The Simulated Evolution of Biochemical Guilds: Reconciling Gaia Theory and Natural Selection

1999 ◽  
Vol 5 (4) ◽  
pp. 291-318 ◽  
Author(s):  
Keith Downing ◽  
Peter Zvirinsky
Keyword(s):  
Natural Selection ◽  
Artificial Life ◽  
Large Scale ◽  
Resource Competition ◽  
Nutrient Recycling ◽  
Nutrient Ratios ◽  
Evolutionary Mechanisms ◽  
Life Model ◽  
Gaia Theory ◽  
Implicit Coordination

Gaia theory, which states that organisms both affect and regulate their environment, poses an interesting problem to Neo-Darwinian evolutionary biologists and provides an exciting set of phenomena for artificial-life investigation. The key challenge is to explain the emergence of biotic communities that are capable, via their implicit coordination, of regulating large-scale biogeochemical factors such as the temperature and chemical composition of the biosphere, but to assume no evolutionary mechanisms beyond contemporary natural selection. Along with providing an introduction to Gaia theory, this article presents simulations of Gaian emergence based on an artificial-life model involving genetic algorithms and guilds of simple metabolizing agents. In these simulations, resource competition leads to guild diversity; the ensemble of guilds then manifests life-sustaining nutrient recycling and exerts distributed control over environmental nutrient ratios. These results illustrate that standard individual-based natural selection is sufficient to explain Gaian self-organization, and they help clarify the relationships between two key metrics of Gaian activity: recycling and regulation.

scholarly journals Changes in selection pressure can facilitate hybridization during biological invasion in a Cuban lizard

2021 ◽  
Vol 118 (42) ◽  
pp. e2108638118
Author(s):  
Dan G. Bock ◽  
Simon Baeckens ◽  
Jessica N. Pita-Aquino ◽  
Zachary A. Chejanovski ◽  
Sozos N. Michaelides ◽  
...  
Keyword(s):  
Natural Selection ◽  
Large Scale ◽  
Limb Length ◽  
Native Range ◽  
Evolutionary Mechanisms ◽  
Invasive Range ◽  
Temporal Sampling ◽  
Contemporary Gene Flow ◽  
Brown Anole ◽  
Show Evidence

Hybridization is among the evolutionary mechanisms most frequently hypothesized to drive the success of invasive species, in part because hybrids are common in invasive populations. One explanation for this pattern is that biological invasions coincide with a change in selection pressures that limit hybridization in the native range. To investigate this possibility, we studied the introduction of the brown anole (Anolis sagrei) in the southeastern United States. We find that native populations are highly genetically structured. In contrast, all invasive populations show evidence of hybridization among native-range lineages. Temporal sampling in the invasive range spanning 15 y showed that invasive genetic structure has stabilized, indicating that large-scale contemporary gene flow is limited among invasive populations and that hybrid ancestry is maintained. Additionally, our results are consistent with hybrid persistence in invasive populations resulting from changes in natural selection that occurred during invasion. Specifically, we identify a large-effect X chromosome locus associated with variation in limb length, a well-known adaptive trait in anoles, and show that this locus is often under selection in the native range, but rarely so in the invasive range. Moreover, we find that the effect size of alleles at this locus on limb length is much reduced in hybrids among divergent lineages, consistent with epistatic interactions. Thus, in the native range, epistasis manifested in hybrids can strengthen extrinsic postmating isolation. Together, our findings show how a change in natural selection can contribute to an increase in hybridization in invasive populations.

scholarly journals Genome size correlates with reproductive fitness in seed beetles

2015 ◽  
Vol 282 (1815) ◽  
pp. 20151421 ◽  
Author(s):  
Göran Arnqvist ◽  
Ahmed Sayadi ◽  
Elina Immonen ◽  
Cosima Hotzy ◽  
Daniel Rankin ◽  
...  
Keyword(s):  
Life History ◽  
Natural Selection ◽  
Genome Size ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Life History Traits ◽  
Single Species ◽  
Reproductive Fitness ◽  
Correlated Evolution ◽  
Seed Beetles

The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the ‘ C -value paradox’. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4–5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution.

scholarly journals Modelling the biogeochemical effects of heterotrophic and autotrophic N<sub>2</sub> fixation in the Gulf of Aqaba (Israel), Red Sea

