Conceptualizing the origin of life in terms of evolution.

In this opinion piece, we discuss how to place evolution in the context of origin-of-life research. Our discussion starts with a popular definition: 'life is a self-sustained chemical system capable of undergoing Darwinian evolution'. According to this definition, the origin of life is the same as the origin of evolution: evolution is the 'end' of the origin of life. This perspective, however, has a limitation, in that the ability of evolution in and of itself is insufficient to explain the origin of life as we know it, as indicated by Spiegelman's and Lincoln and Joyce's experiments. This limitation provokes a crucial question: What conditions are required for replicating systems to evolve into life? From this perspective, the origin of life includes the emergence of life through evolution: evolution is a 'means' of the origin of life. After reviewing Eigen's pioneering work on this question, we mention our ongoing work suggesting that a key condition might be conflicting multi-level evolution. Taken together, there are thus two questions regarding the origin of life: how evolution gets started, and how evolution produces life. Evolution is, therefore, at the centre of the origin of life, where the two lines of enquiry must meet.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Large changes in regulome size herald the main prokaryotic lineages.

Using a large-scale reconstruction of ancestral gene content, we show that radical changes in regulome size occur at the origins of major prokaryotic lineages. Subsequently, the duplication and deletion of regulators slows down in most lineages, except proteobacteria, significantly reducing the scaling of regulators and keeping their average proportion lineage-specific. Our results also suggest that major transitions in prokaryote evolution are related to changes in regulatory capacity rather than proteome innovations.

Pattern analysis of RNA secondary structure similarity and consensus of minimal-energy folding.

We describe an automated procedure to search for consensus structures or substructures in a set of homologous or related RNA molecules. The procedure is based on the calculation of optimal and sub-optimal secondary structures using thermodynamic rules for base-pairing by energy-minimization. A linear representation of the secondary structures of the related RNAs is used so that they can be compared and classified using standard alignment and clusterings programs. We illustrate the method by means of two sets of homologous small RNAs, U2 and U3, and a set of alpha-globin mRNAs and show that biologically interesting consensus structures are obtained.

Spatially induced speciation prevents extinction: the evolution of dispersal distance in oscillatory predator-prey models.

In a discrete-generation, individual-oriented model of predator-prey interactions that exhibits oscillations, we show that the self-structuring of the populations into spiral waves induces a selection pressure for ever-increasing dispersal distances in both populations. As the dispersal distances increase, the sizes of the spatial patterns increase, until they are too large to fit into the limited space. The patterns are then lost and the predators go extinct. This scenario, is, however, not the only outcome. A second selection pressure induced by the spatial boundary can cause reduction of the dispersal distances. Depending on the relative strengths of the two selection pressures, the predators and prey may speciate to give coexistence between short-dispersing boundary quasi-species and far-dispersing spiral quasi-species. Now, when pattern loss occurs, the predators switch to predating on the boundary prey quasi-species and do not go extinct. Also, if the populations reproduce sexually, local gene flow can inhibit the evolution of increasing dispersal distances, and hence the spatial patterns are not lost. Speciation and coexistence can also occur in the sexually reproducing species.

Local T-T cell and T-B cell interactions: a cellular automaton approach.

In this paper we use cellular automata to study growth factor (IL-2) dependent proliferation of helper T cell (Th) and B cell clones at the level of individual cells. We argue that such a spatially- and individual-oriented approach can provide important insights, not obtainable by more conventional modelling approaches in which the immune system is modelled as a well mixed collection of clones. Two questions are examined: (1) under which conditions can a cell which produces its own growth factor (i.e. Th cells) be regulated by it; and (2) if a growth factor is effective only locally, and if both Th and B cells depend on growth factors excreted by Th cells, how can the spatial segregation of T cells and B cells in lymphoid organs and/or at acute infection sites be explained? The results show that, firstly, autocrine regulation can indeed occur in two ways: it can ensure (a) that the cell reacts only on its growth factor when packed inside tissue of arbitrary cells or (b), that the cell reacts only when close to other growth factor producing cells; and secondly, segregation of T cells and B cells results automatically from simple assumptions about the interaction and proliferation of the cells, notwithstanding the fact that proliferation is slowed down by this segregation.

