Is it necessary to assume an apartheid-like social structure in Early Anglo-Saxon England?

It has recently been argued that there was an apartheid-like social structure operating in Early Anglo-Saxon England. This was proposed in order to explain the relatively high degree of similarity between Germanic-speaking areas of northwest Europe and England. Opinions vary as to whether there was a substantial Germanic invasion or only a relatively small number arrived in Britain during this period. Contrary to the assumption of limited intermarriage made in the apartheid simulation, there is evidence that significant mixing of the British and Germanic peoples occurred, and that the early law codes, such as that of King Ine of Wessex, could have deliberately encouraged such mixing. More importantly, the simulation did not take into account any northwest European immigration that arrived both before and after the Early Anglo-Saxon period. In view of the uncertainty of the places of origin of the various Germanic peoples, and their numbers and dates of arrival, the present study adopts an alternative approach to estimate the percentage of indigenous Britons in the current British population. It was found unnecessary to introduce any special social structure among the diverse Anglo-Saxon people in order to account for the estimates of northwest European intrusion into the British population.     

Cumulative cultural evolution and demography

The idea that demographic change may spur or slow down technological change has become widely accepted among evolutionary archaeologists and anthropologists. Two models have been particularly influential in promoting this idea: a mathematical model by Joseph Henrich, developed to explain the Tasmanian loss of culture during the Holocene; and an agent-based adaptation thereof, devised by Powell et al. to explain the emergence of modern behaviour in the Late Pleistocene. However, the models in question make rather strong assumptions about the distribution of skills among social learners and about the selectivity of social learning strategies. Here I examine the behaviour of these models under more conservative and, on empirical and theoretical grounds, equally reasonable assumptions. I show that, some qualifications notwithstanding, Henrich's model largely withstands my robustness tests. The model of Powell et al., in contrast, does not-a finding that warrants a fair amount of skepticism towards Powell et al.'s explanation of the Upper Paleolithic transition. More generally, my evaluation of the accounts of Henrich and of Powell et al. helpfully clarify which inferences their popular models do and not support.     

A model for avian primary moult

The regression methods frequently used to estimate the parameters associated with primary moult in birds are unsatisfactory. Results obtained using least squares regression, and various ad hoc adaptations, are so obviously incorrect that many authors have fitted lines 'by eye' (Newton 1968, Thomas & Dartnall 1971, Elliott et al. 1976, Morrison 1976, Appleton & Minton 1978). In a comparison of seven regression methods, estimates of the average starting date varied between 29 June and 31 July, completion date between 2 and 24 October, and duration of moult between 72 and 109 days for the Redshank Tringo totonus, in spite of the very large sample of 1482 observations (Summers et al. 1983). In this paper we present a new approach to the analysis of primary moult and develop a mathematical model specifically designed for moult data.     

The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate?

Miyata et al. have suggested that the male-to-female mutation rate ratio (alpha) can be estimated by comparing the neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) genes. Rodent silent site X/A comparisons provide very different estimates from X/Y comparisons. We examine three explanations for this discrepancy: (1) statistical biases and artifacts, (2) nonneutral evolution, and (3) differences in mutation rate per germline replication. By estimating errors and using a variety of methodologies, we tentatively reject explanation 1. Our analyses of patterns of codon usage, synonymous rates, and nonsynonymous rates suggest that silent sites in rodents are evolving neutrally, and we can therefore reject explanation 2. We find both base composition and methylation differences between the different sets of chromosomes, a result consistent with explanation 3, but these differences do not appear to explain the observed discrepancies in estimates of alpha. Our finding of significantly low synonymous substitution rates in genomically imprinted genes suggests a link between hemizygous expression and an adaptive reduction in the mutation rate, which is consistent with explanation 3. Therefore our results provide circumstantial evidence in favor of the hypothesis that the discrepancies in estimates of alpha are due to differences in the mutation rate per germline replication between different parts of the genome. This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of alpha, obtained using this method, need to be treated with caution.     

Rational versus anti-rational interpretations of science: an ape-language case-study

Robert Nola (2003) has argued that anti-rationalist interpretations of science fail to adequately explain the process of science, since objective reasons can be causal factors in belief formation. While I agree with Nola that objective reasons can be a cause of belief, in this paper I present a version of the strong programme in the sociology of knowledge, the Interests Thesis, and argue that the Interests Thesis provides a plausible explanation of an episode in the history of ape-language research. Specifically, I examine Terrace, Petitto, Sandess, & Bever (1979, 1980) illegitimate comparison of the signing of their chimpanzee, Nim, with data from human early childhood language development, and argue that Terrace et al.'s interests played a causal role in determining their sceptical beliefs concerning ape linguistic abilities. However, I go on to argue that Terrace et al.'s interests are not the only causal factors in determining their beliefs: objective reasons, associated with the institution of new methodologies, were also causally determinative of Terrace et al.'s sceptical beliefs. Consequently, I argue that belief formation in science is a multi-factorial affair wherein both interests and objective reasons have causal roles. I finish the paper with two conjectures concerning the proper locus of scientific rationality.     

