Explanation and prediction in vegetation science

A definition of vegetation science is given, spanning 6 levels of integration and stressing the interrelations among them. The problems of realism are discussed. The selection of levels is related to the adequate correspondence between conceptualization and research aims. Pattern and process are introduced as the central concepts of vegetation science. The perception of reality is dependent on the spatial and temporal scale chosen. The concept of noise is discussed in relation to stochasticity and randomness of events. Traces of essentialism are found both in classification of communities and habitat ecology. Classification is important, particularly the coexistence of alternative classification approaches. Organicism as a basis of vegetation research is rejected because the organismic view is inadequate on higher integration levels. The concept of function is redefined in a non-teleologic way.Present vegetation ecological research is inductivistic. One possible alternative to inductivism is falsificationism. The major domain of this approach is hypothesis testing, which will become more important. Progress can only be reached by a maximum degree of communication among scientific individuals.Predictive ecology is partly based on historic explanation, partly on complementary approaches. Characters of vegetation worthwhile to be predicted are listed and the necessary requirements for vegetation science to become predictive are discussed. A major requirement is the development of succession and life-history theory. A further elaboration of the individualistic concept will be a main task of vegetation science in the near future.     

Scale dependency and the expression of hierarchical structure in Delphinium patches

Hierarchy theory has provided a valuable conceptual framework for studies of heterogeneity. However, there have been few empirical studies of hierarchical structure and little is known about how hierarchical structure originates or varies among systems. Here, I explore how scale dependency can influence the detection of hierarchical structure. Specifically, I compared how heterogeneity changed with scale in patches of larkspur (Delphinium spp). The distribution of Delphinium nelsonii inflorescences was quite uniform over the range of measured scales (1 m²-2500 m²) and only a single level of patchiness was observed. Aggregations of D. barbeyi inflorescences were much more pronounced and this patchiness was evident at many scales. The number of hierarchical levels and the scales at which patchiness occurred varied both within and between plots of D. barbeyi. Because patchiness was not strongly scale-dependent for either species, discrete patch boundaries and well-defined hierarchical levels were not usually apparent even when multiple scales of patchiness were present. In several cases, the scales of detected patchiness depended on the difference in scale between grain (resolution) and extent. I predict that because of the lack of dominant and strongly scale-dependent processes, microlandscapes such as Delphinium meadows, may be less likely to exhibit well-defined hierarchical structure than larger-scale landscapes, especially those heavily altered by human activities.     

The old REH theory remains unsatisfactory and the new REH theory is problematical - a reply to holmquist and jukes

Summary In response to criticism of REH theory (Fitch 1980), Holmquist and Jukes (1981) have mostly avoided the criticism or misunderstood it. Since they themselves state in their response that Amino acid sequence data alone cannot be used to estimate total nucleotide substitutions, they agree with the criticism. Most of their paper treats the newer theory (here designated as the REHN theory) which attempts to use the nucleotide sequences encoding proteins to better estimate total nucleotide substitutions (Holmquist and Pearl 1980). Since I made no criticism of REHN theory, their comments are frequently beside the point of my original criticism of REH theory. Nevertheless, it is shown here that REHN theory is also unsatisfactory in that: One, the varions are now more clearly defined but in such a way as to preclude the same codon from suffering a nucleotide substitution in more than one evolutionary interval. Two, the set of codons that accepts silent substitutions is identical to the set that accepts amino acid changing nucleotide substitutions. Three, the uncertainty in the REH estimate is considerable in that alternative excellent fits to the same observatuonal data may give alternative REH values that differ significantly even before stochastic variation and selective bias are considered. Four, the fit of their model to data is an irrelevancy where there are zero degrees of freedom.     

Approaching mathematical model of the immune network based DNA Strand Displacement system

One biggest obstacle in molecular programming is that there is still no direct method to compile any existed mathematical model into biochemical reaction in order to solve a computational problem. In this paper, the implementation of DNA Strand Displacement system based on nature-inspired computation is observed. By using the Immune Network Theory and Chemical Reaction Network, the compilation of DNA-based operation is defined and the formulation of its mathematical model is derived. Furthermore, the implementation on this system is compared with the conventional implementation by using silicon-based programming. From the obtained results, we can see a positive correlation between both. One possible application from this DNA-based model is for a decision making scheme of intelligent computer or molecular robot.     

