Functional blueprints: an approach to modularity in grown systems

The engineering of grown systems poses fundamentally different system integration challenges than ordinary engineering of static designs. On the one hand, a grown system must be capable of surviving not only in its final form, but at every intermediate stage, despite the fact that its subsystems may grow unevenly or be subject to different scaling laws. On the other hand, the ability to grow offers much greater potential for adaptation, either to changes in the environment or to internal stresses developed as the system grows. I observe that the ability of subsystems to tolerate stress can be used to transform incremental adaptation into the dynamic discovery of viable growth trajectories for the system as a whole. Using this observation, I propose an engineering approach based on functional blueprints, under which a system is specified in terms of desired performance and means of incrementally correcting deficiencies. I explore how manifold geometric programming can support such an approach by simplifying the construction of distortion-tolerant programs, then demonstrate the functional blueprints approach by applying it to integrate simplified models of tissue growth and vascularization, and further show how the composed system may itself be modulated for use as a component in a more complex design.     

Seagrass landscapes: a terrestrial approach to the marine subtidal environment

Subtidal seagrass habitats are prime candidates for the application of principles derived from landscape ecology. Although seagrass systems are relatively simple compared to their terrestrial counterparts in terms of species diversity and structural complexity, seagrasses do display variation in spatial patterns over a variety of scales. The presence of a moving water layer and its influence on faunal dispersal may be a distinguishing feature impacting ecological processes in the subtidal zone. Studying seagrass-dominated landscapes may provide a novel approach to investigating questions regarding self-similarity of spatial patterns, and offers a new perspective for analysing habitat change in a variety of marine environments.     

Linking habitat use to range expansion rates in fragmented landscapes: a metapopulation approach

Temperature increases because of climate change are expected to cause expansions at the high latitude margins of species distributions, but, in practice, fragmented landscapes act as barriers to colonization for most species. Understanding how species distributions will shift in response to climate change therefore requires techniques that incorporate the combined effects of climate and landscape‐scale habitat availability on colonization rates. We use a metapopulation model (Incidence Function Model, IFM) to test effects of fine‐scale habitat use on patterns and rates of range expansion by the butterfly Hesperia comma. At its northern range margin in Britain, this species has increased its breadth of microhabitat use because of climate warming, leading to increased colonization rates. We validated the IFM by reconstructing expansions in five habitat networks between 1982 and 2000, before using it to predict metapopulation dynamics over 100 yr, for three scenarios based on observed changes to habitat use. We define the scenarios as “cold‐world” (only hot, south‐facing 150–250° hillsides are deemed warm enough), “warm‐world” in which 100–300° hillsides can be populated, and “hot‐world”, where the background climate is warm enough to enable use of all aspects (as increasingly observed). In the simulations, increased habitat availability in the hot‐world scenario led to faster range expansion rates, and to long‐term differences in distribution size and pattern. Thus, fine‐scale changes in the distribution of suitable microclimates led to landscape‐scale changes in population size and colonization rate, resulting in coarse‐scale changes to the species distribution. Despite use of a wider range of habitats associated with climate change, H. comma is still expected to occupy a small fraction of available habitat in 100 yr. The research shows that metapopulation models represent a potential framework to identify barriers to range expansion, and to predict the effects of environmental change or conservation interventions on species distributions and persistence.     

Adaptive walks on changing landscapes: Levins' approach extended

The assumption that trade-offs exist is fundamental in evolutionary theory. Levins (Am. Nat. 96 (1962) 361-372) introduced a widely adopted graphical method for analyzing evolution towards an optimal combination of two quantitative traits, which are traded off. His approach explicitly excluded the possibility of density- and frequency-dependent selection. Here we extend Levins method towards models, which include these selection regimes and where therefore fitness landscapes change with population state. We employ the same kind of curves Levins used: trade-off curves and fitness contours. However, fitness contours are not fixed but a function of the resident traits and we only consider those that divide the trait space into potentially successful mutants and mutants which are not able to invade ('invasion boundaries'). The developed approach allows to make a priori predictions about evolutionary endpoints and about their bifurcations. This is illustrated by applying the approach to several examples from the recent literature.     

