Hierarchical evolutive systems: A mathematical model for complex systems

The notion of an evolutive hierarchical system proposed in this paper is a mathematical model for systems, like organisms, with more or less complex objects. This model, based on category theory, retains the following characteristics of natural systems: they have an internal organization consisting of components with interrelations; they maintain their organization in time though their components are changing; their components are divided into several levels corresponding to the increasing complexity of their own organization, and the system may be studied at any of these levels (e.g. molecular, cellular...). The state of the system at a given instant is modeled by a category whose objects are its components, the state transition by a functor, a complex object by the (direct) limit of a pattern of linked objects (which describes its internal organization). The properties of limits in a category make it possible to ‘measure’ the emergence of properties for a complex object with respect to its components, and to reduce the study of a hierarchical system to that of its components of the lowest degree and their links. Categorical constructions describe the formation of a hierarchical evolutive system stepwise, by means of the operations: absorption of external objects, destruction of some components, formation of new complex objects.     

Autogenesis: the evolution of replicative systems

Questions concerning the nature and origin of living systems and the hierarchy of their evolutionary processes are considered, and several problems which arise in connection with formerly developed theories--the autopoiesis of Maturana & Varela, the POL theory of Haukioja and the earlier developed evolutionary theory of Csányi--are discussed. The organization of living systems, the use of informational terms and the question how reproduction can enter into their characterization, problems of autonomy and identity are included in the list. It is suggested that replication--a copying process achieved by a special network of interrelatedness of components and component-producing processes that produces the same network as that which produced them--characterizes the living organization. The information "used" in this copying process, whether it is stored by special means or distributed in the whole system, is called replicative information. A theoretical model is introduced for the spontaneous emergence of replicative organization, called autogenesis. Autogenesis commences in a system by an organized "small" subsystem, referred to as AutoGenetic System Precursor (AGSP), which conveys replicative information to the system. During autogenesis, replicative information increases in system and compartment(s) form. A compartment is the co-replicating totality of components. The end state of autogenesis is an invariantly self-replicating organization which is unable to undergo further intrinsic organizational changes. It is suggested that replicative unities--such as living organisms--evolve via autogenesis. Levels of evolution emerge as a consequence of the relative autonomy of the autogenetic unities. On the next level they can be considered as components endowed with functions and a new autogenetic process can commence. Thus evolution proceeds towards its end state through the parallel autogenesis of the various levels. In terms of applications, ontogenesis is dealt with in detail as an autogenetic process as is the autogenesis of the biosphere and the global system.     

Biocomplexity: adaptive behavior in complex stochastic dynamical systems

Existing methods of complexity research are capable of describing certain specifics of bio systems over a given narrow range of parameters but often they cannot account for the initial emergence of complex biological systems, their evolution, state changes and sometimes-abrupt state transitions. Chaos tools have the potential of reaching to the essential driving mechanisms that organize matter into living substances. Our basic thesis is that while established chaos tools are useful in describing complexity in physical systems, they lack the power of grasping the essence of the complexity of life. This thesis illustrates sensory perception of vertebrates and the operation of the vertebrate brain. The study of complexity, at the level of biological systems, cannot be completed by the analytical tools, which have been developed for non-living systems. We propose a new approach to chaos research that has the potential of characterizing biological complexity. Our study is biologically motivated and solidly based in the biodynamics of higher brain function. Our biocomplexity model has the following features, (1) it is high-dimensional, but the dimensionality is not rigid, rather it changes dynamically; (2) it is not autonomous and continuously interacts and communicates with individual environments that are selected by the model from the infinitely complex world; (3) as a result, it is adaptive and modifies its internal organization in response to environmental factors by changing them to meet its own goals; (4) it is a distributed object that evolves both in space and time towards goals that is continually re-shaping in the light of cumulative experience stored in memory; (5) it is driven and stabilized by noise of internal origin through self-organizing dynamics. The resulting theory of stochastic dynamical systems is a mathematical field at the interface of dynamical system theory and stochastic differential equations. This paper outlines several possible avenues to analyze these systems. Of special interest are input-induced and noise-generated, or spontaneous state-transitions and related stability issues.     

