Rationality, biology and optimality*

A historical theory of rational norms claims that, if we are supposed to think rationally, this is because it is biologically normal for us to do so. The historical theorist is committed to the view that we are supposed to think rationally only if, in the past, adult humans sometimes thought rationally. I consider whether there is any plausible model of rational norms that can be adopted by the historical theorist that is compatible with the claim that adult human beings are subject to rational norms, given certain plausible empirical assumptions about our history and capabilities. I suggest that there is one such model: this model centres on the idea that a procedure is rational if it has been endorsed (or at least not rejected) by mechanisms that have the function to ensure that the subject learns to reason in a way that approaches a certain kind of optimality. This revised version was published online in July 2006 with corrections to the Cover Date.     

Analysis of the status of subject recruitment in clinical trials in Shandong, China

Although subject recruitment for clinical trials in Shandong has been carried out with an awareness of international regulatory and ethical frameworks, there have been some defects in the recruitment process. The objective of this study is to analyze the current status of subject recruitment in Shandong. We conducted a survey among 198 principal investigators (PIs) and 543 subjects. The results were summarized and calculated as a percentage according to the responses to each question by PIs and subjects. This survey indicated that the ethics committee should strengthen the review of subject recruitment and enhance ethics training among board members. PIs should seek to improve the recruitment process.     

Mutations in ACY1, the gene encoding aminoacylase 1, cause a novel inborn error of metabolism

N-terminal acetylation of proteins is a widespread and highly conserved process. Aminoacylase 1 (ACY1; EC 3.5.14) is the most abundant of the aminoacylases, a class of enzymes involved in hydrolysis of N-acetylated proteins. Here, we present four children with genetic deficiency of ACY1. They were identified through organic acid analyses using gas chromatography-mass spectrometry, revealing increased urinary excretion of several N-acetylated amino acids, including the derivatives of methionine, glutamic acid, alanine, leucine, glycine, valine, and isoleucine. Nuclear magnetic resonance spectroscopy analysis of urine samples detected a distinct pattern of N-acetylated metabolites, consistent with ACY1 dysfunction. Functional analyses of patients' lymphoblasts demonstrated ACY1 deficiency. Mutation analysis uncovered recessive loss-of-function or missense ACY1 mutations in all four individuals affected. We conclude that ACY1 mutations in these children led to functional ACY1 deficiency and excretion of N-acetylated amino acids. Questions remain, however, as to the clinical significance of ACY1 deficiency. The ACY1-deficient individuals were ascertained through urine metabolic screening because of unspecific psychomotor delay (one subject), psychomotor delay with atrophy of the vermis and syringomyelia (one subject), marked muscular hypotonia (one subject), and follow-up for early treated biotinidase deficiency and normal clinical findings (one subject). Because ACY1 is evolutionarily conserved in fish, frog, mouse, and human and is expressed in the central nervous system (CNS) in human, a role in CNS function or development is conceivable but has yet to be demonstrated. Thus, at this point, we cannot state whether ACY1 deficiency has pathogenic significance with pleiotropic clinical expression or is simply a biochemical variant. Awareness of this new genetic entity may help both in delineating its clinical significance and in avoiding erroneous diagnoses.     

Mechanics of curved plasma membrane vesicles: resting shapes, membrane curvature, and in-plane shear elasticity

Highly curved cell membrane structures, such as plasmalemmal vesicles (caveolae) and clathrin-coated pits, facilitate many cell functions, including the clustering of membrane receptors and transport of specific extracellular macromolecules by endothelial cells. These structures are subject to large mechanical deformations when the plasma membrane is stretched and subject to a change of its curvature. To enhance our understanding of plasmalemmal vesicles we need to improve the understanding of the mechanics in regions of high membrane curvatures. We examine here, theoretically, the shapes of plasmalemmal vesicles assuming that they consist of three membrane domains: an inner domain with high curvature, an outer domain with moderate curvature, and an outermost flat domain, all in the unstressed state. We assume the membrane properties are the same in these domains with membrane bending elasticity as well as in-plane shear elasticity. Special emphasis is placed on the effects of membrane curvature and in-plane shear elasticity on the mechanics of vesicle during unfolding by application of membrane tension. The vesicle shapes were computed by minimization of bending and in-plane shear strain energy. Mechanically stable vesicles were identified with characteristic membrane necks. Upon stretch of the membrane, the vesicle necks disappeared relatively abruptly leading to membrane shapes that consist of curved indentations. While the resting shape of vesicles is predominantly affected by the membrane spontaneous curvatures, the membrane shear elasticity (for a range of values recorded in the red cell membrane) makes a significant contribution as the vesicle is subject to stretch and unfolding. The membrane tension required to unfold the vesicle is sensitive with respect to its shape, especially as the vesicle becomes fully unfolded and approaches a relative flat shape.     

