Claims and limits of phylogenetic systematics1

Within the methodology of phylogenetic systematics four hierarchic levels are distinguished: the “Central Claim” (to reconstruct phylogeny), methodoloical postulate (to conclude analysis with a purely dichotomous cladogram if ever possible), method (search for sister-group relationships by character analysis), and “Taxonomic Principle” (establishment of a classification reflecting merely the recognized genealoy). Certain limits of applicability and reliability of traditional phylogenetic systematics are specified: genealogy can only be analysed among taxa with perceptible evolutionary novelties; reticulated genealogy is not yet regarded; events other than cladogenetic ones cannot be recognised. Phylogenetic systematics is an independent method which has not been absorbed by any type of “pattern” or “transformed” cladism. Phylogenetic systematics relies on the theory of evolution, which does not lead into circularity, since phylogenetic systematics does not claim to prove or to explain evolution whatsoever.     

Using Google trends data to assess public understanding on the environmental risks

This study proposes a method to assess the public understanding toward themes related to environment, biodiversity conservation and fishery. Since the Internet traffic is seen as the proxy of the public interest, this article analyzes the related Google Trends data to explore the cognitive map of the public. Patterning changes in the search volume (synchronous increase and decrease) were detected by using the association analysis. Weekly search volumes of the United States for the last 5 years have been gathered and were converted into values ranging between –1 and 1, indicating the gradual level of increase/decrease by the time. Apriori algorithm was used to determine the associations between search volumes of the keywords. As a consequence, several patterns were detected with a significant support indicating synchronous increases/decreases of the volumes. Upon the development of cognitive maps based on the detected patterns, it is found that the terms “Environment” and “Pollution” were the most significant and central terms. The search volume of the terms such as “Conservation,” “Ecology,” “Climate change,” “Invasive species” and “Endangered Species” increases as the search increases in the central terms. Therefore, these terms can be seen as the drivers/triggers of the Google search for some central words. It is apparent that the public has awareness of the central terms and further interest should be provoked and fostered on the environment-related concepts.     

Paraphyly,ancestors, and the goals of taxonomy: A botanical defense of cladism

Cronquist (1987) criticizes cladism for its rejection of paraphyletic groups, which he would retain if he feels they are “conceptually useful.” We argue that paraphyletic higher taxa are artificial classes created by taxonomists who wish to emphasize particular characters or phenetic “gaps,” and that formal recognition of such taxa conveys a misleading picture of common ancestry and character evolution. In our view, classifications should accurately reflect the nested hierarchy of monophyletic groups that is the natural outcome of the evolutionary process. Such systems facilitate the study of evolution and provide an efficient summary of character distributions. Paraphyletic groups, such as “prokaryotes,” “green algae,” “bryophytes,” and “gymnosperms,” should be abandoned, as continued recognition of such groups will only serve to retard progress in understanding evolution. Contrary to Cronquist’s (1987) assertions, cladistic theory is not at odds with standard views on speciation and the existence of ancestors. Groups of interbreeding organisms can continue to exist after giving rise to descendant species, and there are several ways in which such groups, whether extant or extinct, can be incorporated into cladistic classification. In contrast, paraphyletic higher taxa are neither cohesive (integrated by gene flow) nor whole, do not serve as ancestors, and are unacceptable in the phylogenetic system. Fossils may be of great value in assessing phylogenetic relationships and are readily accommodated in cladistic classification. Cladistic studies are helping to answer major questions about plant evolution, and we anticipate increased efforts to develop a truly phylogenetic system.     

Biomolecular information gained through in vitro evolution

An in vitro evolution is a simplified Darwinian evolution in well-controlled surroundings. This evolution process can be modeled as a hill-climbing or adaptive walk on a fitness landscape in sequence space. The evolving molecular system gains at least two kinds of information originating from the converged sequences and the fitness increment of the evolving biopolymer as the adaptive walker. These two represent two aspects of the biomolecular information, its extent and its content, respectively. Here, we review studies related to formulation of the “content” and “extent” of biomolecular information. The two aspects are interconnected through physicochemical properties of the biopolymer, contrary to the case of conventional information, which seems to be independent of matter. The interconnection was analyzed based on the analogy between the evolution process and thermodynamics. The linear combination of the two by a temperature-like fluctuation factor resulted in a free-energy-like monotonically increasing function during the evolution process.     

