Evidence of neutral transcriptome evolution in plants

The transcriptome of an organism is its set of gene transcripts (mRNAs) at a defined spatial and temporal locus. Because gene expression is affected markedly by environmental and developmental perturbations, it is widely assumed that transcriptome divergence among taxa represents adaptive phenotypic selection. This assumption has been challenged by neutral theories which propose that stochastic processes drive transcriptome evolution. To test for evidence of neutral transcriptome evolution in plants, we quantified 18 494 gene transcripts in nonsenescent leaves of 14 taxa of Brassicaceae using robust cross-species transcriptomics which includes a two-step physical and in silico-based normalization procedure based on DNA similarity among taxa. Transcriptome divergence correlates positively with evolutionary distance between taxa and with variation in gene expression among samples. Results are similar for pseudogenes and chloroplast genes evolving at different rates. Remarkably, variation in transcript abundance among root-cell samples correlates positively with transcriptome divergence among root tissues and among taxa. Because neutral processes affect transcriptome evolution in plants, many differences in gene expression among or within taxa may be nonfunctional, reflecting ancestral plasticity and founder effects. Appropriate null models are required when comparing transcriptomes in space and time.

Evolutionary and revolutionary effects of transcomputation

Mathematics in Defence 2011 Abstract. We review transreal arithmetic and present transcomplex arithmetic. These arithmetics have no exceptions. This leads to incremental improvements in computer hardware and software. For example, the range of real numbers, encoded by floating-point bits, is doubled when all of the Not-a-Number(NaN) states, in IEEE 754 arithmetic, are replaced with real numbers. The task of programming such systems is simplified and made safer by discarding the unordered relational operator,leaving only the operators less-than, equal-to, and greater than. The advantages of using a transarithmetic in a computation, or transcomputation as we prefer to call it, may be had by making small changes to compilers and processor designs. However, radical change is possible by exploiting the reliability of transcomputations to make pipelined dataflow machines with a large number of cores. Our initial designs are for a machine with order one million cores. Such a machine can complete the execution of multiple in-line programs each clock tick

Organizing for sustainable procurement: theories, institutions and practice

That construction procurement needs to be re-organized to make it more sustainable implies that there is a problem with the current situation. Starting from this assumption, an overview of construction procurement sets the scene for a discussion of some recent developments relating to organizational frameworks for sustainable construction procurement. Emergent theories dealing with sustainable procurement are considered. There is a plethora of standards and guidance documents for organizing sustainable procurement, originating from a variety of organizations involved. These considerations form the context for approaches being used in practice to achieve sustainable procurement. The Chapter concludes with reflections on why current approaches are insufficient. It seems difficult to persuade clients to spend less money over the life cycle of their buildings. Future directions needed to translate sustainable procurement from rhetoric to reality include the development of suitable incentives and appropriate organizational structures.

An experimental comparison between rival theories of rapid automatized naming performance and its relationship to reading

Two studies investigated the degree to which the relationship between Rapid Automatized Naming (RAN) performance and reading development is driven by shared phonological processes. Study 1 assessed RAN, phonological awareness and reading performance in 1010 children aged 7-10 years. Results showed that RAN deficits occurred in the absence of phonological awareness deficits. These were accompanied by modest reading delays. In structural equation modeling, solutions where RAN was subsumed within a phonological processing factor did not provide a good fit to the data, suggesting that processes outside phonology may drive RAN performance and its association with reading. Study 2 investigated Kail's (1991) proposal that speed of processing underlies this relationship. Children with single RAN deficits showed slower speed of processing than closely matched controls performing normally on RAN. However, regression analysis revealed that RAN made a unique contribution to reading even after accounting for processing speed. Theoretical implications are discussed.