Control of utilization of L-arginine, L-ornithine, agmatine, and putrescine as nitrogen sources in Escherichia coli K-12.

The regulation of the synthesis of the enzymes involved in the utilization of L-arginine, L-ornithine, agmatine, and putrescine as a sole nitrogen source in Escherichia coli K-12 was examined. The synthesis of agmatine ureohydrolase, putrescine aminotransferase, and pyrroline dehydrogenase is dually controlled by catabolite repression and nitrogen availability. Catabolite repression of agmatine ureohydrolase, but not that of putrescine aminotransferase or pyrroline dehydrogenase, is relieved by the addition of cAMP. Agmatine ureohydrolase synthesis in addition is subject to induction by L-arginine and agmatine. Arginine decarboxylase and ornithine decarboxylase synthesis is not sensitive to catabolite repression or to stimulation by nitrogen limitation or subject to substrate induction.     

Visual Assessment of Relative Body Size in a Cichlid Fish,the Oscar,Astronotus ocellatus

In cichlid fishes, fighting ability, success at nest defense, and fecundity are all positively correlated with body size. Selection should therefore favor the evolution of strategies for the assessment of relative body size during intraspecific interactions. The effect of relative body size on agonistic behavior in the oscar (Astronotus ocellatus) was tested using dummies. As predicted by game theory models, attack was strongly correlated with the size of the dummy relative to the subject. The most intense aggression occurred when dummy size was approximately 75% of subject size. These data support the prediciton that perceived body size asymmetries are important determinants of agonistic behavior in these fishes. Further, the results suggest that oscars can visually assess relative body size, and may estimate relative fighting ability without tests of strength. Subject size was positively correlated with intensity of aggressive behavior. Attack and display frequencies were positively correlated with a subject's body size, while latencies to approach and attack dummies were negatively correlated with subject size.     

The genes gmdA, encoding an amidase, and bzuA, encoding a cytochrome P450, are required for benzamide utilization in Aspergillus nidulans

Two unlinked loci, gmdA and bzuA, have previously been identified as being required for the utilization of benzamide as the sole nitrogen source by Aspergillus nidulans. We have cloned each of these genes via direct complementation. The gmdA gene encodes a predicted product belonging to the amidase signature sequence family that displays similarity to AmdS from A. nidulans. However, identity is significantly higher to the amdS gene from Aspergillus niger. The bzuA gene encodes a protein belonging to the cytochrome P450 superfamily and is orthologous to the benzoate para-hydroxylase-encoding gene bphA of A. niger. The bzuA1 mutation prevents the use of benzoate as a carbon source and intracellular accumulation of benzoate results in growth inhibition on benzamide. Northern blot analysis has shown that gmdA expression is subject solely to AreA-dependent nitrogen metabolite repression while bzuA is strongly benzoate inducible and subject to CreA-mediated carbon catabolite repression and a probable inactivation of benzoate induction by glucose. Fluorescence microscopy of a fusion of the N-terminal end of BzuA to green fluorescent protein revealed that this protein localizes to the endoplasmic reticulum.     

Process dynamics, instrumentation and control

A total of 77 references pertaining to the subject were consulted to compose the present review. In addition to their years of publication (1981–1983), the references were selected primarily for their practicality and ability to provide experimental results and confirmation. First, a generalized model illustrating the biochemical reaction engineering considerations is presented. Here the knowledge of reactor and reaction kinetics is emphasized and the need for process instrumentation identified. Recent developments in key process sensors are then discussed in detail along with their utilities in various process situations. Finally, application of control principles and on-line computers to biochemical process operation is given a realistic evaluation by considering the process dynamics and instrumentation capabilities. Future challenges and opportunities from both the reaction engineering and system engineering points of view are carefully assessed. The most recent review relevant to the subject is that by Bull (1983).     

