Are per-incident rape-pregnancy rates higher than per-incident consensual pregnancy rates?

Is a given instance of rape more likely to result in pregnancy than a given instance of consensual sex? This paper undertakes a review and critique of the literature on rape-pregnancy. Next, it presents our own estimation, from U.S. government data, of pregnancy rates for reproductive age victims of penile-vaginal rape. Using data on birth control usage from the Statistical Abstract of the United States, we then form an estimate of rapepregnancy rates adjusted for the substantial number of women in our sample who would likely have been protected by oral contraception or an IUD. Our analysis suggests that per-incident rape-pregnancy rates exceed per-incident consensual pregnancy rates by a sizable margin, even before adjusting for the use of relevant forms of birth control. Possible explanations for this phenomenon are discussed, as are its implications to ongoing debates over the ultimate causes of rape.     

Why are phenotypic mutation rates much higher than genotypic mutation rates?

The evolution of genotypic mutation rates has been investigated in numerous theoretical and experimental studies. Mutations, however, occur not only when copying DNA, but also when building the phenotype, especially when translating and transcribing DNA to RNA and protein. Here we study the effect of such phenotypic mutations. We find a maximum phenotypic mutation rate, umax, that is compatible with maintaining a certain function of the organism. This may be called a phenotypic error threshold. In particular, we find a minimum phenotypic mutation rate, umin, with the property that there is (nearly) no selection pressure to reduce the rate of phenotypic mutations below this value. If there is a cost for lowering the phenotypic mutation rate, then umin is close to the optimum phenotypic mutation rate that maximizes the fitness of the organism. In our model, there is selective pressure to decrease the rate of genotypic mutations to zero, but to decrease the rate of phenotypic mutations only to a positive value. Despite its simplicity, our model can explain part of the huge difference between genotypic and phenotypic mutation rates that is observed in nature. The relevant data are summarized.     

Are rates of species diversification correlated with rates of morphological evolution?

Some major evolutionary theories predict a relationship between rates of proliferation of new species (species diversification) and rates of morphological divergence between them. However, this relationship has not been rigorously tested using phylogeny-based approaches. Here, we test this relationship with morphological and phylogenetic data from 190 species of plethodontid salamanders. Surprisingly, we find that rates of species diversification and morphological evolution are not significantly correlated, such that rapid diversification can occur with little morphological change, and vice versa. We also find that most clades have undergone remarkably similar patterns of morphological evolution (despite extensive sympatry) and that those relatively novel phenotypes are not associated with rapid diversification. Finally, we find a strong relationship between rates of size and shape evolution, which has not been previously tested.     

What's driving false discovery rates?

The "Paris Guidelines" have begun the process of standardizing reporting for proteomics. New bioinformatics tools have improved the process for estimating error rates of peptide identifications. This perspective seeks to consider these advances in the context of proteomics' short history. As increasing numbers of proteomics papers come from biologists rather than technologists, developing consensus standards for estimating error will be increasingly necessary. Standardizing this assessment should be welcomed as a reflection of the growing impact of proteomic technologies.     

Commodity specific rates of temporal discounting: Does metabolic function underlie differences in rates of discounting?

Discounting rates vary as a function of commodity type. Previous studies suggest five potential characteristics of the commodity that could explain these differences: type of reinforcer (primary or secondary), if the commodity is perishable, if the commodity is satiable, if the commodity can be directly consumed, and immediacy of consumption. This paper suggests that these characteristics may best be viewed as related to a more fundamental characteristic: metabolic processing. In order to explore the possibility that metabolic processing underlies changes in discount rates, the difference in discounting between food, money, music CDs, DVDs, and books are compared. Music CDs, DVDs, and books share many characteristics in common with food, including gaining value through a physiological process, but are not directly metabolized. Results are consistent with previous findings of commodity specific discount rates and show that metabolic function plays a role in determining discount rates with those commodities that are metabolized being discounted at a higher rate. These results are interpreted as evidence that the discount rate for different commodities lies along a continuum with those that serve an exchange function rather than a direct function (money) anchoring the low end and those that serve a direct metabolic function capping the high end (food, alcohol, drugs).     

