The fractal nature of nature: power laws,ecological complexity and biodiversity

Underlying the diversity of life and the complexity of ecology is order that reflects the operation of fundamental physical and biological processes. Power laws describe empirical scaling relationships that are emergent quantitative features of biodiversity. These features are patterns of structure or dynamics that are self-similar or fractal-like over many orders of magnitude. Power laws allow extrapolation and prediction over a wide range of scales. Some appear to be universal, occurring in virtually all taxa of organisms and types of environments. They offer clues to underlying mechanisms that powerfully constrain biodiversity. We describe recent progress and future prospects for understanding the mechanisms that generate these power laws, and for explaining the diversity of species and complexity of ecosystems in terms of fundamental principles of physical and biological science.     

Laws of nature and laws of ecology

We address the question of whether there are laws in ecology. Although there has been a great deal of recent interest in this topic, much of the relevant debate has been conducted under some common misconceptions about what laws of nature are. Once these misconceptions are cleared up, the case for ecology having laws is much stronger. Indeed, we suggest that the case for laws in ecology is no better or worse than the case for laws in physics.     

Putting concerns about nature in context: the case of agricultural biotechnology

Concerns about nature are playing increasingly prominent roles in a variety of social debates, including medical biotechnology, environmental protection, and agricultural biotechnology. These concerns are often simply rejected as incoherent: critics argue that there is no good account for how natural states of affairs can have moral value, and that the concept of "nature" is too multifarious and vague to be deployed in moral argument anyway. When these concerns are defended, they are frequently formulated as strong claims that make implausible ontological commitments and that ignore the linkages between these different debates. Agricultural biotechnology provides an especially challenging case study for evaluating concerns about nature. I offer a qualified defense that recognizes these concerns as conceptually linked, attends to social context at appropriate points, and overcomes the charges of incoherence. This defense supports a restrained treatment of concerns about nature in public policy: public policy can neither endorse nor dismiss them. In the case of agricultural biotechnology, this stance probably mandates some form of labeling.     

Biological chromatology. The laws of colour and design in nature

Summary Biochromatology can be defined as the study of the relationships between colours, and between colours and design in nature. Certain laws concerning biochromatics can be formulated in the terminology of the Colour Circle. One of them is that planes in warm colours and planes in cold colours never adjoin. Another law is that design is never polychromatic. It seems that the observed biochromatical facts can be explained with the help of the principle optimal manifestation of colour, which in turn is based on the formative principles of matter itself.     

Fieldwork: man in the system of nature and priority of natural laws in human life

Fieldwork is a branch of inseparable unity of natural and humanitarian sciences; it is aimed at the cultural origin of humanity on the maximum level of its variety. Practically all natural sciences have some space determined by ethnic conscience in nature cognition: ethnodemography, ethnobotany, ethnozoology, etc. Fieldwork guides the research of human culture from the laws of nature. This kind of knowledge is useful to balance human relations with nature and avoid conflicts. Peoples should exchange their wisdom in the dialogue with nature to be more safe. Fieldwork understood as traditional culture only, explaining the variety of ethnoses on our earth, is just the narrow and diachronic level of this branch of knowledge. The cosmological knowledge, where fantasy and not exhausted in its cognition understanding the world of nature are mixed, forms the source of fieldwork and in many respects explains the direction of knowledge: the man finds himself under the open sky, he is the child of nature. Then as time went on there appeared a gradual transition--first nature was creating the man, then by and by he began turning to answer nature by his activity. Nowadays the man is actively creating nature. There are two levels of fieldwork: the ancient one which deals with the origin of ethnoses and the modern one which explores how contemporary life is determined by ethnic specific traits. Fieldwork is the core of multidisciplinary situation in man's knowledge. It is related to such humanitarian sciences: semiotics, culturology, sociology, history, philosophy, literature, linguistics. In the cycle of natural sciences fieldwork stands close to anthropology, geography, biology, demography. Fieldwork as a science has the two main levels--the "sophy" level and the logos "level". The first one discovers wisdom of human life, the second one is aimed at logical structuring of knowledge, here proceed various classifications of peoples.     

Microcins: their nature and genetic determination

A number of gram-negative bacteria are capable of synthesizing the low molecular mass antibiotics microcins, the substances with molecular masses up to 10 000 D possessing a broad range of antibiotic activity. The synthesis is not lethal for the producing cells and is not induced by DNA-damaging agents. The investigated microcins are either of oligopeptide nature or are analogues of methionine. Five types of microcins have been described. The A- and C-types of microcins inhibit protein synthesis, microcins B suppress DNA replication, microcins D and F affect cellular energy potential. Microcin synthesis and immunity to microcins are shown to be plasmid mediated. The role of microcins in ecology of enterobacteria and the ranking among bacterial antibiotics are discussed.     

Glyoxal oxidases: their nature and properties

H₂O₂ has been found to be required for the activity of the main microbial enzymes responsible for lignin oxidative cleavage, peroxidases. Along with other small radicals, it is implicated in the early attack of plant biomass by fungi. Among the few extracellular H₂O₂-generating enzymes known are the glyoxal oxidases (GLOX). GLOX is a copper-containing enzyme, sharing high similarity at the level of active site structure and chemistry with galactose oxidase. Genes encoding GLOX enzymes are widely distributed among wood-degrading fungi especially white-rot degraders, plant pathogenic and symbiotic fungi. GLOX has also been identified in plants. Although widely distributed, only few examples of characterized GLOX exist. The first characterized fungal GLOX was isolated from Phanerochaete chrysosporium. The GLOX from Utilago maydis has a role in filamentous growth and pathogenicity. More recently, two other glyoxal oxidases from the fungus Pycnoporus cinnabarinus were also characterized. In plants, GLOX from Vitis pseudoreticulata was found to be implicated in grapevine defence mechanisms. Fungal GLOX were found to be activated by peroxidases in vitro suggesting a synergistic and regulatory relationship between these enzymes. The substrates oxidized by GLOX are mainly aldehydes generated during lignin and carbohydrates degradation. The reactions catalysed by this enzyme such as the oxidation of toxic molecules and the production of valuable compounds (organic acids) makes GLOX a promising target for biotechnological applications. This aspect on GLOX remains new and needs to be investigated.     

