The Role of Teleological Thinking in Learning the Darwinian Model of Evolution

Human beings are predisposed to think of evolution as teleological—i.e., having a purpose or directive principle—and the ways scientists talk about natural selection can feed this predisposition. This work examines the suggestion that students’ teleological thinking operates as an obstacle when the natural selection evolution model is taught. What we mean by obstacle is an established way of thinking that resists change due to its explanatory power. In light of this approach, the challenges of teaching evolution in biology education have been revised, and improved methodological strategies aimed at a better comprehension of the Darwinian evolution model are suggested.     

Extinction dynamics in mainland-island metapopulations: an N-patch stochastic model

A generalization of the well-known Levins’ model of metapopulations is studied. The generalization consists of (i) the introduction of immigration from a mainland, and (ii) assuming the dynamics is stochastic, rather than deterministic. A master equation, for the probability that n of the patches are occupied, is derived and the stationary probability P _s (n), together with the mean and higher moments in the stationary state, determined. The time-dependence of the probability distribution is also studied: through a Gaussian approximation for general n when the boundary at n = 0 has little effect, and by calculating P(0, t), the probability that no patches are occupied at time t, by using a linearization procedure. These analytic calculations are supplemented by carrying out numerical solutions of the master equation and simulations of the stochastic process. The various approaches are in very good agreement with each other. This allows us to use the forms for P _s 0) and P(0, t) in the linearization approximation as a basis for calculating the mean time for a metapopulation to become extinct. We give an analytical expression for the mean time to extinction derived within a mean field approach. We devise a simple method to apply our mean field approach even to complex patch networks in realistic model metapopulations. After studying two spatially extended versions of this nonspatial metapopulation model—a lattice metapopulation model and a spatially realistic model—we conclude that our analytical formula for the mean extinction time is generally applicable to those metapopulations which are really endangered, where extinction dynamics dominates over local colonization processes. The time evolution and, in particular, the scope of our analytical results, are studied by comparing these different models with the analytical approach for various values of the parameters: the rates of immigration from the mainland, the rates of colonization and extinction, and the number of patches making up the metapopulation.     

New Analytic Results for Speciation Times in Neutral Models

In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the “critical branching process.” We develop an analytic way—as opposed to the common simulation approach—for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.     

Some views on the role of noise in “self”-organizing systems

This paper deals with information transfer from the environment and “self”-organization in open, nonlinear systems far from thermodynamic equilibrium — in the presence of either non-stationary phase jitter noise, or amplitude stationary noise. By “self”-organization we mean here the progressive formation within the system of sequential, ordered (coherent) relationships between appropriate dynamical variables-like for example, the phase differences between the oscillating components of the system. We take up (in Section II) the classical Laser as a specific example and examine in detail the influence of phase jitter noise in the mode (phase) locking process. We find—as expected—that phase fluctuations in the cavity cause degradation of the coherent behaviour (i.e. increase the entropy) of the system — which, however, levels off, or saturates with time. Further (in Section III) we examine systems where the number of self-sustained oscillating components may vary with time in such a way that the maximum entropy of the system increases faster than the overall instantaneous entropy. We put forth the hypothesis that in such cases — because of the increase of the redundancy — the system gets organized not just in spite of, but merely because of the presence of Noise. Possible applications in biological systems (especially concerning a model of cerebral organization) are briefly discussed. It is understood here, that the system has to display some preliminary dynamical structure before the organizing procedure takes over. What happens afterwards is the subject of this paper.     

