On the Evolvability of a Hybrid Ant Colony-Cartesian Genetic Programming Methodology

In this thesis, we design a method that uses Ant Colonies as a Model-based Search to Cartesian Genetic Programming (CGP) to induce computer programs. Candidate problem solutions are encoded using a CGP representation. Ants generate problem solutions guided by pheromone traces of entities and nodes of the CGP representation. The pheromone values are updated based on the paths followed by the best ants, as suggested in the Rank-Based Ant System (ASrank). To assess the evolvability of the system we applied a modified version of the method introduced in [1] to measure rate of evolution which considers variability and neutrality as the major influences in the evolution of a system. Our results show that such method effectively reveals how evolution proceeds under different parameter settings and different environmental scenarios. The proposed hybrid architecture shows high evolvability in a dynamic environment by maintaining a pheromone model that elicits high genotype diversity.

On the Evolvability of a Hybrid Ant Colony-Cartesian Genetic Programming Methodology

In this thesis, we design a method that uses Ant Colonies as a Model-based Search to Cartesian Genetic Programming (CGP) to induce computer programs. Candidate problem solutions are encoded using a CGP representation. Ants generate problem solutions guided by pheromone traces of entities and nodes of the CGP representation. The pheromone values are updated based on the paths followed by the best ants, as suggested in the Rank-Based Ant System (ASrank). To assess the evolvability of the system we applied a modified version of the method introduced in [1] to measure rate of evolution which considers variability and neutrality as the major influences in the evolution of a system. Our results show that such method effectively reveals how evolution proceeds under different parameter settings and different environmental scenarios. The proposed hybrid architecture shows high evolvability in a dynamic environment by maintaining a pheromone model that elicits high genotype diversity.

The current distribution of recently-recruited genes among chromosomes appears increasingly non-random along the evolutionary series from the tetrapoda to the primata

Background: The present availability of full genome sequences of a broad range of animal species across the whole range of evolutionary history enables one to ask questions as to the distribution of genes across the chromosomes. Do newly recruited genes, clade by clade, distribute at random or at non-random locations? Results: We extracted values for the “consensus” ages of the human genes and for their current chromosome locations, from published sources. A quantitative analysis showed that the distribution of newly-added genes among and within the chromosomes appears to be increasingly non-random if one observes animals along the evolutionary series from the tetrapoda through to the great apes, whereas the oldest genes are randomly distributed.Conclusions: Randomization will result from chromosome evolution, but less and less time is available for this process as evolution proceeds. Much of the bunching of recently-added genes arises from new gene formation in gene families, near the location of genes that were recruited in the preceding phylostratum. As examples we cite the KRTAP, ZNF, OR and some minor gene families. We show that bunching can also result from the evolution of the chromosomes themselves when, as for the KRTAP genes, blocks of genes that had previously been on disparate chromosomes become linked together.

Funneled energy landscape unifies principles of protein binding and evolution

Most proteins have evolved to spontaneously fold into native structure and specifically bind with their partners for the purpose of fulfilling biological functions. According to Darwin, protein sequences evolve through random mutations, and only the fittest survives. The understanding of how the evolutionary selection sculpts the interaction patterns for both biomolecular folding and binding is still challenging. In this study, we incorporated the constraint of functional binding into the selection fitness based on the principle of minimal frustration for the underlying biomolecular interactions. Thermodynamic stability and kinetic accessibility were derived and quantified from a global funneled energy landscape that satisfies the requirements of both the folding into the stable structure and binding with the specific partner. The evolution proceeds via a bowl-like evolution energy landscape in the sequence space with a closed-ring attractor at the bottom. The sequence space is increasingly reduced until this ring attractor is reached. The molecular-interaction patterns responsible for folding and binding are identified from the evolved sequences, respectively. The residual positions participating in the interactions responsible for folding are highly conserved and maintain the hydrophobic core under additional evolutionary constraints of functional binding. The positions responsible for binding constitute a distributed network via coupling conservations that determine the specificity of binding with the partner. This work unifies the principles of protein binding and evolution under minimal frustration and sheds light on the evolutionary design of proteins for functions.