Lessons from nature: stimuli-responsive polymers and their biomedical applications

Response to stimulus is a basic process of living systems. Based on the lessons from nature, scientists have been designing useful materials that respond to external stimuli such as temperature, pH, light, electric field, chemicals and ionic strength. These responses are manifested as dramatic changes in one of the following: shape, surface characteristics, solubility, formation of an intricate molecular self-assembly or a sol-to-gel transition. Applications of stimuli-responsive, or 'smart', polymers in delivery of therapeutics, tissue engineering, bioseparations, sensors or actuators have been studied extensively and numerous papers and patents are evidence of rapid progress in this area. Understanding the structure-property relationship is essential for the further development and rational design of new functional smart materials. For example, kinetic and thermodynamic control of the coil-to-globule transition could be achieved through changes in polymer composition and topology.     

Pseudoracemes in papilionoid legumes: their nature, development, and variation

Pseudoracemes in papilionoid legumes: their nature, development, and variation. Cymelike partial inflorescences called fascicles have been reported in the inflorescences of several papilionoid tribes. The total inflorescence is termed a ‘pseudoraceme’ because of the multiple flowers in each bract axil. Pseudoraceme development has been studied in 22 taxa in five papilionoid tribes (Abreae, Desmodieae, Millcttieae, Phaseoleae and Psoraleeae). Two to twelve flowers occur per bract axil among various taxa, with three the most common number.Pongamia pinnata and Clitoris fairchildiana have only two flowers per axil; Vigna radiata, Phaseolus vulgaris, and Apios americana have four to five commonly, and Dioclea aff.ucayalina and Abrus precalorius have up to 12. The ‘fascicle’ usually consists of a triad of three flowers; each triad resembles a dichasial cyme in that the middle flower appears terminal. The middle flower however is subtended by a bract on the abaxial side, so that the middle flower is technically lateral. When the first-order axis elongates, each triad may either remain intact or be separated by axis intervalS. Many variations on the basic triad pattern occur in the species studied: 1.one or two flowers may develop while others that are initiated remain suppressed; 2. Additional flowers may be produced that replicate the first triad; 3. Additional flowers may form medianly only, on the abaxial side. The second-order inflorescence axis which has produced the three flowers persists to produce more flowers in replication of the triad pattern in several taxa (Apios americana, Vigna radiata, Phaseolus vulgaris, and Dioclea aff.ucayalina). In Butea monosperma the second-order inflorescence apex produces subsequent flowers (after the triad) in a helix. In Erylhrina perrieri, there is no indication of a persistent second-order inflorescence apex after the central flower; such a condition could be interpreted as a cyme, except for the abaxial subtending bract. The triad in Psoralea pinnata is a true cyme; the middle flower lacks a subtending bract other than that subtending the entire fascicle. Developmentally, the difference between a cyme and an early-determinate raceme (as in the triad type of pseudoraceme) is rather slight. Comparison of the types of inflorescences described here may indicate how the transition may have occurred between racemes and cymes in the evolution of legumes.     

Memory for events and their spatial context: models and experiments

The computational role of the hippocampus in memory has been characterized as: (i) an index to disparate neocortical storage sites; (ii) a time-limited store supporting neocortical long-term memory; and (iii) a content-addressable associative memory. These ideas are reviewed and related to several general aspects of episodic memory, including the differences between episodic, recognition and semantic memory, and whether hippocampal lesions differentially affect recent or remote memories. Some outstanding questions remain, such as: what characterizes episodic retrieval as opposed to other forms of read-out from memory; what triggers the storage of an event memory; and what are the neural mechanisms involved? To address these questions a neural-level model of the medial temporal and parietal roles in retrieval of the spatial context of an event is presented. This model combines the idea that retrieval of the rich context of real-life events is a central characteristic of episodic memory, and the idea that medial temporal allocentric representations are used in long-term storage while parietal egocentric representations are used to imagine, manipulate and re-experience the products of retrieval. The model is consistent with the known neural representation of spatial information in the brain, and provides an explanation for the involvement of Papez''s circuit in both the representation of heading direction and in the recollection of episodic information. Two experiments relating to the model are briefly described. A functional neuroimaging study of memory for the spatial context of life-like events in virtual reality provides support for the model''s functional localization. A neuropsychological experiment suggests that the hippocampus does store an allocentric representation of spatial locations.     

pi-Turns: types,systematics and the context of their occurrence in protein structures

Background  

For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures.     

The nature and context of exploratory experimentation: an introduction to three case studies of exploratory research

My aim in this article is to introduce readers to the topic of exploratory experimentation and briefly explain how the three articles that follow, by Richard Burian, Kevin Elliott, and Maureen O'Malley, advance our understanding of the nature and significance of exploratory research. I suggest that the distinction between exploratory and theory-driven experimentation is multidimensional and that some of the dimensions are continuums. I point out that exploratory experiments are typically theory-informed even if they are not theory-driven. I also distinguish between research programs and experiments. Research programs that are largely exploratory, such as the ones discussed in these case studies, can involve both exploratory and theory-driven experimentation.