Emergence and biological complexity

Biological networks possess an organization that expresses their potential information. A function, I(X:Y)N, called mutual information of integration, define, on a quantitative basis, three types of organization. If I(X:Y)N=0, the properties of the global system XY can be reduced to the properties of its component sub-systems X and Y. Hence, XY is not a real system displaying collective properties but the mere collection of X and Y. Its properties are the properties of the sub-systems X and Y. If I(X:Y)N>0, the system is integrated. Although it behaves as a coherent whole, it does not possess many collective properties. Last, if I(X:Y)N<0, the system possesses emergent collective properties and can be considered complex for it possesses many collective properties that cannot be predicted from the independent study of component sub-systems X and Y. In a biological system, the emergence of information usually means the emergence of a novel function. This is probably what is occurring with enzymes. If a protein binds two ligands able to interact, and if the condition above is fulfilled, then the protein behaves as an enzyme able to allow a catalytic reaction between the two reagents.     

Chemistry and physics of giant vesicles as biomembrane models

The giant vesicle is becoming an object of intense scrutiny by chemists, biologists, and physicists who are interested in membrane behavior. Recent advances include new models to explain morphological changes, new experimental methods for studying vesicle adhesion, layering and adsorption, and new cataloging of ‘cytomimetic’ processes.     

Naturalising purpose: From comparative anatomy to the ‘adventure of reason’

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality and conservation of forms. Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms.     

An automatic image registration scheme using Tsallis entropy

We have investigated the registration of mammograms based on the Tsallis entropy using mutual information measure. Tsallis entropy has one more parameter ‘q’ and the values of ‘q’ decide the quality of the registration. Existing Tsallis entropy based algorithms are not automatic as they claimed to be. In this article, an automatic affine image registration based on Tsallis entropy is proposed and its performance is analyzed for clinically acquired mammograms for globally registering them. The accuracy is compared with traditionally used mutual information and normalized mutual information based on Shannon entropy. Our algorithm shows promising results with increased accuracy with reduction in number of evaluations. Further, the need for pre-registration in mammogram is discussed in detail. Through this experiment, it is found that the proposed algorithm is effective enough to replace Shannon and existing Tsallis entropy based affine registration schemes.     

Collective behavior in cancer cell populations

In recent years the argument has been made that malignant tumors represent complex dynamic and self‐organizing biosystems. Furthermore, there is increasing evidence that collective cell migration is common during invasion and metastasis of malignant tumors. Here, we argue that cancer systems may be capable of developing multicellular collective patterns that resemble evolved adaptive behavior known from other biological systems including collective sensing of environmental conditions and collective decision‐making. We present a concept as to how these properties could arise in tumors and why the emergence of such swarm‐like patterns would confer advantageous properties to the spatiotemporal expansion of tumors, and consequently, why understanding and ultimately targeting such collectivity should be of interest for basic and clinical cancer research alike.     

Increasing floral diversity for selective enhancement of biological control agents: A double-edged sward?

Floral resource subsidies can have differential effects on insect herbivores compared with the herbivores’ natural enemies. While the nectar of many plant species enhances parasitoid fitness, it may also increase damage by herbivores. This may occur as a result of enhanced herbivore fitness or by enhancing fourth-trophic-level processes, possibly disrupting a trophic cascade as a result. The responses of different arthropod guilds to different floral resource subsidies were compared using Plutella xylostella (Hyponomeutidae), its parasitoid Diadegma semiclausum (Ichneumonidae) and data from two other published herbivore–parasitoid systems. These were Dolichogenidea tasmanica (Braconidae) and its host Epiphyas postvittana, and Copidosoma koehleri (Encyrtidae) and its host Phthorimaea operculella. The parasitoids and hosts in the three systems exhibited differential responses to the nectar sources. The differential response was not explained by morphology, demonstrating that physical access to nectaries alone does not determine the potential of flowers as a food source. For some flowering plants, enhancement of herbivore and parasitoid fitness occurred. Other flowering plants, such as buckwheat and phacelia, conferred a selective enhancement on parasitoids by increasing only their fitness. More effective conservation biocontrol may be achieved by the provision of selective floral resources. Attempts to ‘engineer’ agroecosystems to enhance biological control require an extensive knowledge of the ecology of the herbivore, its enemies and their interactions with potential resource subsidies.     

Information processing organs,mathematical mappings and self-organizing systems

A self-organizing system, which may be biological or man-made, adjusts itself in response to inputs from the surroundings. The input information is processed and transformed, so as to guide the system in accordance with a desired final state. The visual nervous system is considered, to illustrate some possible transformations or mappings, which may be employed by self-organizing systems. The mappings given as examples are linear, but there is evidence also for nonlinear mappings to explain the action of biological systems. The successive stages of adjustment in a self-organizing system can be treated as a feedback control process. Mathematically, feedback control of linear as well as nonlinear systems can be handled by using the principle of contraction mapping. The kind of control considered is flexible in the sense that a desired state of the system as a whole can be achieved through a variety of states of the individual parts. This leads to such questions as equivalence and classification which are also discussed in this paper.     