Theory predicts a rapid transition from niche-structured to neutral biodiversity patterns across a speciation-rate gradient

A central challenge in community ecology is to predict patterns of biodiversity with mechanistic models. The neutral model of biodiversity is a simple model that appears to provide parsimonious and accurate predictions of biodiversity patterns in some ecosystems, even though it ignores processes such as species interactions and niche structure. In a recent paper, we used analytical techniques to reveal why the mean predictions of the neutral model are robust to niche structure in high diversity but not low-diversity ecosystems. In the present paper, we explore this phenomenon further by generating stochastic simulated data from a spatially implicit hybrid niche-neutral model across different speciation rates. We compare the resulting patterns of species richness and abundance with the patterns expected from a pure neutral and a pure niche model. As the speciation rate in the hybrid model increases, we observe a surprisingly rapid transition from an ecosystem in which diversity is almost entirely governed by niche structure to one in which diversity is statistically indistinguishable from that of the neutral model. Because the transition is rapid, one prediction of our abstract model is that high-diversity ecosystems such as tropical forests can be approximated by one simple model—the neutral model—whereas low-diversity ecosystems such as temperate forests can be approximated by another simple model—the niche model. Ecosystems that require the hybrid model are predicted to be rare, occurring only over a narrow range of speciation rates.     

Trade-Offs Between Efficiency and Robustness in Bacterial Metabolic Networks Are Associated with Niche Breadth

The relation between structure and function in biologic networks is a central point of systems biology research. Key functional features—notably, efficiency and robustness—are linked to the topologic structure of a network, and there appears to be a degree of trade-off between these features, i.e., simulation studies indicate that more efficient networks tend to be less robust. Here, we investigate this issue in metabolic networks from 105 lineages of bacteria having a wide range of ecologies. We take quantitative measurements on each network and integrate this network data with ecologic data using a phylogenetic comparative model. In this setting, we find that biologic conclusions obtained with classical phylogenetic comparative methods are sensitive to correlations between model covariates and phylogenetic branch length. To avoid this problem, we propose a revised statistical framework—hierarchical mixed-effect regression—to accommodate phylogenetic nonindependence. Using this approach, we show that the cartography of metabolic networks does indeed reflect a trade-off between efficiency and robustness. Furthermore, ecologic characteristics related to niche breadth are strong predictors of network shape. Given the broad variation in niche breadth seen among species, we predict that there is no universally optimal balance between efficiency and robustness in bacterial metabolic networks and, thus, no universally optimal network structure. These results highlight the biologic relevance of variation in network structure and the potential role of niche breadth in shaping metabolic strategies of efficiency and robustness. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Ransom A. Myers Died March 27th, 2007. He will be missed.     

Responses of blowfly motion-sensitive neurons to reconstructed optic flow along outdoor flight paths

The retinal image flow a blowfly experiences in its daily life on the wing is determined by both the structure of the environment and the animal’s own movements. To understand the design of visual processing mechanisms, there is thus a need to analyse the performance of neurons under natural operating conditions. To this end, we recorded flight paths of flies outdoors and reconstructed what they had seen, by moving a panoramic camera along exactly the same paths. The reconstructed image sequences were later replayed on a fast, panoramic flight simulator to identified, motion sensitive neurons of the so-called horizontal system (HS) in the lobula plate of the blowfly, which are assumed to extract self-motion parameters from optic flow. We show that under real life conditions HS-cells not only encode information about self-rotation, but are also sensitive to translational optic flow and, thus, indirectly signal information about the depth structure of the environment. These properties do not require an elaboration of the known model of these neurons, because the natural optic flow sequences generate—at least qualitatively—the same depth-related response properties when used as input to a computational HS-cell model and to real neurons.     

Cycle-time and residence-time density approximations in a stochastic model for circulatory transport

The concentration of a drug in the circulatory system is studied under two different elimination strategies. The first strategy—geometric elimination—is the classical one which assumes a constant elimination rate per cycle. The second strategy—Poisson elimination—assumes that the elimination rate changes during the process of elimination. The problem studied here is to find a relationship between the residence-time distribution and the cycle-time distribution for a given rule of elimination. While the presented model gives this relationship in terms of Laplace-Stieltjes transform, the aim here is to determine the shapes of the corresponding probability density functions. From experimental data, we expect positively skewed, gamma-like distributions for the residence time of the drug in the body. Also, as some elimination parameter in the model approaches a limit, the exponential distribution often arises. Therefore, we use laguerre series expansions, which yield a parsimonious approximation of positively skewed probability densities that are close to a gamma distribution. The coefficients in the expansion are determined by the central moments, which can be obtained from experimental data or as a consequence of theoretical assumptions. The examples presented show that gamma-like densities arise for a diverse set of cycle-time distributions and under both elimination rules.     