Rethinking genes

The gene is the central construct of twentieth-century biology and evolution. It is a construct because, like “culture” in anthropology, “gene” is widely used and is central to the discipline's discourse, but eludes rigorous definition. Although the gene is acknowledged as a material entity, its membership criteria are unclear and its boundaries are fuzzy—indeed, more than one can occupy the same space at the same time. The purpose of this essay is to bring to light recent refinements in our conception of the gene and their implications for its use in biological anthropology.     

Models for alarm call behaviour

The evolution of alarm call behaviour under individual selection is studied. Four mathematical models of increasing complexity are proposed and analysed. Theoretical conditions for the evolution of “selfish”, “mutualistic”, “altruistic” or “spiteful” alarm calls are established. The models indicate that the hypotheses of benefits of retaining group members or avoiding group detection are not sufficient to explain the evolution of alarm call behaviour, but serve as a complementary factor to facilitate its evolution in most cases. It is hypothesized that the evolution of alarm calls between non-kin should evolve probably when calls are mutualistic, mildly altruistic and there are beneficial group size effects against predation.     

遗传算法在转录因子结合位点识别中的应用

遗传算法是模拟生物进化过程的计算模型,是一种全局优化搜索算法。将遗传算法与转录因子结合位点识别问题相结合的新方法,以一致性序列模型作为保守motif的描述模型,通过对motif序列与待测序列的比对问题进行编码,将其转化成搜索空间中的优化问题,利用遗传算法来搜索最优解,预测转录因子的结合位点。实验结果表明,这种新的方法是有效的,它在占用少量内存的情况下能够准确地识别出待测转录因子结合位点。     

On the “cytosociology” of enzyme action in vivo: A novel thermodynamic correlate of biological evolution

The evolution of enzyme action in vivo is examined, in the light of established thermodynamic correlates of biological evolution. Adopting a “process” view of matter in the “living state,” the authors focus the analysis on the transition-state theory of reaction rates. Thus, the free-energy change associated with the transition-state barrier is seen as a primary target in the evolution of cellular metabolism. The utility and limitations of reductionistic approaches to enzyme evolution, based on the single enzyme, are explored first. Then, canvassing the wealth of evidence on the role of enzyme organization in vivo, the authors synthesize a “cytosociological” view of enzyme evolution. In this view, a composite (resultant) of individual transition-state barriers is deemed a more appropriate “potential function” for modification in the higher evolution of cell metabolism. The suggested direction of evolutionary changes in this function, dictated by the increasing “socialization” of enzyme action in vivo, stands as a novel postulate. This approach is shown to be completely consonant with current thinking on the thermodynamics of biological evolution, and to provide further insight into the nature of material transformations in the “living state”.     

Guest-Editorial Introduction: Converging Evolutionary Patterns in Life and Culture

The natural world demonstrates signs of spatial–temporal order, an order that appears to us through a series of recognizable, recurring and consecutive patterns, i.e. regularities in forms, functions, behaviors, events and processes. These patterns lend insight into the modes and tempos of evolution and thus into the units, levels, and mechanisms that underlie the evolutionary hierarchy. Contributors to this special issue analyze converging patterns in the biological and sociocultural realm across and beyond classic divisions between micro- and macro-evolution; horizontal/reticulate and vertical evolution; phylogeny, ontogeny and ecology; synchronic and diachronic sociocultural and linguistic research; and tree and network diagrams. Explanations are sought in complexity theory, major transitions of evolution, and process and mechanism approaches to change; and consequences for notions such as “life”, “species”, “biological individuality”, “units” and “levels” of evolution are given.     

