuscular tension can be perceived. This theoretical anlysis shows that central processing of signals of intramuscular tension may be required to provide a unique indicator of the external forces on a limb.     

Qualia: The Geometry of Integrated Information

According to the integrated information theory, the quantity of consciousness is the amount of integrated information generated by a complex of elements, and the quality of experience is specified by the informational relationships it generates. This paper outlines a framework for characterizing the informational relationships generated by such systems. Qualia space (Q) is a space having an axis for each possible state (activity pattern) of a complex. Within Q, each submechanism specifies a point corresponding to a repertoire of system states. Arrows between repertoires in Q define informational relationships. Together, these arrows specify a quale—a shape that completely and univocally characterizes the quality of a conscious experience. Φ— the height of this shape—is the quantity of consciousness associated with the experience. Entanglement measures how irreducible informational relationships are to their component relationships, specifying concepts and modes. Several corollaries follow from these premises. The quale is determined by both the mechanism and state of the system. Thus, two different systems having identical activity patterns may generate different qualia. Conversely, the same quale may be generated by two systems that differ in both activity and connectivity. Both active and inactive elements specify a quale, but elements that are inactivated do not. Also, the activation of an element affects experience by changing the shape of the quale. The subdivision of experience into modalities and submodalities corresponds to subshapes in Q. In principle, different aspects of experience may be classified as different shapes in Q, and the similarity between experiences reduces to similarities between shapes. Finally, specific qualities, such as the “redness” of red, while generated by a local mechanism, cannot be reduced to it, but require considering the entire quale. Ultimately, the present framework may offer a principled way for translating qualitative properties of experience into mathematics.     

Automated reporting from gel-based proteomics experiments using the open source Proteios database application

The assembly of data from different parts of proteomics workflow is often a major bottleneck in proteomics. Furthermore, there is an increasing demand for the publication of details about protein identifications due to the problems with false-positive and false-negative identifications. In this report, we describe how the open-source Proteios software has been expanded to automate the assembly of the different parts of a gel-based proteomics workflow. In Proteios it is possible to generate protein identification reports that contain all the information currently required by proteomics journals. It is also possible for the user to specify maximum allowed false positive ratios, and reports are automatically generated with the corresponding score cut-offs calculated. When protein identification is conducted using multiple search engines, the score thresholds that correlate to the predetermined error rate are also explicitly calculated for proteins that appear on the result lists of more than one search engine.     

Arthropodisierung ais biomechanischer Prozeß und die Entstehung der Trilobiten-Konstruktion

The conditions are pointed out under which the body construction of annelids could have been transformed into that of arthropods. As an adaptation to a vagile life near or in the bottom and to an uptaking of food by filtering of particles the parapodia of annelid-like organisms were shifted into a more ventral position. This process required certain bracings by connective tissue and muscles in the body, controlling the body shape. Immobilisation of body parts, initially in the dorsal region, allowed stiff skeletal structures to arise. The sclerotisation caused an increase of efficiency of the motoric system, since the body form was reliably controlled no more by the action of muscles, as in the hydrostatic skeleton systems of worms, but by rigid skeletal plates, to which muscles can be inserted. The result of this transformation were broad and flat arthropod-constructions with ventral food groove, through which the row of endites of the limbs transported a stream of food along the median line to the mouth. On this constructional level the trilobites are the first group with many species. Their structures can be explained as a result of the constructional preconditions of their ancestors and of the adaptations during the transformation, leading from annelid-like hydrostatic skeleton systems to typical arthropods with an exoskeleton-muscle apparatus.     

Contribution of Subcutaneous Connective Tissues to the Epithelialization and Cyst Formation by the Skin Transplanted Subcutaneously

Skins and hollow organs have been shown to form epithelialized cysts when transplanted into subcutaneous tissue of a recipient animal, expanding their surface areas. This system seems to offer a good potential for regenerating organs. We investigated the functional and structural contribution of epithelia and connective tissue compartments in this regeneration system with two experimental systems.