Two Approaches to the Study of the Origin of Life

This paper compares two approaches that attempt to explain the origin of life, or biogenesis. The more established approach is one based on chemical principles, whereas a new, yet not widely known approach begins from a physical perspective. According to the first approach, life would have begun with—often organic—compounds. After having developed to a certain level of complexity and mutual dependence within a non-compartmentalised organic soup, they would have assembled into a functioning cell. In contrast, the second, physical type of approach has life developing within tiny compartments from the beginning. It emphasises the importance of redox reactions between inorganic elements and compounds found on two sides of a compartmental boundary. Without this boundary, “life” would not have begun, nor have been maintained; this boundary—and the complex cell membrane that evolved from it—forms the essence of life.     

Activity patterns of a troop of Japanese monkeys (Macaca fuscata yakui) on Yakushima Island,Japan

Activity patterns of Japanese monkeys (Macaca fuscata) were observed for 240 hr from August to December 1976 on the western slope of Mt. Kuniwari, Yakushima Island, Japan. Activity patterns and the time budget of a habituated wild troop which consisted of 47 animals in August 1976, were studied quantitatively by using the scan-sampling method at 15-min intervals. Six thousand seven hundred and six animals were recorded in 959 scans during the study period and the mean number of animals seen per scan was 7.0. The time budget established for different categories of activity was as follows: inactive—20.9%; moving—22.8%; feeding—23.5%; social grooming—27.9%; self-grooming—1.2%; and other activities—3.7%. Adult males spent less time in feeding and more time in resting or being inactive than females or juveniles. The daily activity patterns were highly variable with respect to time. Intraspecific variations were examined between troops in several regions of Japan and it was noted that the percentages of time devoted to feeding were similar in all areas. Inter-species variations in the activity budgets of several species of primates were also examined. The percentage of time spent in social grooming by Japanese monkeys is exceptionally high compared to that recorded in other species.     

Modelling run-and-tumble chemotaxis in a shear flow

The biased random walk undergone by chemotactic bacteria such as Escherichia coli will be influenced at the microscopic level by flow in the ambient medium. In this paper, we model swimming bacteria being advected and rotated by a simple shear flow. Under certain scaling assumptions, we obtain an advection—diffusion equation for cell density, when the chemotactic response is small, which shows a coupling between the rotation and chemotaxis. We also present an alternative method for calculating the chemotactic flux in an unbounded region which is valid for more general chemotactic responses.     

Key transitions during the evolution of animal phototransduction: novelty, "tree-thinking," co-option, and co-duplication

Biologists are amazed by the intricacy and complexity of biologicalinteractions between molecules, cells, organisms, and ecosystems.Yet underlying all this biodiversity is a universal common ancestry.How does evolution proceed from common starting points to generatethe riotous biodiversity we see today? This "novelty problem"—understandinghow novelty and common ancestry relate—has become of criticalimportance, especially since the realization that genes anddevelopmental processes are often conserved across vast phylogeneticdistances. In particular, two processes have emerged as theprimary generators of diversity in organismal form: duplicationplus divergence and co-option. In this article, we first illustratehow phylogenetic methodology and "tree-thinking" can be usedto distinguish duplication plus divergence from co-option. Second,we review two case studies in photoreceptor evolution—onesuggesting a role for duplication plus divergence, the otherexemplifying how co-option can shape evolutionary change. Finally,we discuss how our tree-thinking approach differs from othertreatments of the origin of novelty that utilized a "linear-thinking"approach in which evolution is viewed as a linear and gradualprogression, often from simple to complex phenotype, drivenby natural selection.     

Analysis of the exponential decay model of the neuron showing frequency threshold effects

The exponential decay model of a neuron has been analyzed using the “random walk” approach of stochastic processes and an “absorbing barrier” solution is obtained forg ^T (s)—the Laplace transform of the output pulse interval density function. An expression for the mean output frequency is derived from this and a variety of input-output curves plotted which show frequency threshold effects in single neurons. Our results are compared with those of other authors obtained by computer simulation techniques, and the significance of these results discussed with reference to the possible behavior of networks constructed of such neuron units.     

