Using niche construction theory to generate testable foraging hypotheses at Liang Bua

Niche construction theory (NCT) has emerged as a promising theoretical tool for interpreting zooarchaeological material. However, its juxtaposition against more established frameworks like optimal foraging theory (OFT) has raised important criticism around the testability of NCT for interpreting hominin foraging behavior. Here, we present an optimization foraging model with NCT features designed to consider the destructive realities of the archaeological record after providing a brief review of OFT and NCT. Our model was designed to consider a foragers decision to exploit an environment given predation risk, mortality, and payoff ratios between different ecologies, like more‐open or more‐forested environments. We then discuss how the model can be used with zooarchaeological data for inferring environmental exploitation by a primitive hominin, Homo floresiensis, from the island of Flores in Southeast Asia. Our example demonstrates that NCT can be used in combination with OFT principles to generate testable foraging hypotheses suitable for zooarchaeological research.     

Uncovering the holes and cracks: from anecdote to testable hypotheses in predation studies

Biological interactions between organisms have long been believed to be very important in structuring communities and, when scaled up over geological time, in the evolution of organisms. Investigations of palaeontological evidence for predator–prey interactions have been popular pursuits, and a number of attractive hypotheses have been proposed which link increased predation pressure with a wide range of morphological and ecological changes which are apparent over the course of the Phanerozoic. In particular studies of fossil drill holes and repair scars in shelly prey have been common targets for research. However, the nature of some of our data has been rather anecdotal and restricted in range. Perhaps we should be more concerned that we are not picking up the true range of natural variability. This paper aims to highlight the sources of variability in our data and, going forward, to urge the collection of quantitative data from many more samples and (palaeo)environmental settings in order that we might properly be able to separate the intrinsic natural variability in our data from robust temporal or spatial trends.     

Proteomic analysis of rat atrial secretory granules: a platform for testable hypotheses

The recent development of powerful proteomic tools has enabled investigators to directly examine the population of proteins present in defined biological systems. We report here the first proteomic analysis of atrial secretory granules. Approximately 100 distinct protein components of the atrial secretory granule proteome were detected using subcellular fractionation and one-dimensional SDS-PAGE in conjunction with peptide mass fingerprinting by MALDI-TOF mass spectrometry. Of this number, 61 proteins were clearly identified by high probability data matches and repeated observation. The majority of the proteome was found to be membrane-associated with the most prominent proteins being peptidylglycine alpha-amidating monooxygenase (PAM) and pro-atrial natriuretic peptide (pro-ANP). This proteomic analysis of the rat atrium secretory granule produced an assembly of proteins with a diverse array of reported functions. The identified proteins fall into seven functional categories: (1) granular transport, docking and fusion; (2) signal transduction; (3) calcium-binding/calcium-dependent; (4) cellular architecture/chaperoning; (5) peptide/protein processing; (6) hormone; (7) proton transport. The novel finding of several protein processing enzymes and signal transduction proteins offer new perspectives on how pro-ANP is stored and processed to ANP during release. Accordingly, defining the proteome of the atrial secretory granule provides a framework for the development of new hypotheses that address key mechanisms governing granule function and ANP secretion.     

地球生物学发展的机遇与挑战*

地球生物学已经引起了人们的广泛关注, 目前面临着机遇与挑战并存的发展局面。得益于现代技术方法的大发展, 地球生物学的研究对象经历了从宏体动植物向微体古生物再向地质微生物和地质病毒的发展, 研究主题从气候环境对生物演化的影响进一步拓展到生物演化如何影响气候环境乃至深地过程, 进而回答生命是如何塑造地球的宜居性这个地球科学的根本性难题。研究对象和研究主题的拓展也提升了地球生物学服务人类社会的能力, 资源能源安全的保障、气候—环境—生物多样性危机的协调应对等都需要地球生物学的支撑。同时, 地球生物学的发展也面临着诸多挑战。它首先需要技术方法的进一步革新来带动认识的创新, 其次需要回答生物演化的驱动力问题, 更需要破解生物演化如何影响深地过程, 包括板块运动、火山活动等地质过程, 只有这样才能全面而正确地评估生物是否改变了宜居地球的演化方向, 以及如何应对当前人类所面临的诸多全球性难题。     

