Learning and selection

Are learning processes selection processes? This paper takes a slightly modified version of the account of selection presented in Hull et al. (Behav Brain Sci 24:511–527, 2001) and asks whether it applies to learning processes. The answer is that although some learning processes are selectional, many are not. This has consequences for teleological theories of mental content. According to these theories, mental states have content in virtue of having proper functions, and they have proper functions in virtue of being the products of selection processes. For some mental states, it is plausible that the relevant selection process is natural selection, but there are many for which it is not plausible. One response to this (due to David Papineau) is to suggest that the learning processes by which we acquire non-innate mental states are selection processes and can therefore confer proper functions on mental states. This paper considers two ways in which this response could be elaborated, and argues that neither of them succeed: the teleosemanticist cannot rely on the claim that learning processes are selection processes in order to justify the attribution of proper functions to beliefs.     

Apoptosis and differentiation of epidermal keratinocytes

We compared some processes characteristic for both apoptosis and terminal differentiation of epidermal keratinocytes. It can be proposed that nonapoptotic programmed cell death takes place during differentiation of keratinocytes. Apoptosis and terminal differentiation of keratinocytes appear to be different processes but some similar molecular mechanisms are involved in these processes.     

Pressurised aeration in wetland macrophytes: Some theoretical aspects of humidity-induced convection and thermal transpiration

The pressurised gas-flows, humidity-induced convection (HIC) and thermal transpiration (TT), which are important for aeration and for greenhouse gas emissions in some wetland macrophytes, are described and discussed. Results obtained from simple mathematical modelling of the processes are presented to illustrate some of their more relevant features. It is emphasised that both processes require the presence of a micro-porous partition having a significantly greater resistance to pressure flow than to diffusion. In particular it is shown that whilst the potential to pressurise by these processes is inversely related to the pore diameters of the partition, the maximum gas flows are generated where pore diameters range from 0.1 to 0.2 μm. Where partitions are a surface feature (e.g. emergent macrophytes) a dominant role for HIC is predicted; where partitions are an embedded feature (e.g. water-lilies) it is deduced that HIC will still play a significant role, but the contribution of TT could be greater.     

Mechanical aspects of cardiac development

Heart development depends on a dynamic interaction between genetic and epigenetic factors. This paper discusses some of the biomechanical processes that help shape the heart in the embryo. First, an overview is given of some of the critical events that occur during cardiac development. Next, mechanics and modeling strategies are discussed for the morphogenetic processes of cardiac tube formation, cardiac looping, myocardial trabeculation, septation, valve formation, and muscle-fiber alignment. Finally, some considerations for future work in this area are listed.     

The degeneration of Y chromosomes

Y chromosomes are genetically degenerate, having lost most of the active genes that were present in their ancestors. The causes of this degeneration have attracted much attention from evolutionary theorists. Four major theories are reviewed here: Muller's ratchet, background selection, the Hill Robertson effect with weak selection, and the 'hitchhiking' of deleterious alleles by favourable mutations. All of these involve a reduction in effective population size as a result of selective events occurring in a non-recombining genome, and the consequent weakening of the efficacy of selection. We review the consequences of these processes for patterns of molecular evolution and variation at loci on Y chromosomes, and discuss the results of empirical studies of these patterns for some evolving Y-chromosome and neo-Y-chromosome systems. These results suggest that the effective population sizes of evolving Y or neo-Y chromosomes are severely reduced, as expected if some or all of the hypothesized processes leading to degeneration are operative. It is, however, currently unclear which of the various processes is most important; some directions for future work to help to resolve this question are discussed.     

Apoptosis and autophagy: regulatory connections between two supposedly different processes

Apoptosis and autophagy are genetically-regulated, evolutionarily-conserved processes that regulate cell fate. Both apoptosis and autophagy are important in development and normal physiology and in a wide range of diseases. Recent studies show that despite the marked differences between these two processes, their regulation is intimately connected and the same regulators can sometimes control both apoptosis and autophagy. In this review, I discuss some of these findings, which provide possible molecular mechanisms for crosstalk between apoptosis and autophagy and suggest that it may be useful to think of these processes as different facets of the same cell death continuum rather than completely separate processes.     

Global patterns in the phylogenetic structure of island mammal assemblages

Assemblage-level phylogenies carry the signature of ecological and evolutionary processes, which may provide useful information on modes of assemblage formation. We present a global-scale analysis of the emergent phylogenetic properties of mammal assemblages on islands, in which we compared the structure of 595 island assemblages with null models constructed under four alternative definitions of regional source pools. Although most assemblages had a structure indistinguishable from random samples, for some mammal taxa, up to 40% of island assemblages were phylogenetically overdispersed. This suggests that in at least some cases, the processes that shape island faunas are not independent of phylogeny. Furthermore, measures of phylogenetic structure were associated in some cases with island geographical features (size, maximum elevation and habitat diversity). Our results suggest that part of the signal of assemblage formation processes is detectable in the phylogenies of contemporary island mammal faunas, though much is obscured by the complexity of these processes.     

