Biophysics; fifty years after Schrödinger

E. Schrödinger described his mechanistic view on life in his book “What is Life?” published in 1944. H. Yukawa stated that life is like a building of bricks. Is life understandable in this manner?In 1950–1960 the generation of structure and function in living cells was shown to be analyzable, step by step, within the theoretical framework of physics. In the 1970's the concept of a molecular machine or unit machine in living cells was clearly presented and the effort to experimentally define unit machines was promoted. Recently, new techniques to directly observe their behaviors have been developed. The machines are not always rigid. In sliding machines, the influx-efflux coupling has been found to be loose. For loose coupling, intramachine flexibility seems to be useful.Living cells can be regarded as an organized system composed of many unit machines, some of which exhibit deterministic behaviors while others exhibit probabilistic behaviors. The cells do not always show a definite response to a given input. We need new statistical mechanics for the study of unit machines and their systems which have complex spatial and temporal structures. They may have a mechanism beyond a simple building of bricks.     

Phylogeography’s past,present, and future: 10 years after

Approximately 20 years ago, Avise and colleagues proposed the integration of phylogenetics and population genetics for investigating the connection between micro- and macroevolutionary phenomena. The new field was termed phylogeography. Since the naming of the field, the statistical rigor of phylogeography has increased, in large part due to concurrent advances in coalescent theory which enabled model-based parameter estimation and hypothesis testing. The next phase will involve phylogeography increasingly becoming the integrative and comparative multi-taxon endeavor that it was originally conceived to be. This exciting convergence will likely involve combining spatially-explicit multiple taxon coalescent models, genomic studies of natural selection, ecological niche modeling, studies of ecological speciation, community assembly and functional trait evolution. This ambitious synthesis will allow us to determine the causal links between geography, climate change, ecological interactions and the evolution and composition of taxa across whole communities and assemblages. Although such integration presents analytical and computational challenges that will only be intensified by the growth of genomic data in non-model taxa, the rapid development of “likelihood-free” approximate Bayesian methods should permit parameter estimation and hypotheses testing using complex evolutionary demographic models and genomic phylogeographic data. We first review the conceptual beginnings of phylogeography and its accomplishments and then illustrate how it evolved into a statistically rigorous enterprise with the concurrent rise of coalescent theory. Subsequently, we discuss ways in which model-based phylogeography can interface with various subfields to become one of the most integrative fields in all of ecology and evolutionary biology.     

Elton’s hypothesis revisited: an experimental test using cogongrass

In the 1950s Charles Elton hypothesized that more diverse communities should be less susceptible to invasion by exotic species (biodiversity–invasibility hypothesis). The biodiversity–invasibility hypothesis postulates that species-rich communities are less vulnerable to invasion because vacant niches are less common and the intensity of interspecific competition is more severe. Field studies were conducted at two sites, a logged site and an unlogged site in Santa Rosa County, Florida, U.S.A, to test Elton’s hypothesis using cogongrass (Imperata cylindrica), a non-indigenous grass invading large areas of the Southeastern United States. The logged site was under 17-year-old loblolly pine prior to clear cutting. The unlogged site, a longleaf pine forest, was at the Blackwater River State Forest. Both the logged site and unlogged site showed no significant relationship between the rate of cogongrass spread and native plant species richness, functional richness, and cover of the invaded community. Increased species or functional richness may increase the use of resources; however, the extensive rhizome/root network possessed by cogongrass and its ability to thrive under shade may allow for its persistence in a diverse community. The results from both the logged and unlogged sites do not support the general hypothesis of Elton that invasion resistance and compositional stability increase with diversity. Biodiversity does not appear to be an important factor for cogongrass invasion in the southern United States. Extrinsic factors in this study prevent the ability to draw a defined causal relationship between native plant diversity and invasibility. Underlying reasons for why no relationship was observed may be simply due to the tremendous competitive ability of cogongrass or the narrow range of species richness, functional richness and cover observed in our study.     

To harness traits for ecology,let’s abandon ‘functionality’

Traits are measurable features of organisms. Functional traits aspire to more. They quantify an organism’s ecology and, ultimately, predict ecosystem functions based on local communities. Such predictions are useful, but only if ‘functional’ really means ‘ecologically relevant’. Unfortunately, many ‘functional’ traits seem to be characterized primarily by availability and implied importance – not by their ecological information content. Better traits are needed, but a prevailing trend is to ‘functionalize’ existing traits. The key may be to invert the process, that is, to identify functions of interest first and then identify traits as quantifiable proxies. We propose two distinct, yet complementary, perspectives on traits and provide a ‘taxonomy of traits’, a conceptual compass to navigate the diverse applications of traits in ecology.     