Breathing metals as a way of life: geobiology in action

Many microbes have the ability to reduce transition metals, coupling this reduction to the oxidation of energy sources in a dissimilatory fashion. Because of their abundance, iron and manganese have been extensively studied, and it is well established that reduction of Mn and Fe account for significant turnover of organic carbon in many environments. In addition, many of the dissimilatory metal reducing bacteria (DMRB) also reduce other metals, including toxic metals like Cr(VI), and radioactive contaminants like U(VI), raising the expectations that these processes can be used for bioremediation. The processes involved in metal reduction remain mysterious, and often progress is slow, as nearly all iron and manganese oxides are solids, which offer particular challenges with regard to imaging and chemical measurements. In particular, the interactions that occur at the bacteria-mineral interfaces are not yet clearly elucidated. One DMRB, Shewanella oneidensis MR-1 offers the advantage that its genome has recently been sequenced, and with the availability of its genomic sequence, several aspects of its metal reducing abilities are now beginning to be seen. As these studies progress, it should be possible to separate several processes involved with metal reduction, including surface recognition, attachment, metal destabilization and reduction, and secondary mineral formation. This revised version was published online in August 2006 with corrections to the Cover Date.     

Setting the stage: the history, chemistry, and geobiology behind RNA

No community-accepted scientific methods are available today to guide studies on what role RNA played in the origin and early evolution of life on Earth. Further, a definition-theory for life is needed to develop hypotheses relating to the "RNA First" model for the origin of life. Four approaches are currently at various stages of development of such a definition-theory to guide these studies. These are (a) paleogenetics, in which inferences about the structure of past life are drawn from the structure of present life; (b) prebiotic chemistry, in which hypotheses with experimental support are sought that get RNA from organic and inorganic species possibly present on early Earth; (c) exploration, hoping to encounter life independent of terran life, which might contain RNA; and (d) synthetic biology, in which laboratories attempt to reproduce biological behavior with unnatural chemical systems.     

Genetic models of homosexuality: generating testable predictions

Homosexuality is a common occurrence in humans and other species, yet its genetic and evolutionary basis is poorly understood. Here, we formulate and study a series of simple mathematical models for the purpose of predicting empirical patterns that can be used to determine the form of selection that leads to polymorphism of genes influencing homosexuality. Specifically, we develop theory to make contrasting predictions about the genetic characteristics of genes influencing homosexuality including: (i) chromosomal location, (ii) dominance among segregating alleles and (iii) effect sizes that distinguish between the two major models for their polymorphism: the overdominance and sexual antagonism models. We conclude that the measurement of the genetic characteristics of quantitative trait loci (QTLs) found in genomic screens for genes influencing homosexuality can be highly informative in resolving the form of natural selection maintaining their polymorphism.     

RNA-ligand chemistry: a testable source for the genetic code

In the genetic code, triplet codons and amino acids can be shown to be related by chemical principles. Such chemical regularities could be created either during the code's origin or during later evolution. One such chemical principle can now be shown experimentally. Natural or particularly selected RNA binding sites for at least three disparate amino acids (arginine, isoleucine, and tyrosine) are enriched in codons for the cognate amino acid. Currently, in 517 total nucleotides, binding sites contain 2.4-fold more codon sequences than surrounding nucleotides. The aggregate probability of this enrichment is 10(-7) to 10(-8), had codons and binding site sequences been independent. Thus, at least some primordial coding assignments appear to have exploited triplets from amino acid binding sites as codons.     

Classification of hypotheses on the evolution of autumn colours

I review the hypotheses that have been proposed to explain the adaptive value of autumn leaf colours. The available adaptive hypotheses can be reduced to the following. Photoprotection: pigments protect against photoinhibition or photooxidation allowing a more efficient recovery of nutrients. Drought resistance: pigments decrease osmotic potential allowing leaves to tolerate water stress. Leaf warming: pigments convert light into heat and warm leaves. Fruit flag: colour attracts animals that help disperse seeds. Coevolution: colour signals that the tree is not a suitable host for insects. Camouflage: colour makes leaves less detectable to herbivores. Anticamouflage: colour enhances conspicuousness of parasites dwelling on leaves to predators or parasitoids. Unpalatability: pigments act as direct anti-feedants against herbivores. Reduced nutrient loss: yellow leaves have less to lose against herbivory. Tritrophic mutualism: colour attracts aphids which attract ants that defend the trees from other insects. For each hypothesis I mention the original references, I define assumptions and predictions, and I discuss briefly conceptual problems and available evidence.     