Homicide and cultural evolution

Homicide rates are suitable materials for the study of “cultural evolution,” because they vary dramatically between societies (hence, are “cultural”) and change gradually rather than saccadically (hence, “evolve”).Sociological models of the sources of variation in homicide rates (“subcultures of violence”; demographic change; “legitimation of violence”; mass media effects) are criticized for inattention to the social context of violence and to the individual motives of the protagonists. Models of culture change that emphasize “transmission” are criticized for treating the culture-bearing person as a passive vessel rather than an active strategist. A satisfactory theory of the “cultural evolution” of violence awaits satisfactory theories of how people apprehend their interests and how they pursue them.     

Cryptic genetic variation can make “irreducible complexity” a common mode of adaptation in sexual populations

The existence of complex (multiple‐step) genetic adaptations that are “irreducible” (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce “irreducibly complex” adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley‐crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.     

Why Are There Still Monkeys?

The question “If humans evolved from monkeys, why are there still monkeys?” reveals a widespread and persistent misconception about the process and pattern of evolution. The concept of “cousins” is central to understanding and overcoming this particular obstacle to evolution education.     

The emergence and significance of heavy-duty scrapers in ancient stone toolkits

Heavy-duty scrapers are documented as a specific morphotype in ancient African and Eurasian toolkits from the Oldowan into the Acheulian. They are characterized by a flat platform perpendicularly oriented to a carinated edge. The convex surface of that edge displays semi-peripheral, unidirectional removals associated with steep retouch and/or crush marks. This morphotype has been described from numerous sites covering a long temporal scale and are diversely referred to in French as “rostro-carénés” or “nucléus-racloirs” and in English as “massive scrapers”, “core scrapers”, “large scrapers”, or “heavy end-scrapers”. Morpho-technological definitions and interpretations are reviewed to track the origin and evolution of heavy-duty scrapers over time and space. Results show that tools referred to as heavy-duty scrapers were made on thick cobbles during the Oldowan, and later, at the onset of the Acheulian, on Large Flakes, while smaller-sized items in Late Acheulian sites assume end-scraper morphologies. But should all of these tools really be grouped under a single denomination? Experimental work explores whether heavy-duty scrapers are the result of knapping processes, or if their morphology could be derived from other kinds of activities. Chronological continuity of the attributes specific to heavy-duty scrapers points to their role in ancient toolkits, suggesting that these scarce but ubiquitous primitive implements are, on equal footing with chopper-cores, one of the oldest morphotypes in the world.     

microRNAs Expression as Novel Genetic Biomarker for Early Prediction and Continuous Monitoring in Pulmonary Cancer

One of the main causes of death in the world is lung cancer. According to the World Health Organization, the annual incidence of lung cancer increases significantly. Moreover, lung cancer accounts for one of the highest mortality rates, mainly due to late detection. Numerous studies have been conducted in order to identify new biomarkers for early diagnosis and for monitoring and evaluation of lung cancer stages. An ideal biomarker candidate is represented by the analysis of microRNAs expression. In this paper, we want to summarize microRNAs expressions in lung cancer. We also want to present the expression of microRNAs depending on the evolution of lung cancer. For this study, we analyzed the studies available in scientific databases, such as PubMed and Scopus. The studies were selected using the search keywords “microRNAs expression,” “lung cancer,” and “genetic biomarkers.” The most significant articles were selected for the study, following rigorous analysis. To evaluate and monitor lung cancer, the expression of microRNAs may be used successfully due to increased specificity and selectivity. However, further studies are needed on the assignment and validation of microRNAs for each type of lung cancer, respectively, for each stage of evolution.     

