Quantitative aspects of the estimation of evolutionary trees

Various approaches to the estimation of evolutionary trees are reviewed, with emphasis on recent developments. It is argued that no approach is 'model-free', that is, without some assumptions about the processes of evolutionary change. A statistical approach provides a general framework and it is accepted that cladistic methodology represents a special case within this framework. The idea of evolutionary convergence is examined in the light of recent discussion of the existence of convergence in molecular evolution. It is concluded that attempts to estimate evolutionary trees are justifiable at least on the grounds that, despite present shortcomings, they are the most appropriate way to analyse comparative data. There are good prospects for further progress.     

Gating or switching? Gating is a better model of prospective timing (a response to 'switching or gating?' by Lejeune)

Lejeune (1998) (Switching or gating? The attentional challenge in cognitive models of psychological time. Behav. Process. 44, 127-45) analyzed and compared two models of prospective timing: the classical switching model and the attentional-gate model. Lejeune argued that a modified switch notion, which can be opened and closed in a frequency which reflects the amount of attentional resources allocated for timing can provide a satisfactory explanation for the impact of attention on prospective timing, and therefore the notion of an 'attentional switch' is favored over adding an 'attentional gate.' In the present analysis, the two competing models are compared in terms of correspondence with the nature of attentional processes, as well as in terms of logical analysis and explanatory power. Based on this comparison, it is argued that gating is a better model of prospective timing than switching.     

Gating or switching? Gating is a better model of prospective timing (a response to 'switching or gating?' by Lejeune)(1)

Lejeune (1998) (Switching or gating? The attentional challenge in cognitive models of psychological time. Behav. Process. 44, 127-45) analyzed and compared two models of prospective timing: the classical switching model and the attentional-gate model. Lejeune argued that a modified switch notion, which can be opened and closed in a frequency which reflects the amount of attentional resources allocated for timing can provide a satisfactory explanation for the impact of attention on prospective timing, and therefore the notion of an 'attentional switch' is favored over adding an 'attentional gate.' In the present analysis, the two competing models are compared in terms of correspondence with the nature of attentional processes, as well as in terms of logical analysis and explanatory power. Based on this comparison, it is argued that gating is a better model of prospective timing than switching.     

Selection on a haploid genotype for discrimination learning performance: Correlation between drone honey bees (Apis mellifera) and their worker progeny (Hymenoptera: Apidae)

Successful bidirectional selection for discriminative olfactory learning is reported for drone honey bees (Apis mellifera). Learning performance was evaluated using a discrimination conditioning procedure that required drones to discriminate between an appetitively reinforced odorant and one that was followed by punishment. Selective breeding produced high- and low-learning-performance lines of worker progeny that diverged from performance of workers whose fathers were selected at random. Furthermore, we show that levels of sucrose-induced sensitization are not correlated to learning performance. These results corroborate earlier findings and further demonstrate the power of selection on a haploid (drone) genotype. In addition, this study now shows that the demonstrated differences in learning performance cannot be completely accounted for by alteration of sucrose-induced sensitization. Thus, using this technique, it may be possible to select for associative conditioning without a pleiotropic increase in sensitization. The honey bee will be ideally suited to these types of correlation analyses in future studies.     

The behavioral plasticity of the edible snail and its neuronal mechanisms]

Published results concerning behavioural habituation, sensitization, long-term processes, environmental conditioning, and conditioned food aversion in terrestrial snail Helix are discussed. Neural mechanisms underlying behavioural changes are considered. Problems of participation of motivational processed and development of plasticity in ontogenesis are reviewed.     

The dynamics of the defensive and feeding conditioned reactions of the edible snail during long-term sensitization]

During the long-term sensitization in a snail there occurs an enhancement of a defensive reaction and a significant decrease of food intake. Defensive conditioning is facilitated and feeding conditioning deteriorated. The results give evidence that a formation of the state of the long-term sensitization is accompanied by a generation of a dominant defense focus.     