Migration and thermotaxis of dictyostelium discoideum slugs, a model study

Dictyostelium discoideum slugs show a pronounced thermotaxis. We have modelled the motion of the D. discoideum slug in the absence and in the presence of a thermal gradient. Our model is an extension of the hybrid cellular automata/partial differential equation model, as formulated by Savill and Hogeweg [J. theor. Biol., (1997) 184, 229-235]. The modelled slugs maintain their shape and crawl, with a velocity depending on slug size, as found in experiments. Moreover, they show thermotactic behaviour: independent of the initial orientation, after some transient process, the slugs start moving along the temperature gradient. The slug behaviour in our model is due to the collective behaviour of the amoebae. Individual amoebae can neither respond to a shallow temperature gradient, nor show differentiation in motion velocity. The behaviour is achieved by a modification of the cyclic AMP waves: differences in temperature alter the excitability of the cell, and thereby the shape of the cyclic AMP wave. Chemotaxis towards cyclic AMP causes the slug to turn. We show that the mechanism still functions at very low signal-to-noise ratios. Copyright 1999 Academic Press.

Structural analysis of a group II intron by chemical modifications and minimal energy calculations.

Folding of the yeast mitochondrial group II intron aI5c has been analysed by chemical modification of the in vitro synthesised RNA with dimethylsulfate and diethylpyrocarbonate. Computer calculations of the intron secondary structure through minimization of free energy were also performed in order to study thermodynamic properties of the intron and to relate these to data obtained from chemical modification. Comparison of the two sets of data with the current phylogenetic model structure of the intron aI5 reveals close agreement, thus lending strong support for the existence of a typical group II intron core structure comprising six neighbouring stem-loop domains. Local discrepancies between the experimental data and the model structures have been analyzed by reference to thermodynamic properties of the structure. This shows that use of the latest refined set of free energy values improves the structure calculation significantly.

Simplicity and complexity in MIRROR universes.

The scientific simplicity principle (OCCAM's razor) has always been strongly enforced by the available modelling tools. Moreover, the concept of simplicity itself is shaped by these (classical) tools. Computer models are less subject to simplicity constraints than other models are. It may be argued that complexity is the preeminent property for biological systems to study. In this paper we discuss our MIRROR modelling methodology in which (a concept of) simplicity is reconciled with biological complexity. Simplicity resides in the simple "TODO" ("do what there is to do") of the "individuals" (molecules, cells, organisms) which inhabit the model universe. The complexity appears in the multiple (levels of) individuals and the multiple levels of observable behavior of the universe. Examples are given of the development of complex, self-regulating social structures by simple interactions of individuals, and the adaptability of TODO based entities is compared to that of evolving entities. On the basis of these examples we sketch a slightly unconventional image of the evolution of complexity in biotic systems and discuss observations on the molecular record of biotic evolution which seem to fit this image.

Interactive instruction on population interactions.

PIP: A tool for teaching and investigating population simulation models, entitled TRICLE (Program for tridimensional representation of trajectories and isoclines) is presented. It can handle deterministic models in terms of differential and difference equations and stochastic models in terms of difference equations. TRICLE works with up to 10 coupled equations, illustrates the structure of the interactions, and incorporates default parameter values and a representation to show dissimilarity of the parameters. Population models are used to demonstrate use of the system; they are not the only use of the TRICLE system. This system provides a graphic presentation of models as static and dynamic states. It relies on the complex pattern recognition of human beings to sense errors in the model of the data.^ieng