On travelling wave solutions in a model for the Belousov-Zhabotinskii reaction.

DNA fragments partially digested by a 3′- or 5′-specific nuclease to produce single chain ends of opposite polarity will form a ring if the ends contain complementary sequences and are allowed to anneal. The frequency of rings can then be used as an assay to determine where and how identical repetitious sequences are arranged in the DNA. Thomas et al. (1973b) showed that all eucaryote chromosomes studied contain similar if not identical repetitious sequences clustered into regions called g-regions. To account for the observed ring frequency under different experimental conditions Thomas, Zimm &; Dancis (1973c) derived equations for two possible models of g-region organization. In the pure tandem model, the repetitious sequences are contiguous and occupy the entire g-region. In the intermittent repetition model, the repetitious sequences are simple copolymers and are irregularly arranged among non-repetitious sequences which are heterogenous in length. In the present paper, the results of Thomas et al. (1973c) are extended to cover the fractional tandem model. In this model, adjacent repetitious sequences are separated by non-repetitious sequences of uniform length. In addition, the equations for both the pure tandem and intermittent repetition models are shown to be special cases of the fractional tandem model but not vice versa.The capabilities and limitations of an analysis of ring formation are demonstrated using data from Drosophila. Although it is not possible to rule out any of the three models, the analysis can limit the ranges of the parameters describing each of the models that are consistent with the data. Previous conclusions that the data could only be explained by a pure tandem model which lacks any intervening unique sequences (Bick, Huang &; Thomas, 1973; Thomas et al., 1973b), are shown to be incorrect, in part because the equations for the fractional tandem model had not then been derived. Thus ring theory equations can be used to show the presence of clusters of similar if not identical sequences from ring-forming experiments, but they may not be able to determine the exact spacing and arrangement of these sequences within the clusters.     

A model for avian primary moult

The regression methods frequently used to estimate the parameters associated with primary moult in birds are unsatisfactory. Results obtained using least squares regression, and various ad hoc adaptations, are so obviously incorrect that many authors have fitted lines ‘by eye’ (Newton 1968, Thomas & Dartnall 1971, Elliott et al. 1976, Morrison 1976, Appleton & Minton 1978). In a comparison of seven regression methods, estimates of the average starting date varied between 29 June and 31 July, completion date between 2 and 24 October, and duration of moult between 72 and 109 days for the Redshank Tringa totanus, in spite of the very large sample of 1482 observations (Summers et al. 1983). In this paper we present a new approach to the analysis of primary moult and develop a mathematical model specifically designed for moult data.     

Evidence for an apartheid-like social structure in early Anglo-Saxon England

The role of migration in the Anglo-Saxon transition in England remains controversial. Archaeological and historical evidence is inconclusive, but current estimates of the contribution of migrants to the English population range from less than 10000 to as many as 200000. In contrast, recent studies based on Y-chromosome variation posit a considerably higher contribution to the modern English gene pool (50-100%). Historical evidence suggests that following the Anglo-Saxon transition, people of indigenous ethnicity were at an economic and legal disadvantage compared to those having Anglo-Saxon ethnicity. It is likely that such a disadvantage would lead to differential reproductive success. We examine the effect of differential reproductive success, coupled with limited intermarriage between distinct ethnic groups, on the spread of genetic variants. Computer simulations indicate that a social structure limiting intermarriage between indigenous Britons and an initially small Anglo-Saxon immigrant population provide a plausible explanation of the high degree of Continental male-line ancestry in England.     

种群趋势指数的方差近似估计式及其应用

根据吴惠龙等（1986）发表的稻纵卷叶螟 Cnaphalocrocis medinalis 的生命表及 Watt 种群趋势指数数学模型,在delta-方法的基础上,本文提出了一种种群趋势指数方差的近似估计法,并应用于评价稻螟赤眼蜂Trichogramma japonicum Ashmead 及化学杀虫剂（甲六粉）对稻纵卷叶螟的控制作用。根据中心极限定律,当样本足够大时,种群趋势指数近似于正态分布。根据近似方差估计量以及 Z-检验方法,取得以下结论：放蜂区明显优于对照区,因其种群趋势指数取值较小,相应的 P 值为 0.0111,该区也明显优于化学杀虫剂处理区,相应的 P 值为 0.0036。杀虫剂处理区差于对照区,因其种群趋势指数值较大（0.3035）,但这种差异并未达到显著水平,P 值为 0.2236。虽然本文的结论近似于吴惠龙等（1986）单纯依据种群趋势指数所得到的结果,但本文的结论更具统计意义,更加可靠。     

