Hume and the argument for biological design

There seems to be a widespread conviction — evidenced, for example, in the work of Mackie, Dawkins and Sober — that it is Darwinian rather than Humean considerations which deal the fatal logical blow to arguments for intelligent design. I argue that this conviction cannot be well-founded. If there are current logically decisive objections to design arguments, they must be Humean — for Darwinian considerations count not at all against design arguments based upon apparent cosmological fine-tuning. I argue, further, that there are good Humean reasons for atheists and agnostics to resist the suggestion that apparent design — apparent biological design and/or apparent cosmological fine-tuning — establishes (or even strongly supports) the hypothesis of intelligent design.     

Development of a serum-free medium using computer-assisted factorial design and analysis

Stepwise screening of media supplements using factorial design and analysis was employed in the development of serum-free medium for a recombinant Chinese hamster ovary cell line. The effects (growth and target protein production) of different combinations were measured at two time points to ensure adequate response. The results were analysed by a computer program specialized in factorial analysis. The formulation deduced from the previous experiment was used as the new basal medium for the next screening. Certain significant nutrients were studied again in a more advanced formulation in order to analyse the potential synergistic effects with new media components. Compared to cells grown in serum-containing medium, cells adapted to the final formulation of the serum-free medium had a comparable growth rate but a four fold increase in the active protein production.Abbreviations ANOVA Analysis of variance - BSA bovine serum albumin - CHO Chinese hamster ovary - FBS fetal bovine serum - MTT 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide - PBS phosphate buffered saline - SFM serum-free medium     

Nutritional environment of soil and roots in and around mycelial blocks of an ectomycorrhizal fungusTricholoma bakamatsutake in an evergreen Fagaceae forest

In the evergreen Fagaceae forests of Japan, an ectomycorrhizal fungusTricholoma bakamatsutake forms shiros or developing mycelial blocks. To determine the physiological characteristics of the mycelial blocks, organic acids of the soil and major nutrient elements of the soil and roots were compared at three types of sites: presently colonized mycelial blocks, previously colonized sites behind the blocks, and uncolonized sites in front of the blocks. The upper part of the mycelial blocks showed the following features compared with the uncolonized site: lower pH (5.1), higher concentrations of oxalic and gluconic acids, lower content of total nitrogen, a similar amount of total carbon, reduced total and available phosphorus, higher content of total calcium and lower content of exchangeable calcium. These findings suggested that the activity of the fungus led to soil acidification by the organic acids, an increase in C/N ratio, depletion of phosphorus and accumulation of calcium.     

The Western Rock lobster Panulirus cygnus (George, 1962) (Decapoda: Palinuridae): the effect of temperature and developmental stage on energy requirements of pueruli

Pueruli of the Western Rock Lobster Panulirus cygnus (George, 1962) are thought to be nonfeeding. Consequently, the metabolic rate is expected to be low during this stage in order to conserve energy reserves. Furthermore, since water temperature potentially has a substantial impact on energetic needs, the puerulus possibly exhibits mechanisms to reduce the effect of temperature on energy consumption. To test these propositions the metabolic rate was measured in post-settlement pueruli and in juveniles at two water temperatures. A respirometer of variable volume (10–50 ml) was designed for this purpose, incorporating a dark-type oxygen sensor. Results were compared with data available from the literature.

Oxygen consumption in pre-molt pueruli and in intermolt juveniles (1.48 to 5.65 μmol O₂· individual⁻¹·h⁻¹ on average) was substantially higher than in post-settlement pueruli (1.06–1.41μmol O₂·ind.⁻¹h⁻¹). These significant changes could only partly be explained through changes in biomass. Furthermore, no significant effect of an increased water temperature (from 18 to 23 ° C) could be detected on the metabolic rate in post-settlement pueruli, and the effect is moderate in pre-molt pueruli (Q₁₀ = 1.95). The water temperature has, however, a substantially greater impact on first and second molt juveniles (Q₁₀ = 2.46 to 4.80).

The energetic demand was calculated from oxygen consumption and indicate that energetic needs of post-settlement pueruli is low compared with both pre-molt pueruli and juveniles. A low energetic demand and a reduced effect of temperature on energy consumption is of considerable benefit to a non-feeding larva, and may provide the puerulus with a means of extending the duration of the non-feeding stage and increasing the chance for survival beyond metamorphosis to the first feeding stage. Results indicate that the energetic demand during metamorphosis may be considerable. It is postulated that energetic requirements of the planktonic (actively swimming) puerulus larvae are considerably higher and are likely to be more temperature dependent.     

Predicting mean and variance of all possible lines and hybrids from designs with partially inbred progenies

Two-factor mating designs at consecutive S_n and S_(n+1) levels (S₀ and S₁ S₁ and S₂, or F₂ and F₃) allow estimation of all components of the variation among homozygous lines and F₁ hybrids that can be derived from a given population. They also allow for the prediction of the mean of these lines and single-cross hybrids. Some tests for the presence of epistasis are possible at the levels of means and of variances. Such mating designs can be very useful for predicting the value of the best possible lines or the best possible F₁ hybrids when it is difficult to produce, at an experimental level for exploratory purposes, either lines or hybrids.     

