Can noise induce chaos?

An important component of the mathematical definition of chaos is sensitivity to initial conditions. Sensitivity to initial conditions is usually measured in a deterministic model by the dominant Lyapunov exponent (LE), with chaos indicated by a positive LE. The sensitivity measure has been extended to stochastic models; however, it is possible for the stochastic Lyapunov exponent (SLE) to be positive when the LE of the underlying deterministic model is negative, and vice versa. This occurs because the LE is a long-term average over the deterministic attractor while the SLE is the long-term average over the stationary probability distribution. The property of sensitivity to initial conditions, uniquely associated with chaotic dynamics in deterministic systems, is widespread in stochastic systems because of time spent near repelling invariant sets (such as unstable equilibria and unstable cycles). Such sensitivity is due to a mechanism fundamentally different from deterministic chaos. Positive SLE's should therefore not be viewed as a hallmark of chaos. We develop examples of ecological population models in which contradictory LE and SLE values lead to confusion about whether or not the population fluctuations are primarily the result of chaotic dynamics. We suggest that "chaos" should retain its deterministic definition in light of the origins and spirit of the topic in ecology. While a stochastic system cannot then strictly be chaotic, chaotic dynamics can be revealed in stochastic systems through the strong influence of underlying deterministic chaotic invariant sets.     

Did farming arise from a misapplication of social intelligence?

The origins of farming is the defining event of human history--the one turning point that has resulted in modern humans having a quite different type of lifestyle and cognition to all other animals and past types of humans. With the economic basis provided by farming, human individuals and societies have developed types of material culture that greatly augment powers of memory and computation, extending the human mental capacity far beyond that which the brain alone can provide. Archaeologists have long debated and discussed why people began living in settled communities and became dependent on cultivated plants and animals, which soon evolved into domesticated forms. One of the most intriguing explanations was proposed more than 20 years ago not by an archaeologist but by a psychologist: Nicholas Humphrey suggested that farming arose from the 'misapplication of social intelligence'. I explore this idea in relation to recent discoveries and archaeological interpretations in the Near East, arguing that social intelligence has indeed played a key role in the origin of farming and hence the emergence of the modern world.     

Neuronal variability: noise or part of the signal?

Sensory, motor and cortical neurons fire impulses or spikes at a regular, but slowly declining, rate in response to a constant current stimulus. Yet, the intervals between spikes often vary randomly during behaviour. Is this variation an unavoidable effect of generating spikes by sensory or synaptic processes ('neural noise') or is it an important part of the 'signal' that is transmitted to other neurons? Here, we mainly discuss this question in relation to sensory and motor processes, as the signals are best identified in such systems, although we also touch on central processes.     

Can a cell be assembled from its constituents?

To date, available are a provisional list of the minimal set of genes required for the functioning and multiplication of a living cell under maximally favorable conditions, methods for the complete chemical synthesis of the minimal genome, and cell-free systems for carrying out all the biochemical reactions comprising the genome replication and expression. The most serious problem that remains on the way to creating an artificial living cell is the need to meet two apparently incompatible requirements: separation of the biochemical reactions from the environment, and exchange between the environment and the cell. A solution to this problem can be provided by molecular colonies (other names: nanocolonies, polonies), which form when RNA or DNA is replicated in a solid medium having pores of a nanometer size. Molecular colonies might also have served as a pre-cellular form of compartmentalization in the RNA World.     

What is signal and what is noise in the brain?

The response of a cortical neuron to a stimulus can show a very large variability when repeatedly stimulated by exactly the same stimulus. This has been quantified in terms of inter-spike-interval (ISI) statistics by several researchers (e.g., [Softky, W., Koch, C., 1993. The highly irregular firing of cortical cells is inconsistent with temporal integration of random EPSPs. J. Neurosci. 13(1), 334-350.]). The common view is that this variability reflects noisy information processing based on redundant representation in large neuron populations. This view has been challenged by the idea that the apparent noise inherent in brain activity that is not strictly related or temporally coupled to the experiment could be functionally significant. In this work we examine the ISI statistics and discuss these views in a recently published model of interacting cortical areas [Knoblauch, A., Palm, G., 2002. Scene segmentation by spike synchronization in reciprocally connected visual areas. I. Local effects of cortical feedback. Biol. Cybernet. 87(3), 151-167.]. From the results of further single neuron simulations we can isolate temporally modulated synaptic input as a main contributor for high ISI variability in our model and possibly in real neurons. In contrast to alternative mechanisms, our model suggests a function of the temporal modulations for short-term binding and segmentation of figures from background. Moreover, we show that temporally modulated inputs lead to ISI statistics which fit better to the neurophysiological data than alternative mechanisms.     

