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PubMed2004

Localization and extinction of bacterial populations under inhomogeneous growth conditions.

The transition from localized to systemic spreading of bacteria, viruses, and other agents is a fundamental problem that spans medicine, ecology, biology, and agriculture science. We have conducted experiments and simulations in a simple one-dimensional system to determine the spreading of bacterial populations that occurs for an inhomogeneous environment under the influence of external convection. Our system consists of a long channel with growth inhibited by uniform ultraviolet (UV) illumination except in a small "oasis", which is shielded from the UV light. To mimic blood flow or other flow past a localized infection, the oasis is moved with a constant velocity through the UV-illuminated "desert". The experiments are modeled with a convective reaction-diffusion equation. In both the experiment and model, localized or extinct populations are found to develop, depending on conditions, from an initially localized population. The model also yields states where the population grows everywhere. Further, the model reveals that the transitions between localized, extended, and extinct states are continuous and nonhysteretic. However, it does not capture the oscillations of the localized population that are observed in the experiment.

Computer Simulation↗
PubMed2006

The dawn of science-based moral reasoning.

In 1998, Edward O. Wilson discussed the biological basis of morality, pointed out that the analysis of its material origins should enable us to fashion a wise ethical consensus, and predicted the dawn of science-based moral reasoning. This article testifies that his prediction was right. Morality, being based on altruism and collaboration, evolved as a socially advantageous biological phenomenon aimed at ensuring the survival of our species, which was structured in small groups at high risk of extinction for the 99.5% of its existence. In the last 0.5%, the advent of agriculture resulted in a demographic explosion that impaired human beings' moral discernment, because the socially detrimental consequences of immoral actions, which had been recognised and condemned promptly in small groups consisting of a few tens of members, were diluted among millions of untouched individuals, thereby becoming less easily recognisable. Nowadays, to test the supposed morality of individual actions and government policies, we should use reason or, in doubtful cases, mathematical modelling to determine their predictable effects on the survival of small theoretical communities. Unless we untenably claim that the unlikelihood of extinction of today's immense societies entitles us to overturn the meaning of morality, all actions and policies that would cause the extinction of small communities should be regarded as indisputably immoral. This article also presents some examples of science-based moral arguments showing the immorality of restrictions and bans on research with human embryonic stem cells and demonstrates that the old concept of the "naturalistic fallacy", which philosophers frequently invoke to dismiss any scientific approach to morality, is no longer tenable, because it increasingly emerges to be a proof of what may well be defined the "philosophical fallacy".

Biological Evolution↗
PubMed2005

Population modeling for a captive squirrel monkey colony.

Population modeling for a squirrel monkey colony breeding in a captive laboratory environment was approached with the use of two different mathematical modeling techniques. Deterministic modeling was used initially on a spreadsheet to estimate future census figures for animals in various age/sex classes. Historical data were taken as input parameters for the model, combined with harvesting policies to calculate future population figures in the colony. This was followed by a more sophisticated stochastic model that is capable of accommodating random variations in biological phenomena, as well as smoothing out measurement errors. Point estimates (means) for input parameters used in the deterministic model are replaced by probability distributions fitted into historical data from colony records. With the use of Crystal Ball (Decisioneering, Inc., Denver, CO) software, user-selected distributions are embedded in appropriate cells in the spreadsheet model. A Monte Carlo simulation scheme running within the spreadsheet draws (on each cycle) random values for input parameters from the distribution embedded in each relevant cell, and thus generates output values for forecast variables. After several thousand runs, a distribution is formed at the output end representing estimates for population figures (forecast variables) in the form of probability distributions. Such distributions provide the decision-maker with a mathematical habitat for statistical analysis in a stochastic setting. In addition to providing standard statistical measures (e.g., mean, variance, and range) that describe the location and shape of the distribution, this approach offers the potential for investigating crucial issues such as conditions surrounding the plausibility of extinction.

Animals↗
PubMed2002

Mechanism and biological role of nitric oxide binding to cytochrome c'.