Regulation of the Actin Cytoskeleton Transformation in the Cell by ARP2/3 Complex. Review

The cytoskeleton is formed by a network of protein filaments, including microtubules, actin filaments and intermediate filaments. Filaments permeate the entire cytoplasm; they are involved in maintaining the cell shape, they organize and anchor the organelles, they control the transport of various molecules, cell division and provide signal transduction. To implement these diverse and complex functions, the components of the cytoskeleton must be very dynamic and mobile, be able to rebuilt quickly and interact with each other. This is due to the presence of a large number of actin-binding proteins—nucleators, activators, inactivators of polymerization and depolymerization of actin filaments. This review describes the regulation of actin dynamics by the Arp2/3 complex. In the cell, this complex is in an inactive state. Its activation occurs after it’s interaction with activators. Activators change the conformation and spatial arrangement of the domains of the Arp2/3 complex, providing its interaction with the monomeric and polymeric actin. Activators of the Arp2/3 complex have been known for a long time and include such proteins as WASp and WAVE. All activators possess a specific VCA domain, which is responsible for their binding to the Arp2/3 complex. The structure of the complex with bound activators has been studied using various physical-chemical methods. The inactivators of the complex only recently attracted specific attention of the investigators. At present, at least five different proteins are known to inactivate the Arp2/3 complex by binding to its various subunits. Examples of inactivators are coronin, Gmf and arpin. The structure of the Arp2/3 complex with inactivators was recently published and showed that despite their binding to different subunits of the complex, all inactivators transform the Arp2/3 complex into an “open” state, moving the actin-like Arp subunits apart from each other. Studies of the spatial organization of actin-binding proteins are necessary for understanding the patterns of interaction between them while providing the vital activity of the cell. These data can later be used in the search for new ligands to prevent metastasis of tumor cells.     

A supramolecular light-harvesting complex from chloroplast photosystem-II membranes.

In this study, we report on the composition of a photosystem-II antenna preparation which contains three chlorophyll-a/b proteins (CP), CP29, CP24 and light-harvesting complex (LHC) II obtained from Zea mays grana membranes as previously described [Dainese, P. & Bassi, R. (1991) J. Biol. Chem. 266, 8136-8142]. We demonstrate that the three chlorophyll proteins are present in the preparation with a 3:3:9 molar ratio and that they form a supramolecular antenna complex which represents one third of the photosystem-II antenna system. Phosphorylation experiments show that this complex is involved in the mechanism of regulation of excitation-energy distribution between photosystems: phosphorylation of the membranes induces dissociation of the LHCII moiety from the CP29-CP24 moiety and changes in the aggregation state of LHCII components of the CP29-CP24-LHCII complex. The LHCII subpopulations of the complex are shown to be distinct from the total LHCII population by isoelectrofocusing analysis. On the basis of these data and in the light of the stoichiometry of photosystem-II chlorophyll-binding proteins, we propose a model for the organization of photosystem-II antenna system.     

A systems approach to animal communication

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function varies in different states of the system. We provide a brief overview of the current state of the field, including a focus on select studies that highlight the dynamic nature of animal signalling. We then introduce core concepts from systems biology (redundancy, degeneracy, pluripotentiality, and modularity) and discuss their relationships with system properties (e.g. robustness, flexibility, evolvability). We translate systems concepts into an animal communication framework and accentuate their utility through a case study. Finally, we demonstrate how consideration of the system-level organization of animal communication poses new practical research questions that will aid our understanding of how and why animal displays are so complex.     

Multifractal growth in periphyton communities

Periphyton is an aquatic community composed by algae, bacteria, fungi, and other microorganisms that can develop a complex architecture comparable to tropical forests. We analyzed the spatial pattern of a periphyton community along a succession developed in experimental tanks. Our aim was to identify regularities that may help us to explain the patchiness of this community. Therefore, we estimated the spatial pattern of periphyton biomass using a non‐destructive image analysis technique to obtain a temporal series of the spatial distribution. These were analyzed using multifractal techniques. Multifractals are analogous to fractals but they look at the geometry of quantities instead of the geometry of pattern. To use these techniques the object of study must show scale invariance and then can be characterized by a spectra of fractal dimensions. Self‐organization describes the evolution of complex structures that emerge spontaneously driven internally by variations of the system itself. The spatial distribution of biomass showed scale invariance at all stages of succession and as the periphyton developed in a homogeneous landscape, in a demonstration of self‐organized behavior. Self‐organization to a critical state (SOC) is presented in the complex systems literature as a general explanation for scale invariance in nature. SOC requires a mechanism where the history of past events in a place influence the actual dynamics, this was termed ecological memory. The scale invariance was found from the very beginning of the succession thus self‐organized criticality is a very improbable explanation for the pattern because there would be not enough time for the build‐up of ecological memory. Positive interactions between algae and bacteria, and the existence of different spatial scales of colonization and growth are the likely causes of this pattern. Our work is a demonstration of how large scale patterns emerge from local biotic interactions.     