Motherhood, evolutionary psychology and mirror neurons or: ‘Grammar is politics by other means’

Through a close analysis of socio-biologist Sarah Blaffer Hrdy’s work on motherhood and ‘mirror neurons’ it is argued that Hrdy’s claims exemplify how research that ostensibly bases itself on neuroscience, including in literary studies ‘literary Darwinism’, relies after all not on scientific, but on political assumptions, namely on underlying, unquestioned claims about the autonomous, transparent, liberal agent of consumer capitalism. These underpinning assumptions, it is further argued, involve the suppression or overlooking of an alternative, prior tradition of feminist theory, including feminist science criticism.

The ebbing hegemon? An evolutionary perspective on the emergence of holistic governance and the efficient role of Institutional Investors in Environmental, Social and Governance issues (ESG)

This paper seeks to chronicle the roots of corporate governance form its narrow shareholder perspective to the current bourgeoning stakeholder approach while giving cognizance to institutional investors and their effective role in ESG in light of the King Report III of South Africa. It is aimed at a critical review of the extant literature from the shareholder Cadbury epoch to the present day King Report novelty. We aim to: (i) offer an analytical state of corporate governance in the Anglo-Saxon world, Middle East and North Africa (MENA), Far East Asia and Africa; and (ii) illuminate the lead role the king Report of South Africa is playing as the bellwether of the stakeholder approach to corporate governance as well as guiding the role of institutional investors in ESG.

Rerum cognoscere causas: part I - How do the ideas of system dynamics relate to traditional social theories and the voluntarism/determinism debate?

This is the first half of a two-part paper which deals with the social theoretic assumptions underlying system dynamics. The motivation is that clarification in this area can help mainstream social scientists to understand how our field relates to their literature, methods and concerns. Part I has two main sections. The aim of the first is to answer the question: How do the ideas of system dynamics relate to traditional social theories? The theoretic assumptions of the field are seldom explicit but rather are implicit in its practice. The range of system dynamics practice is therefore considered and related to a framework - widely used in both operational research (OR) and systems science - that organises the assumptions behind traditional social theoretic paradigms. Distinct and surprisingly varied groupings of practice are identified, making it difficult to place system dynamics in any one paradigm with any certainty. The difficulties of establishing a social theoretic home for system dynamics are exemplified in the second main section. This is done by considering the question: Is system dynamics deterministic? An analysis shows that attempts to relate system dynamics to strict notions of voluntarism or determinism quickly indicate that the field does not fit with either pole of this dichotomous, and strictly paradigmatic, view. Part I therefore concludes that definitively placing system dynamics with respect to traditional social theories is highly problematic. The scene is therefore set for Part II of the paper, which proposes an innovative and potentially fruitful resolution to this problem.

Patterns of maximum body size evolution in Cenozoic land mammals: eco-evolutionary processes and abiotic forcing

There is accumulating evidence that macroevolutionary patterns of mammal evolution during the Cenozoic follow similar trajectories on different continents. This would suggest that such patterns are strongly determined by global abiotic factors, such as climate, or by basic eco-evolutionary processes such as filling of niches by specialization. The similarity of pattern would be expected to extend to the history of individual clades. Here, we investigate the temporal distribution of maximum size observed within individual orders globally and on separate continents. While the maximum size of individual orders of large land mammals show differences and comprise several families, the times at which orders reach their maximum size over time show strong congruence, peaking in the Middle Eocene, the Oligocene and the Plio-Pleistocene. The Eocene peak occurs when global temperature and land mammal diversity are high and is best explained as a result of niche expansion rather than abiotic forcing. Since the Eocene, there is a significant correlation between maximum size frequency and global temperature proxy. The Oligocene peak is not statistically significant and may in part be due to sampling issues. The peak in the Plio-Pleistocene occurs when global temperature and land mammal diversity are low, it is statistically the most robust one and it is best explained by global cooling. We conclude that the macroevolutionary patterns observed are a result of the interplay between eco-evolutionary processes and abiotic forcing

Testing substorm theories: The need for multipoint observations

The requirement for multipoint observations to test theories of magnetospheric substorms is reviewed. A wide variety of such theories have been proposed, but these cannot be properly evaluated because we do not understand how the various features of a substorm are causally linked. In terms of explaining certain substorm features, some theories may be mutually-exclusive rivals. But this is not always the case, making it possible that theories may be either combined into a synthesis model or loosely connected in a more modular view of substorms. Some key questions are defined which require multipoint in-situ measurements, combined with remote sensing observations, of the development and relationship of the major substorm features.