For catch bonds, it all hinges on the interdomain region

Tensile mechanical force was long assumed to increase the detachment rates of biological adhesive bonds (Bell, 1978). However, in the last few years, several receptor-ligand pairs were shown to form "catch bonds," whose lifetimes are enhanced by moderate amounts of force. These include the bacterial adhesive protein FimH binding to its ligand mannose (Thomas et al., 2002; Thomas et al., 2006), blood cell adhesion proteins P- and L-selectin binding to sialyl Lewis X (sLe(X))-containing ligands (Marshall et al., 2003; Evans et al., 2004; Sarangapani et al., 2004), and the myosin-actin motor protein interaction (Guo and Guilford, 2006). The structural mechanism behind this counterintuitive force-enhanced catch bond behavior is of great interest.     

Eliminating bovine tuberculosis in cattle and badgers: insight from a dynamic model

Bovine tuberculosis (BTB) is a multi-species infection that commonly affects cattle and badgers in Great Britain. Despite years of study, the impact of badgers on BTB incidence in cattle is poorly understood. Using a two-host transmission model of BTB in cattle and badgers, we find that published data and parameter estimates are most consistent with a system at the threshold of control. The most consistent explanation for data obtained from cattle and badger populations includes within-host reproduction numbers close to 1 and between-host reproduction numbers of approximately 0.05. In terms of controlling infection in cattle, reducing cattle-to-cattle transmission is essential. In some regions, even large reductions in badger prevalence can have a modest impact on cattle infection and a multi-stranded approach is necessary that also targets badger-to-cattle transmission directly. The new perspective highlighted by this two-host approach provides insight into the control of BTB in Great Britain.     

Two explanations of the dawn chorus compared: how monotonically changing light levels favour a short break from singing

I used optimality modelling to compare two of the most plausible and general explanations for the dawn and dusk peaks in bird song output. Kacelnik's explanation is that foraging is inefficient in poor light, but that social interactions are less affected, making singing more worthwhile than foraging. McNamara et al.'s explanation is based on stochasticity in foraging success and overnight energy requirements; it has been extensively analysed with stochastic dynamic programming models. Both explanations are now incorporated into this sort of model. I used various functions to link success of foraging and singing to time of day, but assumed that above some light level there is no further effect. Kacelnik's explanation has as strong an effect as stochasticity in generating dawn and dusk choruses. It also predicts short pauses in the singing output just after the dawn chorus and before the dusk chorus. The former arises because birds delay foraging when it will become more profitable later, until foraging success reaches a plateau, when the energetic debt accumulated makes them forage. The principle of this see-saw double switch in behaviours may apply to other explanations for the dawn chorus, and to other shifts in behaviour when conditions change gradually. The model predicts that from day to day cloud cover determines when a dawn chorus starts, but that overnight temperature and wind strength have more effect on chorus intensity and duration. I discuss what sort of observational and experimental data on singing routines would better test this model. Copyright 2002 The Association for the Study of Animal Behaviour. Published by Elsevier Science Ltd. All rights reserved.     

The evolution of sea urchin sperm bindin

Sea urchins have been model organisms for the study of fertilization for more than a century. Fertilization in sea urchins happens externally, which facilitates the study of sperm-egg attachment and fusion, and means that all of the molecules involved in gamete recognition and fusion are associated with the gametes. Sea urchin sperm bindin was the first "gamete recognition protein" to be isolated and characterized (Vacquier and Moy 1977), and bindin has since been studied by developmental biologists interested in fertilization, by biochemists interested in membrane fusion and by evolutionary biologists interested in reproductive isolation and speciation. Research on bindin was last reviewed thirteen years ago by Vacquier et al. (1995) in an article titled "What have we learned about sea urchin sperm bindin?" in which the authors reviewed the identification, isolation and early molecular examinations of bindin. Research since then has focused on bindin's potential role in fusing egg and sperm membranes, comparisons of bindin between distantly related species, studies within genera linking bindin evolution to reproductive isolation, and studies within species looking at fertilization effects of individual bindin alleles. In addition, the egg receptor for bindin has been cloned and sequenced. I review this recent research here.     

Two of these or two of those?

Symmetrically dividing neuroepithelial cells may produce two daughters that are both proliferating or both postmitotic, as highlighted by Zigman et al. in this issue of Neuron and Sanada and Tsai in a recent issue of Cell. Here, I will attempt to offer a simple explanation why these results may be so different.     

