'Nothing exists for one cause' : putting biology back into evolution

The opening phrase of the title is from Charles Darwin’s notebooks (Schweber 1977). It is a double reminder, firstly that mainstream evolutionary theory is not just about describing nature but is particularly looking for mechanisms or ‘causes’, and secondly, that there will usually be several causes affecting any particular outcome. The second part of the title is our concern at the almost universal rejection of the idea that biological mechanisms are sufficient for macroevolutionary changes, thus rejecting a cornerstone of Darwinian evolutionary theory. Our primary aim here is to consider ways of making it easier to develop and to test hypotheses about evolution. Formalizing hypotheses can help generate tests. In an absolute sense, some of the discussion by scientists about evolution is little better than the lack of reasoning used by those advocating intelligent design. Our discussion here is in a Popperian framework where science is defined by that area of study where it is possible, in principle, to find evidence against hypotheses – they are in principle falsifiable. However, with time, the boundaries of science keep expanding. In the past, some aspects of evolution were outside the current boundaries of falsifiable science, but increasingly new techniques and ideas are expanding the boundaries of science and it is appropriate to re-examine some topics. It often appears that over the last few decades there has been an increasingly strong assumption to look first (and only) for a physical cause. This decision is virtually never formally discussed, just an assumption is made that some physical factor ‘drives’ evolution. It is necessary to examine our assumptions much more carefully. What is meant by physical factors ‘driving’ evolution, or what is an ‘explosive radiation’. Our discussion focuses on two of the six mass extinctions, the fifth being events in the Late Cretaceous, and the sixth starting at least 50,000 years ago (and is ongoing). Cretaceous/Tertiary boundary; the rise of birds and mammals. We have had a long-term interest (Cooper and Penny 1997) in designing tests to help evaluate whether the processes of microevolution are sufficient to explain macroevolution. The real challenge is to formulate hypotheses in a testable way. For example the numbers of lineages of birds and mammals that survive from the Cretaceous to the present is one test. Our first estimate was 22 for birds, and current work is tending to increase this value. This still does not consider lineages that survived into the Tertiary, and then went extinct later. Our initial suggestion was probably too narrow in that it lumped four models from Penny and Phillips (2004) into one model. This reduction is too simplistic in that we need to know about survival and ecological and morphological divergences during the Late Cretaceous, and whether Crown groups of avian or mammalian orders may have existed back into the Cretaceous. More recently (Penny and Phillips 2004) we have formalized hypotheses about dinosaurs and pterosaurs, with the prediction that interactions between mammals (and groundfeeding birds) and dinosaurs would be most likely to affect the smallest dinosaurs, and similarly interactions between birds and pterosaurs would particularly affect the smaller pterosaurs. There is now evidence for both classes of interactions, with the smallest dinosaurs and pterosaurs declining first, as predicted. Thus, testable models are now possible. Mass extinction number six: human impacts. On a broad scale, there is a good correlation between time of human arrival, and increased extinctions (Hurles et al. 2003; Martin 2005; Figure 1). However, it is necessary to distinguish different time scales (Penny 2005) and on a finer scale there are still large numbers of possibilities. In Hurles et al. (2003) we mentioned habitat modification (including the use of Geogenes III July 2006 31 fire), introduced plants and animals (including kiore) in addition to direct predation (the ‘overkill’ hypothesis). We need also to consider prey switching that occurs in early human societies, as evidenced by the results of Wragg (1995) on the middens of different ages on Henderson Island in the Pitcairn group. In addition, the presence of human-wary or humanadapted animals will affect the distribution in the subfossil record. A better understanding of human impacts world-wide, in conjunction with pre-scientific knowledge will make it easier to discuss the issues by removing ‘blame’. While continued spontaneous generation was accepted universally, there was the expectation that animals continued to reappear. New Zealand is one of the very best locations in the world to study many of these issues. Apart from the marine fossil record, some human impact events are extremely recent and the remains less disrupted by time.

Efficient preconditioning of the method of lines for solving nonlinear two-sided space-fractional diffusion equations

A standard method for the numerical solution of partial differential equations (PDEs) is the method of lines. In this approach the PDE is discretised in space using �finite di�fferences or similar techniques, and the resulting semidiscrete problem in time is integrated using an initial value problem solver. A significant challenge when applying the method of lines to fractional PDEs is that the non-local nature of the fractional derivatives results in a discretised system where each equation involves contributions from many (possibly every) spatial node(s). This has important consequences for the effi�ciency of the numerical solver. First, since the cost of evaluating the discrete equations is high, it is essential to minimise the number of evaluations required to advance the solution in time. Second, since the Jacobian matrix of the system is dense (partially or fully), methods that avoid the need to form and factorise this matrix are preferred. In this paper, we consider a nonlinear two-sided space-fractional di�ffusion equation in one spatial dimension. A key contribution of this paper is to demonstrate how an eff�ective preconditioner is crucial for improving the effi�ciency of the method of lines for solving this equation. In particular, we show how to construct suitable banded approximations to the system Jacobian for preconditioning purposes that permit high orders and large stepsizes to be used in the temporal integration, without requiring dense matrices to be formed. The results of numerical experiments are presented that demonstrate the effectiveness of this approach.

