The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law

Before the Darwinian revolution many biologists considered organic forms to be determined by natural law like atoms or crystals and therefore necessary, intrinsic and immutable features of the world order, which will occur throughout the cosmos wherever there is life. The search for the natural determinants of organic form-the celebrated "Laws of Form"-was seen as one of the major tasks of biology. After Darwin, this Platonic conception of form was abandoned and natural selection, not natural law, was increasingly seen to be the main, if not the exclusive, determinant of organic form. However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form. We speculate that it is unlikely that the folds will prove to be the only case in nature where a set of complex organic forms is determined by natural law, and suggest that natural law may have played a far greater role in the origin and evolution of life than is currently assumed.     

Intrasexual selection predicts the evolution of signal complexity in lizards

Sexual selection has often been invoked in explaining extravagant morphological and behavioural adaptations that function to increase mating success. Much is known about the effects of intersexual selection, which operates through female mate choice, in shaping animal signals. The role of intrasexual selection has been less clear. We report on the first evidence for the coevolution of signal complexity and sexual size dimorphism (SSD), which is characteristically produced by high levels of male male competition. We used two complementary comparative methods in order to reveal that the use of complex signals is associated with SSD in extant species and that historical increases in complexity have occurred in regions of a phylogenetic tree characterized by high levels of pre-existing size dimorphism. We suggest that signal complexity has evolved in order to improve opponent assessment under conditions of high male male competition. Our findings suggest that intrasexual selection may play an important and previously underestimated role in the evolution of communicative systems.     

Comparative genomics and the study of evolution by natural selection

Genomics profoundly affects most areas of biology, including ecology and evolutionary biology. By examining genome sequences from multiple species, comparative genomics offers new insight into genome evolution and the way natural selection moulds DNA sequence evolution. Functional divergence, as manifested in the accumulation of nonsynonymous substitutions in protein-coding genes, differs among lineages in a manner seemingly related to population size. For example, the ratio of nonsynonymous to synonymous substitution (d_N/d_S) is higher in apes than in rodents, compatible with Ohta's nearly neutral theory of molecular evolution, which suggests that the fixation of slightly deleterious mutations contributes to protein evolution at an extent negatively correlated with effective population size. While this supports the idea that functional evolution is not necessarily adaptive, comparative genomics is uncovering a role for positive Darwinian selection in 10–40% of all genes in different lineages, estimates that are likely to increase when the addition of more genomes gives increased power. Again, population size seems to matter also in this context, with a higher proportion of fixed amino acid changes representing advantageous mutations in large populations. Genes that are particularly prone to be driven by positive selection include those involved with reproduction, immune response, sensory perception and apoptosis. Genetic innovations are also frequently obtained by the gain or loss of complete gene sequences. Moreover, it is increasingly realized, from comparative genomics, that purifying selection conserves much more than just the protein-coding part of the genome, and this points at an important role for regulatory elements in trait evolution. Finally, genome sequencing using outbred or multiple individuals has provided a wealth of polymorphism data that gives information on population history, demography and marker evolution.     

Evolution: natural selection in the evolution of humans and chimps

We now have more or less full sequences of both human and chimp genomes, allowing comparison that sheds light on their evolution. A few hundred genes show significant evidence for adaptive evolution in the two lineages, but the actual number might be much higher. Natural selection has eliminated about 75% of amino acid changes in coding sequence since the split of the human and chimpanzee genomes.     

Iterative design of a simulation-based module for teaching evolution by natural selection

Background

This research builds on a previous study that looked at the effectiveness of a simulation-based module for teaching students about the process of evolution by natural selection. While the previous study showed that the module was successful in teaching how natural selection works, the research uncovered some weaknesses in the design. In this paper, we used design-based research to investigate how design changes to the module affected not only students' understanding of the concepts but also their usage of misconceptions in the assessments. We present results from two studies. In study 1, we looked at gains in understanding on a pre and post-assessment for students who used the revised version of the module. We also examined misconception uses in their answer selections. In study 2, we compared the performance on a summative assessment between students who used the revised version and students who used the original version of the module. We also looked at misconception uses in their answer selections.