The binding of nitric oxide to ferric and ferrous Chromatium vinosum cytochrome c' was studied. The extinction coefficients for the ferric and ferrous nitric oxide complexes were measured. A binding model that included both a conformational change and dissociation of the dimer into subunits provided the best fit for the ferric cytochrome c' data. The NO (nitric oxide) binding affinity of the WT ferric form was found to be comparable to the affinities displayed by the ferric myoglobins and hemoglobins. Using an improved fitting model, positive cooperativity was found for the binding of NO to the WT ferric and ferrous forms, while anticooperativity was the case for the Y16F mutant. Structural explanations accounting for the binding are proposed. The NO affinity of ferrous cytochrome c' was found to be much lower than the affinities of myoglobins, hemoglobins, and pentacoordinate heme models. Structural factors accounting for the difference in affinities were analyzed. The NO affinity of ferrous cytochrome c' was found to be in the range typical of receptors and carriers. In addition, cytochrome c' was found to react with cytosolic light-irradiated membranes in the presence of succinate and carbon monoxide. With these results, a biochemical model of cytochrome c' functioning as a nitric oxide carrier was proposed.

Amino Acid Substitution↗
PubMed1999

A model of prebiotic replication: survival of the fittest versus extinction of the unfittest.

A model of prebiotic replication discussed by Szathmary and Maynard Smith (1997) is refined in accordance with Lifson's (1997) theory on the crucial stages in the origin of animate matter. The refined model accounts for two processes associated with replication: (1) Replicators always decompose at some rate. (2) Replicators deplete their reactants at a rate equal to the rate of their own replication. Consequently, replicators and their reactants are linked by a non-linear feedback process that keeps them within limits and leads them toward a steady state. The model suggests that: (a) All competing replicators, including those which replicate at sub-exponential "parabolic" and super-exponential "hyperbolic" rates, are subject to natural selection. (b) Survival/extinction is determined by positive/negative net-replication irrespective of the mechanism of replication. (c) Being fit/unfit is the consequence of survival/extinction rather than its cause. In other words, natural selection and survival of the fit is the outcome of continual extinction of the unfit.

Animals↗
PubMed1975

Reversible extinction of the morphogen in bone matrix by reduction and oxidation of disulfide bonds.

Beta-Mercaptoethanol (beta-ME) or dithiothreitol (DTT) reduction extinguishes the capacity of bone matrix gelatin to produce new bone following implantation in a muscle pouch. If the reducing solution is used in concentrations of 50 mmoles/l or less, the extinction can be partially reversed by bubbling of oxygen through the solution for one hour. Sulfhydryl group blocking reagents prevent reoxidation of reduced bone gelatin, and restoration of the bone morphogenetic property (BMP). Unspecific borohydride reduction at 37 degrees destroys bone yield irreversibly, but at 2 degrees reduction of free aldehyde groups in bone gelatin does not prevent beta-ME and DTT reversible extinction. These observations are interpreted to suggest that the disulphide linkage may be an essential part of the biologically active conformation of either a non-collagenous bone morphogenetic polypeptide firmly bound to collagen or a collagen by-product entrapped within a water insoluble gel matrix.

Animals↗
PubMed2004

Ecology: compensating for extinction.

Food web interactions allow communities to compensate for the loss of species. Compensation of this kind may reshuffle communities so that today's resilient species are tomorrow's vulnerable species, creating a false impression of ecosystem stability following the first wave of extinction.

Biodiversity↗
PubMed2004

Climbing and the daily energy cost of locomotion in wild chimpanzees: implications for hominoid locomotor evolution.

As noted by previous researchers, the chimpanzee postcranial anatomy reflects a compromise between the competing demands of arboreal and terrestrial locomotion. In this study, we measured the distance climbed and walked per day in a population of wild chimpanzees and used published equations to calculate the relative daily energy costs. Results were used to test hypotheses regarding the arboreal-terrestrial tradeoff in chimpanzee anatomy, specifically whether arboreal adaptations serve to minimize daily locomotor energy costs by decreasing the energy spent climbing. Our results show that chimpanzees spend approximately ten-times more energy per day on terrestrial travel than on vertical climbing, a figure inconsistent with minimizing energy costs in our model. This suggests non-energetic factors, such as avoiding falls from the canopy, may be the primary forces maintaining energetically costly climbing adaptations. These analyses are relevant to anatomical comparisons with living and extinct hominoids.