Weak convergence of discrete time non-markovian processes related to selection models in population genetics

We consider discrete time stochastic processes defined by solutions to some non-linear difference equations whose coefficients are autocorrelated random sequences. It is proved that these processes converge weakly in D[0, T] to diffusion processes, under the assumption that the random sequences satisfy some mixing condition. Diffusion approximation for stochastic selection models in population genetics is discussed, as the application of this limit theorem.     

Statistical phylogeography

While studies of phylogeography and speciation in the past have largely focused on the documentation or detection of significant patterns of population genetic structure, the emerging field of statistical phylogeography aims to infer the history and processes underlying that structure, and to provide objective, rather than ad hoc explanations. Methods for parameter estimation are now commonly used to make inferences about demographic past. Although these approaches are well developed statistically, they typically pay little attention to geographical history. In contrast, methods that seek to reconstruct phylogeographic history are able to consider many alternative geographical scenarios, but are primarily nonstatistical, making inferences about particular biological processes without explicit reference to stochastically derived expectations. We advocate the merging of these two traditions so that statistical phylogeographic methods can provide an accurate representation of the past, consider a diverse array of processes, and yet yield a statistical estimate of that history. We discuss various conceptual issues associated with statistical phylogeographic inferences, considering especially the stochasticity of population genetic processes and assessing the confidence of phylogeographic conclusions. To this end, we present some empirical examples that utilize a statistical phylogeographic approach, and then by contrasting results from a coalescent-based approach to those from Templeton's nested cladistic analysis (NCA), we illustrate the importance of assessing error. Because NCA does not assess error in its inferences about historical processes or contemporary gene flow, we performed a small-scale study using simulated data to examine how our conclusions might be affected by such unconsidered errors. NCA did not identify the processes used to simulate the data, confusing among deterministic processes and the stochastic sorting of gene lineages. There is as yet insufficient justification of NCA's ability to accurately infer or distinguish among alternative processes. We close with a discussion of some unresolved problems of current statistical phylogeographic methods to propose areas in need of future development.     

Patterns and processes in the early evolution of the tetrapod ear

This article reviews some of the latest information on the evolution of the tetrapod ear region as seen in the fossil record. It looks at the changes that can be documented across the fish-tetrapod transition, the patterns that they show and what can be inferred of the processes that brought some of them about. These processes include an increased role for neural crest, and heterochronic processes such as pedomorphosis. The earliest tetrapods show a common pattern of a short stout stapes with a large stapedial foramen, that primitively contacted the palatal bones and probably supported the braincase. Modifications to this pattern can be seen in tandem with changes to the occiput and are bound up with changes to jaw and breathing mechanisms. By the Late Carboniferous, tetrapods had diversified into a range of groups showing a wide variety of otic morphologies, some of which were probably tympanic, while others were not, and some which are very different from those found in extant tetrapods. In amniotes, the evolution of a tympanic ear appears to correlate with consolidation and integration of the occiput to the skull roof. Competing phylogenies suggest different numbers of iterations for the origin of a tympanic ear, but a minimum of four separate occasions is implied.     

Detecting density dependence

Populations that persist do so, not by a juggling act balancing their rate of increase against a pot-pourri of unpredictable environmental factors, but rather by one or more processes that are broadly density-dependent, at least at some time or in some place. Detecting such density dependence is clearly of major importance in ecology. Unfortunately, many existing life table studies which set out with the aim of quantifying such processes are flawed by their lack of attention to within-generation factors causing differential birth and/or death rates between individuals. These factors can be very important to population regulation and are easily overlooked in analyses using only average population estimates.     

Protein synthesis-dependent long-term functional plasticity: methods and techniques

There is growing interest in late-LTP and late-LTD, that is, distinct forms of functional plasticity that require somatic functions such as protein synthesis in addition to the transient synaptic processes that are required for short lasting forms. Interestingly, to date only these forms of lasting plastic events could be detected in healthy, freely moving animals and thus, they are considered as physiological cellular models of learning and memory formation. Late-LTP and -LTD are characterized by 'synaptic tagging' or 'capture' and 'synaptic cross-tagging', but there are only a few laboratories that can currently perform experiments studying these properties. In brain slice work, there are many different approaches to investigate these processes using different methodological variations: some allow slices to rest for long periods before the experiment starts, others do not; some run their experiments at near to physiological temperatures, others at lower temperatures; some stimulate frequently, others do not.     

Translational research involving oxidative stress and diseases of aging

There is ample mounting evidence that reactive oxidant species are exacerbated in inflammatory processes, many pathological conditions, and underlying processes of chronic age-related diseases. Therefore there is increased expectation that therapeutics can be developed that act in some fashion to suppress reactive oxidant species and ameliorate the condition. This has turned out to be more difficult than at first expected. Developing therapeutics for indications in which reactive oxidant species are an important consideration presents some unique challenges. We discuss important questions including whether reactive oxidant species should be a therapeutic target, the need to recognize the fact that an antioxidant in a defined chemical system may be a poor antioxidant operationally in a biological system, and the importance of considering that reactive oxidant species may accompany the disease or pathological system rather than being a causative factor. We also discuss the value of having preclinical models to determine if the processes that are important in causing the disease under study are critically dependent on reactive oxidant species events and if the therapeutic under consideration quells these processes. In addition we discuss measures of success that must be met in commercial research and development and in preclinical and clinical trials and discuss as examples our translational research effort in developing nitrones for the treatment of acute ischemic stroke and as anti-cancer agents.     