Results

In study 1, we saw a significant improvement in the pre-post assessment for students who used the revised version. In study 2, we did not find a significant difference on the overall performance outcome between students who used the revised and those that used the original version of the module. In both studies, however, we saw a  lower use of misconceptions after students used the revised module. In particular, we saw less use of the adaptive mutation misconception, the belief that mutations are adaptive responses to the environment and are biased towards advantageous mutations. This is promising because in the previous study there was no evidence of decreased use of this misconception.

Conclusions

Students showed learning gains on all targeted key concepts, and reduced expression of all targeted misconceptions, which was not found previously for students using the older workbook version of the module. In particular, the revised version appears to help students overcome the adaptive mutation misconception. This article demonstrates how design-based research can contribute to the ongoing improvement of evidence-based instruction in undergraduate biology classrooms.

     

Why the evolution of resistance to anthropogenic toxins normally involves major gene changes: the limits to natural selection

Standard population genetic theory suggests that adaptation should normally be achieved by the spread of many genes each of small effect (polygenes), and that adaptation by major genes should be unusual. Such models depend on consideration of the rates of acquisition of adaptation. In practice, adaptation to pollutants and anthropogenic toxins has most frequently been achieved by the spread of major genes. A simple model is developed to explain this discrepancy, in which the determining factor is not the rate of spread, but the maximum response achievable under the two contrasting models of polygenic or major gene inheritance. In the short term, for a given mean and genetic variance, characters in which the additive genetic variance is produced by the segregation of many genes of small effect at intermediate gene frequencies are unable to produce as large a response to directional selection as characters in which the variance is caused by genes of large effect at low frequency. If the target for selection is a long way from the mean prior to selection (as it may well be for adaptation to novel anthropogenic stresses) then adaptation can only be achieved by species possessing major genes. The model is discussed with reference to the example of heavy metal tolerance in plants.     

Fluctuating natural selection accounts for the evolution of diversification bet hedging

Natural environments are characterized by unpredictability over all time scales. This stochasticity is expected on theoretical grounds to result in the evolution of ‘bet-hedging’ traits that maximize the long term, or geometric mean fitness even though such traits do not maximize fitness over shorter time scales. The geometric mean principle is thus central to our interpretation of optimality and adaptation; however, quantitative empirical support for bet hedging is lacking. Here, I report a quantitative test using the timing of seed germination—a model diversification bet-hedging trait—in Lobelia inflata under field conditions. In a phenotypic manipulation study, I find the magnitude of fluctuating selection acting on seed germination timing—across 70 intervals throughout five seasons—to be extreme: fitness functions for survival are complex and multimodal within seasons and significantly dissimilar among seasons. I confirm that the observed magnitude of fluctuating selection is sufficient to account for the degree of diversification behaviour characteristic of individuals of this species. The geometric mean principle has been known to economic theory for over two centuries; this study now provides a quantitative test of optimality of a bet-hedging trait in nature.     

Evidence that a major determinant for the identity of a transfer RNA is conserved in evolution

We observed recently that a single G3.U70 base pair in the amino acid acceptor stem of an Escherichia coli alanine tRNA is a major determinant for its identity. Inspection of tRNA sequences shows that G3.U70 is unique to alanine in E. coli and is present in eucaryotic cytoplasmic alanine tRNAs. We show here that single nucleotide changes of G3.U70 to A3.U70 or to G3.C70 eliminate in vitro aminoacylation of an insect and of a human alanine tRNA by the respective homologous synthetase. Compared to the influence of G3.U70, other sequence variations in tRNAAla have a relatively small effect on aminoacylation by the insect and human enzymes. In addition, while these eucaryotic tRNAs have nucleotide differences from E. coli alanine tRNA, they are heterologously charged only with alanine when expressed in E. coli. The results indicate a functional role for G3.U70 that is conserved in evolution. They also suggest that the sequence differences between E. coli and the eucaryotic alanine tRNAs at sites other than the conserved G3.U70 do not create major determinants for recognition by any other bacterial enzyme.     

