On the use of the Price equation

This paper distinguishes two categories of questions that the Price equation can help us answer. The two different types of questions require two different disciplines that are related, but nonetheless move in opposite directions. These disciplines are probability theory on the one hand and statistical inference on the other. In the literature on the Price equation this distinction is not made. As a result of this, questions that require a probability model are regularly approached with statistical tools. In this paper, we examine the possibilities of the Price equation for answering questions of either type. By spending extra attention on mathematical formalities, we avoid the two disciplines to get mixed up. After that, we look at some examples, both from kin selection and from group selection, that show how the inappropriate use of statistical terminology can put us on the wrong track. Statements that are 'derived' with the help of the Price equation are, therefore, in many cases not the answers they seem to be. Going through the derivations in reverse can, however, be helpful as a guide how to build proper (probabilistic) models that do give answers.     

Nucleolar targeting: the hub of the matter

The nucleolus is a dynamic structure that has roles in various processes, from ribosome biogenesis to regulation of the cell cycle and the cellular stress response. Such functions are frequently mediated by the sequestration or release of nucleolar proteins. Our understanding of protein targeting to the nucleolus is much less complete than our knowledge of membrane‐spanning translocation systems—such as those involved in nuclear targeting—and the experimental evidence reveals that few parallels exist with these better‐characterized systems. Here, we discuss the current understanding of nucleolar targeting, explore the types of sequence that control the localization of a protein to the nucleolus, and speculate that certain subsets of nucleolar proteins might act as hub proteins that are able to bind to multiple protein targets. In parallel to other subnuclear structures, such as PML bodies, the proteins that are involved in the formation and maintenance of the nucleolus are inexorably linked to nucleolar trafficking.     

The variances of the distributions of the combinations of the sexes within mammalian litters: Notes to mark the centenary of the problem

It is 100 years since Gini noted that in some samples of litters of mice and rabbits, the variances of the distributions of the combinations of the sexes are sub-binomial. In other words, in contrast with binomial expectation, there are too many litters in which the sexes are equally balanced, and there are too few unisexual litters. In the intervening years, this finding has been replicated in a number of further species, but no explanation has become established. Potential explanations are reviewed here, and it is suggested that the most likely cause is that, at the time of formation of the zygotes, p, the probability that a zygote will be male, varies from one zygote to another within litters, thus constituting an example of Poisson variation. And it is a standard result in probability theory that such variation causes sub-binomial variance.     

Vortical flow in the utricle and the ampulla: a computational study on the fluid dynamics of the vestibular system

We present a computational study of the fluid dynamics in healthy semicircular canals (SCCs) and the utricle. The SCCs are the primary sensors for angular velocity and are located in the vestibular part of the inner ear. The SCCs are connected to the utricle that hosts the utricular macula, a sensor for linear acceleration. The transduction of angular motion is triggered by the motion of a fluid called endolymph and by the interaction of this fluid with the sensory structures of the SCC. In our computations, we observe a vortical flow in the utricle and in the ampulla (the enlarged terminal part of the SCCs) which can lead to flow velocities in the utricle that are even higher than those in the SCCs. This is a fundamentally new result which is in contrast to the common belief that the fluid velocities in the utricle are negligible from a physiological point of view. Moreover, we show that the wall shear stresses in the utricle and the ampulla are maximized at the positions of the sensory epithelia. Possible physiological and clinical implications are discussed.     