Effects of modeling and lineage on fishing behavior in the small-eared bushbaby (otolemur garnettii)

Thirty-eight bushbabies(Otolemur garnettii)were subjects in an observational learning study. We exposed them to one of three modeling conditions: (1) fishing model—one that actually performed fishing behavior; (2) nonfishing model—one that performed as a model in every way except performance of fishing behavior; and (3) no model. We assessed them with regard to latency to approach the fishbowl, latency to make an initial fishing attempt, duration of time spent in the vicinity of the fishbowls, and number of actual fishing attempts. Results indicate that subjects that were exposed to either fishing or nonfishing models were faster to approach the fishbowls and spent more time in the vicinity of the fishbowls than animals in the no-model condition Lineage, i.e., whether or not the animals’ parents fished, rather than modeling condition, was the best predictor of the latency to initial fishing attempt and the number of attempts made.     

Utilizing intraluminal pressure differences to predict esophageal bolus flow dynamics

Successful esophageal emptying depends on the generation of a sustained intrabolus pressure (IBP) sufficient to overcome esophagogastric junction (EGJ) obstruction. Our aim was to develop a manometric analysis paradigm that describes the bolus driving pressure difference and the flow permissive time for esophageal bolus transit. Twenty normal subjects were studied with a 36-channel manometry assembly (1-cm spacing) during two 5- and one 10-ml barium swallows and concurrent fluoroscopy. Bolus domain pressure plots were generated by plotting bolus domain pressure (BDP) and EGJ relaxation pressure. BDP was defined as the pressure midway between the peristaltic ramp-up and the proximal margin of the EGJ. The flow permissive time was defined as the period where the BDP was > or = EGJ relaxation pressure. The mean BDP was 11.7 +/- 1.0 mmHg (SE), and the mean flow permissive time was 3.9 +/- 0.4 s for 5-ml swallows in normal controls. The mean BDP difference during flow was 4.0 +/- 1.0 mmHg. There was no significant difference in the fluoroscopic transit time and the flow permissive time calculated from the BDP plots (5 ml: fluoroscopy 3.4 +/- 0.2 s; BDP 3.9 +/- 0.4 s, P > 0.05). BDP plots provide a reliable measurement of IBP and its relationship with EGJ relaxation. The time available for flow can be readily delineated from this analysis, and the driving pressure responsible for flow can be accurately described and quantified. This may help predict abnormal bolus transit and the underlying mechanical properties of the EGJ.     

The temporal dimension of marine speciation

Speciation is a process that occurs over time and, as such, can only be fully understood in an explicitly temporal context. Here we discuss three major consequences of speciation’s extended duration. First, the dynamism of environmental change indicates that nascent species may experience repeated changes in population size, genetic diversity, and geographic distribution during their evolution. The present characteristics of species therefore represents a static snapshot of a single time point in a species’ highly dynamic history, and impedes inferences about the strength of selection or the geography of speciation. Second, the process of speciation is open ended—ecological divergence may evolve in the space of a few generations while the fixation of genetic differences and traits that limit outcrossing may require thousands to millions of years to occur. As a result, speciation is only fully recognized long after it occurs, and short-lived species are difficult to discern. Third, the extinction of species or of clades provides a simple, under-appreciated, mechanism for the genetic, biogeographic, and behavioral ‘gaps’ between extant species. Extinction also leads to the systematic underestimation of the frequency of speciation and the overestimation of the duration of species formation. Hence, it is no surprise that a full understanding of speciation has been difficult to achieve. The modern synthesis—which united genetics, development, ecology, biogeography, and paleontology—greatly advanced the study of evolution. Here we argue that a similarly synthetic approach must be taken to further our understanding of the origin of species.     