Distribution of P-protein in Mature Sieve Elements of Cucurbita maxima Seedlings Subjected to Prolonged Darkness

A study has been made of the structure of the sieve tubes inthe phloem of seedlings of Cucurbita maxima kept in total darknessfor 2 or 3 days. All cytoplasmic components were found to beparietal in their distribution. The parietal system was closelyapplied to the cell membrane and appeared to be supported bya continuous framework of endoplasmic reticulum (ER) with whichP-protein was intimately associated. The ER-P-protein complexwas highly compact in some sieve elements and loosened to variousdegrees in others. The pores in the sieve plates were eitherunobstructed or occluded by components of the parietal complexin various ways, occlusion not always being accompanied by noticeabledisruption of the parietal system. In visibly undisturbed sievetubes, in which the ER-P-protein complex was in a highly compactstate, occlusion appeared accidental, arbitrary and withoutany alignment of the components present in the pores. It issuggested that the distribution of the cytoplasmic componentsin the parietal position represents a true-to-life conditionof the sieve tube, preserved due to control of the ‘surge’artefact to which transporting sieve tubes are susceptible.However, the organization of sieve tube probably changes withthe state of transport and the highly compact condition of theER-P-protein complex as well as unobstructed or arbitrarilyobstructed sieve plate pores represent a state of ‘rest’or low transport. Cucurbita maxima, P-protein, sieve elements, phloem, seedlings     

The Arabidopsis ESCRT protein�Cprotein interaction network

In yeast, endosomal sorting of monoubiquitylated transmembrane proteins is performed by a subset of the 19 "class E vacuolar protein sorting" proteins. The core machinery consists of 11 proteins that are organised in three complexes termed ESCRT I-III (endosomal sorting complex required for transport I-III) and is conserved in eukaryotic cells. While the pathway is well understood in yeast and animals, the plant ESCRT system is largely unexplored. At least one sequence homolog for each ESCRT component can be found in the Arabidopsis genome. Generally, sequence conservation between yeast/animals and the Arabidopsis proteins is low. To understand details about participating proteins and complex organization we have performed a systematic pairwise yeast two hybrid analysis of all Arabidopsis proteins showing homology to the ESCRT core machinery. Positive interactions were validated using bimolecular fluorescence complementation. In our experiments, most putative ESCRT components exhibited interactions with other ESCRT components that could be shown to occur on endosomes suggesting that despite their low homology to their yeast and animal counterparts they represent functional components of the plant ESCRT pathway.     

The Ecological Component of Ecological Risk Assessment: Lessons from a Field Experiment

To improve ecological relevance, regulatory agencies are promoting assessments of effects at higher levels of organization, an objective that requires an understanding of current ecological theories. One such theory, hierarchy theory, contends that the effects of a disturbance acting at one level of organization (e.g., population) are not, as a rule, transmitted to higher levels of organization (e.g., community). Conversely, effects at higher levels of organization only occur if lower level variables have been affected. Further, responses to disturbance depend on disturbance history. In this study, I determined the effects of a disturbance treatment at the population, guild, and community levels of organization for vegetation in five wetlands with a disturbance history ranging from highly to rarely disturbed. The 2-year field experiment revealed that the effects of the disturbance treatment were most strongly felt at the population level of organization in wetlands without a history of disturbance. These observed impacts took place against a backdrop of constant change. Thus, the eventual disappearance of treatment effects was not due to a return to the pre-treatment state, but rather a return to a trajectory similar to that exhibited by the control plots. The implications of these results for ecological risk assessment are: (1) the observed effects of a stressor in a system cannot be extrapolated to other systems unless they have similar disturbance histories, (2) detecting effects before they become serious requires monitoring at lower levels of organization, (3) recovery to a naturally innate state is not a viable concept, and (4) the traditional approach of using one post-treatment measurement to determine if reference and impact sites differ is of very questionable value.     