Evolutionary consequences of coevolving targets

Most evolutionary optimization models incorporate a fitness evaluation that is based on a predefined static set of test cases or problems. In the natural evolutionary process, selection is of course not based on a static fitness evaluation. Organisms do not have to combat every existing disease during their lifespan; organisms of one species may live in different or changing environments; different species coevolve. This leads to the question of how information is integrated over many generations. This study focuses on the effects of different fitness evaluation schemes on the types of genotypes and phenotypes that evolve. The evolutionary target is a simple numerical function. The genetic representation is in the form of a program (i.e., a functional representation, as in genetic programming). Many different programs can code for the same numerical function. In other words, there is a many-to-one mapping between "genotypes" (the programs) and "phenotypes". We compare fitness evaluation based on a large static set of problems and fitness evaluation based on small coevolving sets of problems. In the latter model very little information is presented to the evolving programs regarding the evolutionary target per evolutionary time step. In other words, the fitness evaluation is very sparse. Nevertheless the model produces correct solutions to the complete evolutionary target in about half of the simulations. The complete evaluation model, on the other hand, does not find correct solutions to the target in any of the simulations. More important, we find that sparse evaluated programs are better generalizable compared to the complete evaluated programs when they are evaluated on a much denser set of problems. In addition, the two evaluation schemes lead to programs that differ with respect to mutational stability; sparse evaluated programs are less stable than complete evaluated programs.

In silico evolved lac operons exhibit bistability for artificial inducers, but not for lactose.

Bistability in the lac operon of Escherichia coli has been widely studied, both experimentally and theoretically. Experimentally, bistability has been observed when E. coli is induced by an artificial, nonmetabolizable, inducer. However, if the lac operon is induced with lactose, the natural inducer, bistability has not been demonstrated. We derive an analytical expression that can predict the occurrence of bistability both for artificial inducers and lactose. We find very different conditions for bistability in the two cases. Indeed, for artificial inducers bistability is predicted, but for lactose the condition for bistability is much more difficult to satisfy. Moreover, we demonstrate that in silico evolution of the lac operon generates an operon that avoids bistability with respect to lactose, but does exhibit bistability with respect to artificial inducers. The activity of this evolved operon strikingly resembles the experimentally observed activity of the operon. Thus our computational experiments suggest that the wild-type lac operon, which regulates lactose metabolism, is not a bistable switch. Nevertheless, for engineering purposes, this operon can be used as a bistable switch with artificial inducers.

Shapes in the shadow: evolutionary dynamics of morphogenesis.

This article investigates the evolutionary dynamics of morphogenesis. In this study, morphogenesis arises as a side-effect of maximization of number of cell types. Thus, it investigates the evolutionary dynamics of side-effects. Morphogenesis is governed by the interplay between differential cell adhesion, gene-regulation, and intercellular signaling. Thus, it investigates the potential to generate complex behavior by entanglement of relatively "boring" processes, and the (automatic) coordination between these processes. The evolutionary dynamics shows all the hallmarks of evolutionary dynamics governed by nonlinear genotype phenotype mapping: for example, punctuated equilibria and diffusion on neutral paths. More striking is the result that interesting, complex morphogenesis occurs mainly in the "shadow" of neutral paths which preserve cell differentiation, that is, the interesting morphologies arise as mutants of the fittest individuals. Characteristics of the evolution of such side-effects in the shadow appear to be the following: (1) The specific complex morphologies are unique (or at least very rare) among the set of de novo initiated evolutionary histories. (2) Similar morphologies are reinvented at large temporal distances during one evolutionary history and also when evolution is restarted after the main cell differentiation pattern has been established. (3) A mosaic-like evolution at the morphological level, where different morphological features occur in many combinations, while at the genotypic level recombination is not implemented and genotypes diverge linearly and at a constant rate.

Evolving mechanisms of morphogenesis: on the interplay between differential adhesion and cell differentiation.

Differential cell adhesion, mediated by e.g. integrin and cadherins/catenines, plays an important role in morphogenesis and it has been shown that there is intimate cross-talk between their expression and modification, and inter-cellular signalling, cell differentiation, cell growth and apoptosis. In this paper, we introduce and use a formal model to explore the morphogenetic potential of the interplay between these processes. We demonstrate the formation of interesting morphologies. Initiated by cell differentiation, differential cell adhesion leads to a long transient of cell migrations, e.g. engulfing and intercalation of cells and cell layers. This transient can be sustained dynamically by further cell differentiation, and by cell growth/division and cell death which are triggered by the (also long range) forces (stretching and squeezing) generated by the cell adhesion. We study the interrelation between modes of cell differentiation and modes of morphogenesis. We use an evolutionary process to zoom in on gene-regulation networks which lead to cell differentiation. Morphogenesis is not selected for but appears as a side-effect. The evolutionary dynamics shows the hallmarks of evolution on a rugged landscape, including long neutral paths. We show that a combinatorially large set of morphologies occurs in the vicinity of a neutral path which sustains cell differentiation. Thus, an almost linear molecular phylogeny gives rise to mosaic evolution on the morphological level.