Uses of respect and uses of the human embryo

In most parts of the world, research on the human embryo is subject to tight controls. In the United Kingdom it is restricted by means of both a fourteen-day time limit and the permitted purposes of the research. One of the ways in which the argument for these restrictions has been put is in terms of respect. That is, the human embryo is said to be the kind of thing that is worthy of a measure of respect such that there are limits to what can be done to it. This paper considers some of the ways in which this principle of respect has been understood as well as some objections to the very idea that research resulting in the destruction of the human embryo can claim to show that embryo respect. It will be argued that an account of 'respectful destruction' can be articulated on the grounds of our shared finitude as human moral agents, and in particular on the grounds of our shared lack of certainty regarding the moral status of the embryo.     

Parallel tion in the context of character analysis

For the establishment of polarity of character transformation prior to phylogenetic analysis, various logical and biological criteria are discussed; some are rejected on grounds of liability to systematic error, circularity or unwarranted assumptions aboutParallel tion is used as a non-polar term, with forward and reverse to indicate polarity. A computer program for the detection of parallel tion is described which takes taxa in groups of four. The characters, with two derived: two primitive states or three derived: one primitive state, are listed according to the distribution of states over the four taxa. To each of the 15 phylogenies there corresponds a compatible pair of character patterns. Discordant 2: 2 patterns are unconditionally incompatible (Le Quesne test failure), discordant 3: 1 patterns are incompatible conditional upon correct scoring of polarity. For any putative phylogeny the concordant and discordant characters are identified. In cases of competing alternatives these character sets have to be weighed against one another. Character weighting is discussed; it is argued that it is the individual character transformation which should be weighted, in each direction separately.     

Logical identification of all steady states: The concept of feedback loop characteristic states

Biological regulatory systems can be described in terms of non-linear differential equations or in logical terms (using an “infinitely non-linear” approximation). Until recently, only part of the steady states of a system could be identified on logical grounds. The reason was that steady states frequently have one or more variable located on a threshold (see below); those steady states were not detected because so far no logical status was assigned to threshold values. This is why we introduced logical scales with values 0,¹θ, 1²θ, 2, ..., in which¹θ,²θ, ... are the logical values assigned to the successive thresholds of the scale. We thus have, in addition to the regular logical states,singular states in which one or more variables is located on a threshold. This permits identifyingall the steady states on logical grounds. It was noticed that each feedback loop (or reunion of disjointed loops) can be characterized by a logical state located at the thresholds at which the variables of the loop operate. This led to the concept ofloop-characteristic state, which, as we will see, enormously simplifies the analysis.The core of this paper is a formal demonstration that among the singular states of a system, only loop-characteristic states can be steady. Reciprocally, given a loop-characteristic state, there are parameter values for which this state is steady; in this case, the loop is effective (i.e. it generates multistationarity if it is a positive loop, homeostasis if it is a negative loop). This not only results in the above-mentioned radical simplification of the identification of the steady states, but in an entirely new view of the relation between feedback loops and steady states.     

Actions,Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized

Behavioral evidence suggests that instrumental conditioning is governed by two forms of action control: a goal-directed and a habit learning process. Model-based reinforcement learning (RL) has been argued to underlie the goal-directed process; however, the way in which it interacts with habits and the structure of the habitual process has remained unclear. According to a flat architecture, the habitual process corresponds to model-free RL, and its interaction with the goal-directed process is coordinated by an external arbitration mechanism. Alternatively, the interaction between these systems has recently been argued to be hierarchical, such that the formation of action sequences underlies habit learning and a goal-directed process selects between goal-directed actions and habitual sequences of actions to reach the goal. Here we used a two-stage decision-making task to test predictions from these accounts. The hierarchical account predicts that, because they are tied to each other as an action sequence, selecting a habitual action in the first stage will be followed by a habitual action in the second stage, whereas the flat account predicts that the statuses of the first and second stage actions are independent of each other. We found, based on subjects'' choices and reaction times, that human subjects combined single actions to build action sequences and that the formation of such action sequences was sufficient to explain habitual actions. Furthermore, based on Bayesian model comparison, a family of hierarchical RL models, assuming a hierarchical interaction between habit and goal-directed processes, provided a better fit of the subjects'' behavior than a family of flat models. Although these findings do not rule out all possible model-free accounts of instrumental conditioning, they do show such accounts are not necessary to explain habitual actions and provide a new basis for understanding how goal-directed and habitual action control interact.     