植物与草食动物之间的协同适应及进化

通常协同进化是指一个物种 (或种群 )的遗传结构由于回应于另一个物种 (或种群 )遗传结构的变化而发生的相应改变。广义的理解 ,协同进化是相互作用的物种之间的互惠进化。生物之间、特别是植物与草食动物之间的协同适应与进化 ,已经成为生物进化、生态、遗传等学科十分关注的问题 ,可能成为生物学中各学科研究的交汇点或结点。作者具体阐述了 :(1)生物之间协同进化的研究意义 ,包括对生物学与生态学的价值 ;(2 )生物之间协同进化研究的限制或困难 ,诸如时间、研究对象、进化等级尺度和研究方法的限制 ;(3)植物与草食动物之间协同进化的主要研究对象 (系统 ) ,即昆虫传粉系统、昆虫诱导植物反应系统、种子散布系统、以及大型草食动物采食与植物反应系统 ;(4 )植物与草食动物之间协同进化的主要研究内容 ,包括适应特征 (性状 )——物种的可塑性 ,以及适应机制——物种适应过程与策略两个方面 ;(5 )植物与草食动物之间协同进化研究的存在问题及研究方向     

Smart plants: Memory and communication without brains

The immobility of plants is consistent with their principal function: collecting light to provide photosynthetic substrate for the biological system. Their immobility does impose limitations on some basic requirements, such as the need for pollination, for seed dispersal, and for protection against herbivores. Meeting these 3 needs will logically necessitate some ability for plant communication – at least a capability for beneficial adaptive behavior. Three types of plant behavior provide evidence of memory and communication abilities: a capability for memory, a capability for measuring time, and extensive evidence of chemical signaling systems. These may provide benefits for genetic outcrossing, seed dispersal and protection – beneficial adaptive behaviors. The chemical signaling system constitutes a wireless communication network that draws mobile animals into assisting plant functions that require mobility. Plants share their chemical signaling systems most frequently with insects and birds. These beneficial adaptable behaviors may be interpreted as some type of consciousness.     

Instability helps virtual flies to mate

In this paper we perform a bifurcation analysis for a discrete time dynamical system, describing the behavior of a virtual fly, developed by Böddeker and Egelhaaf (2003). Like real blowflies, the virtual counterparts exhibit a dichotomous behavior: they catch small targets but follow big objects at a constant distance. We consider this model for targets on linear and on circular trajectories. Then we transform the system into a ‘‘frozen’’ form, such that the position of the target is fixed. It turns out that the loss of stability of a fixed point in the frozen system due to a Neimark-Sacker bifurcation, explains the dichotomous behavior of the virtual fly.     

Eugenic and sexual folklores and the castration of sex offenders in the Netherlands (1938–1968)

This contribution questions the positive/negative eugenics dichotomy that typifies the historiography on the eugenic movement in the Netherlands and the claim that this movement was mostly marginal because only positive eugenics was pursued. From 1938 to 1968 in the Netherlands, after a decade of debates, 400 sex offenders who had been committed to asylums for the criminally insane were ‘voluntarily’ and ‘therapeutically’ castrated. For political reasons debates on castration, meant to create consensus, eliminated any reference to or connotation with eugenics, yet these policies were unthinkable without them. This article shows that thinking about social and sexual problems and their solutions in the 1930s were permeated by eugenic folklore which in turn was informed by sexual folklore. Both eugenic and sexual lore, as common sense, or as ways of knowing, were about individual and collective loss of self control which was referred to with a catch-all phrase: ‘hypersexuality’. Although sexual classifications used in diagnosing sex offenders suggested the existence of discrete sexual categories, homosexuality for instance was not seen as a sexual alternative or as an identity but as the extent to which an offender suffered from a form of hypersexuality that threatened the fabric of society.     

RNA and RNP as new molecular parts in synthetic biology

Synthetic biology has a promising outlook in biotechnology and for understanding the self-organizing principle of biological molecules in life. However, synthetic biologists have been looking for new molecular "parts" that function as modular units required in designing and constructing new "devices" and "systems" for regulating cell function because the number of such parts is strictly limited at present. In this review, we focus on RNA/ribonucleoprotein (RNP) architectures that hold promise as new "parts" for synthetic biology. They are constructed with molecular design and an experimental evolution technique. So far, designed self-folding RNAs, RNA (RNP) enzymes, and nanoscale RNA architectures have been successfully constructed by utilizing Watson-Crick base-pairs together with specific RNA-RNA or RNA-protein binding motifs of known defined 3D structures. Riboregulators for regulating targeted gene expression have also been designed and produced in vitro as well as in vivo. Lately, RNA and ribonucleoprotein complexes have been strongly attracting the attention of molecular biologists because a variety of noncoding RNAs discovered in nature perform spatiotemporal gene expressions. Thus we hope that newly accumulating knowledge on naturally occurring RNAs and RNP complexes will provide a variety of new parts, devices and systems for synthetic biology.     