Microcosm study of ion mobilization and greenhouse gas evolution in soils of a plantation-forested subtropical coastal catchment

This study examined the potential for Fe mobilization and greenhouse gas (GHG, e.g. CO2, and CH4) evolution in SEQ soils associated with a range of plantation forestry practices and water-logged conditions. Intact, 30-cm-deep soil cores collected from representative sites were saturated and incubated for 35 days in the laboratory, with leachate and headspace gas samples periodically collected. Minimal Fe dissolution was observed in well-drained sand soils associated with mature, first-rotation Pinus and organic Fe complexation, whereas progressive Fe dissolution occurred over 14 days in clear-felled and replanted Pinus soils with low organic matter and non-crystalline Fe fractions. Both CO2 and CH4 effluxes were relatively lower in clear-felled and replanted soils compared with mature, first-rotation Pinus soils, despite the lack of statistically significant variations in total GHG effluxes associated with different forestry practices. Fe dissolution and GHG evolution in low-lying, water-logged soils adjacent to riparian and estuarine, native-vegetation buffer zones were impacted by mineral and physical soil properties. Highest levels of dissolved Fe and GHG effluxes resulted from saturation of riparian loam soils with high Fe and clay content, as well as abundant organic material and Fe-metabolizing bacteria. Results indicate Pinus forestry practices such as clear-felling and replanting may elevate Fe mobilization while decreasing CO2 and CH4 emissions from well-drained, SEQ plantation soils upon heavy flooding. Prolonged water-logging accelerates bacterially mediated Fe cycling in low-lying, clay-rich soils, leading to substantial Fe dissolution, organic matter mineralization, and CH4 production in riparian native-vegetation buffer zones.

Tracking the magmatic evolution of island arc volcanism : insights from a high-precision Pb isotope record of Montserrat, Lesser Antilles

The volcanic succession on Montserrat provides an opportunity to examine the magmatic evolution of island arc volcanism over a ∼2.5 Ma period, extending from the andesites of the Silver Hills center, to the currently active Soufrière Hills volcano (February 2010). Here we present high-precision double-spike Pb isotope data, combined with trace element and Sr-Nd isotope data throughout this period of Montserrat's volcanic evolution. We demonstrate that each volcanic center; South Soufrière Hills, Soufrière Hills, Centre Hills and Silver Hills, can be clearly discriminated using trace element and isotopic parameters. Variations in these parameters suggest there have been systematic and episodic changes in the subduction input. The SSH center, in particular, has a greater slab fluid signature, as indicated by low Ce/Pb, but less sediment addition than the other volcanic centers, which have higher Th/Ce. Pb isotope data from Montserrat fall along two trends, the Silver Hills, Centre Hills and Soufrière Hills lie on a general trend of the Lesser Antilles volcanics, whereas SSH volcanics define a separate trend. The Soufrière Hills and SSH volcanic centers were erupted at approximately the same time, but retain distinctive isotopic signatures, suggesting that the SSH magmas have a different source to the other volcanic centers. We hypothesize that this rapid magmatic source change is controlled by the regional transtensional regime, which allowed the SSH magma to be extracted from a shallower source. The Pb isotopes indicate an interplay between subduction derived components and a MORB-like mantle wedge influenced by a Galapagos plume-like source.

Relative entropy rate based model selection for linear hybrid system filters of uncertain nonlinear systems

Hybrid system representations have been exploited in a number of challenging modelling situations, including situations where the original nonlinear dynamics are too complex (or too imprecisely known) to be directly filtered. Unfortunately, the question of how to best design suitable hybrid system models has not yet been fully addressed, particularly in the situations involving model uncertainty. This paper proposes a novel joint state-measurement relative entropy rate based approach for design of hybrid system filters in the presence of (parameterised) model uncertainty. We also present a design approach suitable for suboptimal hybrid system filters. The benefits of our proposed approaches are illustrated through design examples and simulation studies.

