Principles for Consciousness in Integrated Cognitive Control

In this article we will argue that given certain conditions for the evolution of bi- \ud ological controllers, these will necessarily evolve in the direction of incorporating \ud consciousness capabilities. We will also see what are the necessary mechanics for \ud the provision of these capabilities and extrapolate this vision to the world of artifi- \ud cial systems postulating seven design principles for conscious systems. This article \ud was published in the journal Neural Networks special issue on brain and conscious- \ud ness

Biophysics of magnetic orientation: strengthening the interface between theory and experimental design

The first demonstrations of magnetic effects on the behaviour of migratory birds and homing pigeons in laboratory and field experiments, respectively, provided evidence for the longstanding hypothesis that animals such as birds that migrate and home over long distances would benefit from possession of a magnetic sense. Subsequent identification of at least two plausible biophysical mechanisms for magnetoreception in animals, one based on biogenic magnetite and another on radical-pair biochemical reactions, led to major efforts over recent decades to test predictions of the two models, as well as efforts to understand the ultrastructure and function of the possible magnetoreceptor cells. Unfortunately, progress in understanding the magnetic sense has been challenged by: (i) the availability of a relatively small number of techniques for analysing behavioural responses to magnetic fields by animals; (ii) difficulty in achieving reproducible results using the techniques; and (iii) difficulty in development and implementation of new techniques that might bring greater experimental power. As a consequence, laboratory and field techniques used to study the magnetic sense today remain substantially unchanged, despite the huge developments in technology and instrumentation since the techniques were developed in the 1950s. New methods developed for behavioural study of the magnetic sense over the last 30 years include the use of laboratory conditioning techniques and tracking devices based on transmission of radio signals to and from satellites. Here we consider methodological developments in the study of the magnetic sense and present suggestions for increasing the reproducibility and ease of interpretation of experimental studies. We recommend that future experiments invest more effort in automating control of experiments and data capture, control of stimulation and full blinding of experiments in the rare cases where automation is impossible. We also propose new experiments to confirm whether or not animals can detect magnetic fields using the radical-pair effect together with an alternate hypothesis that may explain the dependence on light of responses by animals to magnetic field stimuli

Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control

Standard virulence evolution theory assumes that virulence factors are maintained because they aid parasitic exploitation, increasing growth within and/or transmission between hosts. An increasing number of studies now demonstrate that many opportunistic pathogens (OPs) do not conform to these assumptions, with virulence factors maintained instead because of advantages in non-parasitic contexts. Here we review virulence evolution theory in the context of OPs and highlight the importance of incorporating environments outside a focal virulence site. We illustrate that virulence selection is constrained by correlations between these external and focal settings and pinpoint drivers of key environmental correlations, with a focus on generalist strategies and phenotypic plasticity. We end with a summary of key theoretical and empirical challenges to be met for a fuller understanding of OPs

Presence and rehabilitation: toward second-generation virtual reality applications in neuropsychology

Virtual Reality (VR) offers a blend of attractive attributes for rehabilitation. The most exploited is its ability to create a 3D simulation of reality that can be explored by patients under the supervision of a therapist. In fact, VR can be defined as an advanced communication interface based on interactive 3D visualization, able to collect and integrate different inputs and data sets in a single real-like experience. However, "treatment is not just fixing what is broken; it is nurturing what is best" (Seligman & Csikszentmihalyi). For rehabilitators, this statement supports the growing interest in the influence of positive psychological state on objective health care outcomes. This paper introduces a bio-cultural theory of presence linking the state of optimal experience defined as "flow" to a virtual reality experience. This suggests the possibility of using VR for a new breed of rehabilitative applications focused on a strategy defined as transformation of flow. In this view, VR can be used to trigger a broad empowerment process within the flow experience induced by a high sense of presence. The link between its experiential and simulative capabilities may transform VR into the ultimate rehabilitative device. Nevertheless, further research is required to explore more in depth the link between cognitive processes, motor activities, presence and flow

Restart could optimize the probability of success in a Bernoulli trial

Recently noticed ability of restart to reduce the expected completion time of first-passage processes allows appealing opportunities for performance improvement in a variety of settings. However, complex stochastic processes often exhibit several possible scenarios of completion which are not equally desirable in terms of efficiency. Here we show that restart may have profound consequences on the splitting probabilities of a Bernoulli-like first-passage process, i.e. of a process which can end with one of two outcomes. Particularly intriguing in this respect is the class of problems where a carefully adjusted restart mechanism maximizes probability that the process will complete in a desired way. We reveal the universal aspects of this kind of optimal behaviour by applying the general approach recently proposed for the problem of first-passage under restart.Comment: 6 pages and 3 figures in the main text + 4 pages of supplementary informatio

Experimental approaches to unravel proximate mechanisms of parasitoid searching and patch leaving behaviour