A new index for the intensity of natural selection.

A new index for the intensity of natural selection is proposed, based upon the double exponential model for fitness functions. This index is defined as a variance and is such that a value of zero indicates no selection while a value of one indicates quite strong selection. The use of the index is demonstrated using published data on the survival of human infants with different birth weights and gestation times.     

Self-organization and natural selection in the evolution of complex despotic societies

Differences between related species are usually explained as separate adaptations produced by individual selection. I discuss in this paper how related species, which differ in many respects, may evolve by a combination of individual selection, self-organization, and group-selection, requiring an evolutionary adaptation of only a single trait. In line with the supposed evolution of despotic species of macaques, we take as a starting point an ancestral species that is egalitarian and mildly aggressive. We suppose it to live in an environment with abundant food and we put the case that, if food becomes scarce and more clumped, natural selection at the level of the individual will favor individuals with a more intense aggression (implying, for instance, biting and fierce fighting). Using an individual-centered model, called DomWorld, I show what happens when the intensity of aggression increases. In DomWorld, group life is represented by artificial individuals that live in a homogeneous world. Individuals are extremely simple: all they do is flock together and, upon meeting one another, they may perform dominance interactions in which the effects of winning and losing are self-reinforcing. When the intensity of aggression in the model is increased, a complex feedback between the hierarchy and spatial structure results; via self-organization, this feedback causes the egalitarian society to change into a despotic one. The many differences between the two types of artificial society closely correspond to those between despotic and egalitarian macaques in the real world. Given that, in the model, the organization changes as a side effect of the change of one single trait proper to an egalitarian society, in the real world a despotic society may also have arisen as a side effect of the mutation of a single trait of an egalitarian species. If groups with different intensities of aggression evolve in this way, they will also have different gradients of hierarchy. When food is scarce, groups with the steepest hierarchy may have the best chance to survive, because at least a small number of individuals in such a group may succeed in producing offspring, whereas in egalitarian societies every individual is at risk of being insufficiently fed to reproduce. Therefore, intrademic group selection (selection within an interbreeding group) may have contributed to the evolution of despotic societies.     

Forms of natural selection controlling the genomic evolution in nodule bacteria

The role of different forms of natural selection in the evolution of genomes in root nodule bacteria (rhizobia) is analyzed for the first time. In these nitrogen-fixing symbionts of leguminous plants, two types of genome organization are revealed: (i) unitary type, where over 95% of genetic information is encoded by chromosomes (5.3–5.5 Mb in Azorhizobium, 7.0–7.8 Mb in Mesorhizobium, 7.3–10.1 Mb in Bradyrhizobium); (ii) multipartite type, where up to 50% of genetic information is allocated to plasmids or chromids which may exceed 2 Mb in size and usually control the symbiotic properties (pSyms) in fast-growing rhizobia (Rhizobium, Sinorhizobium, Neorhizobium). Emergence of fast-growing species with narrow host ranges are correlated to the extension of extrachromosomal parts of genomes, including the increase in pSyms sizes (in Sinorhizobium). An important role in this evolution is implemented by diversifying selection since the genomic diversity evolved in rhizobia owing to symbiotic interactions with highly divergent legumes. However, analysis of polymorphism in nod genes (encoding synthesis of lipo-chitooligosaccharide signaling Nod factors) suggests that the impacts of diversifying selection are restricted to the bacterial divergence for host specificity and do not influence the overall genome organization. Since the extension of rhizobia genome diversity results from the horizontal sym gene transfer occurring with low frequencies, we suggest that this extension is due to the frequency-dependent selection anchoring the rare genotypes in bacterial populations. It is implemented during the rhizobia competition for nodulation encoded by the functionally diverse cmp genes. Their location in different parts of bacterial genomes may be considered as an important factor of their adaptive diversification implemented in the host-associated microbial communities.     