Instability of supersonic cold streams feeding galaxies – IV. Survival of radiatively cooling streams

ABSTRACT We study the effects of Kelvin–Helmholtz Instability (KHI) on the cold streams that feed massive haloes at high redshift, generalizing our earlier results to include the effects of radiative cooling and heating from a UV background, using analytic models and high resolution idealized simulations. We currently do not consider self-shielding, thermal conduction, or gravity. A key parameter in determining the fate of the streams is the ratio of the cooling time in the turbulent mixing layer which forms between the stream and the background following the onset of the instability, $t_{\rm cool,\, mix}$, to the time in which the mixing layer expands to the width of the stream in the non-radiative case, tshear. This can be converted into a critical stream radius, Rs, crit, such that $R_{\rm s}/R_{\rm s,crit}=t_{\rm shear}/t_{\rm cool,\, mix}$. If Rs < Rs, crit, the non-linear evolution proceeds similarly to the non-radiative case studied by Mandelker et al. If Rs > Rs,crit, which we find to almost always be the case for astrophysical cold streams, the stream is not disrupted by KHI. Rather, background mass cools and condenses on to the stream, and can increase the mass of cold gas by a factor of ∼3 within 10 stream sound crossing times. The mass entrainment induces thermal energy losses from the background and kinetic energy losses from the stream, which we model analytically. Roughly half of the dissipated energy is radiated away from gas with $T \lt 5\times 10^4\, {\rm K}$, suggesting much of it will be emitted in Ly α.

The propagation of choked jet outflows in power-law external media

ABSTRACT Observations of both gamma-ray bursts (GRBs) and active galactic nuclei (AGNs) point to the idea that some relativistic jets are suffocated by their environment before we observe them. In these ‘choked’ jets, all the jet’s kinetic energy is transferred into a hot and narrow cocoon of near-uniform pressure. We consider the evolution of an elongated, axisymmetric cocoon formed by a choked jet as it expands into a cold power-law ambient medium ρ ∝ R−α, in the case where the shock is decelerating (α < 3). The evolution proceeds in three stages, with two breaks in behaviour: the first occurs once the outflow has doubled its initial width, and the second once it has doubled its initial height. Using the Kompaneets approximation, we derive analytical formulae for the shape of the cocoon shock, and obtain approximate expressions for the height and width of the outflow versus time in each of the three dynamical regimes. The asymptotic behaviour is different for shallow ($\alpha \leq 2$) and steep (2 < α < 3) density profiles. Comparing the analytical model to numerical simulations, we find agreement to within ∼15 per cent out to 45 deg from the axis, but discrepancies of a factor of 2–3 near the equator. The shape of the cocoon shock can be measured directly in AGNs, and is also expected to affect the early light from failed GRB jets. Observational constraints on the shock geometry provide a useful diagnostic of the jet properties, even long after jet activity ceases.

Perspectives from Montiaceae (Portulacineae) Evolution. II. Ecological Evolution, Phylogenetic Comparative Analysis, and the Principle of Evolutionary Idiosyncraticity

The present paper reviews evidence for ecological evolution of Montiaceae. Montiaceae (Portulacineae) comprise a family of ca. 275 species and ca. 25 subspecific taxa of flowering plants distributed mainly in extreme western America, with additional endemism elsewhere, including other continents and islands. They have diversified repeatedly across steep ecological gradients. Based on narrative analysis, I argue that phylogenetic transitions from annual to perennial life history have been more frequent than suggested by computational phylogenetic reconstructions. I suggest that a reported phylogenetic correlation between the evolution of life history and temperature niche is coincidental and not causal. I demonstrate how statistical phylogenetic comparative analysis (PhCA) missed evidence for marked moisture niche diversification among Montiaceae. I discount PhCA evidence for the relation between Montiaceae genome duplication and ecological diversification. Based on the present analysis of Montiaceae evolution, I criticize the premise of the prevalent statistical approach to PhCA, which tests Darwinian deterministic hypotheses against stochastic evolutionary null models. I discuss theoretical/empirical evidence that evolution is neither stochastic, nor Darwinistically-determined, but idiosyncratic. Idiosyncraticity describes the outcome of a stochastically perturbed nonlinear chaos-like process. The Principle of Evolutionary Idiosyncraticity (PEI) is based on the evolutionary theory of Natural Drift, which maintains that determinism in evolution is a property of the organism and not, as maintained by the theory of Natural Selection, its traits or its milieu. This determinism is characteristic of chaotic functions, which are absolutely determinate, generate self-similarity, but remain absolutely unpredictable. PEI explains precisely observations that evolution proceeds not linearly, but chaotically, producing both quasi-linear fractal-like patterns and non-linear jumps. PEI has ramifications for all areas of macroevolutionary research. In particular, it demonstrates both the fallacy and futility of the statistical PhCA approach that interprets evolutionary causes in terms of evolutionary correlations. However, statistical methods of PhCA can be applied heuristically and fruitfully to reveal idiosyncraticity and discover evolutionary novelty. This, in turn, is demonstrated by the emergence of statistical anomalies in evolutionary analyses of Montiaceae.