Animals exploit complex environments in an optimal way, often with limited brain capacities. Interestingly, it is largely unknown, how they do so. This thesis comprises five studies investigating proximate mechanisms modulating the searching behaviour of parasitoid wasps. These organisms serve as excellent organisms for such questions due to their tight link of searching success and fitness. While the first study assumed a simple motor response to serve as a heuristic, yet effective, mechanism, the remaining studies focussed on the role of octopamine [OA] and dopamine [DA]. Both substances being essential in the assessment of reward and aversive stimuli, respectively. Neither the assumed motor response could be met nor did OA or DA reveal any consistent effects with respect to the assessment of rewards and costs. DA slightly impacted the movement pattern. Treatment with OA revealed numerous effects, in total indicating an influence on stress level. Both is in line with studies on other species. Yet, although OA significantly influences searching behaviour, the underlying mechanism is considerably more complex than initially assumed. Last, it was shown that a generalisation on the basis of a few studies and stimuli with respect to the role of OA in the integration of rewards is a simplification

Humans, geometric similarity and the Froude number: is ''reasonably close'' really close enough?

Summary Understanding locomotor energetics is imperative, because energy expended during locomotion, a requisite feature of primate subsistence, is lost to reproduction. Although metabolic energy expenditure can only be measured in extant species, using the equations of motion to calculate mechanical energy expenditure offers unlimited opportunities to explore energy expenditure, particularly in extinct species on which empirical experimentation is impossible. Variability, either within or between groups, can manifest as changes in size and/or shape. Isometric scaling (or geometric similarity) requires that all dimensions change equally among all individuals, a condition that will not be met in naturally developing populations. The Froude number (Fr), with lower limb (or hindlimb) length as the characteristic length, has been used to compensate for differences in size, but does not account for differences in shape. To determine whether or not shape matters at the intraspecific level, we used a mechanical model that had properties that mimic human variation in shape. We varied crural index and limb segment circumferences (and consequently, mass and inertial parameters) among nine populations that included 19 individuals that were of different size. Our goal in the current work is to understand whether shape variation changes mechanical energy sufficiently enough to make shape a critical factor in mechanical and metabolic energy assessments. Our results reaffirm that size does not affect mass-specific mechanical cost of transport (Alexander and Jayes, 1983) among geometrically similar individuals walking at equal Fr. The known shape differences among modern humans, however, produce sufficiently large differences in internal and external work to account for much of the observed variation in metabolic energy expenditure, if mechanical energy is correlated with metabolic energy. Any species or other group that exhibits shape differences should be affected similarly to that which we establish for humans. Unfortunately, we currently do not have a simple method to control or adjust for size–shape differences in individuals that are not geometrically similar, although musculoskeletal modeling is a viable, and promising, alternative. In mouse-to-elephant comparisons, size differences could represent the largest source of morphological variation, and isometric scaling factors such as Fr can compensate for much of the variability. Within species, however, shape differences may dominate morphological variation and Fr is not designed to compensate for shape differences. In other words, those shape differences that are “reasonably close” at the mouse-to-elephant level may become grossly different for within-species energetic comparisons

Unveiling the Crucial Intermediates in Androgen Production

Significance: The human enzyme cytochrome P450 17A1 (CYP17A1) catalyzes the critical step in the biosynthesis of the male sex hormones, and, as such, it is a key target for the inhibition of testosterone production that is necessary for the progression of certain cancers. CYP17A1 catalyzes two distinct types of chemical transformations. The first is the hydroxylation of the steroid precursors pregnenolone and progesterone. The second is a different reaction involving carbon–carbon (C-C) bond cleavage, the mechanism of which has been actively debated in the literature. Using a combination of chemical and biophysical methods, we have been able to trap and characterize the active intermediate in this C-C lyase reaction, an important step in the potential design of mechanism-based inhibitors for the treatment of prostate cancers. Abstract: Ablation of androgen production through surgery is one strategy against prostate cancer, with the current focus placed on pharmaceutical intervention to restrict androgen synthesis selectively, an endeavor that could benefit from the enhanced understanding of enzymatic mechanisms that derives from characterization of key reaction intermediates. The multifunctional cytochrome P450 17A1 (CYP17A1) first catalyzes the typical hydroxylation of its primary substrate, pregnenolone (PREG) and then also orchestrates a remarkable C17–C20 bond cleavage (lyase) reaction, converting the 17-hydroxypregnenolone initial product to dehydroepiandrosterone, a process representing the first committed step in the biosynthesis of androgens. Now, we report the capture and structural characterization of intermediates produced during this lyase step: an initial peroxo-anion intermediate, poised for nucleophilic attack on the C20 position by a substrate-associated H-bond, and the crucial ferric peroxo-hemiacetal intermediate that precedes carbon–carbon (C-C) bond cleavage. These studies provide a rare glimpse at the actual structural determinants of a chemical transformation that carries profound physiological consequences

Restoring the mauri of coastal dune lake ecosystems : the case study of Lake Waiorongomai, Ōtaki, Aotearoa/New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Resource and Environmental Planning, at Massey University, Palmerston North, Aotearoa/New Zealand