Conditioning and sensitization in the edible snail: the neurophysiological and metabolic characteristics]

Electrophysiological parameters and bound calcium (Ca(b)) level dynamics during sensitization development or conditioning of food aversion were studied in the command neurons of defense behaviour in the snail Helix lucorum. Responses evoked by a testing sensory stimulus were facilitated 50-60 min after the first sensitizing stimulation, while conditioned responses appeared 80-90 min after the first conditioning. It was the most essential electrophysiological difference between the long-term sensitization and conditioning. Analysis of the Ca(b)) dynamics in the neurons showed significant differences in calcium-dependent metabolism during the sensitization and conditioning, likely underlying the electrophysiological differences.     

Population cycles produced by delayed density dependence in an annual plant

In contrast to insect and animal populations, little attention has been directed to the study of cycles in plant populations. It has been argued on theoretical grounds that plants present stable dynamics. Nevertheless, there are examples where plant populations appear to exhibit oscillatory dynamics, but the oscillatory signal is variable and comes from very short time series data. Using a combination of time series, models, and empirical results, we present evidence of population cycles for Descurania sophia in a 16-year field experiment. Endogenous and exogenous causal mechanisms were studied to identify processes underlying this temporal dynamic. Our results show a 4-year cycle produced by delayed density dependence. We suggest that high nutrient levels might be responsible for the observed dynamics of D. sophia. Our results suggest that although plant population dynamics may be stabilized by direct density dependence, delayed density dependence could destabilize dynamics.     

An analytical short- and long-term memory model of presynaptic plasticity

A mathematical model, called the Learning Gate Model (LGM), that describes phenomena responsible for biological synaptic plasticity, is presented. The functionality of the model are mainly based on the work of Kandel and colleagues on the most elementary forms of learning observed in the Aplysia Californica marine mollusc. In particular, emphasis is placed on the double temporal dynamics of synaptic plasticity and the temporal specificity of classical conditioning. By properly modeling the effect of the binding of Ca⁺⁺ ions to the serotonin-sensitive adenylate cyclase enzyme, it is shown how a positively accelerated learning curve can be obtained for sensitization and classical conditioning. Phenomena of spontaneous recovery and second-order conditioning are reproduced through simulations. Mathematical analyses of the temporal trace of conditioned stimulus and of the Short-Term Memory steady state are also given.     

IQ, visuospatial ability and the gender divide: a reply to Bilalić and Mcleod

Bilalic and McLeod's arguments fall short on several grounds.There are excellent logical reasons to expect strong ability/chess expertise links and specific research evidence to date is sparse, with mixed findings. Data are presented from Georgia, which has a high female participation rate in chess, which suggest that differing gender motivation levels and participation rates impact relatively little on chess performance differences at the extreme.     

The evolution of dominance: Haldane v Fisher revisited.

Fisher's model for the evolution of dominance indicates that the accumulation of dominance modifiers will be accelerated by (1) an increased frequency of the mutant heterozygote, (2) increased selection for the phenotype of the normal homozygote. The model has been criticised by Haldane on the grounds that point (1) is not fulfilled, that is dominance appears to be more common in populations with a low frequency of mutant heterozygotes (populations of inbreeders). In support of Fisher's model it is argued that intense selection for the wild type phenotype is more common in inbreeders than outbreeders. This situation should promote the accumulation of dominance modifiers (point (2) above).     