Continuous fermentation systems for alcohol production

Many batch fermentation processes are operated throughout the world for the production of alcohol (ethanol) from sugar-based feedstocks but very few truly continuous processes are in operation. This review compares the two modes of operation and some advantages of the continuous processes are examined. Possible markets for continuous processes are identified and some possible explanations for the, as yet, lack of wide acceptance of continuous processes are offered. Seven different commercially available processes are reviewed.     

Line-of-descent and genealogical processes,and their applications in population genetics models

A variety of results for genealogical and line-of-descent processes that arise in connection with the theory of some classical selectively neutral population genetics models are reviewed. While some new results and derivations are included, the principle aim is to demonstrate the central importance and simplicity of genealogical Markov chains in this theory. Considerable attention is given to “diffusion time scale” approximations of such genealogical processes. A wide variety of results pertinent to (diffusion approximations of) the classical multiallele single-locus Wright-Fisher model and its relatives are simplified and unified by this approach. Other examples where such genealogical processes play an explicit role, such as the infinite sites and infinite alleles models, are discussed.     

Density dependence at some time and place?

There appears to be widespread acceptance that for a population to persist, some demographic parameter must be density dependent at some place or time. In this paper, we question the veracity and heuristic value of treating this statement as a general principle of ecology. We also point out that some processes that have recently been defined as density dependent are, in fact, not. Taken in its original sense, density dependence implies a change in demographic rates based on biological (generally negative) feedback. Situations exist, however, in which demographic rates change in relation to density without negative biological feedback. For example, per capita recruitment in marine populations will decrease as local population size increases even as absolute numbers of arriving larvae do not change. The failure to separate these density-related processes from true density-dependent processes affects our understanding of population regulation and of the way in which the natural world functions. Furthermore, focusing solely on density-dependent processes and their role in population regulation neglects to address numerous density-independent processes like disturbance and climatic variation that may have important impacts in determining population size. Received: 20 January 1999 / Accepted: 12 January 2000     

Profiling and Identification of Small rDNA-Derived RNAs and Their Potential Biological Functions

Small non-coding RNAs constitute a large family of regulatory molecules with diverse functions. Notably, some small non-coding RNAs matched to rDNA have been identified as qiRNAs and small guide RNAs involved in various biological processes. However, a large number of small rDNA-derived RNAs (srRNAs) are usually neglected and yet to be investigated. We systematically investigated srRNAs using small RNA datasets generated by high-throughput sequencing, and found srRNAs are mainly mapped to rRNA coding regions in sense direction. The datasets from immunoprecipitation and high-throughput sequencing demonstrate that srRNAs are co-immunoprecipitated with Argonaute (AGO) proteins. Furthermore, the srRNA expression profile in mouse liver is affected by diabetes. Overexpression or inhibition of srRNAs in cultured cells shows that srRNAs are involved in various signaling pathways. This study presents a global view of srRNAs in total small RNA and AGO protein complex from different species, and demonstrates that srRNAs are correlated with diabetes, and involved in some biological processes. These findings provide new insights into srRNAs and their functions in various physiological and pathological processes.     

Biological applications of the theory of birth-and-death processes

In this review, we discuss applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described. Birth-and-death processes, with some straightforward additions such as innovation, are a simple, natural and formal framework for modeling a vast variety of biological processes such as population dynamics, speciation, genome evolution, including growth of paralogous gene families and horizontal gene transfer and somatic evolution of cancers. We further describe how empirical data, e.g. distributions of paralogous gene family size, can be used to choose the model that best reflects the actual course of evolution among different versions of birth-death-and-innovation models. We conclude that birth-and-death processes, thanks to their mathematical transparency, flexibility and relevance to fundamental biological processes, are going to be an indispensable mathematical tool for the burgeoning field of systems biology.     

Modelling and simulation techniques for membrane biology

One of the most important aspects of Computational Cell Biology is the understanding of the complicated dynamical processes that take place on plasma membranes. These processes are often so complicated that purely temporal models cannot always adequately capture the dynamics. On the other hand, spatial models can have large computational overheads. In this article, we review some of these issues with respect to chemistry, membrane microdomains and anomalous diffusion and discuss how to select appropriate modelling and simulation paradigms based on some or all the following aspects: discrete, continuous, stochastic, delayed and complex spatial processes.     

Osteoporosis: pathogenesis and clinical intervention

Osteoporosis is a very common disorder and much has been learnt in recent years about the many pathogenic processes that contribute to bone loss and fragility. Drug treatments are now available to prevent bone loss and reduce fracture, and there are prospects for modifying some of the pathogenic processes themselves. In common with other structures, the tissues of the musculoskeletal system undergo many changes with aging, and some of the commonest skeletal disorders are seen in the elderly. The changes in bone lead to osteoporosis and fractures, whereas muscle changes (sarcopenia) contribute to frailty, and changes in cartilage lead to osteoarthritis.