Dispase-separated epidermis often forms epithelialized cysts when combined with dermal connective tissue whereas dispase-separated epidermis alone does not form cysts or epithelialize, indicating the functional importance of the dermal connective tissue in the regeneration process.

When GFP rats were used as donors for the skin, the donor-derived tissue was composed of whole epidermis and parts of the connective tissue cells and blood vessels under the newly epithelialized portion of the cyst wall. Small capillaries of granulation tissues were shown to be of recipient origin, but some large vessels were of donor origin. These results showed the significant functional and structural contribution of dermal connective tissue in the regeneration of the skin in subdermal transplant.     

The role of cleavage in the localization of developmental potential in the Ctenophore Mnemiopsis leidyi

This study defines the time period during which the cellular components that specify comb plates and photocytes become localized in different parts of blastomeres prior to their segregation to separate daughter cells. At the two-cell stage the factors which specify comb plates are localized at the aboral pole of the blastomeres. There is not a significant localization of the factors which specify comb plates and photocytes along the tentacular axis of the embryo. At the four-cell stage, the factors which specify comb plates become localized at one end of the tentacular axis of the blastomeres; however, the factors which specify photocytes have not yet become localized. At the eight-cell stage, the factors which specify these two cell types are segregated to different blastomeres.The role of cleavage in setting up these localized regions of developmental potential has been studied by reversibly inhibiting selected cleavages. After the first division, the pattern of cleavage that follows a period of cleavage inhibition corresponds to the pattern occurring in untreated embryos that began development at the same time. This situation is similar to the “clock” system, which controls many aspects of the pattern of cleavage in sea urchin embryos. The extent to which the factors that specify comb plates and photocytes become localized in a given region of a blastomere is correlated with the kind of cleavage which occurs after a block. Most of the activity involved in localizing developmental potential takes place during cleavage.     

Contribution of Subcutaneous Connective Tissues to the Epithelialization and Cyst Formation by the Skin Transplanted Subcutaneously

Skins and hollow organs have been shown to form epithelialized cysts when transplanted into subcutaneous tissue of a recipient animal, expanding their surface areas. This system seems to offer a good potential for regenerating organs. We investigated the functional and structural contribution of epithelia and connective tissue compartments in this regeneration system with two experimental systems.Key Words: skin, epithelialization, transplantation, GFP, epidermis, cystDispase-separated epidermis often forms epithelialized cysts when combined with dermal connective tissue whereas dispase-separated epidermis alone does not form cysts or epithelialize, indicating the functional importance of the dermal connective tissue in the regeneration process.When GFP rats were used as donors for the skin, the donor-derived tissue was composed of whole epidermis and parts of the connective tissue cells and blood vessels under the newly epithelialized portion of the cyst wall. Small capillaries of granulation tissues were shown to be of recipient origin, but some large vessels were of donor origin. These results showed the significant functional and structural contribution of dermal connective tissue in the regeneration of the skin in subdermal transplant.     

Identification of nerve plexi in connective tissues of the sea cucumber Holothuria glaberrima by using a novel nerve-specific antibody

The echinoderm nervous system is one of the least studied among invertebrates, partly because the tools available to study the neurobiology of this phylum are limited. We have now produced a monoclonal antibody (RN1) that labels a nervous system component of the sea cucumber Holothuria glaberrima. Western blots show that our antibody recognizes a major band of 66 kDa and a minor band of 53 kDa. Immunohistological experiments show that, in H. glaberrima, the antibody distinctly labels most of the known nervous system structures and some components that were previously unknown or little studied. A surprising finding was the labeling of nervous plexi within the connective tissue compartments of all organs studied. Double labeling with holothurian neuropeptides and an echinoderm synaptotagmin showed that RN1 labeled most, if not all, of the fibers labeled by these neuronal markers, but also a larger component of cells and fibers. The presence of a distinct connective tissue plexus in holothurians is highly significant since these organisms possess mutable connective tissues that change viscosity under the control of the nervous system. Therefore, the cells and fibers recognized by our monoclonal antibodies may be involved in controlling tensility changes in echinoderm connective tissue.     