2018 ◽  
Vol 15 (24) ◽  
pp. 7379-7401 ◽  
Author(s):  
Angela M. Kuhn ◽  
Katja Fennel ◽  
Ilana Berman-Frank
Keyword(s):  
Water Column ◽  
Red Sea ◽  
N2 Fixation ◽  
Large Scale ◽  
Gulf Of Aqaba ◽  
Nutrient Concentrations ◽  
Nutrient Ratios ◽  
Biogeochemical Models ◽  
Deep Waters ◽  
Direct Measurements

Abstract. Recent studies demonstrate that marine N2 fixation can be carried out without light by heterotrophic N2 fixers (diazotrophs). However, direct measurements of N2 fixation in aphotic environments are relatively scarce. Heterotrophic as well as unicellular and colonial photoautotrophic diazotrophs are present in the oligotrophic Gulf of Aqaba (northern Red Sea). This study evaluates the relative importance of these different diazotrophs by combining biogeochemical models with time series measurements at a 700 m deep monitoring station in the Gulf of Aqaba. At this location, an excess of nitrate, relative to phosphate, is present throughout most of the water column and especially in deep waters during stratified conditions. A relative excess of phosphate occurs only at the water surface during nutrient-starved conditions in summer. We show that a model without N2 fixation can replicate the observed surface chlorophyll but fails to accurately simulate inorganic nutrient concentrations throughout the water column. Models with N2 fixation improve simulated deep nitrate by enriching sinking organic matter in nitrogen, suggesting that N2 fixation is necessary to explain the observations. The observed vertical structure of nutrient ratios and oxygen is reproduced best with a model that includes heterotrophic as well as colonial and unicellular autotrophic diazotrophs. These results suggest that heterotrophic N2 fixation contributes to the observed excess nitrogen in deep water at this location. If heterotrophic diazotrophs are generally present in oligotrophic ocean regions, their consideration would increase current estimates of global N2 fixation and may require explicit representation in large-scale models.

scholarly journals What is a good pattern of life model? Guidance for simulations

SIMULATION ◽  
2018 ◽  
Vol 95 (8) ◽  
pp. 693-706
Author(s):  
Barry G Silverman ◽  
Gnana Bharathy ◽  
Nathan Weyer
Keyword(s):  
Large Scale ◽  
First Generation ◽  
Hybrid Approach ◽  
Daily Activities ◽  
Human Behaviors ◽  
The World ◽  
Life Model ◽  
Good Pattern ◽  
Definition Of

We have been modeling an ever-increasing scale of applications with agents that simulate the pattern of life (PoL) and real-world human behaviors in diverse regions of the world. The goal is to support sociocultural training and analysis. To measure progress, we propose the definition of a measure of goodness for such simulated agents, and review the issues and challenges associated with first-generation (1G) agents. Then we present a second generation (2G) agent hybrid approach that seeks to improve realism in terms of emergent daily activities, social awareness, and micro-decision making in simulations. We offer a PoL case study with a mix of 1G and 2G approaches that was able to replace the pucksters and avatar operators needed in large-scale immersion exercises. We conclude by observing that a 1G PoL simulation might still be best where large-scale, pre-scripted training scenarios will suffice, while the 2G approach will be important for analysis or if it is vital to learn about adaptive opponents or unexpected or emergent effects of actions. Lessons are shared about ways to blend 1G and 2G approaches to get the best of each.

Run4Life project: A step forward in NPK recovery from source-separated wastewaters.

2020 ◽  
Author(s):  
Gemma Torres Sallan ◽  
Eduard Borras ◽  
Martí Aliaguilla ◽  
Daniele Molognoni ◽  
Sonia Sanchis ◽  
...  
Keyword(s):  
Ammonium Nitrate ◽  
Large Scale ◽  
Business Models ◽  
Nutrient Recycling ◽  
Sewage Treatment ◽  
Domestic Wastewater ◽  
Organic Fertilizers ◽  
Nutrient Recovery ◽  
Npk Fertilizers ◽  
Recovery Rates