Did cathelicidins, a family of multifunctional host-defense peptides, arise from a cysteine protease inhibitor?

Cystatins, the cysteine protease inhibitors, and the cathelin-like domain (CLD) of the antimicrobial cathelicidins are classified into the same superfamily because of their overall structural similarity. However, their evolutionary relationship has remained obscure owing to low sequence similarity. Structural similarity of two proteins often provides evidence for divergent evolution; however, structural convergence can not be completely ruled out in this case. Conserved gene structure and related function provide new evidence in favor of a common ancestral origin for cystatins and CLDs. On the basis of two observations, the C-terminal location of the cathelicidin antimicrobial domain and evolutionary gain of one 3' intron, I propose a gradual evolution model to explain how the AMD evolved from the ancestral cystatin scaffold.     

Can anomalous signal of sulfur become a tool for solving protein crystal structures?

A general method for solving the phase problem from native crystals of macromolecules has long eluded structural biology. For well diffracting crystals this goal can now be achieved, as is shown here, thanks to modern data collection techniques and new statistical phasing algorithms. Using solely a native crystal of tetragonal hen egg-white lysozyme, a protein of 14 kDa molecular mass, it was possible to detect the positions of the ten sulfur and seven chlorine atoms from their anomalous signal, and proceed from there to obtain an electron-density map of very high quality.     

Can a death signal half-life be used to sense the distance to a lesion site in axons?

Neuron response to injury depends on the distance to the lesion site, which means that neurons are capable of sensing this distance. Several mechanisms explaining how neurons can do this have been proposed and it is possible that neurons use a combination of several mechanisms to make such measurements. In this paper we investigate the feasibility of the simplest mechanism, which is based on the hypothesis that death signals, produced at the lesion site, propagate toward the neuron soma. The signals are propelled by dynein motors. If signals have a finite half-life, they decay as they propagate. By measuring the concentration of death signals arriving to the soma, neurons should thus be able to determine the distance to the injury site. We develop and solve a transport equation based on the above model. We investigate how a death signal distribution depends on the dynein velocity distribution. We evaluate the efficiency of such a mechanism by investigating the sensitivity of death signal concentration at the soma to the distance to the injury site. By using the hypothesis that system performance is optimized by evolution, we evaluate death signal half-lives that would maximize this sensitivity.     

Evolutionary theory of bacterial quorum sensing: when is a signal not a signal?

The term quorum sensing (QS) is used to describe the communication between bacterial cells, whereby a coordinated population response is controlled by diffusible molecules produced by individuals. QS has not only been described between cells of the same species (intraspecies), but also between species (interspecies) and between bacteria and higher organisms (inter-kingdom). The fact that QS-based communication appears to be widespread among microbes is strange, considering that explaining both cooperation and communication are two of the greatest problems in evolutionary biology. From an evolutionary perspective, intraspecies signalling can be explained using models such as kin selection, but when communication is described between species, it is more difficult to explain. It is probable that in many cases this involves QS molecules being used as 'cues' by other species as a guide to future action or as manipulating molecules whereby one species will 'coerce' a response from another. In these cases, the usage of QS molecules cannot be described as signalling. This review seeks to integrate the evolutionary literature on animal signalling with the microbiological literature on QS, and asks whether QS within bacteria is true signalling or whether these molecules are also used as cues or for the coercion of other cells.     

Can a reductionist be a pluralist?