The following Figures have been removed for copyright reasons but may be accessed via their sources listed in the bibliography (page numbers in the captions): 1.2.1 (p.13); 2.2.1 (p.48); 4.2.3 (p.166); 4.2.4 (p.168); 4.3.1 (p.184); 4.3.4 (p.191); 4.3.5 (p.194); 4.3.6 (p.198); 4.3.7 (p.203); 4.3.8 (p.205); 4.3.9 (p.208); 6.0.1 (p.326); & 6.3.11 (p.392).This doctoral thesis documents and analyses a six-year, hapū-led, iwi-and community-supported, kaupapa-Māori-based (Māori-cultural-values-based) project that resulted in the transformative change of a dune lake ecosystem (which included people i.e., a whānau Māori ecosystem). Lake Waiorongomai, just north of Ōtaki, is a culturally-significant ancestral landscape and wāhi tapu (sacred site) for local whānau (extended families), hapū (sub-tribes) and iwi (tribes). The mana (prestige), mauri (life force) and ecological wellbeing of this wāhi tapu was diminished as a result of forest clearance, hydrological modification of the lake catchment, and the effects of pastoral farming activities. Attempts over the last three decades to bring Māori land owners and hapū members together to re-instate the mana and mauri of the dune lake ecosystem met with limited success. This thesis documents and seeks to better understand: (i) the conditions that gave rise to a successful restoration project; and (ii) the factors that empowered this hapū-led project. The study shows that conditions that contributed to a successful project involved: (i) collective land owner, local hapū and iwi support; (ii) a kaupapa Māori approach; (iii) project activities guided by the expression of rangatiratanga (sovereignty) and the contributions of a kaitiaki team who were appointed by hapū members; and (iv) the engagement of a kaupapa Māori researcher to support the hapū initiative and their revitalisation aspirations. Transformative change in this case study was change that had positive effects on physical, cultural, social, psychological and spiritual wellbeing. In the Lake Waiorongomai restoration project, the outcomes that had positive effects for the whānau Māori ecosystem include, but are not limited to: (i) fencing the lake with a 50m riparian margin; (ii) fencing the Waiorongomai Stream with a 10m riparian margin; (iii) community involvement in planting more than 3000 native plants, translocating over 1000 harakeke (swamp flax), and trapping over 100 pests (including stoats and ferrets); and (iv) reconnection of whānau and hapū members to the lake, through regular wānanga and ongoing restoration activities such as winter planting days. The habitat within the lake and surrounding wetlands provided opportunities to observe amongst other things threatened species such as the tiny button daisy, raoriki (swamp buttercup), fennel-leaved pond weed, matuku (bittern), kotuku ngutupapa (royal spoonbill), kotuku (white heron), parera (grey ducks), weweia (dab chicks) and pūweto (spotless crake). The improvement in the wellbeing of two species, inanga (whitebait) and watercress, over the course of the study is of particular note, since these species hold customary value for whānau and hapū. A central focus of this research is the relationship that ecological wellbeing and whānau, hapū, iwi wellbeing are inextricably linked. In summary, this hapū-led, community supported project took initial, confident steps in reclaiming, reframing and re-instating the mana and mauri of this whānau Māori ecosystem. This thesis argues that transformative changes were generated by empowering factors that were closely linked with: (i) the creation of a project space that allowed the free expression of kaupapa and tikanga (customs) in a socially and culturally mediated journey; (ii) whānau and hapū members’ expressions of kaupapa and tikanga that enhanced the success of this project; (iii) contributions of iwi members, councils and the wider community; (iv) the sharing and developing of mātauranga (knowledge) including through the involvement of learning institutes (e.g. whare wānanga, kura kaupapa, kōhanga reo and university students); and (v) a synthesis of Māori and Western restoration and research methods (including ecological monitoring). These empowering factors assisted in affirming to local hapū members that their expressions of kaupapa and tikanga were crucial in generating initial lake ecosystem wellbeing improvements including the enhancement of mauri. Two key lessons can be drawn from the role of these various factors in transformative change. First, no individual contribution was enough to ensure the success of the restoration. However, when a safe kaupapa and tikanga space was created for the inclusion of all contributors, the total effect was more than the sum of the individual parts (i.e., a synergistic outcome resulted). Second, the results indicate that it is highly unlikely that a Western methodological approach on its own would have been as successful in achieving a project outcome of this kind. A comparison of the key characteristics of kaupapa Māori and action research showed that a kaupapa Māori research methodology was the most appropriate for this case study. As such, this thesis may enhance current action research theory and method by showing how it could be responsive to cultural values, knowledge, customs and language in a real-world, wicked problem context of this kind. In documenting and exploring the various conditions and factors that made this restoration project possible, this thesis provides environmental planners and policy makers a real-world window into how transformative and progressive communityecosystem outcomes can be achieved in a Māori cultural context through the use of a kaupapa Māori approach

In silico case studies of compliant robots: AMARSI deliverable 3.3

In the deliverable 3.2 we presented how the morphological computing ap- proach can significantly facilitate the control strategy in several scenarios, e.g. quadruped locomotion, bipedal locomotion and reaching. In particular, the Kitty experimental platform is an example of the use of morphological computation to allow quadruped locomotion. In this deliverable we continue with the simulation studies on the application of the different morphological computation strategies to control a robotic system