&lt;p&gt;Domestic wastewater (WW) is an important carrier of nutrients usually wasted away by current centralised sewage treatment plants. The Run4Life project proposes an alternative strategy for increasing circularity of WW treatment systems and improving nutrient recovery rates and material qualities. This is based on a decentralised treatment of segregated black water (BW), kitchen waste and grey water combining existing and innovative technologies.&lt;/p&gt;&lt;p&gt;Run4Life is currently improving innovative nutrient recovery technologies, these being: (i) an ultra-low flush vacuum toilet, which uses around 0.5L/flush, thus less water than conventional vacuum toilets, allowing concentration of BW compared to conventional toilets and vacuum toilets. (ii) Bio-electrochemical systems for nitrogen recovery, which recovers up to 12.8 g/m&lt;sup&gt;2&lt;/sup&gt;*d of Nitrogen present in blackwater as liquid fertilizer (ammonium nitrate) iii) (Hyper-)thermophilic anaerobic digestion, which aims to recover the phosphorous and nitrogen in the hygienised effluent in a one-step treatment and ready for use as fertilisers. &amp;#160;&lt;/p&gt;&lt;p&gt;Nutrient recycling technologies from domestic WW are demonstrated at large scale in four demonstration sites where decentralised WW treatment systems are implemented: Ghent (Belgium, 430 houses), Helsingborg (Sweden, 320 apartments), Sneek (The Netherlands, 32 houses), and Vigo (Spain, 1 office building). This will result in solid and liquid NPK fertilizers being recovered in the form of struvite, ammonium nitrate, calcium phosphate, organic fertilizers and reclaimed water.&lt;/p&gt;&lt;p&gt;The environmental, economic and societal impact of the obtained fertilizers is being tested by means of ecotoxicology tests, pot experiments, field trials, and by a selection of key performance indicators based on European, national and regional legislation present in the four different countries. Life cycle assessments are being performed for each technology and demonstration site, and active measures such as knowledge brokerage activities are being developed as an engagement strategy to advocate the institutional, legal and social acceptance of the Run4Life nutrient recovery technologies and fertilizers produced.&amp;#160; In addition, new business models which can benefit from the Run4Life project are currently being assessed.&lt;/p&gt;&lt;p&gt;It is expected that, by the end of the project, more than 90% of the water will be reused, and that nutrient recovery rates will achieve 100%.&lt;/p&gt;

Natural selection for costly nutrient recycling in simulated microbial metacommunities

2012 ◽  
Vol 312 ◽  
pp. 1-12 ◽  
Author(s):  
Richard A. Boyle ◽  
Hywel T.P. Williams ◽  
Timothy M. Lenton
Keyword(s):  
Natural Selection ◽  
Nutrient Recycling ◽  
Selection For

The ulam Programming Language for Artificial Life

2016 ◽  
Vol 22 (4) ◽  
pp. 431-450 ◽  
Author(s):  
David H. Ackley ◽  
Elena S. Ackley
Keyword(s):  
Software Engineering ◽  
Computational Model ◽  
Programming Language ◽  
Artificial Life ◽  
Large Scale ◽  
Living Systems ◽  
Traditional Architecture ◽  
Surface Appearance ◽  
Best Effort ◽  
Large Scale Systems

Traditional digital computing demands perfectly reliable memory and processing, so programs can build structures once then use them forever—but such deterministic execution is becoming ever more costly in large-scale systems. By contrast, living systems, viewed as computations, naturally tolerate fallible hardware by repairing and rebuilding structures even while in use—and suggest ways to compute using massive amounts of unreliable, merely best-effort hardware. However, we currently know little about programming without deterministic execution, in architectures where traditional models of computation—and deterministic ALife models such as the Game of Life—need not apply. This expanded article presents ulam, a language designed to balance concurrency and programmability upon best-effort hardware, using lifelike strategies to achieve robust and scalable computations. The article reviews challenges for traditional architecture, introduces the active-media computational model for which ulam is designed, and then presents the language itself, touching on its nomenclature and surface appearance as well as some broader aspects of robust software engineering. Several ulam examples are presented; then the article concludes with a brief consideration of the couplings between a computational model and its physical implementation.

scholarly journals A Simple Model of Unbounded Evolutionary Versatility as a Largest-Scale Trend in Organismal Evolution

2000 ◽  
Vol 6 (2) ◽  
pp. 109-128 ◽  
Author(s):  
Peter D. Turney
Keyword(s):  
Natural Selection ◽  
Simple Model ◽  
Computational Model ◽  
Local Adaptation ◽  
Large Scale ◽  
Changing Environment ◽  
Local Environments ◽  
Global Trend ◽  
Evolutionary Pace ◽  
Biological Organisms

The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but empirical and theoretical arguments undermine this belief. Natural selection results in organisms that are well adapted to their local environments, but it is not clear how local adaptation can produce a global trend. In this paper, I present a simple computational model, in which local adaptation to a randomly changing environment results in a global trend towards increasing evolutionary versatility. In this model, for evolutionary versatility to increase without bound, the environment must be highly dynamic. The model also shows that unbounded evolutionary versatility implies an accelerating evolutionary pace. I believe that unbounded increase in evolutionary versatility is a large-scale trend in evolution. I discuss some of the testable predictions about organismal evolution that are suggested by the model.

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