A new hypothesis for the evolution of biological electron transport

A new hypothesis for the evolution of biological electron transport is presented. According to this hypothesis biological electron transport originated close to the potential of the hydrogen electrode and evolved in various advantageous directions including, when molecular oxygen became available on the Earth, that of the oxygen electrode. This implies stepwise evolution along and across the potential scale. The hypothesis is based mainly on existing information obtained from studies of primary and tertiary structural relationships of proteins. It is hoped to provide a framework for closer understanding of both evolution and mechanisms of cellular oxidation-reduction as well as energy coupling reactions.     

Evaluating the role of natural selection in the evolution of gene regulation

Surveys of gene expression reveal extensive variability both within and between a wide range of species. Compelling cases have been made for adaptive changes in gene regulation, but the proportion of expression divergence attributable to natural selection remains unclear. Distinguishing adaptive changes driven by positive selection from neutral divergence resulting from mutation and genetic drift is critical for understanding the evolution of gene expression. Here, we review the various methods that have been used to test for signs of selection in genomic expression data. We also discuss properties of regulatory systems relevant to neutral models of gene expression. Despite some potential caveats, published studies provide considerable evidence for adaptive changes in gene expression. Future challenges for studies of regulatory evolution will be to quantify the frequency of adaptive changes, identify the genetic basis of expression divergence and associate changes in gene expression with specific organismal phenotypes.     

An experimental demonstration of Fisher's principle: evolution of sexual proportion by natural selection.

Most sexually reproducing species have sexual proportions around 1:1. This major biological phenomenon remained unexplained until 1930, when FISHER proposed that it results from a mechanism of natural selection. Here we report the first experimental test of his model that obeys all its assumptions. We used a naturally occurring X-Y meiotic drive system--the sex-ratio trait of Drosophila mediopunctat--to generate female-biased experimental populations. As predicted by FISHER, these populations evolved toward equal sex proportions due to natural selection, by accumulation of autosomal alleles that direct the parental reproductive effort toward the rare sex. Classical Fisherian evolution is a rather slow mechanism: despite a very large amount of genetic variability, the experimental populations evolved from 16% of males to 32% of males in 49 generations and would take 330 generations (29 years) to reach 49%. This slowness has important implications for species potentially endangered by skewed sexual proportions, such as reptiles with temperature sex determination.     

The evolution of patient selection criteria and indications for extracorporeal life support in pediatric cardiopulmonary failure: next time, let's not eat the bones

Bill James, baseball statistician and author, tells the story of hungry cavemen sitting about a campfire, waiting for tomatoes to ripen. One has the inspiration to throw an ox on the fire, and the first barbecue ensued and was endured. After eating, the conversation goes something like this. "There were some good parts." "Yeah, but there were some bad parts." And the smart one says, "This time, let's not eat the bones." The evolution of patient selection criteria for the use of extracorporeal support (ECLS) is a bit like those cavemen and their first barbecued ox. Extracorporeal life support technology and application to patient care is the unique result of a long standing history of ambitious attempt, evaluation, debate, collaboration and extension.     

Adaptive walks on behavioural landscapes and the evolution of optimal behaviour by natural selection

Summary One of the main challenges to the adaptationist programme in general and to the use of optimality models in behavioural and evolutionary ecology in particular is that natural selection need not optimise fitness. This challenge is addressed by considering the evolution of optimal patch choice by natural selection. The behavioural model is based on a state variable approach in which a strategy consists of a sequence denoting the patch to be visited as a function of the organism's state and time. The optimal strategy maximises expected terminal reproduction. The fitnesses of alternative strategies are computed by iteration of the associated equations for fitness; this characterises the adaptive behavioural landscape. There may be enormous numbers of strategies that have near optimal fitnesses. A population model is used to connect frequencies of behavioural types from one generation to the next. Theories on adaptive walks on fitness landscapes are considered in the context of behaviour. The main result is that within the context of optimality arguments at selective equilibrium, sub-optimal behaviours can persist. General implications for research in behavioural ecology, including tests of behavioural theories, are discussed.