Helix movements and the reconstruction of the haem pocket during the evolution of the cytochrome c family

Analysis of cytochromes c (tuna), c2 (Rhodospirillum rubrum), c550 (Paracoccus denitrificans) and c551 (Pseudomonas aeruginosa) shows that they contain 48 residues identifiable as homologous from superposition of the structures. The other 34 to 64 residues are in loops that vary greatly in sequence, length and conformation, or in alpha-helices that are found in only some of the structures. Of the 48 homologous residues, 17 are in three segments which pack onto the haem faces. In all four structures, these segments have the same conformations, and the same locations relative to the haem. The other 31 residues are in three alpha-helices which are in contact with each other. These form the back and one side of the haem pocket. In cytochrome c551 the positions of the three alpha-helices have shifted and rotated, in comparison with cytochromes c and c2, by up to 5 A and 25 degrees relative to the haem. These shifts, facilitated by mutations at the helix-helix interfaces, are related to the reconstruction of the propionic acid side of the haem pocket described by Almassy & Dickerson (1978). Together these effects produce alternative structures for the haem pocket. This mechanism of adaptation to mutation contrasts with that observed in the globins. In the globins, mutations also produce changes in helix interfaces and shifts of packed helices, but in the globins these shifts are coupled to conserve the structure of the haem pocket.     

From the cytoplasm into the cilium: Bon voyage

The primary cilium compartmentalizes a tiny fraction of the cell surface and volume, yet many proteins are highly enriched in this area and so efficient mechanisms are necessary to concentrate them in the ciliary compartment. Here we review mechanisms that are thought to deliver protein cargo to the base of cilia and are likely to interact with ciliary gating mechanisms. Given the immense variety of ciliary cytosolic and transmembrane proteins, it is almost certain that multiple, albeit frequently interconnected, pathways mediate this process. It is also clear that none of these pathways is fully understood at the present time. Mechanisms that are discussed below facilitate ciliary localization of structural and signaling molecules, which include receptors, G-proteins, ion channels, and enzymes. These mechanisms form a basis for every aspect of cilia function in early embryonic patterning, organ morphogenesis, sensory perception and elsewhere.     

On the role of the engrailed+ gene in the internal organs of Drosophila.

Our purpose is to assess the effects of lethal alleles of engrailed on cells of the internal organs of Drosophila. Using nuclear transplantation we make mosaic flies that contain regions made by engrailed-lethal cells that are genetically labelled. We find that engrailed-lethal cells cause defects in some parts of the epidermis and central nervous system. Most of the internal organs of the fly are assessed and of those, all organs and tissues derived from the endoderm or the splanchnic and somatic mesoderm are normal; flies carrying engrailed-lethal cells in large areas of these organs are viable. We postulate that segments of the mesoderm are single units of cell lineage and that, unlike the ectoderm, they are not subdivided into anterior and posterior compartments.     

Assessing the impacts of fire on the vegetation resources that are available to the local communities of the seasonal wetlands of the Okavango, Botswana, in the context of different land uses and key government policies

The Okavango wetlands in north western Botswana are the most fire-prone environment in Botswana. Most of these fires are anthropogenic. The fires in this environment are thought to impact the environment negatively and therefore practices that are associated with extensive use of fire have been strongly criticized. Despite this, there has been little work done to understand how these fires impact the wetlands environment and its dynamics, especially the vegetation resources that are used by the local communities in the wetlands. The objective of the study was to identify fire spatial and temporal trends in relation to settlement distribution, through the use of remote sensing, socio-economic and phytosociological surveys. The fire history results show that geographically there has not been any significant change in vegetation structure and that in fact fires may have promoted biodiversity. The results of analysis show an overall variance on vegetation structure of 23% whereas the rest are unaccounted for. There is a strong association between settlements, ethnicities, literacy and fire occurrences. The most fire-prone areas are inhabited by communities that have used fire in the past for various resource use practices.     

Genetic matches and the logic of the law

In a recent article Levine and Kobilinsky (1997) point out that current methods in forensic DNA 'identification' are inadequate because the commercial kits commonly used in forensic practice do not detect the true genotype, but rather a genotype based on convenient categorization. For this reason, Levine and Kobilinsky argue that statistics attached to such categorizations are invalid. The authors believe that the arguments of Levine and Kobilinsky are logically flawed. This revised version was published online in July 2006 with corrections to the Cover Date.     