Rational design of peptide-based inhibitors of trypanothione reductase as potential antitrypanosomal drugs

Summary The rational design of ligands for the substrate-binding site of a homology-modelled trypanothione reductase (TR) was performed. Peptides were designed to be selective for TR over human glutathione reductase (GR). The design process capitalized on the proposed differences between the activesites of TR and human GR, subsequently confirmed by the TR crystal structure. Enzyme kinetics confirmed that forT. cruzi TR benzoyl-Leu-Arg-Arg-ß-naphthylamide was an inhibitor (K_i 13.8µM) linearly competitive with the native substrate, trypanothione disulphide, and did not inhibit glutathione reductase.     

The making of the minibody: An engineered β-protein for the display of conformationally constrained peptides

Conformationally constraining selectable peptides onto a suitable scaffold that enables their conformation to be predicted or readily determined by experimental techniques would considerably boost drug discovery process by reducing the gap between the discovery of a peptide lead and the design of a peptidomimetic with a more desirable pharmacological profile. With this in mind, we designed the minibody, a 61-residue β-protein aimed at retaining some desirable features of immunogloblin variable domains, such as tolerance to sequence variability in selected regions of the protein and predictability of main chain conformation of the same regions, based on the ‘canonical structures’ model. To test the ability of the minibody scaffold to support functional sites we also designed a metal binding version of the protein by suitably choosing the sequences of its loops. The minibody was produced both by chemical syntyhesis and expression in E. coli and charactgerized by size exclusion chromatography, UV CD (circular dichroism) spectroscopy and metal binding activity. All our data supported the model, but a more detailed structural characterization of the molecule was impaired by its low soubility. We were able to overcome this problem both by further; mutagenesis of the framework and by addition of a solublizing motif. The minibody is being used to select constrained human IL-6 peptidic ligands from a library displayed on the surface of the f1 bacteriophage.     

Gene technology-based antimetabolite design: the use of an in vitro protein expression system to facilitate antimetabolite design for virally-induced human diseases and malignant conditions

A precondition for the chemotherapeutic treatment of a variety of virally-induced human diseases and malignant conditions is a highly selective interaction of the drug molecule to be used with it's biological target. To ensure the development of novel, effective drugs, it is essential that the biological target is well characterised with regard to it's structure and activity. Such characterisation relies upon adequate amounts of pure target being available. One of the most important enzymatic importers for antimetabolites is the enzyme thymidine kinase. In this article an in vitro protein expression system is described which facilitates the production of milligram amounts of pure and biologically active thymidine kinase, from a number of important biological sources. Results have shown that the in vitro produced enzyme has the exact biochemical propeties of the in vivo enzyme. Thus the in vitro protein expression system is an ideal vechicle to facilitate an in depth investigation of the enzyme's biological properties.     

Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry

Globular proteins have high packing densities as a result of residue side chains in the core achieving a tight, complementary packing. The internal packing is considered the main determinant of native protein structure. From that point of view, we present here a method of energy minimization using an automata network to predict a set of amino acid sequences and their side-chain conformations from a desired backbone geometry for de novo design of proteins. Using discrete side-chain conformations, that is, rotamers, the sequence generation problem from a given backbone geometry becomes one of combinatorial problems. We focused on the residues composing the interior core region and predicted a set of amino acid Sequences and their side-chain conformations only from a given backbone geometry. The kinds of residues were restricted to six hydrophobic amino acids (Ala, Ile, Met, Leu, Phe, and Val) because the core regions are almost always composed of hydrophobic residues. The obtained sequences were well packed as was the native sequence. The method can be used for automated sequence generation in the de novo design of proteins. © 1994 Wiley-Liss, Inc.     

Denitrification measurements in aquatic sediments: A comparison of three methods

Measurements of denitrification using the acetylene inhibition,¹⁵N isotope tracer, and N₂ flux methods were carried out concurrently using sediment cores from Vilhelmsborg sø, Denmark, in an attempt to clarify some of the limitations of each technique. Three experimental treatments of overlying water were used: control, nitrate enriched, and ammonia enriched water. The N₂ flux and¹⁵N tracer experiments showed high rates of coupled nitrification/denitrification in the sediments. The acetylene inhibition method did not capture any coupled nitrification/denitrification. This could be explained by acetylene inhibition of nitrification. A combined¹⁵N tracer/acetylene inhibition experiment demonstrated that acetylene inhibition of N₂O reduction was incomplete and the method, therefore, only measured approximately 50% of the denitrification due to nitrate from the overlying water. Similar rates of denitrification due to nitrate in the overlying water were measured by the N₂ flux method and the acetylene inhibition method, after correcting for the 50% efficiency of acetylene inhibition. Rates of denitrification due to nitrate from the overlying water measured by the¹⁵N tracer method, however, were only approximately 35% or less of those measured by the acetylene inhibition or N₂ flux methods.