Functional biotic homogenization of bird communities in disturbed landscapes

Aim  Worldwide, functional homogenization is now considered to be one of the most prominent forms of biotic impoverishment induced by current global changes. Yet this process has hardly been quantified on a large scale through simple indices, and the connection between landscape disturbance and functional homogenization has hardly been established. Here we test whether changes in land use and landscape fragmentation are associated with functional homogenization of bird communities at a national scale.
Location  France.
Methods  We estimated functional homogenization of a community as the average specialization of the species present in that community. We studied the spatial variation of this community specialization index (CSI) using 1028 replicates from the French Breeding Bird Survey along spatial gradients of landscape fragmentation and recent landscape disturbance, measured independently, and accounting for spatial autocorrelation.
Results  The CSI was very sensitive to both measures of environmental degradation: on average, 23% of the difference in the CSI values between two sample sites was attributed to the difference in fragmentation and the disturbance between sites. This negative correlation between CSI and sources of landscape degradation was consistent over various habitats and biogeographical zones.
Main conclusions  We demonstrate that the functional homogenization of bird communities is strongly positively correlated to landscape disturbance and fragmentation. We suggest that the CSI is particularly effective for measuring functional homogenization on both local and global scales for any sort of organism and with abundance or presence–absence data.     

Habitat size and number in multi-habitat landscapes: a model approach based on species-area curves

This paper discusses species diversity in simple multi-habitat environments. Its main purpose is to present simple mathematical and graphical models on how landscape patterns affect species numbers. The idea is to build models of species diversity in multi-habitat landscapes by combining species-area curves for different habitats. Predictions are made about how variables such as species richness and species overlap between habitats influence the proportion of the total landscape each habitat should constitute, and how many habitats it should be divided into in order to be able to sustain the maximal number of species. Habitat size and numbers are the only factors discussed here, not habitat spatial patterns. Among the predictions are: 1) where there are differences in species diversity between habitats, optimal landscape patterns contain larger proportions of species rich habitats. 2) Species overlap between habitats shifts the optimum further towards larger proportions of species rich habitat types. 3) Species overlap also shifts the optimum towards fewer habitat types. 4) Species diversity in landscapes with large species overlap is more resistant to changes in landscape (or reserve) size. This type of model approach can produce theories useful to nature and landscape management in general, and the design of nature reserves and national parks in particular.     

Functional landscape heterogeneity and animal biodiversity in agricultural landscapes

Biodiversity in agricultural landscapes can be increased with conversion of some production lands into 'more-natural'- unmanaged or extensively managed - lands. However, it remains unknown to what extent biodiversity can be enhanced by altering landscape pattern without reducing agricultural production. We propose a framework for this problem, considering separately compositional heterogeneity (the number and proportions of different cover types) and configurational heterogeneity (the spatial arrangement of cover types). Cover type classification and mapping is based on species requirements, such as feeding and nesting, resulting in measures of 'functional landscape heterogeneity'. We then identify three important questions: does biodiversity increase with (1) increasing heterogeneity of the more-natural areas, (2) increasing compositional heterogeneity of production cover types and (3) increasing configurational heterogeneity of production cover types? We discuss approaches for addressing these questions. Such studies should have high priority because biodiversity protection globally depends increasingly on maintaining biodiversity in human-dominated landscapes.     

Gustatory processing: a dynamic systems approach

Recent gustatory studies have provided a growing body of evidence that taste processing is dynamic and distributed, and the taste system too complex to be adequately described by traditional feed-forward models of taste coding. Current research demonstrates that neuronal responses throughout the gustatory neuroaxis are broad, variable and temporally structured, as a result of the fact that the taste network is extensive and heavily interconnected, containing modulatory pathways, many of which are reciprocal. Multimodal influences (e.g. olfactory and somatosensory) and effects of internal state (e.g. attention and expectation), shown in both behavioral and neuronal responses to taste stimuli, add further complexity to neural taste responses. Future gustatory research should extend to more brain regions, incorporate more connections, and analyze behaviors and neuronal responses in both time- and state-dependent manners.     