Age Factors↗
PubMed2005

Dependence of the enhanced optical scattering efficiency relative to that of absorption for gold metal nanorods on aspect ratio, size, end-cap shape, and medium refractive index.

The current intense interest in the properties of plasmonic nanostructures for their applications in chemical and biochemical sensors, medical diagnostics and therapeutics, and biological imaging is fundamentally based on their enhanced optical absorption and scattering properties. In this study, the optical extinction, absorption, and scattering efficiencies were calculated as a function of shape definition, aspect ratio, surrounding medium, and material selection. The discrete dipole approximation method was used, which is known to be a very useful and versatile computational tool for particles with any arbitrary shape. Relative contribution of scattering to the total extinction for the longitudinal mode was found to be significantly dependent on the aspect ratio of the nanorod in a somewhat complex manner, different from a typical linear relationship for the resonance wavelength. A slight elongation of Au nanosphere gives rise to a drastic increase in the relative scattering efficiency, which eventually reaches a maximum and begins to decrease with further increase in the aspect ratio. This is ascribed to the increasing absorptive contribution from the larger imaginary dielectric function of the metal particle in the longer wavelength region where the red-shifted excitation of the longitudinal resonance mode occurs. For transverse mode exhibiting the blue-shift in the resonance peak, on the contrary, the absorption efficiency is relatively enhanced compared to the scattering efficiency with increasing aspect ratio. This is thought to result from the dominant effect of the interband transition present in this wavelength region. Besides the dependence of plasmonic characteristics on the aspect ratio of nanorod, the DDA results for a small change of the end-cap shape and the index of the surrounding medium lead us to conclude that there exist two competing key factors: a weighting factor assigned to the shape parameter and the dielectric function of the metal particle, which control the relative enhancement in the scattering and absorption as well as the linearity of resonance wavelength with regard to the aspect ratio.

Journal Article↗
PubMed2004

Microbialite resurgence after the Late Ordovician extinction.

Microbialites, including biogenic stromatolites, thrombolites and dendrolites, were formed by various microbial mats that trapped and bound sediments or formed the locus of mineral precipitation. Microbialites were common and diverse during the Proterozoic, but declined in abundance and morphological diversity when multicellular life diversified during the Cambrian Radiation. A second decline occurred during the Ordovician Radiation of marine animals, and from then until the present microbialites have been confined largely to high-stress environments where multicellular organisms are rare. The microbialite declines in the Phanerozoic are attributed to disruption of the mats by animals. A resurgence of stromatolite abundance and size during reduced animal diversity after the Permian extinction has been documented anecdotally. Here we show, with statistical support, that a microbialite resurgence also occurred after the Late Ordovician extinction event in western North America. The resurgences were associated with loss of mat-inhibiting animals, providing insights into shallow-water community structures after extinction events.

Animals↗
PubMed1981

Immigration and extinction probabilities for individual species: relation to incidence functions and species colonization curves.

We develop a dynamic model of island biogeography based on immigration and extinction probabilities of individual species rather than on the usual biogeographic parameters of the number of species immigrating or going extinct per unit time. In the real world, these probabilities vary enormously among species, and three field studies suggest lognormal distributions. Based on such distributions of individual probabilities, our model proceeds by calculating the conditional probability of species occurrence--the likelihood that a given species will occur on a given island--as a function of total species number on the island. The model succeeds in predicting two observed features of species communities; (i) staggered, sigmoidally-shaped incidence functions ("differing area requirements of different species") and (ii) concave immigration and extinction curves.

Animals↗
PubMed2002

Short-term studies underestimate 30-generation changes in a butterfly metapopulation.