Writers' rooms: theories of contemporary authorship in portraits of creative spaces

This article analyzes two series of photographs and essays on writers’ rooms published in England and Canada in 2007 and 2008. The Guardian’s Writers Rooms series, with photographs by Eamon McCabe, ran in 2007. In the summer of 2008, The Vancouver International Writers and Readers Festival began to post its own version of The Guardian column on its website by displaying, each week leading up to the Festival in September, a different writer’s “writing space” and an accompanying paragraph. I argue that these images of writers’ rooms, which suggest a cultural fascination with authors’ private compositional practices and materials, reveal a great deal about theoretical constructions of authorship implicit in contemporary literary culture. Far from possessing the museum quality of dead authors’ spaces, rooms that are still being used, incorporating new forms of writing technology, and having drafts of manuscripts scattered around them, can offer insight into such well-worn and ineffable areas of speculation as inspiration, singular authorial genius, and literary productivity.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

A central process in evolution is the recruitment of genes to regulatory networks. We engineered immotile strains of the bacterium Pseudomonas fluorescens that lack flagella due to deletion of the regulatory gene fleQ. Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway. Step 1 mutations increase intracellular levels of phosphorylated NtrC, a distant homologue of FleQ, which begins to commandeer control of the fleQ regulon at the cost of disrupting nitrogen uptake and assimilation. Step 2 is a switch-of-function mutation that redirects NtrC away from nitrogen uptake and towards its novel function as a flagellar regulator. Our results demonstrate that natural selection can rapidly rewire regulatory networks in very few, repeatable mutational steps.

Evolutionary rewiring of bacterial regulatory networks

Bacteria have evolved complex regulatory networks that enable integration of multiple intracellular and extracellular signals to coordinate responses to environmental changes. However, our knowledge of how regulatory systems function and evolve is still relatively limited. There is often extensive homology between components of different networks, due to past cycles of gene duplication, divergence, and horizontal gene transfer, raising the possibility of cross-talk or redundancy. Consequently, evolutionary resilience is built into gene networks – homology between regulators can potentially allow rapid rescue of lost regulatory function across distant regions of the genome. In our recent study [Taylor, et al. Science (2015), 347(6225)] we find that mutations that facilitate cross-talk between pathways can contribute to gene network evolution, but that such mutations come with severe pleiotropic costs. Arising from this work are a number of questions surrounding how this phenomenon occurs.

Sex differences in the programming effects of prenatal stress on psychopathology and stress responses: an evolutionary perspective

There is strong evidence from animal studies that prenatal stress has different effects on male and female offspring. In general, although not always, prenatal stress increases anxiety, depression and stress responses, both hypothalamic–pituitary–adrenal and cardiovascular, in female offspring rather than in male. Males are more likely to show learning and memory deficits. There have been few studies so far in humans which differentiate effects of prenatal stress on male and female psychopathology. Some studies support the animal models, but the evidence is inconsistent. The mediating mechanisms for any sex specific effects are little understood, but there is evidence that placental function can differ depending on the sex of the fetus. We suggest that there may be an evolutionary reason for any sex differences in the long term effects of prenatal stress. In a stressful environment it may be adaptive for females, who are more likely to stay in one place and look after children, to be more vigilant, alert to danger and thus show more stress responsiveness. This can give rise to a more anxious or depressed phenotype. With males it may be more adaptive to go out and explore new environments, compete with other males, and be more aggressive. For this it may help to be less responsive to external stressors. More research is needed into sex differences in the effects of prenatal stress in humans, to test these ideas.