Individual- and population-based diversity in restriction-modification systems.

Restriction-modification (RM) systems are cognate gene complexes that code for an endonuclease and a methylase. They are often thought to have developed in bacteria as protection against invading genetic material, e.g., phage DNA. The high diversity of RM systems, as observed in nature, is often ascribed to the coevolution of RM systems (which 'invent' novel types) and phages. However, the extent to which phages are insensitive to RM systems casts doubts on the effectiveness of RM systems as protection against infection and thereby on the reason for the diversity of RM systems. We present an eco-evolutionary model in order to study the evolution of the diversity of RM systems. The model predicts that in general diversity of RM systems is high. More importantly, the diversity of the RM systems is expressed either at the individual level or at the population level. In the first case all individuals carry RM systems of all sequence specificities, whereas in the second case they carry only one RM system or no RM systems at all. Nevertheless, in the second case the same number of sequence specificities are present in the population.

Energy directed folding of RNA sequences.

A modification of Nussinov's algorithm (1) for (planar) secondary structure generation is described. Our algorithm postpones decisions on matches involving destabiling loops until they prove to be energetically more favourable than more local matches. We present, moreover, an alternative way of representing secondary structures which avoids unwarranted suggestions on higher order neighbourhood, can be automated easily, allows for any amount of annotation of the sequences, makes comparison of alternate foldings easy and is pleasing to the eye. 5S RNA sequences are used to illustrate the methods.

Colicin diversity: a result of eco-evolutionary dynamics.

Colicins are plasmids that are carried in Escherichia coli. They code for a toxic protein and for proteins that confer on the host immunity against this toxin. When bacteria carry plasmids their growth rate is reduced. At the same time, the production of toxins makes it possible for colicinogenic bacteria to invade bacterium strains that are not immune. In natural bacterium populations there is a high diversity of colicin types. The reason for the maintenance of this diversity has been the subject of much recent debate. We have studied a simple eco-evolutionary model of the interaction of bacteria with colicins and show that high diversity of colicins is to be expected. We find two different dynamical modes each with a high diversity: a hyperimmunity mode and a multitoxicity mode. Bacteria are immune to most toxins in the first mode but in fact produce very few toxins. In the second mode bacteria are immune only to those toxins that they actually produce. In the second mode toxin levels per bacterium are much higher, whereas immunity levels per bacterium are lower.

Evolution of the immune repertoire with and without somatic DNA recombination.

Repertoire of an immune system is a set of antigen receptors each having a unique specificity to bind an antigen. In many vertebrate species, antigen receptors are produced via combinatorial arrangements of DNA segments in specialized immune cells. Due to this molecular mechanism, repertoire of vertebrate species is potentially very large. The diversity of repertoire is thought to guarantee recognition of most ill-causing micro-organisms. In vertebrate species however, similar editing of DNA segments has not been demonstrated to take place. Immune system of invertebrate species therefore seems to operate in a distinct manner from that of vertebrate species. Using an evolutionary model in which organisms struggle to fight infections, we attempt to understand why some species use a more diverse set of antigen receptors than others. Individuals in our model either use somatic DNA recombination to produce antigen receptors (as in vertebrates) or do not use such a mechanism (as in vertebrates). We found that individuals having an invertebrate-like immune system came to employ only a few antigen receptors to recognize a set of pathogens whereas those with a vertebrate-like immune system use a larger set of more specific antigen receptors to recognize the same set of pathogens. Our interpretation of this finding is that because the genetics of the immune system imposed different constraints on the evolutionary process, two distinct recognition strategies have been adapted by these species.