Linear and nonlinear propagation of localised plasmon in metallic nanostructures

A major challenge in modern photonics and nano-optics is the diffraction limit of light which does not allow field localisation into regions with dimensions smaller than half the wavelength. Localisation of light into nanoscale regions (beyond its diffraction limit) has applications ranging from the design of optical sensors and measurement techniques with resolutions as high as a few nanometres, to the effective delivery of optical energy into targeted nanoscale regions such as quantum dots, nano-electronic and nano-optical devices. This field has become a major research direction over the last decade. The use of strongly localised surface plasmons in metallic nanostructures is one of the most promising approaches to overcome this problem. Therefore, the aim of this thesis is to investigate the linear and non-linear propagation of surface plasmons in metallic nanostructures. This thesis will focus on two main areas of plasmonic research –– plasmon nanofocusing and plasmon nanoguiding. Plasmon nanofocusing – The main aim of plasmon nanofocusing research is to focus plasmon energy into nanoscale regions using metallic nanostructures and at the same time achieve strong local field enhancement. Various structures for nanofocusing purposes have been proposed and analysed such as sharp metal wedges, tapered metal films on dielectric substrates, tapered metal rods, and dielectric V-grooves in metals. However, a number of important practical issues related to nanofocusing in these structures still remain unclear. Therefore, one of the main aims of this thesis is to address two of the most important of issues which are the coupling efficiency and heating effects of surface plasmons in metallic nanostructures. The method of analysis developed throughout this thesis is a general treatment that can be applied to a diversity of nanofocusing structures, with results shown here for the specific case of sharp metal wedges. Based on the geometrical optics approximation, it is demonstrated that the coupling efficiency from plasmons generated with a metal grating into the nanofocused symmetric or quasi-symmetric modes may vary between ~50% to ~100% depending on the structural parameters. Optimal conditions for nanofocusing with the view to minimise coupling and dissipative losses are also determined and discussed. It is shown that the temperature near the tip of a metal wedge heated by nanosecond plasmonic pulses can increase by several hundred degrees Celsius. This temperature increase is expected to lead to nonlinear effects, self-influence of the focused plasmon, and ultimately self-destruction of the metal tip. This thesis also investigates a different type of nanofocusing structure which consists of a tapered high-index dielectric layer resting on a metal surface. It is shown that the nanofocusing mechanism that occurs in this structure is somewhat different from other structures that have been considered thus far. For example, the surface plasmon experiences significant backreflection and mode transformation at a cut-off thickness. In addition, the reflected plasmon shows negative refraction properties that have not been observed in other nanofocusing structures considered to date. Plasmon nanoguiding – Guiding surface plasmons using metallic nanostructures is important for the development of highly integrated optical components and circuits which are expected to have a superior performance compared to their electronicbased counterparts. A number of different plasmonic waveguides have been considered over the last decade including the recently considered gap and trench plasmon waveguides. The gap and trench plasmon waveguides have proven to be difficult to fabricate. Therefore, this thesis will propose and analyse four different modified gap and trench plasmon waveguides that are expected to be easier to fabricate, and at the same time acquire improved propagation characteristics of the guided mode. In particular, it is demonstrated that the guided modes are significantly screened by the extended metal at the bottom of the structure. This is important for the design of highly integrated optics as it provides the opportunity to place two waveguides close together without significant cross-talk. This thesis also investigates the use of plasmonic nanowires to construct a Fabry-Pérot resonator/interferometer. It is shown that the resonance effect can be achieved with the appropriate resonator length and gap width. Typical quality factors of the Fabry- Pérot cavity are determined and explained in terms of radiative and dissipative losses. The possibility of using a nanowire resonator for the design of plasmonic filters with close to ~100% transmission is also demonstrated. It is expected that the results obtained in this thesis will play a vital role in the development of high resolution near field microscopy and spectroscopy, new measurement techniques and devices for single molecule detection, highly integrated optical devices, and nanobiotechnology devices for diagnostics of living cells.

Orthopedic bone plates : evolution in structure implementation technique and biomaterial

With many important developments over the last century, nowadays orthopedic bone plate now excels over other types of internal fixators in bone fracture fixation. The developments involve the design, material and implementation techniques of the plates. This paper aims to review the evolution in implementation technique and biomaterial of the orthopedic bone plates. Plates were initially used to fix the underlying bones firmly. Accordingly, Compression plate (CP), Dynamic compression plate (DCP), Limited contact dynamic compression plate (LC-DCP) and Point contact fixator (PC-Fix) were developed. Later, the implementation approach was changed to locking, and the Less Invasive Stabilization System (LISS) plate was introduced as a result. Finally, a combination of both of these approaches has been used by introducing the Locking Compression Plate (LCP). Currently, precontoured LCPs are mainly used for bone fracture fixation. In parallel with structure and implementation techniques, numerous advances have occurred in biomaterials of the plates. Titanium and stainless steel alloys are now the most common biomaterials in production of orthopedic bone plates. However, regarding the biocompatibility, bioactivity and biodegradability characteristics of Mg alloys, Ta alloys, SMAs, carbon fiber composites and bioceramics, these materials are considered as potentially suitable for plates. However, due to poor mechanical properties, they have very limited applications. Therefore, further studies are required in future to solve these problems and make them feasible for heavy-duty bone plates.