A Simple Self-Maintaining Metabolic System: Robustness,Autocatalysis, Bistability

A living organism must not only organize itself from within; it must also maintain its organization in the face of changes in its environment and degradation of its components. We show here that a simple (M,R)-system consisting of three interlocking catalytic cycles, with every catalyst produced by the system itself, can both establish a non-trivial steady state and maintain this despite continuous loss of the catalysts by irreversible degradation. As long as at least one catalyst is present at a sufficient concentration in the initial state, the others can be produced and maintained. The system shows bistability, because if the amount of catalyst in the initial state is insufficient to reach the non-trivial steady state the system collapses to a trivial steady state in which all fluxes are zero. It is also robust, because if one catalyst is catastrophically lost when the system is in steady state it can recreate the same state. There are three elementary flux modes, but none of them is an enzyme-maintaining mode, the entire network being necessary to maintain the two catalysts.     

Dependence of the Parameters of Visual Evoked Potentials on the Parameters of a Complex Visual Stimulus (Tests on Humans)

We recorded visual evoked potentials, VEP, elicited by presentation of a reversal chess pattern; 35 healthy persons were examined. A recording electrode was in point Oz, according to the 10-20 system; dimensions of the chess pattern square fields and their contrast varied from 1.8 to 120 and from 2 to 100%, respectively. Peak latencies, PL, of the N75 component depended on the contrast of stimulus elements in a U-like manner with the minimum within a 20-25% range. The PL of the P100 component monotonically increased with a decrease in the contrast, while the dependence of the PL of N145 was complex: a trend toward a decrease with a decrease in contrast to 30%, a local maximum in about 25%, a decrease and stabilization within a 15-4% range, and a sharp increase at the minimum contrast. The amplitude of N75 decreased with decrease in contrast down to 20-25% and then stabilized; the amplitude of P100 decreased in an S-like mode, with a plateau within 25-4%. The dependence of the N145 amplitude was complex, with a plateau-like maximum at 30-15% contrast. The amplitudes of the negative VEP components, N75 and N145, increased with an increase in the square dimensions to 7.5 and then decreased. Changes in the P100 amplitude included two phases, with a local minimum within an angular dimension range of 30-15^O. The PL of all analyzed components in general increased with a decrease in the angular dimension of the pattern components. The above data are discussed considering concepts on the genesis of different VEP components and on the existence of specialized channels in the visual system, which are responsible for detection of different parameters of a visual object. The complex dynamics of the PL of the analyzed VEP components and of the P100 amplitude related to variation of the contrast and angular dimensions of the elements of a complex stimulus are considered to be determined by a module principle of the organization of the elements constituting different levels of the visual system and by transformations of the receptive fields of these elements on the level of cortical modules, which are related to changes in the stimulus parameters.     

Cognitive Learning,Monitoring and Assistance of Industrial Workflows Using Egocentric Sensor Networks

Today, the workflows that are involved in industrial assembly and production activities are becoming increasingly complex. To efficiently and safely perform these workflows is demanding on the workers, in particular when it comes to infrequent or repetitive tasks. This burden on the workers can be eased by introducing smart assistance systems. This article presents a scalable concept and an integrated system demonstrator designed for this purpose. The basic idea is to learn workflows from observing multiple expert operators and then transfer the learnt workflow models to novice users. Being entirely learning-based, the proposed system can be applied to various tasks and domains. The above idea has been realized in a prototype, which combines components pushing the state of the art of hardware and software designed with interoperability in mind. The emphasis of this article is on the algorithms developed for the prototype: 1) fusion of inertial and visual sensor information from an on-body sensor network (BSN) to robustly track the user’s pose in magnetically polluted environments; 2) learning-based computer vision algorithms to map the workspace, localize the sensor with respect to the workspace and capture objects, even as they are carried; 3) domain-independent and robust workflow recovery and monitoring algorithms based on spatiotemporal pairwise relations deduced from object and user movement with respect to the scene; and 4) context-sensitive augmented reality (AR) user feedback using a head-mounted display (HMD). A distinguishing key feature of the developed algorithms is that they all operate solely on data from the on-body sensor network and that no external instrumentation is needed. The feasibility of the chosen approach for the complete action-perception-feedback loop is demonstrated on three increasingly complex datasets representing manual industrial tasks. These limited size datasets indicate and highlight the potential of the chosen technology as a combined entity as well as point out limitations of the system.     