Causal mechanisms of evolution and the capacity for niche construction

Ernst Mayr proposed a distinction between “proximate”, mechanistic, and “ultimate”, evolutionary, causes of biological phenomena. This dichotomy has influenced the thinking of many biologists, but it is increasingly perceived as impeding modern studies of evolutionary processes, including study of “niche construction” in which organisms alter their environments in ways supportive of their evolutionary success. Some still find value for this dichotomy in its separation of answers to “how?” versus “why?”questions about evolution. But “why is A?” questions about evolution necessarily take the form “how does A occur?”, so this separation is illusory. Moreover, the dichotomy distorts our view of evolutionary causality, in that, contra Mayr, the action of natural selection, driven by genotype-phenotype-environment interactions which constitute adaptations, is no less “proximate” than the biological mechanisms which are altered by naturally selected genetic variants. Mayr’s dichotomy thus needs replacement by more realistic, mechanistic views of evolution. From a mechanistic viewpoint, there is a continuum of adaptations from those evolving as responses to unchanging environmental pressures to those evolving as the capacity for niche construction, and intermediate stages of this can be identified. Some biologists postulate an association of “phenotypic plasticity” (phenotype-environment covariation with genotype held constant) with capacity for niche construction. Both “plasticity” and niche construction comprise wide ranges of adaptive mechanisms, often fully heritable and resulting from case-specific evolution. Association of “plasticity” with niche construction is most likely to arise in systems wherein capacity for complex learning and behavioral flexibility have already evolved.     

Abstracts: Albany 2007, The 15th Conversation

Abstract

Forty nine molecular dynamics simulations of unfolding trajectories of the segment B1 of streptococcal protein G (GB1) provide a direct demonstration of the diversity of unfolding pathway and give a statistically utmost unfolding pathway under the physical property space. Twelve physical properties of the protein were chosen to construct a 12-dimensional property space. Then the 12-dimentional property space was reduced to a 3-dimentional principle component property space. Under the property space, the multiple unfolding trajectories look like “trees”, which have some common characters. The “root of the tree” corresponds to the native state, the “bole” homologizes the partially unfolded conformations, and the “crown” is in correspondence to the unfolded state. These unfolding trajectories can be divided into three types. The first one has the characters of straight “bole” and “crown” corresponding to a fast two-state unfolding pathway of GB1. The second one has the character of “the standstill in the middle tree bole”, which may correspond to a three-state unfolding pathway. The third one has the character of “the circuitous bole” corresponding to a slow two-state unfolding pathway. The fast two-state unfolding pathway is a statistically utmost unfolding pathway or preferred pathway of GB1, which occupies 53% of 49 unfolding trajectories. In the property space all the unfolding trajectories construct a thermal unfolding pathway ensemble of GB1. The unfolding pathway ensemble resembles a funnel that is gradually emanative from the native state ensemble to the unfolded state ensemble. In the property space, the thermal unfolded state distribution looks like electronic cloud in quantum mechanics. The unfolded states of the independent unfolding simulation trajectories have substantial overlaps, indicating that the thermal unfolded states are confined by the physical property values, and the number of protein unfolded state are much less than that was believed before.     

The distance between bacterial species in sequence space

Despite the revolution caused by information from macromolecular sequences, the basis of bacterial classification remains the genus and the species. How do these terms relate to the variety of bacteria that exist on earth? In this paper, the inter- and intraspecies differences in amino acid sequence of several bacterial electron transport proteins, cytochromesc, and blue copper proteins are compared. For the soil and water organisms studied, bacterial species can be classed as “tight” when there is little intraspecies variation, or “loose” when this variation is large. For this set of proteins and organisms, interspecies variation is much larger than that within a species. Examples of “tight” species arePseudomonas aeruginosa andRhodobacter sphaeroides, whilePseudomonas stutzeri andRhodopseudomonas palustris are loose species. The results are discussed in the context of the origin and age of bacterial species, and the distribution of genomes in “sequence space.” The situation is probably different for commensal or pathogenic bacteria, whose population structure and evolution are linked to the properties of another organism.     

Optimization by simulating molecular evolution

Based on the analogy between mathematical optimization and molecular evolution and on Eigen's quasi-species model of molecular evolution, an evolutionary algorithm for combinatorial optimization has been developed. This algorithm consists of a versatile variation scheme and an innovative decision rule, the essence of which lies in a radical revision of the conventional philosophy of optimization: A number of configurations of variables with better values, instead of only a single best configuration, are selected as starting points for the next iteration. As a result the search proceeds in parallel along a number of routes and is unlikely to get trapped in local optima. An important innovation of the algorithm is introduction of a constraint to let the starting points always keep a certain distance from each other so that the search is able to cover a larger region of space effectively. The main advantage of the algorithm is that it has more chances to find the global optimum and as many local optima as possible in a single run. This has been demonstrated in preliminary computational experiments.