SENSORY ANALYSIS PROCEDURES AND VIEWPOINTS: INTELLECTUAL HISTORY,CURRENT DEBATES,FUTURE OUTLOOKS1

This paper presents the intellectual history of product testing (sensory analysis). It traces the history from two separate streams; the expert (and expert panelist), and the empiricist (sociologist, followed by experimental psychologist). Sensory analysis in the last decade of the 20th century is host to many of the same intellectual arguments in these two fields as were current a half century ago, or longer, in psychology. What has been absent is a set of worldviews and organizing principles around which the field can grow and mature more rapidly. The paper presents three major organizing subject areas for sensory analysis: individual differences (sensory segmentation), sensory-instrumental analysis (reverse engineering), and cognitive approaches (mixed modeling and optimization of physical and conceptual variables). These three subject areas and their organizing principles provide sensory analysis with a vision of future research and application that accord with the scientific heritage and extend current procedures.     

Rights and responsibilities in rural South Africa: implications for gender,generation, and personhood

In the rural Eastern Cape, South Africa, contests over the meaning and merit of human rights feature prominently in intergenerational and intergendered conflicts. In this article I identify and analyse a tension between amalungelo (a socially embedded and relational form of rights) and irhayti (a Xhosaization of the English ‘[human] right’) as a means of exploring the interpersonal tensions that arise through the production and contestation of the subject positions that human rights set in motion. Using the examples of elders’ complaints of neglect, and of young men's accusations of human rights violations on the part of women, I ground this investigation in men's and elders’ explanations of how human rights enable morally reprehensible actions, and are implicated in what they perceive to be a climate of interpersonal neglect. In analysing these claims, I show that gendered and generational conflict in this region is grounded in uncertainty about the content of gendered and generational subject positions themselves, and speaks to the relative moral value of autonomous versus relational forms of personhood. Moreover, I show that where inequality and interdependence are intrinsic to the ways in which gendered and generational subject positions are constituted and understood, human rights serve both to destabilize the content of these subject positions in ways that render appropriate gendered and generational sociality unclear, and also to bring into question the relative moral value of autonomous versus more relational forms of personhood.     

ADP-ribosyl transferase,rearrangement of DNA,and cell differentiation

Cell differentiation is the process by which genetic information is selectively expressed to produce cells with various morphologies and functions. The integrated changes necessary for this fundamentally important process have recently been the subject of intense study. This review will summarize data from several laboratories correlating differentiation with the activity of the enzyme ADP-ribosyl transferase and with changes in single-strand DNA breaks in various diverse eukaryotic systems. We will then discuss the implications of these observations for differentiation in general, including the possibility that rearrangement of genetic material is a widespread mechanism for controlling gene expression.     

Cloning, expression, and regulation of the Pseudomonas cepacia protocatechuate 3,4-dioxygenase genes.

The genes for the alpha and beta subunits of the enzyme protocatechuate 3,4-dioxygenase (EC 1.13.11.3) were cloned from the Pseudomonas cepacia DBO1 chromosome on a 9.5-kilobase-pair PstI fragment into the broad-host-range cloning vector pRO2317. The resultant clone was able to complement protocatechuate 3,4-dioxugenase mutations in P. cepacia, Pseudomonas aeruginosa, and Pseudomonas putida. Expression studies showed that the genes were constitutively expressed and subject to catabolite repression in the heterologous host. Since the cloned genes exhibited normal induction patterns when present in P. cepacia DBO1, it was concluded that induction was subject to negative control. Regulatory studies with P. cepacia wild-type and mutant strains showed that protocatechuate 3,4-dioxygenase is induced either by protocatechuate or by beta-carboxymuconate. Further studies of P. cepacia DBO1 showed that p-hydroxybenzoate hydroxylase (EC 1.14.13.2), the preceding enzyme in the pathway, is induced by p-hydroxybenzoate and that beta-carboxymuconate lactonizing enzyme, which catalyzes the reaction following protocatechuate 3,4-dioxygenase, is induced by both p-hydroxybenzoate and beta-ketoadipate.     

A class of latent Markov models for capture-recapture data allowing for time, heterogeneity, and behavior effects

We propose an extension of the latent class model for the analysis of capture-recapture data which allows us to take into account the effect of a capture on the behavior of a subject with respect to future captures. The approach is based on the assumption that the variable indexing the latent class of a subject follows a Markov chain with transition probabilities depending on the previous capture history. Several constraints are allowed on these transition probabilities and on the parameters of the conditional distribution of the capture configuration given the latent process. We also allow for the presence of discrete explanatory variables, which may affect the parameters of the latent process. To estimate the resulting models, we rely on the conditional maximum likelihood approach and for this aim we outline an EM algorithm. We also give some simple rules for point and interval estimation of the population size. The approach is illustrated by applying it to two data sets concerning small mammal populations.     