Pluralism is often put forth as a counter-position to reductionism. In this essay, I argue that reductionism and pluralism are in fact consistent. I propose that there are several potential goals for reductions and that the proper form of a reduction should be considered in tandem with the goal that it aims to achieve. This insight provides a basis for clarifying what version(s) of reductionism are currently defended, for explicating the notion of a fundamental level of explanation, and for showing how one can be both a reductionist and a pluralist.     

How far can a juxtacrine signal travel?

Juxtacrine signalling is the process of cell communication in which ligand and receptors are both anchored in the cell membrane. We develop three mathematical models for this process, involving different mathematical representations of the dynamics of membrane-bound ligand and free and bound receptors, within an epithelial sheet. We consider the dynamics of this system following a localized disturbance, such as would be provided by a source of ligand or by the generation of a free edge via wounding. We study the ability of the juxtacrine mechanism to transmit a signal away from this disturbance, and show analytically that the spatial half-life of the signal can in fact be arbitrarily large. This result is quite general, since we use a generic reaction kinetic scheme; the key assumption is that ligand and receptor production are both upregulated by binding. Moreover, the result applies to all three of our model formulations. We conclude by discussing applications of the result to the particular case of the transforming growth factor alpha binding to epidermal growth factor receptor in epidermal wound healing.     

Can migrants escape from density dependence?

Migration is thought to maximize growth by enabling individuals to escape from density dependence, but this has rarely been tested at the individual level in natural populations. We employed linear mixed modeling of the spacing between consecutive scale growth rings to reconstruct individual growth profiles of a paradigmatic fish migrant, the sea trout (Salmo trutta) and related these to estimates of year class strength over a 13‐year period. Variation in scale growth was 1.3 times greater among individuals than within individuals in freshwater and 10 times greater at sea. Scale growth was inversely related to year class strength, both in freshwater (before migration) and at sea (after migration). Competition for patchily distributed resources is the most plausible explanation of the negative density‐dependent growth observed in freshwater and, to a lesser extent, in the marine environment. Our study provides some of the strongest evidence for a role of density dependence in determining partial migrations because although migrants can maximize growth by moving into the sea, they do not appear to become free from density dependence constraints completely. This has implications for conservation and suggests that sea trout and other anadromous fish displaying partial migrations may not be best managed on a river by river basis, but rather from a broader, coastal perspective.     

Can biochar reduce soil greenhouse gas emissions from a Miscanthus bioenergy crop?

Energy production from bioenergy crops may significantly reduce greenhouse gas (GHG) emissions through substitution of fossil fuels. Biochar amendment to soil may further decrease the net climate forcing of bioenergy crop production, however, this has not yet been assessed under field conditions. Significant suppression of soil nitrous oxide (N₂O) and carbon dioxide (CO₂) emissions following biochar amendment has been demonstrated in short‐term laboratory incubations by a number of authors, yet evidence from long‐term field trials has been contradictory. This study investigated whether biochar amendment could suppress soil GHG emissions under field and controlled conditions in a Miscanthus × Giganteus crop and whether suppression would be sustained during the first 2 years following amendment. In the field, biochar amendment suppressed soil CO₂ emissions by 33% and annual net soil CO₂ equivalent (eq.) emissions (CO₂, N₂O and methane, CH₄) by 37% over 2 years. In the laboratory, under controlled temperature and equalised gravimetric water content, biochar amendment suppressed soil CO₂ emissions by 53% and net soil CO₂ eq. emissions by 55%. Soil N₂O emissions were not significantly suppressed with biochar amendment, although they were generally low. Soil CH₄ fluxes were below minimum detectable limits in both experiments. These findings demonstrate that biochar amendment has the potential to suppress net soil CO₂ eq. emissions in bioenergy crop systems for up to 2 years after addition, primarily through reduced CO₂ emissions. Suppression of soil CO₂ emissions may be due to a combined effect of reduced enzymatic activity, the increased carbon‐use efficiency from the co‐location of soil microbes, soil organic matter and nutrients and the precipitation of CO₂ onto the biochar surface. We conclude that hardwood biochar has the potential to improve the GHG balance of bioenergy crops through reductions in net soil CO₂ eq. emissions.