Molecular Organization of Soluble Type III Secretion System Sorting Platform Complexes

Many medically relevant Gram‐negative bacteria use the type III secretion system (T3SS) to translocate effector proteins into the host for their invasion and intracellular survival. A multi-protein complex located at the cytosolic interface of the T3SS is proposed to act as a sorting platform by selecting and targeting substrates for secretion through the system. However, the precise stoichiometry and 3D organization of the sorting platform components are unknown. Here we reconstitute soluble complexes of the Salmonella Typhimurium sorting platform proteins including the ATPase InvC, the regulator OrgB, the protein SpaO and a recently identified subunit SpaO_C, which we show to be essential for the solubility of SpaO. We establish domain–domain interactions, determine for the first time the stoichiometry of each subunit within the complexes by native mass spectrometry and gain insight into their organization using small-angle X‐ray scattering. Importantly, we find that in solution the assembly of SpaO/SpaO_C/OrgB/InvC adopts an extended L-shaped conformation resembling the sorting platform pods seen in in situ cryo-electron tomography, proposing that this complex is the core building block that can be conceivably assembled into higher oligomers to form the T3SS sorting platform. The determined molecular arrangements of the soluble complexes of the sorting platform provide important insights into its architecture and assembly.     

Tritium planigraphy: A tool for studying the spatial structure of proteins and their complexes

The review is devoted to tritium planigraphy and its applications in solving a broad scope of problems in modern molecular and physicochemical biology. The method is based on nonselective substitution of tritium for hydrogen in the hydrocarbon parts of target molecules. It furnishes information on the steric accessibility of the components of a system under study (macromolecule within a complex amino acid residues, and even separate atomic groupings in a macromolecule) that characterizes the structure of the entire object. The technique is applicable to specimens in different phase states and has no limitations in respect of the target molecular mass. Tritium planigraphy is especially important in the cases when the biological macromolecules cannot be examined by the conventional methods (X-ray analysis and NMR spectroscopy). The review summarizes the studies of protein accessible surface and spatial arrangement, and outlines the approaches to modeling the protein 3D structure and probing into the spatial organization of theEscherichia coli ribosome and virus particles.     

Organization of the native ribosome–translocon complex at the mammalian endoplasmic reticulum membrane

BackgroundIn eukaryotic cells, many proteins have to be transported across or inserted into the endoplasmic reticulum membrane during their biogenesis on the ribosome. This process is facilitated by the protein translocon, a highly dynamic multi-subunit membrane protein complex.Scope of reviewThe aim of this review is to summarize the current structural knowledge about protein translocon components in mammals.Major conclusionsVarious structural biology approaches have been used in synergy to characterize the translocon in recent years. X-ray crystallography and cryoelectron microscopy single particle analysis have yielded highly detailed insights into the structure and functional mechanism of the protein-conducting channel Sec61, which constitutes the functional core of the translocon. Cryoelectron tomography and subtomogram analysis have advanced our understanding of the overall structure, molecular organization and compositional heterogeneity of the translocon in a native membrane environment. Tomography densities at subnanometer resolution revealed an intricate network of interactions between the ribosome, Sec61 and accessory translocon components that assist in protein transport, membrane insertion and maturation.General significanceThe protein translocon is a gateway for approximately one third of all synthesized proteins and numerous human diseases are associated with malfunctioning of its components. Thus, detailed insights into the structure and molecular organization of the translocon will not only advance our understanding of membrane protein biogenesis in general, but they can potentially pave the way for novel therapeutic approaches against human diseases.     