On the importance of homology in the age of phylogenomics

Homology is perhaps the most central concept of phylogenetic biology. Molecular systematists have traditionally paid due attention to the homology statements that are implied by their alignments of orthologous sequences, but some authors have suggested that manual gene-by-gene curation is not sustainable in the phylogenomics era. Here, we show that there are multiple ways to efficiently screen for and detect homology errors in phylogenomic data sets. Application of these screening approaches to two phylogenomic data sets, one for birds and another for mammals, shows that these data are replete with homology errors including alignments of different exons to each other, alignments of exons to introns, and alignments of paralogues to each other. The extent of these homology errors weakens the conclusions of studies based on these data sets. Despite advances in automated phylogenomic pipelines, we contend that much of the long, difficult, and sometimes tedious work of systematics is still required to guard against pervasive homology errors. This conclusion is underscored by recent studies that show that just a few outlier genes can impact phylogenetic results at short, tightly spaced internodes that are deep in the Tree of Life. The view that widespread DNA sequence alignment errors are not a major concern for rigorous systematic research is not tenable. If a primary goal of phylogenomics is to resolve the most challenging phylogenetic problems with the abundant data that are now available, researchers must employ effective procedures to screen for and correct homology errors prior to performing downstream phylogenetic analyses.     

ECVAM's role in the implementation of the Three Rs concept in the field of biologicals

Biologicals can be defined as products that are derived from living organisms or are produced by them. They include vaccines, hormones, monoclonal and polyclonal antibodies, blood products and rDNA products. The production of conventionally produced biologicals requires an extensive batch-related quality control, to ensure that these products are both safe and potent. As several of the control tests rely on animal models, it is inevitable that the large numbers of animals are used. Many initiatives have been undertaken in the last few decades to reduce and refine the use of animals in this area. ECVAM has been involved in many activities to support the development, validation and implementation of these Three Rs methods. The role that ECVAM has played in a number of validation studies is summarised. It is concluded that ECVAM should continue to support the activities that have been shown to be successful, preferably in collaboration with the regulatory bodies.     

From the cytoplasm into the cilium: Bon voyage

The primary cilium compartmentalizes a tiny fraction of the cell surface and volume, yet many proteins are highly enriched in this area and so efficient mechanisms are necessary to concentrate them in the ciliary compartment. Here we review mechanisms that are thought to deliver protein cargo to the base of cilia and are likely to interact with ciliary gating mechanisms. Given the immense variety of ciliary cytosolic and transmembrane proteins, it is almost certain that multiple, albeit frequently interconnected, pathways mediate this process. It is also clear that none of these pathways is fully understood at the present time. Mechanisms that are discussed below facilitate ciliary localization of structural and signaling molecules, which include receptors, G-proteins, ion channels, and enzymes. These mechanisms form a basis for every aspect of cilia function in early embryonic patterning, organ morphogenesis, sensory perception and elsewhere.     

Does the heterogeneity of autism undermine the neurodiversity paradigm?

The neurodiversity paradigm is presented by its proponents as providing a philosophical foundation for the activism of the neurodiversity movement. Its central claims are that autism and other neurodivergent conditions are not disorders because they are not intrinsically harmful, and that they are valuable, natural and/or normal parts of human neurocognitive variation. This paper: (a) identifies the non‐disorder claim as the most central of these, based on its prominence in the literature and connections with the practical policy claims that the paradigm is supposed to support; (b) describes the heterogeneity of autism at the behavioural and causal levels, and argues that at the behavioural level this encompasses ways of being autistic that are harmful in ways that cannot be not wholly attributed to discrimination or unjust social arrangements, challenging the claim that autism is not a disorder; (c) considers and rejects responses to this challenge based on separation of high‐ and low‐functioning autism, separation of autism from co‐occurring conditions, and viewing autism as part of an individual’s identity. Two of these responses fail for reasons that are themselves connected with the behavioural and/or causal heterogeneity of autism.     