Reviews of Publications

Book reviewed in this article:
Flowers of the Himalaya , by Oleg Polunin and Adam Stainton.
A Guide to the Vegetation of Britain and Europe , by Oleg Polunin and Martin Walters.
The Experimental Biology of Bryophytes, edited by A. F. Dyer & J. G. Duckett.
A Birdwatcher's Miscellany, edited by Rob Hume.
The Moths and Butterjlies of Great Britain and Ireland, Volume 10, Noctuidae (Part II) and Agaristidae, edited by J. Heath.
Atlas of Butterjlies in Britain and Ireland, by J. Heath, E. Pollard & J. A. Thomas.
Colour Identification Guide to Butterjlies of the British Isles, revised edition by T. G. Howarth.
The World of Butterjlies, An Illustrated Encyclopaedia, by V. Sbordoni & S.Forestiero.
Colour Identijcation Guide to Moths of the British Isles, by Bernard Skinner.
The Biology of Buttegies, edited by R. I. Vane-Wright & P. R. Ackery.
Australian Grasses, by Nancy T. Burbidge, revised by Surrey W. L. Jacobs.
Collins Guide to Grasses, Sedges, Rushes and Ferns, by R. Fitter & A. Fitter. Collins.
Grasses of the Soviet Union, by N. N. Tsvelev, edited by A. A. Fedorov.
The European Garden Flora, Volume 2, Monocotyledons (Part ZZ), edited by S. M Walters et al.
Grasses, 3rd edition, by C. E. Hubbard, revised by J. C. E. Hubbard.     

Induction of gene expression in Dictyostelium by prestarvation factor, a factor secreted by growing cells

During growth, Dictyostelium cells continuously secrete a factor, PSF, that accumulates in proportion to cell density. At sufficient concentration, it triggers the production of discoidin I and certain lysosomal enzymes. Our earlier studies demonstrated these effects of PSF on protein and enzyme levels [Clarke et al., Differentiation 34:79-87, 1987; Clarke et al., Dev Genet 9: 315-326, 1988]. In the present study, we have examined whether PSF induces increased mRNA levels. By Northern blot analysis, we have found that discoidin I mRNA accumulates in exponentially growing NC4 cells as the cells reach high density; significant levels of mRNA are detectable in cells growing either on plates or in suspension, beginning about four generations before the end of exponential growth. High levels of discoidin I mRNA are also found in low-density cells grown in the presence of buffer conditioned by high-density cells. These results indicate that PSF induces the accumulation of discoidin I mRNA. Other "early developmental" genes, pCZ22 and the early I genes (16, 18, and 111), are also expressed in exponentially growing cells at high density or in the presence of conditioned buffer. We conclude that several genes previously found to be preferentially expressed very early in development are actually induced during late exponential growth by PSF.     

Modeling effects of local extinctions on culture change and diversity in the paleolithic

The persistence of early stone tool technologies has puzzled archaeologists for decades. Cognitively based explanations, which presume either lack of ability to innovate or extreme conformism, do not account for the totality of the empirical patterns. Following recent research, this study explores the effects of demographic factors on rates of culture change and diversification. We investigate whether the appearance of stability in early Paleolithic technologies could result from frequent extinctions of local subpopulations within a persistent metapopulation. A spatially explicit agent-based model was constructed to test the influence of local extinction rate on three general cultural patterns that archaeologists might observe in the material record: total diversity, differentiation among spatially defined groups, and the rate of cumulative change. The model shows that diversity, differentiation, and the rate of cumulative cultural change would be strongly affected by local extinction rates, in some cases mimicking the results of conformist cultural transmission. The results have implications for understanding spatial and temporal patterning in ancient material culture.     

A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments

MOTIVATION: A common task in analyzing microarray data is to determine which genes are differentially expressed across two kinds of tissue samples or samples obtained under two experimental conditions. Recently several statistical methods have been proposed to accomplish this goal when there are replicated samples under each condition. However, it may not be clear how these methods compare with each other. Our main goal here is to compare three methods, the t-test, a regression modeling approach (Thomas et al., Genome Res., 11, 1227-1236, 2001) and a mixture model approach (Pan et al., http://www.biostat.umn.edu/cgi-bin/rrs?print+2001,2001a,b) with particular attention to their different modeling assumptions. RESULTS: It is pointed out that all the three methods are based on using the two-sample t-statistic or its minor variation, but they differ in how to associate a statistical significance level to the corresponding statistic, leading to possibly large difference in the resulting significance levels and the numbers of genes detected. In particular, we give an explicit formula for the test statistic used in the regression approach. Using the leukemia data of Golub et al. (Science, 285, 531-537, 1999), we illustrate these points. We also briefly compare the results with those of several other methods, including the empirical Bayesian method of Efron et al. (J. Am. Stat. Assoc., to appear, 2001) and the Significance Analysis of Microarray (SAM) method of Tusher et al. (PROC: Natl Acad. Sci. USA, 98, 5116-5121, 2001).