Ventilatory support: a dynamical systems approach

Misunderstanding of the dynamical behavior of the ventilatory system, especially under assisted ventilation, may explain the problems encountered in ventilatory support monitoring. Proportional assist ventilation (PAV) that theoretically gives a breath by breath assistance presents instability with high levels of assistance. We have constructed a mathematical model of interactions between three objects: the central respiratory pattern generator modelled by a modified Van der Pol oscillator, the mechanical respiratory system which is the passive part of the system and a controlled ventilator that follows its own law. The dynamical study of our model shows the existence of two crucial behaviors, i.e. oscillations and damping, depending on only two parameters, namely the time constant of the mechanical respiratory system and a cumulative interaction index. The same result is observed in simulations of spontaneous breathing as well as of PAV. In this last case, increasing assistance leads first to an increase of the tidal volume (V_T), a further increase in assistance inducing a decrease in V_T, ending in damping of the whole system to an attractive fixed point. We conclude that instabilities observed in PAV may be explained by the different possible dynamical behaviors of the system rather than changes in mechanical characteristics of the respiratory system.     

CODEX,a neural network approach to explore signaling dynamics landscapes

Current studies of cell signaling dynamics that use live cell fluorescent biosensors routinely yield thousands of single‐cell, heterogeneous, multi‐dimensional trajectories. Typically, the extraction of relevant information from time series data relies on predefined, human‐interpretable features. Without a priori knowledge of the system, the predefined features may fail to cover the entire spectrum of dynamics. Here we present CODEX, a data‐driven approach based on convolutional neural networks (CNNs) that identifies patterns in time series. It does not require a priori information about the biological system and the insights into the data are built through explanations of the CNNs'' predictions. CODEX provides several views of the data: visualization of all the single‐cell trajectories in a low‐dimensional space, identification of prototypic trajectories, and extraction of distinctive motifs. We demonstrate how CODEX can provide new insights into ERK and Akt signaling in response to various growth factors, and we recapitulate findings in p53 and TGFβ‐SMAD2 signaling.     

Linking ecological and social systems in cities: urban planning in Finland as a case

The loss of urban green space as a result of urbanization threatens the overall biodiversity of urban areas, and prompts us to consider the importance of existing urban nature more carefully. Because urban ecological systems are in intense interaction with human-social systems, it is fruitful to create an interdisciplinary research and planning framework to ensure the maintenance of biodiversity in urban areas. For this purpose, we adapted a suitable theoretical and conceptual scheme for the setting of Finnish urban development, which provides an example of a situation where a lot of nature has so far remained inside and around urban area. The adapted scheme focuses on the land use change as a result of urban land use planning and development, and may provide a way to address the important variables and feedback mechanisms between information flowing from ecological systems and drivers from the social system. Furthermore, we outlined a more specific framework around the Finnish urban detailed planning process in order to study the interactions between these systems further. After addressing ecology-oriented questions of quantity, quality and needs of urban nature, and human-oriented drivers, such as flow and incorporation of information, knowledge, values and institutions, we identified several challenges in integrating the components of ecological and social systems. Creating common conceptual ground for different actors and disciplines, improving communication in the process, matching contradictory values and perceptions, and improving stakeholder participation would be in the best interest of nature and people of urban areas.     

Complex systems in pulmonary medicine: a systems biology approach to lung disease

The lung is a highly complex organ that can only be understood by integrating the many aspects of its structure and function into a comprehensive view. Such a view is provided by a systems biology approach, whereby the many layers of complexity, from the molecular genetic, to the cellular, to the tissue, to the whole organ, and finally to the whole body, are synthesized into a working model of understanding. The systems biology approach therefore relies on the expertise of many disciplines, including genomics, proteomics, metabolomics, physiomics, and, ultimately, clinical medicine. The overall structure and functioning of the lung cannot be predicted from studying any one of these systems in isolation, and so this approach highlights the importance of emergence as the fundamental feature of systems biology. In this paper, we will provide an overview of a systems biology approach to lung disease by briefly reviewing the advances made at many of these levels, with special emphasis on recent work done in the realm of pulmonary physiology and the analysis of clinical phenotypes.     

Taking a systems approach to ecological systems

Increasingly, there is interest in a systems‐level understanding of ecological problems, which requires the evaluation of more complex, causal hypotheses. In this issue of the Journal of Vegetation Science, Soliveres et al. use structural equation modeling to test a causal network hypothesis about how tree canopies affect understorey communities. Historical analysis suggests structural equation modeling has been under‐utilized in ecology.