GLOBIO3: A Framework to Investigate Options for Reducing Global Terrestrial Biodiversity Loss

The GLOBIO3 model has been developed to assess human-induced changes in biodiversity, in the past, present, and future at regional and global scales. The model is built on simple cause–effect relationships between environmental drivers and biodiversity impacts, based on state-of-the-art knowledge. The mean abundance of original species relative to their abundance in undisturbed ecosystems (MSA) is used as the indicator for biodiversity. Changes in drivers are derived from the IMAGE 2.4 model. Drivers considered are land-cover change, land-use intensity, fragmentation, climate change, atmospheric nitrogen deposition, and infrastructure development. GLOBIO3 addresses (i) the impacts of environmental drivers on MSA and their relative importance; (ii) expected trends under various future scenarios; and (iii) the likely effects of various policy response options. GLOBIO3 has been used successfully in several integrated regional and global assessments. Three different global-scale policy options have been evaluated on their potential to reduce MSA loss. These options are: climate-change mitigation through expanded use of bio-energy, an increase in plantation forestry, and an increase in protected areas. We conclude that MSA loss is likely to continue during the coming decades. Plantation forestry may help to reduce the rate of loss, whereas climate-change mitigation through the extensive use of bioenergy crops will, in fact, increase this rate of loss. The protection of 20% of all large ecosystems leads to a small reduction in the rate of loss, provided that protection is effective and that currently degraded protected areas are restored. Author Contributions  RA—Writing, study design, data analyses; MvO—Writing, research; LM— Writing, data analyses; CN—Contribution to method; MB—Research, data analyses; BtB—Contribution to method.     

Mathematical models of predator/prey/plant interactions in a patch environment

Several tritrophic systems are characterized by local over-exploitation of the food source. Interactions between predatory mites, spider mites and their host plants are an example of such systems: either the spider mites over-exploit local patches of host plants or the spider mites are exterminated by predatory mites. It is often stated that modelling the overall population dynamics of such systems in a realistic way would soon lead to an unmanageable edifice. We advocate, however, the use of physiologically structured population models as a both general and formal mathematical framework. The advantage is that analytically tractable models may be obtained from the complex ‘master’ model by time-scale arguments or special choices of model ingredients. In this way a network of models can be derived, each concentrating on a particular aspect, all inadequate to cover the entire spectrum, but together (we hope) providing a coherent set of insights the relative importance of which can be assessed by computer experiments on the ‘master’ model. In this paper a rather realistic model of predator/prey interactions in an ensemble of host-plant patches is presented and, as an example of our approach, some special cases are derived from that model. Their analysis provided some first, useful insights. It is shown that prolonged duration of the prey-dispersal phase and prey dispersal from predator (-invaded prey) patches may result in a stable steady state, whereas a humped plant-production function may — under certain conditions — result in two stable steady states.     

Evolutionary Robotic Approaches in Primate Gait Analysis

Understanding how primates move is particularly challenging because many of the experimentation techniques that would normally be available are unsuitable for ethical and conservation reasons. We therefore need to develop techniques that can maximize the data available from minimally intrusive experimentation. One approach for achieving this is to use evolutionary robotic techniques to build a musculoskeletal simulation and generate movement patterns that optimize some global parameter such as economy or performance, or to match existing kinematic data. If the simulation has a sufficiently high biofidelity and can match experimentally measured performance criteria then we can use it to predict aspects of locomotor mechanics that would otherwise be impossible to measure. This approach is particularly valuable when studying fossil primates because it can be based entirely on morphology and can generate movements spontaneously. A major question in human evolution is the origin of bipedal running and the role of elastic energy storage. By using an evolutionary robotics model of humanoid running we can show that elastic storage is required for efficient, high-performance running. Elasticity allows both energy recovery to minimize total energy cost and also power amplification to allow high performance. The most important elastic energy store on the human hind limb is the Achilles tendon: a feature that is at best weakly expressed among the African great apes. By running simulations both with and without this structure we can demonstrate its importance, and we suggest that identification of the presence or otherwise of this tendon—perhaps by calcaneal morphology or Sharpey’s fibers—is essential for identifying when and where in the fossil record human style running originated.