Can extinction rates be estimated without fossils?

There is considerable interest in the possibility of using molecular phylogenies to estimate extinction rates. The present study aims at assessing the statistical performance of the birth-death model fitting approach to estimate speciation and extinction rates by comparison to the approach considering fossil data. A simulation-based approach was used. The diversification of a large number of lineages was simulated under a wide range of speciation and extinction rate values. The estimators obtained with fossils performed better than those without fossils. In the absence of fossils (e.g. with a molecular phylogeny), the speciation rate was correctly estimated in a wide range of situations; the bias of the corresponding estimator was close to zero for the largest trees. However, this estimator was substantially biased when the simulated extinction rate was high. On the other hand the estimator of extinction rate was biased in a wide range of situations. Surprisingly, this bias was lesser with medium-sized trees. Some recommendations for interpreting results from a diversification analysis are given.     

Why have child pedestrian death rates fallen?

Pedestrian injuries are a leading cause of childhood mortality and disability. Over the past two decades in Britain child pedestrian death rates have fallen despite large increases in traffic volume. In this paper Roberts examines the likely reasons for this decline. He argues that neither prevention programmes nor improvements in medical care are a plausible explanation and that the decline is most likely the result of a substantial reduction in children''s traffic exposure. He believes, however, that restricting children''s traffic exposure exacerbates socioeconomic differentials in childhood mortality and denies children their right to mobility. Roberts is convinced that one answer is for British transport policy to be aimed at providing mobility equitably rather than struggling to meet the ever increasing demands of car travel.     

Otolith accretion rates: Does size really matter?

This study examined the relationship between otolith size and growth in juvenile cod (Gadus morhua L.). Two groups of juvenile cod were reared under different food ration and temperature regimes to obtain fish of similar somatic size but with different sized otoliths. The two groups were subjected to alternating temperature regimes and intermediate ration levels. Large otoliths grew significantly faster than the small ones and variation between individuals was extensive. The ratio of otolith growth during cold and warm temperature exposure did not differ between groups, and the observed growth pattern is therefore not attributable to differential growth within individual temperature periods. The ratio decreased with otolith size, presumably as a result of ontogenetic decrease in otolith protein composition. These results suggest that processes coupled to the metabolic rate of the endolymphatic epithelium are the key driver behind otolith growth.     

Can varying inbreeding depression select for intermediary selfing rates?

We study the evolution of the self-fertilization of an annual hermaphroditic plant under varying inbreeding depression. While classical population genetic models treat inbreeding depression as a constant parameter, recent empirical research has shown that changing environmental conditions can make inbreeding depression vary. Here, we create a simple phenotypic model, assuming variable inbreeding depression. We investigate how different types of variability (spatial, temporal, and spatiotemporal variability) affect the evolution of selfing rates in three models. Two main results, which differ from the classical predictions, emerge from this study. First, we find that fluctuating environments, which influence the magnitude of inbreeding depression, are able to select for evolutionarily stable intermediary selfing rates. Second, we show that spatiotemporal variation of inbreeding depression can lead to the development and the maintenance of polymorphic selfing rates within a population.     

Phylogeny and evolutionary rates of G protein α subunit genes

Summary Rooted phylogenetic trees for a total of 34 genes encoding the stimulatory (s), inhibitory (i), transducin (t), G_x (x), G_z (z), G₁₁ (11), G₁₂ (12), G₁₃ (13), G₁₆ (16), G_q (q), and other (o) G protein a subunits have been constructed. The analysis shows that the G₁₂ (12 and 13), G_q (11, 16, and q), and G_s (s genes) groups form one cluster, and the G_x (x and z genes), G_i (i genes), G_t (t1 and t2), and G_o (o genes) groups form another cluster. During mammalian evolution, the rates of synonymous substitutions for these genes were estimated to be between 1.77 × 10^–9/site/year and 5.63 × 10^–9/site/year, whereas those of nonsynonymous substitutions were between 0.008 × 10^–9/site/year and 0.067 × 10^–9/site/year. These evolutionary rates are similar to those for histone genes, suggesting equally important biological functions of the G protein a subunits. Offprint requests to: S. Yokoyama     