Realized vs apparent reduction in enemies of the European starling

Release from parasites, pathogens or predators (i.e. enemies) is a widely cited ‘rule of thumb’ to explain the proliferation of nonindigenous species in their introduced regions (i.e. the ‘enemy release hypothesis’, or ERH). Indeed, profound effects of some parasites and predators on host populations are well documented. However, some support for the ERH comes from studies that find a reduction in the species richness of enemies in the introduced range, relative to the native range, of particular hosts. For example, data on helminth parasites of the European starling in both its native Eurasia and in North America support a reduction of parasites in the latter. However, North American ‘founder’ starlings were likely not chosen randomly from across Eurasia. This could result in an overestimation of enemy release since enemies affect their hosts on a population level. We control for the effects of subsampling colonists and find, contrary to previous reports, no evidence that introduced populations of starlings experienced a reduction in the species richness of helminth parasites after colonization of North America. These results highlight the importance of choosing appropriate contrast groups in biogeographical analyses of biological invasions to minimize the confounding effects of ‘propagule biases’.     

Informatics - genome and genetic databases

Databases for biologists are becoming increasingly important. Some of these can be regarded as ‘core’ resources, such as the bibliographic databases, whereas others are of greater interest to specialists. As comparative genomics develops, however, even databases limited in their scope (e.g. to a single organism) are of great interest to a wider community.     

Grazing impact in relation to livestock watering points

Animals use and impact on habitats unevenly. A prime example is the ‘piosphere’, the zone of ecological impact focused around a livestock watering point, particularly in dry areas. The piosphere provides a good context for studying the ecological effects of large herbivores, and for applying ecological information to land management. Much of the literature on piospheres is in journals outside mainstream ecology, and this article provides ecologists with an introductory review of the topic and its wider ramifications.     

Microsatellites: consensus and controversy

Microsatellite DNA loci have recently been adopted for many biological applications. Comparative studies across a wide range of species has revealed many details of their mutational properties and evolutionary life cycles. Experience shows that a full understanding of these processes is essential to ensure the effective use of microsatellites as analytical tools. In this article, we review the controversies that have arisen as biologists have taken up this new technology and the emerging consensus that has resulted from their debates. We point to the need for comparative DNA sequencing studies to produce input data for a new generation of theoretical models of microsatellite behaviour. We conclude by presenting our own conceptual model, ‘Snakes and Ladders’, as an aid to theory development.     

Invasion of a Top Predator into an Epipelagic Ecosystem can bring a Paradoxical Top-Down Trophic Control

We apply mathematical modeling to explore different scenarios of invasion of a top predator (carnivorous zooplankton or planktivorous fish) into an epipelagic plankton ecosystem. We use a ‘minimal’ model of three nonlinear ordinary differential equations (nutrient–phytoplankton–herbivores) with the top predator density as a time-dependent parameter. The ecosystem shows different types of response, which can be described in terms of top-down trophic control. Our investigation indicates that under certain conditions the plankton ecosystem model demonstrates a surprising kind of response: in a wide range of realistic ecosystem parameters the invasion of the top predator leads to a prominent increase in the average density of zooplankton and to a resulting decrease of phytoplankton density. This phenomenon is opposite to the ‘typical’ top–down control when the carnivore pressure decreases zooplankton density which, in turn, increases phytoplankton biomass. We call the revealed type of top-down control ‘paradoxical’. Examples of such a response in natural aquatic ecosystems were reported earlier but no clear explanation has been provided hitherto. In this paper, we analyze possible mechanisms of ‘paradoxical top–down control’ and show that it can occur in eutrophic epipelagic ecosystems subject to high rate of cross-pycnocline exchange.     

Swarms of particle agents with harmonic interactions

Summary Agent-based modeling is a powerful methodology to describe the occurence of complex behavior in biological systems. The interaction of a large number of individuals (agents) may for example lead to the emergence of new forms of collective motion. In this paper, we investigate a particle-based approach to the coherent motion of a swarm with parabolic (i. e. harmonic) interactions between the agents. It is based on generalized Langevin equations for the particle agents, which take into account (i) energetic conditions for active motion, (ii) linear attractive forces between each two agents. The complex collective motion observed can be explained as the result of these different influences: the active motion of the agents, which is driven by the energy-take up, would eventually lead to a spatial dispersion of the swarm, while the mutual interaction of the agents results in a tendency of spatial concentration. In addition to particle-based computer simulations, we also provide a mathematical framework for investigating the collective dynamics. Dedicated to the memory of Michael Conrad