植物叶片衰老机理的几种假说

关于植物叶片衰老已有很多工作,对于衰老的机理提出了许多假说。本文汇总、介绍了其中几种主要假说。     

Two hypotheses on the causes of male homosexuality and paedophilia

This note considers two hypotheses on the causes of homosexuality and paedophilia in men, viz. the hypotheses of maternal immunity and of postnatal learning. According to the maternal immune hypothesis, there is progressive immunization of some mothers to male-specific antigens by each succeeding male fetus, and there are concomitantly increasing effects of anti-male antibodies on the sexual differentiation of the brain in each succeeding male fetus. An attempt is made to assess the status of this hypothesis within immunology. Knowledge of the properties of anti-male antibodies is meagre and there has been little direct experimentation on them, let alone on their effects on the developing male fetal brain. Moreover until the relevant antigens are identified, it will not be possible to test mothers of male homosexuals or paedophiles for the presence of such antibodies. Yet until this experimentation has been done, it would seem premature to regard the hypothesis as more than a very provisional explanatory tool. The evidence in relation to the postnatal learning hypothesis is quite different. There is an abundance of data suggesting that male homosexuals and paedophiles report having experienced more sexual abuse (however defined) in childhood (CSA) than do heterosexual controls. The question revolves round the interpretation of these data. Many (though not all) of these studies are correlational and thus subject to the usual qualifications concerning such data. However, there are grounds for supposing that some of the reports are veridical, and there is support from a longitudinal study reporting a small but significant increase in paedophilia in adulthood following CSA. To summarize: most boys who experience CSA do not later develop into homosexuals or paedophiles. However, the available evidence suggests that a few do so as a result of the abuse.     

Two hypotheses on the feedback regulation of pancreatic enzyme secretion

We review the mechanisms underlying the feedback regulation of pancreatic enzyme secretion in response to a meal. Pancreatic enzyme secretion in the rat and pig is known to be regulated by a negative feedback mechanism mediated by intestinal trypsin and chymotrypsin. Such a mechanism has recently been noted in humans. The presence of these enzymes in the small intestine suppresses pancreatic enzyme secretion, whereas their removal increases it. Two novel peptides have been proposed to account for the stimulation of pancreatic enzyme secretion in response to feeding trypsin inhibitor. One was assumed to be present in rat pancreatic juice and the other to be spontaneously secreted from the rat small intestine. In either case, trypsin and trypsin inhibitors do not directly interact with the luminal surface of the small intestine, but their actions are mediated by a trypsin-sensitive, cholecystokinin-releasing peptide. This is a novel explanation of the well-recognized stimulation of pancreatic enzyme secretion in response to dietary protein intake.     

12种有毒植物的化感效应比较研究

以油菜、燕麦、反枝苋和狗尾草为受体,采用室内生物测定法和盆栽法,研究了甘肃天祝天然草地12种有毒植物的化感作用.结果表明:离体条件下,黄花棘豆、臭蒿、节烈角茴香和露蕊乌头植株水浸液对4种受体植物化感作用较强,其综合化感效应值(M)分别为-0.781 5、-0.685 9、-0.667 0和-0.643 2;其次是密花香薷、醉马草、美丽凤毛菊、甘肃马先蒿、迷果芹和异叶青兰,其M值均低于-0.4;对受体植物化感作用较弱的是乳白香青(M值为-0.343 9)和铁棒锤(M值为-0.262 5).黄花棘豆植株对盆栽的油菜、燕麦、反枝苋和狗尾草幼苗生长有较强的抑制作用,综合化感效应M值分别为-0.529 6、-0.356 2、-0.520 1和-0.588 4.可见黄花棘豆表现出较强的化感作用,具有一定的开发利用价值.