Synonymous nucleotide substitution rates of β-tubulin and histone genes conform to high overall genomic rates in rodents but not in sea urchins

Summary Sea urchin and rodent genomes have been posited to evolve rapidly as indicated by divergences in single copy nuclear DNA sequences. We have examined whether the synonymous substitution rates of three highly conserved genes, -tubulin, histone H4, and histone H3, adhere to these high genomic substitution rates by comparing sequences between two sea urchins,Strongylocentrotus purpuratus andLytechinus pictus, and between rodents and humans. Whereas the rate of change between the 3 untranslated regions of the -tubulin cDNA ofS. purpuratus (Sp-1), sequenced in this study, and ofL. pictus (Lp-3) was consistent with the overall rate of change estimated from previous DNA hybridization results between these species, the synonymous substitution rates for the carboxyl domains of these -tubulins, as well as for the late histones H4 and H3, were significantly depressed. In contrast, synonymous nucleotide substitution rates between rodents and between rodent and human for the carboxyl domain proper of identical -tubulin isotypes and for histone H4 and H3.1 did not differ from the overall rate of change for the rodent genomes. Moreover, an analysis of paralogous human and mouse -tubulin sequences supported the conclusion that the synonymous substitution rates in the mouse were higher than those in the human. Differences in constraint on evolutionary change were not evident strictly from the conserved amino acid sequences and base compositions of these genes. Other constraining influences seemed more relevant to the departure of the synonymous substitution rates of the sea urchin -tubulin and histone coding regions from the average genomic rate.     

Unemployment rates: an alternative to the Jarman index?

OBJECTIVE--To compare the Jarman index with alternative deprivation measures with regard to its usefulness to district health authorities as an indicator of need at small area level. DESIGN--The Jarman index (UPA (8)), Townsend''s index of material deprivation, the Scottish Development Department''s index, the Department of the Environment''s basic index, and unemployment rates were compared in respect of their correlation with measures of morbidity by electoral ward in a typical English district health authority. Measures of morbidity comprised standardised mortality ratios, admission rates (standardised and non-standardised), and permanent sickness rates. Spearman rank correlation coefficients were calculated for each combination of measures and were then ranked for each of the deprivation indices. SETTING--The 59 electoral wards of the Central Nottinghamshire Health Authority. RESULTS--The Jarman index consistently ranked lower in respect of its correlation with measures of morbidity than did the other deprivation measures. Current unemployment rates correlated well with morbidity measures, in particular with hospital admission rates, with correlations ranging from 0.669 to 0.830 for average and standardised all age admission rates. CONCLUSIONS--The Jarman index seems to be the least appropriate of these indices for health authority use. Unemployment rate merits further consideration as a simple, up to date marker for deprivation and consequent need for health service provision.     

Different evolution rates within the lens-specificβ-crystallin gene family

Summary We have determined the sequence of a rat A3/A1-crystallin complementary DNA (cDNA) clone and the (partial) sequence of the human B3-crystallin gene. Calculation of the ratio of silent to nonsynonymous substitution between orthologous A3/A1-, B3-, and other - and -crystallin sequences revealed that the region encoding the two globular domains of the A3/A1-crystallin sequence is the best conserved during evolution, much better than the corresponding region of the B1-, B3-, or the -crystallin sequences, and even better (at least in the rodent/frog comparison) that the well-conserved A-crystallin sequence. Remarkably, the rate of change of the A3/A1-crystallin coding sequence does not differ in the rodent and primate lineages, in contrast with previous findings concerning the evolution rates of the A- or -crystallin sequences in these two lineages. Comparison of the regions that encode the four motifs of the -crystallin between orthologous mammalian sequences showed that the extent of nonsynonymous substitution in each of these four homologous motif regions is the same. However, when the orthologous -crystallin genes of more distantly related species (mammals vs chicken or frog) are compared, the extent of nonsynonymous substitution is higher in the regions encoding the external motifs I and III than in the regions encoding the internal motifs II and IV. This phenomenon is also observed when paralogous members of the /-crystallin supergene family are compared.     