Retracing and rewriting Hooke’s Micrographia book for teaching history of science

The history of science is an important component to acquire for achieving scientific literacy. In this study, a collaborative activity was applied in which the students were presented with the historical context in which Robert Hooke lived and developed the first register of the microscopic world. Furthermore, the students explored the environment using a microscope made by themselves, employing PET bottles and lenses obtained from CD or DVD readers and, finally, they drew and described selected objects, and collaboratively rewrote a ‘new version’ of Hooke’s classical book ‘Micrographia’. The study was performed in a secondary school, with 12- to 15-year-old students, and the hypothesis was that the planned intervention could enlarge students’ perception of historical aspects of the scientific discovery of the microscopic world, to a greater extent than traditional classes involving lectures and textbooks. The comparison was evaluated using a quantitative tool, called the History-Word-Association test (HWAT), which aims to evaluate the general vision of students regarding the agents, historical period and sociocultural circumstance involved in the issue addressed. The students that participated in the planned didactic activity showed a significant improvement in identification and retention of ideas associated with the history of the discovery of the microscopic world.     

Invasion or retreat? The fate of exotic invaders on the northern prairies, 40?years after cattle grazing

Despite the detrimental impacts of invasive plants on native biodiversity, ecosystem function, and management cost, few studies have focused on the long-term persistence of invaders. Here, we use a unique, long-term dataset to examine the recovery of northern rough fescue prairie communities, 41?years after the removal of livestock from Riding Mountain National Park, Manitoba, Canada. Our 1973 data suggest that summer grazing of plains?? rough fescue (Festuca hallii (Vasey) Piper) leads to its displacement from the plant community and increased dominance by exotic invaders. After 41?years of recovery time, historic grazing intensity remained an excellent predictor of community structure and composition. Areas classified as heavily grazed in 1973 remained characterized by exotic grasses and had significantly lower richness and diversity. While some exotic invaders persisted despite 41?years of community recovery, others were ephemeral. For example, both Poa pratensis (L.) and Bromus inermis (Leyss.) persisted, increasing in abundance across all classes of grazing intensity, suggesting that their control requires active restoration of the invaded areas. In contrast, passive restoration may be possible for a subset of ephemeral exotic species such as Taraxacum officinale, which had virtually disappeared from invaded prairies by 2010. Our long-term data provide a rare perspective into the long-term dynamics of plant invasions. Based on our findings, conservation managers will need to consider the dichotomy between persistent and ephemeral invaders and their impact on the recovery of northern prairie communities as they focus their restoration efforts against the mounting impacts of exotic plant invaders.     

The sliding theory of cytoplasmic streaming: fifty years of progress

Fifty years ago, an important paper appeared in Botanical Magazine Tokyo. Kamiya and Kuroda proposed a sliding theory for the mechanism of cytoplasmic streaming. This pioneering study laid the basis for elucidation of the molecular mechanism of cytoplasmic streaming—the motive force is generated by the sliding of myosin XI associated with organelles along actin filaments, using the hydrolysis energy of ATP. The role of the actin–myosin system in various plant cell functions is becoming evident. The present article reviews progress in studies on cytoplasmic streaming over the past 50 years.     

CWM and Rao’s quadratic diversity: a unified framework for functional ecology

Assessing the effects of environmental constraints on community structure often relies on methods that consider changes in species functional traits in response to environmental processes. Various indices have been proposed to measure relevant aspects of community trait composition from different viewpoints and perspectives. Among these, the ‘community-weighted mean trait value’ (CWM) and the Rao coefficient have been widely used in ecological research for summarizing different facets of functional composition and diversity. Analyzing changes in functional diversity of bee communities along a post-fire successional gradient in southern Switzerland we show that these two measures may be used to describe two complementary aspects of community structure, such as the mean and the dispersion of functional traits within a given species assemblage. While CWM can be adequately used to summarize shifts in mean trait values within communities due to environmental selection for certain functional traits, the Rao coefficient can be effectively applied to analyze patterns of trait convergence or divergence compared to a random expectation.     

Palaeolimnology in the English Lakes — some questions and answers over fifty years

In a review of work on 10 of the very numerous lakes of the English Lake District — work which involved co-operation between palaeolimnologists from different disciplines and between palaeo- and neolimnologists — the questions asked by the researchers are listed and it is shown which kind of lake has provided constructive answers. Complete and conformable sediment profiles covering the last ca 14 000 years are found in these lakes, but no single profile is optimal for study of the whole period. Knowledge of the pattern of sediment accumulation is necessary before the record in microfossils and changing sediment composition can be interpreted with confidence. The demonstration that the sediment-source material of these open lakes must have been largely allochthonous established the importance of the sediment column as a record of changes through time in the composition and stability of the soils of each catchment. These changes illustrate the influence of:

The world’s largest parrotfish has slow growth and a complex reproductive ecology

Coral Reefs - The bumphead parrotfish (Bolbometopon muricatum) is an iconic coral reef species of commercial, subsistence, and cultural value that has faced severe declines across the Indo-Pacific....     

