A density functional theory study of phenyl formation initiated by ethynyl radical (C2H•) and ethyne (C2H2)

An ab initio computational density functional theory (DFT) was used to study the formation of the first cyclic molecule (phenyl) initiated by the ethynyl radical (C₂H•). The study covers a competition reaction between the addition reactions of C₂H• with ethyne (C₂H₂) and some molecular re-arrangement schemes. The minimum energy paths of the preferred cyclic formation route were characterized. A thorough thermochemical analysis was performed by evaluating the differences in the energy of activation (ΔE), enthalpy (ΔH), and Gibb's free energy (ΔG) of the optimized stable and transition state (TS) molecules. The reaction temperatures were set to normal (T = 298 K) and combustion (T = 1,200 K) conditions.

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Higher order multipole moments for molecular dynamics simulations

In conventional force fields, the electrostatic potential is represented by atom-centred point charges. This choice is in principle arbitrary, but technically convenient. Point charges can be understood as the first term of multipole expansions, which converge with an increasing number of terms towards the accurate representation of the molecular potential given by the electron density distribution. The use of multipole expansions can therefore improve the force field accuracy. Technically, the implementation of atomic multipoles is more involved than the use of point charges. Important points to consider are the orientation of the multipole moments during the trajectory, conformational dependence of the atomic moments and stability of the simulations which are discussed here.

Adaptationism and the adaptive landscape

Debates over adaptationism can be clarified and partially resolved by careful consideration of the ‘grain’ at which evolutionary processes are described. The framework of ‘adaptive landscapes’ can be used to illustrate and facilitate this investigation. We argue that natural selection may have special status at an intermediate grain of analysis of evolutionary processes. The cases of sickle-cell disease and genomic imprinting are used as case studies.

Leitlinien zur molekulargenetischen Diagnostik: Fragiles-X und Fragiles-X assoziiertes Tremor/Ataxie Syndrom

Ohne Zusammenfassung

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Individual variability of behavioural responses by Wandering Albatrosses (Diomedea exulans) to human disturbance

Sub-Antarctic Marion Island has had a permanent research station for 50 years and the islands Wandering Albatrosses have been intensively studied for 20 years. The reactions of breeding birds to approaches by a human on foot were recorded. Three response variables were calculated: intensity of vocal reaction (IVR), intensity of non-vocal reaction (INR) and overall response index (ORI). At 5 m from the nest, twice as many birds stood and/or vocalised as at 15 m. Nearest neighbour distance, age and gender did not explain individual variability of responses. Study colony birds had higher IVR scores than non-study colony birds; birds at colonies closest to the station had the highest ORI scores. A better breeding record was associated with lower IVR and ORI scores, but a causative relationship remains to be demonstrated. A minimum viewing distance of 25 m is recommended for breeding Wandering Albatrosses.

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The rise and fall of the adaptive landscape?

The discussion of the adaptive landscape in the philosophical literature appears to be divided along the following lines. On the one hand, some claim that the adaptive landscape is either “uninterpretable” or incoherent. On the other hand, some argue that the adaptive landscape has been an important heuristic, or tool in the service of explaining, as well as proposing and testing hypotheses about evolutionary change. This paper attempts to reconcile these two views.

Towards dynamical system models of language-related brain potentials

Event-related brain potentials (ERP) are important neural correlates of cognitive processes. In the domain of language processing, the N400 and P600 reflect lexical-semantic integration and syntactic processing problems, respectively. We suggest an interpretation of these markers in terms of dynamical system theory and present two nonlinear dynamical models for syntactic computations where different processing strategies correspond to functionally different regions in the system’s phase space.

Responses of marine organisms to physical and chemical impacts

Studies on the effects of a variety of exogenous and anthropogenic environmental factors, including endocrine disruptors, heavy metals, UV light, high temperature, and others, on marine organisms have been presented at the 2nd Bilateral Seminar Italy–Japan held in November 2006. Reports were discussed in order to reveal the current situation of marine ecosystems, aiming at evaluation and prediction of environmental risks.

Objects limit human comprehension

This paper demonstrates that the human visual system, the primary sensory conduit for primates, processes ambient energy in a way that obligatorily constructs the objects that we ineluctably perceive. And since our perceptual apparatus processes information only in terms of objects (along with the properties and movements of objects), we are limited in our ability to comprehend ‘what is’ when we move beyond our ordinary world of midsize objects—as, for example, when we address the micro microworld of quantum physics.

Steric Effects in Release of Amides from Linkers in Solid-Phase Synthesis. Molecular Mechanics Modeling of Key Step in Peptide and Combinatorial Chemistry

   Acidolytic release of an amide from a solid support by C–N bond cleavage is an ubiquitous and crucial step in many solid-phase syntheses. We have used molecular modeling of a pseudo-equilibrium to explore substituent and steric effects in the release of peptides. The high acid-lability of the backbone amide linkage (BAL), which releases sec. amides, compared to C-terminal amide anchoring, which releases primary amides, was rationalized by steric relief upon cleavage. Thus, the relative stability of the carbenium ion formed from the linker in the acidolytic release is an insufficient measure of the lability of a linkage. In addition, predictions indicated that steric effects from the C^α-substituent in a BAL anchored amino acid residue should accelerate the acidolytic release. The finding that steric crowding leads to increased acid-lability will be important for further development and use of handles.

Hennigian Phylogenetic Systematics and the ‘Groundplan’ vs. ‘Post-Groundplan’ Approaches: A Reply to Kukalová-Peck

The recent contribution by Jarmila Kukalová-Peck on Hennigian phylogenetics and hexapod limb evolution is critically evaluated.

Forty Years of ‘The Strategy’: Levins on Model Building and Idealization

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is concerned, at its core, with justifying the use of multiple, idealized models in population biology.

The Ethics of Birth and Death: Gender Infanticide in India

This paper discusses the persistent devaluation of the girl child in India and the link between the entrenched perception of female valuelessness and the actual practice of infanticide of girl babies or foetuses. It seeks to place female infanticide, or ‘gendercide,’ within the context of Western-derived conceptions of ethics, justice and rights. To date, current ethical theories and internationally purveyed moral frameworks, as well as legal and political declarations, have fallen short of an adequate moral appraisal of infanticide. This paper seeks to rethink the issue.

Sexual selection and mate choice in evolutionary psychology

The importance of mate choice and sexual selection has been emphasized by the majority of evolutionary psychologists. This paper assesses three cases of work on mate choice and sexual selection in evolutionary psychology: David Buss on cross-cultural human mate preferences, Randy Thornhill and Steve Gangestad on the link between mate preferences and fluctuating asymmetry, and Geoffrey Miller on the role of Fisher’s runaway process in human evolution. A mixture of conceptual and empirical problems in each case highlights the general weakness of work in evolutionary psychology on these issues.

Realistic threshold policy with hysteresis to control predator–prey continuous dynamics

This paper introduces a threshold policy with hysteresis (TPH) for the control of one-predator one-prey models. The models studied are the Lotka–Volterra and Rosenzweig–MacArthur two species density-dependent predator–prey models and the Arditi–Ginzburg nondimensional ratio-dependent model. The proposed policy (TPH) changes the dynamics of the system in such a way that a bounded oscillation is achieved confined to a region that does not allow extinction of either species. The policy can be designed by a suitable choice of so called virtual equilibrium points in a simple and intuitive manner.