A general method to determine sampling windows for nonlinear mixed effects models with an application to population pharmacokinetic studies

Optimal design methods have been proposed to determine the best sampling times when sparse blood sampling is required in clinical pharmacokinetic studies. However, the optimal blood sampling time points may not be feasible in clinical practice. Sampling windows, a time interval for blood sample collection, have been proposed to provide flexibility in blood sampling times while preserving efficient parameter estimation. Because of the complexity of the population pharmacokinetic models, which are generally nonlinear mixed effects models, there is no analytical solution available to determine sampling windows. We propose a method for determination of sampling windows based on MCMC sampling techniques. The proposed method attains a stationary distribution rapidly and provides time-sensitive windows around the optimal design points. The proposed method is applicable to determine sampling windows for any nonlinear mixed effects model although our work focuses on an application to population pharmacokinetic models.

Nonlinear H_infinity control of UAVs for collision avoidance in gusty environments

This paper proposes a nonlinear H_infinity controller for stabilization of velocities, attitudes and angular rates of a fixed-wing unmanned aerial vehicle (UAV) in a windy environment. The suggested controller aims to achieve a steady-state flight condition in the presence of wind gusts such that the host UAV can be maneuvered to avoid collision with other UAVs during cruise flight with safety guarantees. This paper begins with building a proper model capturing flight aerodynamics of UAVs. Then a nonlinear controller is developed with gust attenuation and rapid response properties. Simulations are conducted for the Shadow UAV to verify performance of the proposed con- troller. Comparative studies with the proportional-integral-derivative (PID) controllers demonstrate that the proposed controller exhibits great performance improvement in a gusty environment, making it suitable for integration into the design of flight control systems for cruise flight of UAVs.

Insights into historical drainage evolution based on the phylogeography of the chevron snakehead fish (Channa striata) in the Mekong Basin

1. The phylogeography of freshwater taxa is often integrally linked with landscape changes such as drainage re-alignments that may present the only avenue for historical dispersal for these taxa. Classical models of gene flow do not account for landscape changes and so are of little use in predicting phylogeography in geologically young freshwater landscapes. When the history of drainage formation is unknown, phylogeographical predictions can be based on current freshwater landscape structure, proposed historical drainage geomorphology, or from phylogeographical patterns of co-distributed taxa. 2. This study describes the population structure of a sedentary freshwater fish, the chevron snakehead (Channa striata), across two river drainages on the Indochinese Peninsula. The phylogeographical pattern recovered for C. striata was tested against seven hypotheses based on contemporary landscape structure, proposed history and phylogeographical patterns of codistributed taxa. 3. Consistent with the species ecology, analysis of mitochondrial and microsatellite loci revealed very high differentiation among all sampled sites. A strong signature of historical population subdivision was also revealed within the contemporary Mekong River Basin (MRB). Of the seven phylogeographical hypotheses tested, patterns of co-distributed taxa proved to be the most adequate for describing the phylogeography of C. striata. 4. Results shed new light on SE Asian drainage evolution, indicating that the Middle MRB probably evolved via amalgamation of at least three historically independent drainage sections and in particular that the Mekong River section centred around the northern Khorat Plateau in NE Thailand was probably isolated from the greater Mekong for an extensive period of evolutionary time. In contrast, C. striata populations in the Lower MRB do not show a phylogeographical signature of evolution in historically isolated drainage lines, suggesting drainage amalgamation has been less important for river landscape formation in this region.

Emergent innovation through the co-evolution of informal and formal media economies

Well-established distinctions between amateur and professional are blurring as the impact of social media, changes in cultural consumption, and crises in copyright industries’ business models are felt across society and economy. I call this the increasingly rapid co-evolution of the formal market and informal household sectors and analyse it through the concept of ‘social network markets’ – individual choices are made on the basis of other’s choices and such networked preferencing is enhanced by the growing ubiquity of social media platforms. This may allow us better to understand sources of disruption and innovation in audiovisual production and distribution in wealthy Western markets which are as significant as those posed by informal practices outside the West. I examine what is happening around the monetization and professionalization of online video (YouTube, for example) and the socialization of professional production strategies (transmedia, for example) as innovation from the margins.