Long-wavelength chlorophylls in photosystem I of cyanobacteria: Origin,localization, and functions

The structural organization of photosystem I (PSI) complexes in cyanobacteria and the origin of the PSI antenna long-wavelength chlorophylls and their role in energy migration, charge separation, and dissipation of excess absorbed energy are discussed. The PSI complex in cyanobacterial membranes is organized preferentially as a trimer with the core antenna enriched with long-wavelength chlorophylls. The contents of long-wavelength chlorophylls and their spectral characteristics in PSI trimers and monomers are species-specific. Chlorophyll aggregates in PSI antenna are potential candidates for the role of the long-wavelength chlorophylls. The red-most chlorophylls in PSI trimers of the cyanobacteria Arthrospira platensis and Thermosynechococcus elongatus can be formed as a result of interaction of pigments peripherally localized on different monomeric complexes within the PSI trimers. Long-wavelength chlorophylls affect weakly energy equilibration within the heterogeneous PSI antenna, but they significantly delay energy trapping by P700. When the reaction center is open, energy absorbed by long-wavelength chlorophylls migrates to P700 at physiological temperatures, causing its oxidation. When the PSI reaction center is closed, the P700 cation radical or P700 triplet state (depending on the P700 redox state and the PSI acceptor side cofactors) efficiently quench the fluorescence of the long-wavelength chlorophylls of PSI and thus protect the complex against photodestruction.     

Oligomers of Tha4 organize at the thylakoid Tat translocase during protein transport

The Tat (twin arginine translocation) systems of thylakoids and bacteria transport fully folded protein substrates without breaching the permeability barrier of the membrane. Two components of the thylakoid system, cpTatC and Hcf106, compose a precursor-bound receptor complex. The third component, Tha4, assembles with the precursor-bound receptor complex for the translocation step and is thought to compose at least part of the protein-conducting channel. Here, we used two different cross-linking approaches to explore the organization of Tha4 in the translocase. These cross-linking techniques showed that transition to an active protein transport state resulted in an alignment of the Tha4 amphipathic helix and C-terminal tail domains to form Tha4 oligomers. Oligomerization required functional Tha4, a twin arginine signal peptide, and an active cpTatC-Hcf106 receptor complex. The spectrum of oligomers obtained was independent of the mature folded domain of the precursor. We propose a trapdoor mechanism for translocation whereby aligned oligomers of Tha4 amphipathic helices fold into the membrane to allow formfitting passage of precursor proteins.     

Interactions among genomic structure, function, and evolution revealed by comprehensive analysis of the Arabidopsis thaliana genome

The genome in a higher organism consists of a number of types of nucleotide sequence-specialized components, with each having tens of thousands of members or elements. It is crucial for our understanding of how a genome as an entity is organized, functions, and evolves to determine how these components are organized in the genome and how they relate with each other; however, no such knowledge is available. Here, we report a comprehensive analysis of the organization and interaction of all 40 components constituting the genome of the plant model species, Arabidopsis thaliana, at the whole-genome and chromosome levels. The 40 components include (i) 6 genome structural components consisting of GC%, genes, retrotransposons, DNA transposons, simple repeats, and low complex repeats; (ii) 3 evolutionarily critical features consisting of recombination rate, nucleotide substitutions, and nucleotide insertions/deletions; and (iii) 31 categories of genes with different functions and numbers of functions. We show that the distributions of 39 of the 40 components of the genome (excepting GC%) deviate significantly from the random distribution model and different types of the genome components are significantly correlated. These results remained to be true even when the genomic regions, such as centromeric regions, where transposable and repeat elements are abundant were excluded from the analyses. These findings suggest that DNA molecules contained in the Arabidopsis genome are each organized and structured from their constituting components in an unambiguous manner and that different types of the components that constitute or characterize the genome interact. The analysis also showed that each chromosome consists of a similar set of the components at similar densities, suggesting that the unique organization and interaction pattern of the components in each chromosome may represent, at least in part, the identity of a chromosome or a genome at the genome level, thus partly accounting for the phenotypic variation among different species. The data also provide comprehensive and new insights into many phenomena significant in genome biology, with which we particularly discuss the variation of genetic recombination. The variation of genetic recombination rate along a chromosomal arm is shaped, not only by the distribution of simple repeats, retrotransposons, DNA transposons, and nucleotide substitutions, but also by the functions of genes contained, especially those with multiple functions, suggesting that variation of genetic recombination along a chromosomal arm is the result of interactions among the components constituting local genome structure, function, and evolution.