The limits of subfunctionalization

Background  

The duplication-degeneration-complementation (DDC) model has been proposed as an explanation for the unexpectedly high retention of duplicate genes. The hypothesis proposes that, following gene duplication, the two gene copies degenerate to perform complementary functions that jointly match that of the single ancestral gene, a process also known as subfunctionalization. We distinguish between subfunctionalization at the regulatory level and at the product level (e.g within temporal or spatial expression domains).     

The limits of brain determinacy

The genes do not control everything that happens in a cell or an organism, because thermally induced molecular movements and conformation changes are beyond genetic control. The importance of uncontrolled events has been argued from the differences between isogenic organisms reared in virtually identical environments, but these might alternatively be attributed to subtle, undetected differences in the environment. The present review focuses on the uncontrolled events themselves in the context of the developing brain. These are considered at cellular and circuit levels because even if cellular physiology was perfectly controlled by the genes (which it is not), the interactions between different cells might still be uncoordinated. A further complication is that the brain contains mechanisms that buffer noise and others that amplify it. The final resultant of the battle between these contrary mechanisms is that developmental stochasticity is sufficiently low to make neurobehavioural defects uncommon, but a chance component of neural development remains. Thus, our brains and behaviour are not entirely determined by a combination of genes-plus-environment.     

The limits of phosphorus removal in wetlands

The phosphorus concentrations exported from wetlands are explored via data and a first order model. The graph of outlet concentration versus areal phosphorus loading is used to display these data and the model. For a given wetland, data and models show that P concentrations show an S curve response to increasing P loadings. The lower plateau is the background concentration and the upper plateau is the inlet concentration. The position of the ascending limb between the two plateaus is positioned differently for different wetlands. Phosphorus (P) removal in wetlands is often typified by a stable decreasing gradient of P concentrations from inlet to outlet, and an accompanying stable decreasing gradient in P assimilation. Limits to removal are inherent in the physical, chemical and biological processes. A lower outlet concentration limit exists because of the P cycle in the un-impacted wetland. The loading at which the outlet concentration departs from background, the lower knee in the loading curve, varies from wetland to wetland. An upper outlet concentration limit is imposed by the source concentration for extremely high inflows. The first order mass balance equation interpolates between these limits. The model gives further insights about performance within an overall envelope. The water carrying capacity of the wetland precludes flows in excess of the hydraulic conveyance capacity, thus limiting the possible P loadings to the system. Conversely, extremely low hydraulic loadings cause the wetland to be dominated by atmospheric additions and losses. The central tendency of inter-system data in the North American Database is shown to be inadequate to draw generalized conclusions about ecosystem processes in an individual wetland. The proposed one gram rule of Richardson, et al. (1997) is shown to be an over-simplification.     

Child abuse: The limits of sociobiology

A review of five population based studies indicates that rates of child abuse tend to be highest among young male children from poor families. Children from very large families, children from families with a history of marital disruption, and defective children are also at a high risk of abuse. Perpetrators are more apt to be fathers or stepparents than would be expected on the basis of their representation in families of abused children. Biological mothers are least apt to abuse their children.Although these data are consistent with an evolutionary model of child abuse, many of these findings are also consistent with alternative (especially economic) models for abuse. An attempt is made to develop testable predictions for child abuse that are consistent with evolutionary theory and inconsistent with more conventional models.     

The limits and frontiers of desiccation-tolerant life

Drying to equilibrium with the air is lethal to most speciesof animals and plants, making drought (i.e., low external waterpotential) a central problem for terrestrial life and a majorcause of agronomic failure and human famine. Surprisingly, awide taxonomic variety of animals, microbes, and plants do toleratecomplete desiccation, defined as water content below 0.1 g H₂Og^–1 dry mass. Species in five phyla of animals and fourdivisions of plants contain desiccation-tolerant adults, juveniles,seeds, or spores. There seem to be few inherent limits on desiccationtolerance, since tolerant organisms can survive extremely intenseand prolonged desiccation. There seems to be little phylogeneticlimitation of tolerance in plants but may be more in animals.Physical constraints may restrict tolerance of animals withoutrigid skeletons and to plants shorter than 3 m. Physiologicalconstraints on tolerance in plants may include control by hormoneswith multiple effects that could link tolerance to slow growth.Tolerance tends to be lower in organisms from wetter habitats,and there may be selection against tolerance when water availabilityis high. Our current knowledge of limits to tolerance suggeststhat they pose few obstacles to engineering tolerance in prokaryotesand in isolated cells and tissues, and there has already beenmuch success on this scientific frontier of desiccation tolerance.However, physical and physiological constraints and perhapsother limits may explain the lack of success in extending toleranceto whole, desiccation-sensitive, multicellular animals and plants.Deeper understanding of the limits to desiccation tolerancein living things may be needed to cross this next frontier.     

Signal sequences. The limits of variation

Variations in length and composition of the charged N-terminal, central hydrophobic and polar C-terminal regions in a large sample of signal sequences have been mapped, both as a function of the overall length of the sequence, and in an absolute sense, i.e. various "extremes" have been sought. The results show subtle differences between eukaryotic and prokaryotic sequences, but the general impression of signal sequences as being highly variable is reinforced. Criteria for a "minimal" signal sequence are suggested and discussed.     

The limits and relationships of the acanthomorph teleosts

The phylogenetic status of the speciose euteleostean assemblage, the Acanthomorpha, is investigated. For the purposes of cladistic analysis attention is centred upon an examination of euteleostean buccal ligament systems, the occipital and ethmoid regions of the neurocranium, and the posttemporal/neurocranial association.
In this study four derived morphological features are identified which support the monophyly of the Acanthomorpha, and the previously 'problematical' genus Polymixia is determined to be the sistergroup of all the remaining acanthomorphs. The phylogenetic integrity of the sistergroup of the entire Acanthomorpha, the Myctophiformes (sensu Rosen, 1973), is attested by the presence of four derived features, and the monophyly of its major subdivisions (the Myctophidae and Neoscopelidae) is resolved.
Additional problems of euteleostean systematics and systematic methodology are discussed.     

The limits of reductionism in the life sciences

In the contemporary life sciences more and more researchers emphasize the "limits of reductionism" (e.g. Ahn et al. 2006a, 709; Mazzocchi 2008, 10) or they call for a move "beyond reductionism" (Gallagher/Appenzeller 1999, 79). However, it is far from clear what exactly they argue for and what the envisioned limits of reductionism are. In this paper I claim that the current discussions about reductionism in the life sciences, which focus on methodological and explanatory issues, leave the concepts of a reductive method and a reductive explanation too unspecified. In order to fill this gap and to clarify what the limits of reductionism are I identify three reductive methods that are crucial in the current practice of the life sciences: decomposition, focusing on internal factors, and studying parts in isolation. Furthermore, I argue that reductive explanations in the life sciences exhibit three characteristics: first, they refer only to factors at a lower level than the phenomenon at issue, second, they focus on internal factors and thus ignore or simplify the environment of a system, and, third, they cite only the parts of a system in isolation.