Functions of the LE sensory neurons inAplysia

Mechanosensory neurons which innervate the siphon and have their cell bodies in the LE cluster of the abdominal ganglion ofAplysia have revealed many cellular and molecular processes that may play general roles in learning and memory. It was initially suggested that these cells are largely responsible for triggering the gill-withdrawal reflex evoked by weak siphon stimulation, and that most of this effect is mediated by their monosynaptic connections to gill motor neurons. This implied a simple link between plasticity at these synapses and modifications of the reflex during learning. We review more recent studies from several laboratories showing that the LE cells are not activated by very weak tactile stimuli that elicit the gill-withdrawal reflex, and that an unidentified population of siphon sensory neurons has lower mechanosensory thresholds and produces shorter latency responses. Furthermore, the direct connections between LE cells and gill motor neurons make a minor contribution when the reflex is elicited in pinned siphon preparations by light stimuli that weakly activate the LE cells. Because weak mechanical stimulation of the unrestrained siphon causes little or no LE cell activation, it is unlikely that, under natural conditions, sensitization or conditioning of reflex responses elicited by light siphon touch depends upon plasticity of LE cell synapses onto either motor or interneurons. The LE cells appear to function as nociceptors because they are tuned to noxious stimuli and, like mammalian nociceptors, show peripheral sensitization following nociceptive activation. This sensitization and the profound activity-dependent potentiation of LE synapses indicate that LE cell contributions to defensive reflexes should be largest during and after intense activation of the LE cells by noxious stimulation (with the LE cell plasticity contributing to long-lasting memory of peripheral injury). The LE sensory neurons offer special opportunities for direct tests of this and other hypotheses about specific mnemonic functions of fundamental mechanisms of neural plasticity.     

Reduced intensity conditioning for hematopoietic stem cell transplantation: has it achieved all it set out to?

At its inception, reduced intensity conditioning (RIC) was heralded as a means to limit toxicity after hematopoietic stem cell transplantation (HSCT), especially for the older patient demographic. The aim was to promote the inherent anti-leukemic activity of the transplant whilst reducing toxicity and transplant-related mortality (TRM). More than 10 years on, much has been learnt about the role of conditioning in determining outcomes after transplantation. The use of RIC as a preparative regimen has increased the number of patients that can benefit from HSCT because the initial therapy is less toxic. However, many of the early pioneers of RIC quickly realized that the toxicity from graft-versus-host disease (GvHD) was equally as potent as that from conditioning. Furthermore, questions remain concerning the efficacy of RIC regimens in retaining anti-leukemic immunity, especially in cases of aggressive disease. The undoubted synergy between chemotherapeutic and immunologic treatment of malignancy means that reduction of conditioning intensity to minimal levels may not be entirely logical.     

Hempel's view on functional explanation some critical comments

Summary Functional explanations are regarded as a special type of explanation by many biologists. Philosophers of science tend to agree that they are weak forms of the common modes of explanation, although the elucidation of the logical structure involved is difficult. The present paper shows that Hempel's reconstruction of functional explanations is inadequate on pragmatic grounds. Thus his conclusion that such explanations are necessarily weak is also objectionable. There is no reason for allotting functional explanations a special logical status.     

Differential effects of selective opioid peptide antagonists on the acquisition of pavlovian fear conditioning.

Pretreatment with opioid antagonists enhances acquisition of Pavlovian fear conditioning. The present experiments attempted to characterize the type of opioid receptor responsible for this effect using a procedure that assessed the fear of rats to a chamber previously associated with electric shock (1 mA, 0.75 s). Freezing, a species-typical immobility, was employed as an index of fear. Two mu opioid antagonists, CTOP (40 ng) and naloxonazine (10 micrograms), enhanced conditioning. On the other hand, the kappa antagonist nor-binaltorphimine reduced conditioning. Two delta antagonist treatments (16-methyl cyprenorphine and naltrindole) had no reliable effect on acquisition. Thus the enhancement of conditioning appears to be mediated by mu receptors. Previous research has shown that the conditional fear produced by these procedures caused an analgesia that is also mediated by mu receptors. It is argued that the enhancement effect occurs because of an antagonism of this analgesia and that the analgesia normally acts to regulate the level of fear conditioning.     

UNDIGNIFIED BIOETHICS

The concept of dignity is pervasive in bioethics. However, some bioethicists have argued that it is useless on three grounds: that it is indeterminate; that it is reactionary; and that it is redundant. In response, a number of defences of dignity have recently emerged. All of these defences claim that when dignity is suitably clarified, it can be of great use in helping us tackle bioethical controversies. This paper rejects such defences of dignity. It outlines the four most plausible conceptions of dignity: dignity as virtuous behaviour; dignity as inherent moral worth; Kantian dignity; and dignity as species integrity. It argues that while each conception is coherent, each is also fundamentally flawed. As such, the paper argues for a bioethics without dignity: an ‘undignified bioethics.’