Most studies of rare and endangered species are based on work carried out within one generation, or over one to a few generations of the study organism. We report the results of a study that spans 30 generations (years) of the entire natural range of a butterfly race that is endemic to 35 km(2) of north Wales, UK. Short-term studies (surveys in single years and dynamics over 4 years) of this system led to the prediction that the regional distribution would be quite stable, and that colonization and extinction dynamics would be relatively unimportant. However, a longer-term study revealed unexpectedly high levels of population turnover (local extinction and colonization), affecting 18 out of the 20 patches that were occupied at any time during the period. Modelling the system (using the 'incidence function model' (IFM) for metapopulations) also showed higher levels of colonization and extinction with increasing duration of the study. The longer-term dynamics observed in this system can be compared, at a metapopulation level, with the increased levels of variation observed with increasing time that have been observed in single populations. Long-term changes may arise from local changes in the environment that make individual patches more or less suitable for the butterfly, or from unusual colonization or extinction events that take metapopulations into alternative states. One implication is that metapopulation and population viability analyses based on studies that cover only a few animal or plant generations may underestimate extinction threats.

Animals↗
PubMed1989

The present, past and future of human-caused extinctions.

This paper re-evaluates whether we are really at the start of a mass extinction caused by humans. I consider the present, past and future of human-caused extinctions. As regards the present, estimates of extinction rates based on Red Data Books underestimate real values by a large factor, because the books evaluate only those species that have attracted specific attention and searches. Especially in tropical areas with few resident biologists, many poorly known species go extinct without having been the object of specific attention, and others disappear even before being described. A 'green list' of species known to be secure is needed to complement 'red books' of species known to be extinct. As regards the past, it is now clear that the first arrival of humans at any oceanic island with no previous human inhabitants has always precipitated a mass extinction in the island biota. Well-known victims include New Zealand's moas, Madagascar's giant lemurs, and scores of bird species on Hawaii and other tropical Pacific islands. Late-Pleistocene or Holocene extinctions of large mammals after the first arrival of humans in North America, South America and Australia may also have been caused by humans. Hence human-caused mass extinction is not a hypothesis for the future but an event that has been underway for thousands of years. As regards the future, consideration of the main mechanisms of human-caused extinctions (overhunting, effects of introduced species, habitat destruction, and secondary ripple effects) indicates that the rate of extinction is accelerating.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1991

[The wisdom of the animal body].

In 1932 CANNON described the physiological wisdom of the body. This cannot exist without morphological wisdom. Since morphology is a formative process, both kinds of wisdom depend on the same formative forces. These forces are the forces of consciousness at all levels. Their existence is proved by the fact that they can be eliminated by narcosis. The wisdom of these forces is twofold: Firstly, the wisdom of need sensation which lasts only until the need is satisfied. This is the conscious intelligence of the body which is responsible for restraint in all living beings. Secondly, the wisdom, or better, the prudence of need satisfaction which requires knowledge and appropriate tools. The organs of the body are these tools. Knowledge belongs to the intellect which knows how to handle material. This is achieved in all prehuman species subconsciously and is demonstrated in all structures built by cells and animals. Only the human mind can be unwise and imprudent; but man, being free, is also able to be wise and prudent and so prevent the extinction of the earthly creation.

Animal Population Groups↗
PubMed1997

Emergence of collective strategies in a prey-predator game model.

The emergence of collective strategies in a prey-predator system is studied. We use the term "collective" in the sense of the collective motion of defense or attack often found in behaviors of animal groups. In our prey-predator system, both prey and predators move around on a two-dimensional plane, interacting by playing a game; predators can score by touching the backside of a prey. Thresholds are assumed for the scores of both prey and predators. The species with the higher scores can reproduce more, and that with the lower scores will be diminished. As a result, strategies as collective motions are observed; these consist of rotating cluster motions, line formations, disordered but one-way marching, and random swarming. In particular, the strategy of random swarming encourages symbiosis in the sense that it is associated with a low extinction probability for the whole system.

Animals↗