Gulf War Syndrome: A Reaction to Psychiatry’s Invasion of the Military?

Following the 1991 Gulf War, a number of soldiers who fought there began to complain of various symptoms and disorders, the collection of which came to be known as Gulf War syndrome (GWS). A debate has raged about the nature and cause of this illness, with many suggesting that it is a psychiatric condition. GWS continues to be a contested illness, yet there is no disputing that many Gulf veterans are ill. This article considers the way in which GWS sufferers understand their illness to be physical in nature and the way in which they negotiate and resist psychological theories of their illness. Based on 14 months of ethnographic fieldwork in the United Kingdom, data for this article were collected mainly by in-depth, semistructured interviews with GWS sufferers, their family members, doctors, and scientists, as well as healthy Gulf veterans. A total of 93 informants were interviewed, including 67 UK Gulf veterans, most of whom were ill. The paper argues that despite the increasing presence of psychiatry in military discourse, GWS reveals the way that people are able to transform, negotiate and even negate its power and assumptions.     

The rebound effect through industrial ecology’s eyes: a review of LCA-based studies

Purpose

Industrial ecology academics have embraced with great interest the rebound effect principle operationalised within energy economics. By pursuing more comprehensive assessments, they applied tools such as life cycle assessment (LCA) to appraise the environmental consequences of the rebound effect. As a result, the mainstream rebound mechanism was broadened and a diversity of (sometimes inconsistent) definitions and approaches unveiled. To depict the state of play, a comprehensive literature review is needed.

Methods

A literature review has been carried out by targeting scientific documents relevant for the integration of the rebound effect into LCA-based studies. The search was conducted using two approaches: (1) via online catalogues using a defined search criterion and (2) via cross-citation analysis from the documents identified through the first approach.

Results and discussion

By analysing a total of 42 works yielded during our review, it was possible to bring together the various advantages of the life cycle perspective, as well as to identify the main inconsistencies and uninformed claims present in literature. Concretely, three main advantages have been identified and are discussed: (1) the representation of the rebound effect as a multi-dimensional, life cycle estimate, (2) the improvement of the technology explicitness and (3) the broadening of the consumption and production factors leading to the rebound effect. Also, inconsistencies on the definition and classification of the rebound effect have been found among studies.

Conclusions

The review contributes a number of valuable insights to understand how the rebound effect has been treated within the industrial ecology and LCA fields. For instance, the conceptual and methodological refinements introduced by these fields represent a step forward from traditional viewpoints, making the study of the rebound effect more comprehensive and meaningful for environmental assessment and policy making. However, the broadened scope of this new approach unveiled some conceptual inconsistencies, which calls for a common framework. This framework would help the LCA community to consistently integrate the rebound effect as well as to create a common language with other disciplines, favouring learning and co-evolution. We believe that our findings can serve as a starting point in order to delineate such a common framework.     

Feeding ecology of Lilian’s Lovebird Agapornis lilianae in Liwonde National Park,Malawi

Lilian's Lovebird Agapornis lilianae is a small, near-threatened parrot resident in mopane Colophospermum mopane woodlands. We investigated its diet and foraging behaviour in Liwonde National Park, Malawi. We expected that Lilian's Lovebirds would show little specialisation for a particular food source but generally feed on available seeds, fruits, flowers and other items as observed in other lovebirds. Lilian's Lovebirds fed on 30 different plant species. Lilian's Lovebirds were observed feeding in six habitat types in Liwonde National Park and adjacent areas during the wet season, and four in the dry season. In the wet season lovebirds (23% of observations) foraged in grassy wetland (dambo) areas the most, whilst in the dry season they foraged in grasslands with tree cover (18%) the most. In mopane woodland, foraging flock sizes differed significantly between the wet (mean = 19.8 ± 1.0 lovebirds) and dry season (mean = 33.6 ± 2.3 lovebirds). Grass seeds were lovebirds’ main food source from December to June. The nutritional analysis of preferred foods showed that grass seeds have a relatively high protein and energy content. Grass seed availability is reduced with savanna burning and so early season burning (before May–June) in areas in and outside the park is not recommended.