Intelligent design and the NFL theorems

Another look is taken at the model assumptions involved in William Dembski’s (2002a, No Free Lunch: Why Specified Complexity Cannot be Purchased without Intelligence. Roman & Littlefield, Lanham, MA) use of the NFL theorems from optimization theory to disprove the Darwinian theory of evolution by natural selection, and his argument is shown to be irrelevant to evolutionary biology.     

一类具有饱和反应率的脉冲免疫接种的SIS模型

研究了具饱和传染率的脉冲免疫接种SIS模型,得到了无病周期解全局渐近稳定的充分条件和系统持续生存的充分条件．     

黑曲霉纤维素酶高产固态培养基的快速优选研究

研究采用正交设计,对影响黑曲霉 Ｆ_２７产纤维素酶的 １０个营养因素在较少水平下进行初选,从中选出对产酶影响显著的４个因素．在此基础上采用均匀设计,在较多水平下进行较少次数的试验,将试验结果用微机逐步回归处理,得到最优回归方程,由回归方程计算出预测极值点和预测极值、优化出高产纤维素酶固态培养基配方．经试验验证,试验实测值和预测值基本相符, ＣＭＣａｓｅ活力平均达 ３７０５Ｕ／ｇ, ＦＰＡ活力平均达 ７．４Ｕ／ｇ．表明对于多因子试验,应用正交设计结合均匀设计的试验方法是快速、简便、可行的．     

Optimization of bio-hydrogen production from biodiesel wastes by Klebsiella pneumoniae

Biodiesel wastes containing glycerol were utilized by Klebsiella pneumoniae DSM 2026 to produce hydrogen. The optimization of medium components was performed using both Plackett-Burman and uniform design methods. Using the Plackett-Burman design, glycerol, yeast extract, NH(4)Cl, KCl and CaCl2 were found to be the most important components, which were further investigated by uniform design and second-order polynomial stepwise regression analysis. The optimized medium containing 20.4 g.L(-1) glycerol, 5.7 g.L(-1) KCl, 13.8 g.L(-1) NH(4)Cl, 1.5 g.L(-1) CaCl(2) and 3.0 g.L(-1) yeast extract resulted in 5.0-fold increased level of hydrogen (57.6 mL/50 mL medium) production compared to initial level (11.6 mL/50 mL medium) after 24 h of fermentation The optimization of fermentation condition (pH, temperature and inoculum) was also conducted. When the strain grew in the optimized medium under optimal fermentation condition in a 5-L stirred tank bioreactor for batch production, hydrogen yield and production reached 0.53 mol/mol and 117.8 mmol/L, respectively. The maximum hydrogen evolution rate was 17.8 mmol/(L.h). Furthermore, 1,3-propanediol (6.7 g.L(-1)) was also obtained from the liquid medium as a by-product.     

Bayesian Inference in Semiparametric Mixed Models for Longitudinal Data

Summary .  We consider Bayesian inference in semiparametric mixed models (SPMMs) for longitudinal data. SPMMs are a class of models that use a nonparametric function to model a time effect, a parametric function to model other covariate effects, and parametric or nonparametric random effects to account for the within-subject correlation. We model the nonparametric function using a Bayesian formulation of a cubic smoothing spline, and the random effect distribution using a normal distribution and alternatively a nonparametric Dirichlet process (DP) prior. When the random effect distribution is assumed to be normal, we propose a uniform shrinkage prior (USP) for the variance components and the smoothing parameter. When the random effect distribution is modeled nonparametrically, we use a DP prior with a normal base measure and propose a USP for the hyperparameters of the DP base measure. We argue that the commonly assumed DP prior implies a nonzero mean of the random effect distribution, even when a base measure with mean zero is specified. This implies weak identifiability for the fixed effects, and can therefore lead to biased estimators and poor inference for the regression coefficients and the spline estimator of the nonparametric function. We propose an adjustment using a postprocessing technique. We show that under mild conditions the posterior is proper under the proposed USP, a flat prior for the fixed effect parameters, and an improper prior for the residual variance. We illustrate the proposed approach using a longitudinal hormone dataset, and carry out extensive simulation studies to compare its finite sample performance with existing methods.     