Assessing the structural complexity of manufacturing systems configurations

Modern manufacturing systems are increasingly required to be flexible and adaptable to changing market demands, which adds to their structural and operational complexity. One of the major challenges at the early design stages is to select a manufacturing system configuration that both satisfies the production functional requirements and is easy to operate and manage. A new metric for assessing the structural complexity of manufacturing system configurations is presented in this paper. The proposed complexity metric incorporates the quantity of information using an entropy approach. It accounts for the complexity inherent in the various modules in the manufacturing system through the use of an index derived from a newly developed manufacturing systems classification code. The code captures the effect of various component types and technologies used in a manufacturing system on the system’s structural complexity. The presented metric would be helpful in selecting the least complex manufacturing system configuration that meets the requirements. An engine cylinder head production system is used to illustrate the application of the proposed methodology in comparing feasible but different manufacturing system configurations capable of producing the cylinder head based on their structurally inherent complexity.     

The Codes of Recognition

This paper is divided into two parts. Part I focuses on the manner in which the components of the face recognition system work together so that a perceiver, within several hundred milliseconds after seeing a familiar face, is able to both identify the face of the perceived and recall elements of the history of past encounters with the perceived. Face recognition plays a crucial role in enabling both human and nonhuman primates to interact in collaborative social groups. This critical function is accomplished through the unidirectional coded transfer of informational elements from one component to another. Although these informational elements themselves are not meaningful to the perceiving agent, they do nevertheless contain essential bits of information that are necessary for the final formation of the meaningful message. The structural components of the system are identified and the manner in which informational elements are coded and transferred sequentially from component to component in the brain of the perceiver is described. The independent, physically separated components in the face recognition system are bridged by an additional component, an “adaptor”, that mediates the transfer of informational elements from one component to another. The nature of the independent systems, and the manner by which the bridging or adaptor apparatus enables coded information transfer from one system to another is discussed. Part II focuses on the analysis of recognition in human-designed sign systems such as Braille and Morse code. Recognition in human-designed sign systems is notable for the stability of the link between sign and meaning. Face recognition is characterized as being subjective, indicating that the meaning of a sign (face) to a perceiver is variable and dependent on context, whereas human-devised sign recognition is characterized as being objective, indicating that the meaning of a sign is context independent and invariant. Human-designed sign systems require the presence in brain of a referent world. An example of a referent world is the set of letters of the alphabet. Representations of this set are installed in the brain through social mediated learning. Human-designed sets of signs (e.g., Braille, and written text) are created to correspond, via a code enabling adaptor structure, to referent worlds in the brain. Human-designed sign systems are the foundations for literacy, a capability only found in humans.     

Differential activation of M26-containing meiotic recombination hot spots in Schizosaccharomyces pombe

Certain genomic loci, termed hot spots, are predisposed to undergo genetic recombination during meiosis at higher levels relative to the rest of the genome. The factors that specify hot-spot potential are not well understood. The M26 hot spot of Schizosaccharomyces pombe is dependent on certain trans activators and a specific nucleotide sequence, which can function as a hot spot in a position- and orientation-independent fashion within ade6. In this report we demonstrate that a linear element (LE) component, Rec10, has a function that is required for activation of some, but not all, M26-containing hot spots and from this we propose that, with respect to hot-spot activity, there are three classes of M26-containing sequences. We demonstrate that the localized sequence context in which the M26 heptamer is embedded is a major factor governing whether or not this Rec10 function is required for full hot-spot activation. Furthermore, we show that the rec10-144 mutant, which is defective in full activation of ade6-M26, but proficient for activation of other M26-containing hot spots, is also defective in the formation of LEs, suggesting an intimate link between higher-order chromatin structure and local influences on hot-spot activation.     

Restricting restriction

Systems biology is a new, fashionable and well-funded discipline, which to quote from a recent review aims to 'examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism em leader ' (Kitano, H. (2002) Science 295:1662-1664). Systems biology will do this by profiting from the vast amounts of biological information that are available in the genomics era and make extensive use of computer modelling. But: 'many breakthroughs in experimental devices, advanced software and analytical methods are required before the achievements of system biology can live up to their much-touted potential'. This edition of Molecular Microbiology contains a paper that is the product of traditional experimental biology but which could serve as a test case for systems biology. The paper shows how bacteria integrate such disparate subsystems as DNA restriction, homologous recombination and regulated proteolysis to protect their chromosomes from degradation. When systems biology can predict this level of choreography, it will be a mature discipline.     