Enzymatic evolution driven by entropy production

We show that the structural evolution of enzymes is largely influenced by the entropy produced in the enzymatic process. We have computed this quantity for the case in which the process has unstable and metastable intermediate states. By assuming that the kinetics takes place along a potential barrier, we have found that the behavior of the total entropy produced is a non-monotonic function of the intermediate state energy. By diminishing the number of metastable intermediate states, the total entropy produced decreases and consequently the enzyme kinetics and the thermodynamic efficiency are enhanced. Minimizing locally the total entropy produced for an enzymatic process with metastable intermediate states, the kinetics and the thermodynamic efficiency are raised. In contrast, in the absence of metastable intermediate states, a maximum of the entropy produced results in an improvement of the kinetic performance although the thermodynamic efficiency diminishes. Our results show that the enzymatic evolution proceeds not only to enhance the kinetics but also to optimize the total entropy produced.

Pulsed evolution shaped modern vertebrate body sizes

The relative importance of different modes of evolution in shaping phenotypic diversity remains a hotly debated question. Fossil data suggest that stasis may be a common mode of evolution, while modern data suggest some lineages experience very fast rates of evolution. One way to reconcile these observations is to imagine that evolution proceeds in pulses, rather than in increments, on geological timescales. To test this hypothesis, we developed a maximum-likelihood framework for fitting Lévy processes to comparative morphological data. This class of stochastic processes includes both an incremental and a pulsed component. We found that a plurality of modern vertebrate clades examined are best fitted by pulsed processes over models of incremental change, stationarity, and adaptive radiation. When we compare our results to theoretical expectations of the rate and speed of regime shifts for models that detail fitness landscape dynamics, we find that our quantitative results are broadly compatible with both microevolutionary models and observations from the fossil record.

The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals

Inter-specific body mass allometries can evolve from the natural selection of mass, with ±1/4 and ±3/4 exponents following from the geometry of intra-specific interactions when density dependent foraging occurs in two spatial dimensions (2D, Witting, 1995). The corresponding values for three dimensional interactions (3D) are ±1/6 and ±5/6.But the allometric exponents in mobile organisms are more diverse than the prediction. The exponent for mass specific metabolism tends to cluster around −1/4 and −1/6 in terrestrial and pelagic vertebrates, but it is strongly positive in prokaryotes with an apparent value around 5/6 (DeLong et al., 2010). And a value around zero has been reported in protozoa, and on the macro evolutionary scale from prokaryotes over larger unicells to multicellular vertebrates (Makarieva et al., 2005, 2008).I show that mass specific metabolism can be selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, and that this selection of metabolism and mass is sufficient to explain metabolic exponents that decline from 5/6 over zero to −1/6 in 3D, and from 3/4 over zero to −1/4 in 2D. The decline follows from a decline in the importance of mass specific metabolism for the selection of mass, and it suggestsi) that the body mass variation in prokaryotes is selected from primary variation in mass specific metabolism,ii) that the variation in multicellular animals are selected from primary variation in the handling and/or densities of the underlying resources,iii) that protozoa are selected as an intermediate lifeform between prokaryotes and multicellular animals, andiv) that macro evolution proceeds along an upper bound on mass specific metabolism.