Meiofauna and the origins of the Metazoa*

Possible alternative habitats and life-styles of the original metazoan are considered. It is argued from the dominance of the benthic habitat in present-day groups that the original metazoan habitat was benthic rather than planktonic. Similarly, plesiomorphic metazoan taxa tend to be holobenthic rather than pelago-benthic. It is therefore probable that the early Metazoa were holobenthic. The concept of plesiohabitats and apohabitats in the evolution of taxa is presented. This leads to the proposition that the early metazoans were interstitial bionts of fine sand. Finally, the controversy concerning the aerobic or anaerobic origin of the Metazoa is considered. It is shown that competition theory predicts that plesiomorphic taxa are likely to remain in plesiohabitats. Diagrams showing the possible evolution of major taxa in relation to available habitats are presented. It is concluded that the earliest Metazoa could have evolved in anaerobic marine sand and that the early Plathelminthomorpha and Aschelminthes did so.     

Potential hazards of biotechnology: the viewpoint from the United Kingdom

(1) There is a danger that our science may be severely restricted in the future if we do not as scientists take action to inform the public. (2) Scientists are agreed that some governmental controls are essential, but there is an urgent need that these should be applied uniformly worldwide. (3) The situation has changed rapidly now that the scientists are poised to demonstrate that genetic engineering has advanced to the stage where it can be applied to the field. Only in that way can we, as scientists, demonstrate that biotechnology can help humanity to overcome the problems of health, disease, and decent living which threaten to get progressively worse.     

Exophthalmos from the standpoint of the ophthalmologist

There are many causes of abnormal protrusion of one or both eyes, the most common of which is imbalance of the glands of internal secretion. Among other causes are a variety of tumors that originate behind the eye or that extend to that location from other parts in the body. Infections can extend to the orbit behind the eye from the neighboring structures such as the paranasal sinuses. Infection may also extend to the orbit from distant areas by way of the blood and cause exophthalmos.     

The political left rolls with the good and the political right confronts the bad: connecting physiology and cognition to preferences

We report evidence that individual-level variation in people's physiological and attentional responses to aversive and appetitive stimuli are correlated with broad political orientations. Specifically, we find that greater orientation to aversive stimuli tends to be associated with right-of-centre and greater orientation to appetitive (pleasing) stimuli with left-of-centre political inclinations. These findings are consistent with recent evidence that political views are connected to physiological predispositions but are unique in incorporating findings on variation in directed attention that make it possible to understand additional aspects of the link between the physiological and the political.     

Exploring the temporal consequences of chasing the elements in Rosen's relational diagrams

In the work 'Life Itself', Rosen showed that a formal mechanism cannot be 'closed to efficient cause'. Additionally, he claimed that organisms are 'closed to efficient cause' and that, by logical extension, organisms cannot be mechanisms. This paper shows that it is possible for mechanisms to be 'nearly closed to efficient cause', with the requirement that some unentailed efficient-cause agents are placed inside the system. Populations of these 'nearly closed to efficient cause' systems can be defined based on the ability to isolate each component in its own 'reaction chamber'. Diagrams from these populations are drawn from a couple of different perspectives, and comments are made on how these diagrams can be related to the more conventional language of chemistry.     

Zebra stripes and tiger stripes: the spatial frequency distribution of the pattern compared to that of the background is significant in display and crypsis

Some striped animals are camouflaged in their natural environment, whereas others are conspicuous. Mammals are known to have spatial frequency analysers in their visual mechanism, and it is suggested that the spatial characteristics of a striped pattern are different in camouflaged and conspicuous animals. Fourier analysis of the stripes of the zebra shows spatial frequencies in the pattern that are unlikely to be present so strongly in their natural background scene. A similar analysis of the camouflaging stripes of a tiger show that the distribution of spatial frequencies are similar to that in the background scene.