海洋生态修复:概念、类型与实施路径选择

生态修复是我国生态文明建设的重要内容。在对生态修复相关概念梳理的基础上,从公共物品治理视角对海洋生态修复主体、修复标准、修复路径及修复措施保障等关键环节进行论述,研究表明：污染和破坏者作为赔偿型海洋生态修复的主体,可通过自行修复和委托修复等方式,将受损海洋生态修复到破坏前的基线水平;国家作为补偿型海洋生态修复的主体,依据边际成本收益分析法确定最优修复规模,通过政府市场采购和创建市场等经济激励型路径实施生态修复以增加公众福利。未来我国海洋生态修复应重点关注修复的资金保障、监督制度以及生态修复的技术研发和修复完成后的成本收益评估等。     

Short-wavelength light sensitivity of circadian, pupillary, and visual awareness in humans lacking an outer retina

As the ear has dual functions for audition and balance, the eye has a dual role in detecting light for a wide range of behavioral and physiological functions separate from sight. These responses are driven primarily by stimulation of photosensitive retinal ganglion cells (pRGCs) that are most sensitive to short-wavelength ( approximately 480 nm) blue light and remain functional in the absence of rods and cones. We examined the spectral sensitivity of non-image-forming responses in two profoundly blind subjects lacking functional rods and cones (one male, 56 yr old; one female, 87 yr old). In the male subject, we found that short-wavelength light preferentially suppressed melatonin, reset the circadian pacemaker, and directly enhanced alertness compared to 555 nm exposure, which is the peak sensitivity of the photopic visual system. In an action spectrum for pupillary constriction, the female subject exhibited a peak spectral sensitivity (lambda(max)) of 480 nm, matching that of the pRGCs but not that of the rods and cones. This subject was also able to correctly report a threshold short-wavelength stimulus ( approximately 480 nm) but not other wavelengths. Collectively these data show that pRGCs contribute to both circadian physiology and rudimentary visual awareness in humans and challenge the assumption that rod- and cone-based photoreception mediate all "visual" responses to light.     

Moments,cumulants, and polygenic dynamics

A new approach for describing the evolution of polygenic traits subject to selection and mutation is presented. Differential equations for the change of cumulants of the allelic frequency distribution at a particular locus and for the cumulants of the distributions of genotypic and phenotypic values are derived. The derivation is based on the assumptions of random mating, no sex differences, absence of random drift, additive gene action, linkage equilibrium, and Hardy-Weinberg proportions. Cumulants are a set of parameters that, like moments, describe the shape of a probability density. Compared with moments, however, they have properties that make them a much more convenient tool for investigating polygenic traits. Applications to directional and stabilizing selection are given.     

The alpha, but not the beta, isoform of the human thromboxane A2 receptor is a target for prostacyclin-mediated desensitization

In this study, we examined the effects the prostacyclin receptor (IP) agonist cicaprost exhibited on U46619-mediated thromboxane A(2) receptor (TP) signaling in platelets and compared it to that which occurs in human embryonic kidney (HEK) 293 cells stably overexpressing the individual TPalpha or TPbeta isoforms. Consistent with previous studies, cicaprost abrogated U46619-mediated platelet aggregation and mobilization of intracellular calcium ([Ca(2+)](i)). In HEK 293 cells, signaling by TPalpha, but not TPbeta, was subject to IP-mediated desensitization in a protein kinase A-dependent, protein kinase C-independent manner. Desensitization of TPalpha signaling was independent of the nature of the IP agonist used, the level of IP expression, or the subtype of G(q) protein. Signaling by TP(Delta)(328), a truncated variant of TP devoid of the divergent residues of the TPs, or by TPalpha(S329A), a site-directed mutant of TPalpha, were insensitive to IP agonist activation. Whole cell phosphorylations established that TPalpha, but not TPbeta or TPalpha(S329A), is subject to IP-mediated phosphorylation and that TPalpha phosphorylation is inhibited by H-89. Thus, we conclude that TPalpha, but not TPbeta, is subject to cross-desensitization by IP mediated through direct protein kinase A phosphorylation at Ser(329) and propose that TPalpha may be the isoform physiologically relevant to TP:IP-mediated vascular hemostasis.