Test Study on the Excitation Spectrum of the CO ⃛Ar van der Waals Molecule

In the present contribution, we performed ab initio Møller-Plesset perturbation theory second-order (MP2) calculations in the framework of the supermolecule approach on the vertical excitation spectra of the weakly bound van der Waals CO-Ar molecule in its "near T-shaped" most stable ground state structure, as a guideline for future theoretical and experimental work. These test calculations indicate a ground CO ( X 1 D )- Ar ( 1 S ) interaction with R e =3.72 Å, D e =109 cm -1 and D o =92 cm -1 . They also indicate an excited CO ( A 1 @ )- Ar ( 1 S ) interaction with R e =3.55 Å, D e =141 cm -1 and D o =121 cm -1 . A red shift of 29 cm -1 for the CO ( X 1 D )- Ar ( 1 S ) M CO ( A 1 @ )- Ar ( 1 S ) vertical excitation energy, with respect to the corresponding CO ( X 1 D ) M CO ( A 1 @ ) excitation in the absence of Ar, can be obtained by comparing the corresponding D o values.     

DFT modelling of hydrogen on Cu(110)- and (111)-type clusters

Density Functional Theory (DFT) calculations using gaussian 98 have been performed on hydrogen adsorbed on clusters representing the (110) and (111) surfaces of Cu. Clusters were constructed to model different adsorption sites, and at least two different size clusters were used for each site. On the (111) surface, hydrogen prefers to adsorb in a hollow site, though with the hcp variant being favoured by the adsorption energy, and the fcc alternative by the vibrational frequencies. On the (110) surface, the "fcc" site on a (1 2 2) reconstructed surface is preferred.     

Common alien plants are more competitive than rare natives but not than common natives

Success of alien plants is often attributed to high competitive ability. However, not all aliens become dominant, and not all natives are vulnerable to competitive exclusion. Here, we quantified competitive outcomes and their determinants, using response‐surface experiments, in 48 pairs of native and naturalised alien annuals that are common or rare in Germany. Overall, aliens were not more competitive than natives. However, common aliens (invasive) were, despite strong limitation by intraspecific competition, more competitive than rare natives. This is because alien species had higher intrinsic growth rates than natives, and common species had higher intrinsic growth rates than rare ones. Strength of interspecific competition was not related to status or commonness. Our work highlights the importance of including commonness in understanding invasion success. It suggests that variation among species in intrinsic growth rates is more important in competitive outcomes than inter‐ or intraspecific competition, and thus contributes to invasion success and rarity.     

Water as a complex system: its role in ligand diffusion, general anesthesia, and sleep

The work and inspiration of Robert Rosen is stated and expressed in personal tones. The concept of passages through water (H2O) near protein surfaces is reviewed in terms of its influence on ligand diffusion to an effector. This is offered as a target for interference by a non-specific general anesthetic agent. In view of the similarities between this anesthetic state and sleep, this mechanism is proposed to be operative for the sleep/wake states. Based on this mechanism and other factors, nitrogen (N2) is proposed as an exogenous sleep factor.     

Recent advancement in the discovery and development of COX-2 inhibitors: Insight into biological activities and SAR studies (2008–2019)

Cyclooxygenase-2 is a very important physiological enzyme playing key roles in various biological functions especially in the mechanism of pain and inflammation, among other roles, making it a molecule of high interest to the pharmaceutical community as a target. COX 2 enzyme is induced only during inflammatory processes or cancer and reflects no role in the guarding stomach lining. Thus, selective COX-2 inhibition can significantly reduce the adverse effects including GI tract damage and hepatotoxic effects of traditional NSAIDs like aspirin, ibuprofen, etc. Recent developments on COX-2 inhibitors is primarily focused on improving the selectivity index of the drug towards COX-2 along with enhancing the potency of the drug by modifying the scaffolds of Coxibs currently in the market like Celecoxib, Indomethacin, Oxaprozin, etc. We have reported the progress on new COX-2 inhibitors in the last decade (2008–2019) focussing on five heterocyclic rings- Pyrazole, Indole, Oxazole, Pyridine and Pyrrole. The addition of various moieties to these core rings and their structure-activity relationship along with their molecular modelling data have been explored in the article. This review aims to aid medicinal chemists in the design and discovery of better COX-2 inhibitors constructed on these five heterocyclic pharmacophores.