Molecular clock of silent substitution: At least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes

Summary For each of eleven different types of nuclear genes, comparisons of the protein coding sequences were made between human, mouse and rat pairwisely, and the evolutionary rate of silent substitution, v _S ^nucl. , was estimated. It is shown that the v _S ^nucl. is not only very high (=5.37×10^–9/site/yr), but also approximately uniform for different genes regardless of the types, which confirms our previous results (Miyata et al. 1980b). This is in sharp contrast to the rate of protein evolution which differes greatly from protein to protein. Furthermore the v _S ^nucl. is shown to be approximately constant with respect to different divergence times, at least within a short time period (75 Myr). Based on these observations, we propose a new molecular clock which has several advantages over a protein clock. Using this clock, we show that the rate of amino acid replacement in the immunoglobulin Ck gene of b4 rabbit is unexpectedly high, almost comparable to the rate of silent changes. This rate may be the highest one for protein evolution that we know so far. We further examine the rate of silent substitutions in mitochondrial genes comparing mouse and rat. Surprisingly the rate is extremely high (35×10^–9/site/yr), at least 6-times as high as the corresponding rate of nuclear genes. Based on the estimate, we discuss a possible origin of the rapid rate found in mitochondrial DNA.     

关帝山林区景观要素沿环境梯度分布趋势的研究

 应用空间趋势面分析法研究森林景观空间格局,阐明其技术路线和工作步骤,并提出在ARC／INFO支持下的统一网格样点图上取样法。通过对不同景观要素生态潜力的定量化,对关帝山天然次生林区景观要素沿环境梯度的分布趋势进行了研究。试图从高度异质的复杂景观中,揭示景观要素的空间分布规律及其控制机制。结果表明：在研究地区30～50km的空间尺度上,水平地理位置对景观要素空间分布格局的影响极为有限,景观要素总体空间分布格局更多地受地形特征和干扰格局的综合控制,海拔、坡向和坡度是控制研究地区景观要素空间分布格局的基本因素,在不同海拔带上,坡向和坡度对景观要素空间分布格局的影响作用,在方向和强度上都有明显差别。本文应用空间趋势面分析法进一步对这些差别进行了详细分析,并得出了一些基本规律,这将有利于促进研究地区森林可持续经营和景观规划与管理水平的提高。     

Improving ethanol tolerance of a self-flocculating yeast by optimization of medium composition

High ethanol tolerance is a desired property of industrial yeast strains for efficient ethanol fermentation. In this study, the impact of medium composition on ethanol tolerance of the self-flocculating yeast SPSC01 was investigated using a chemically defined medium. Single-factor experiments revealed that besides magnesium and calcium, zinc also exhibited significant protective effect against ethanol toxicity; addition of 0.02 g/l zinc sulfate significantly increased cell viability in the ethanol shock treatment. Metal ions of manganese, cobalt, and ferrous failed to promote ethanol tolerance, although addition of 0.02 g/l cobalt increased ethanol production without apparent influence on ethanol tolerance. Furthermore, Uniform Design method was employed to obtain the medium with high cell viability, and the key nutrient factors in the medium composition were revealed to be (NH₄)₂SO₄, K₂HPO₄, vitamin mixtures, and the metal ions of magnesium, calcium and zinc. The optimized combination of metal ions addition was (g/l): MgSO₄ 0.4, CaCl₂ 0.2, ZnSO₄ 0.01. The highest cell viability (90.2%) of SPSC01 against ethanol shock treatment was observed in the optimized medium, which demonstrated significant improvement of ethanol tolerance of the self-flocculating yeast.     

Population-Based Reversible Jump Markov Chain Monte Carlo

We present an extension of population-based Markov chain MonteCarlo to the transdimensional case. A major challenge is thatof simulating from high- and transdimensional target measures.In such cases, Markov chain Monte Carlo methods may not adequatelytraverse the support of the target; the simulation results willbe unreliable. We develop population methods to deal with suchproblems, and give a result proving the uniform ergodicity ofthese population algorithms, under mild assumptions. This resultis used to demonstrate the superiority, in terms of convergencerate, of a population transition kernel over a reversible jumpsampler for a Bayesian variable selection problem. We also givean example of a population algorithm for a Bayesian multivariatemixture model with an unknown number of components. This isapplied to gene expression data of 1000 data points in six dimensionsand it is demonstrated that our algorithm outperforms some competingMarkov chain samplers. In this example, we show how to combinethe methods of parallel chains (Geyer, 1991), tempering (Geyer& Thompson, 1995), snooker algorithms (Gilks et al., 1994),constrained sampling and delayed rejection (Green & Mira,2001).