Attack Robustness and Centrality of Complex Networks

Many complex systems can be described by networks, in which the constituent components are represented by vertices and the connections between the components are represented by edges between the corresponding vertices. A fundamental issue concerning complex networked systems is the robustness of the overall system to the failure of its constituent parts. Since the degree to which a networked system continues to function, as its component parts are degraded, typically depends on the integrity of the underlying network, the question of system robustness can be addressed by analyzing how the network structure changes as vertices are removed. Previous work has considered how the structure of complex networks change as vertices are removed uniformly at random, in decreasing order of their degree, or in decreasing order of their betweenness centrality. Here we extend these studies by investigating the effect on network structure of targeting vertices for removal based on a wider range of non-local measures of potential importance than simply degree or betweenness. We consider the effect of such targeted vertex removal on model networks with different degree distributions, clustering coefficients and assortativity coefficients, and for a variety of empirical networks.     

Involvement of the suboesophageal and thoracic ganglia in the control of antennal movements in crickets

In crickets (Gryllus campestris, Gryllus bimaculatus) the contribution of the suboesophageal ganglia (SOG) and thoracic ganglia to the generation of antennal movements during visual tracking, walking and flight was investigated by the transection of connectives. Transection of one circumoesophageal connective abolished the movements and postures of the antenna ipsilateral to the lesion, while the contralateral antenna behaved normally. Simple antennal reflexes remained. Transection of one neck connective reduced fast components of antennal movements during tracking and walking. During flight the ipsilateral antenna could not be maintained in a prolonged forward position. Antennal movements during tracking and walking appeared normal after transection of one connective between pro- and mesothoracic ganglia. However, the antennal flight posture required uninterrupted connections between brain and mesothoracic ganglion. The ablation of more posterior ganglia had no effect on the antennal behaviours investigated. Recordings from an antennal motor nerve revealed a unilateral net excitation relayed via the SOG to the brain. Two ascending interneurones with activity closely correlated with antennal movements are candidates for such a relay function. The data show that the brain is not sufficient to generate antennal movements and postures as integral parts of several behaviours. The SOG and the thoracic ganglia are required in addition. Accepted: 12 March 1997     

微重力环境影响植物生长发育的研究进展

微重力是最独特的空间环境条件之一,研究微重力对不同植物种类以及不同植物部位的影响是空间生物学的重要内容之一,对于建立生物再生式生命保障系统意义重大。生物再生式生命保障系统是未来开展长期载人空间活动的核心技术,其优势在于能在一个密闭的系统内持续再生氧气,水和食物等高等动物生活必需品,植物部件是生物再生式生命保障系统的重要组成部分。了解和掌握微重力对植物生长发育的影响,有助于采取有效的作业制度确保其正常生长发育和繁殖,是成功建立生物再生式生命保障系统的首要关键。该文就植物在空间探索中的地位和作用,地面模拟微重力的装置以及国内外有关微重力对植物的影响做一综述。现有的研究结果包括,未来长期的载人航天任务需要植物通过光合作用为生物再生式生命保障系统提供部分动物营养、洁净水以及清除系统中的固体废物和二氧化碳;三维随机回旋装置是目前地面上模拟微重力效应的主要装置之一,尤其适用于植物材料的长期模拟微重力处理;国内外有关微重力对植物影响的报道生理生化水平多集中在植物的生长发育和生理反应,比如表型变化或者与重力相关的激素或者钙离子的再分配,细胞或亚细胞水平主要有细胞壁、线粒体、叶绿体以及细胞骨架等,基因和蛋白质表达水平的研究对象主要为拟南芥。由于实验方法和材料之间的差异,微重力对不同植物或者植物不同部位在各个水平的影响效果并不一致,未来需要开展更多的相关研究工作。