How do biomolecular systems speed up and regulate rates?

The viability of a biological system depends upon careful regulation of the rates of various processes. These rates have limits imposed by intrinsic chemical or physical steps (e.g., diffusion). These limits can be expanded by interactions and dynamics of the biomolecules. For example, (a) a chemical reaction is catalyzed when its transition state is preferentially bound to an enzyme; (b) the folding of a protein molecule is speeded up by specific interactions within the transition-state ensemble and may be assisted by molecular chaperones; (c) the rate of specific binding of a protein molecule to a cellular target can be enhanced by mechanisms such as long-range electrostatic interactions, nonspecific binding and folding upon binding; (d) directional movement of motor proteins is generated by capturing favorable Brownian motion through intermolecular binding energy; and (e) conduction and selectivity of ions through membrane channels are controlled by interactions and the dynamics of channel proteins. Simple physical models are presented here to illustrate these processes and provide a unifying framework for understanding speed attainment and regulation in biomolecular systems.     

Strand symmetry of mutation rates in theβ-globin region

Summary It has been suggested that there may be inequalities in the types of substitution on the two DNA strands (in particular, in the frequencies of transversions from R to Y and from Y to R) due to a higher error rate on the lagging than the leading strand during replication. Reexamination of 11 kb of the -globin region sequenced in six primates fails to confirm this suggestion. Examination of the 73-kb -globin region sequenced in humans shows that the frequency of pyrimidines in different parts of this region is more variable than expected in a random sequence, but the pattern is more consistent with nonrandomness generated by DNA turnover mechanisms than with strand asymmetry due to a higher error rate on the lagging strand.     

Whole body synthesis rates of DHA from α-linolenic acid are greater than brain DHA accretion and uptake rates in adult rats

Docosahexaenoic acid (DHA) is important for brain function, however, the exact amount required for the brain is not agreed upon. While it is believed that the synthesis rate of DHA from α-linolenic acid (ALA) is low, how this synthesis rate compares with the amount of DHA required to maintain brain DHA levels is unknown. The objective of this work was to assess whether DHA synthesis from ALA is sufficient for the brain. To test this, rats consumed a diet low in n-3 PUFAs, or a diet containing ALA or DHA for 15 weeks. Over the 15 weeks, whole body and brain DHA accretion was measured, while at the end of the study, whole body DHA synthesis rates, brain gene expression, and DHA uptake rates were measured. Despite large differences in body DHA accretion, there was no difference in brain DHA accretion between rats fed ALA and DHA. In rats fed ALA, DHA synthesis and accretion was 100-fold higher than brain DHA accretion of rats fed DHA. Also, ALA-fed rats synthesized approximately 3-fold more DHA than the DHA uptake rate into the brain. This work indicates that DHA synthesis from ALA may be sufficient to supply the brain.     

Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes

Molecular simulations are often used to analyse the stability of protein–ligand complexes. The stability can be characterised by exit rates or using the exit time approach, i.e. by computing the expected holding time of the complex before its dissociation. However determining exit rates by straightforward molecular dynamics methods can be challenging for stochastic processes in which the exit event occurs very rarely. Finding a low variance procedure for collecting rare event statistics is still an open problem. In this work we discuss a novel method for computing exit rates which uses results of Robust Perron Cluster Analysis (PCCA+). This clustering method gives the possibility to define a fuzzy set by a membership function, which provides additional information of the kind ‘the process is being about to leave the set’. Thus, the derived approach is not based on the exit event occurrence and, therefore, is also applicable in case of rare events. The novel method can be used to analyse the temperature effect of protein–ligand systems through the differences in exit rates, and, thus, open up new drug design strategies and therapeutic applications.