The biology and evolution of bird songs.
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Animals↗
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Results for “Biological Evolution”
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Reflections on an unsolved problem of biology: the evolution of senescence and death.
The evolutionary theory of senescence is based largely on principles first outlined by Williams in 1957, and consists of two relatively independent parts. The first part builds on ideas first put forward by Medawar, Haldane and others, to explain how something as negative as senescence could have been positively selected in evolution, particularly since most animals in the wild do not reach an age where senescence is expressed. Williams proposed that the genes responsible for the negative effects of senecence (senescence effector genes) were fixed in evolution by a process he called antagonistic pleiotropy, wherein a subset of genes selected because they confer a reproductive advantage early in life may have harmful effects in the post-reproductive period; negative selection against these harmful effects fails because, as pointed out by Medawar, the force of natural selection declines with age. The evolutionary history of senescence-causing genes is seen as a nondirected accumulation of genes selected on a basis independent of senescence per se. In the second portion of his paper, Williams made a series of predictions about how the age of organisms at reproductive maturity, fecundity, lifespan and the timing of the onset of senescence would all interact in the life history of a species. These latter predictions, which do not depend at all on details of the mechanisms of selection of senescence effector genes, have been validated by numerous experiments over the past several decades. On the other hand, it has become increasingly evident that the senescence effector genes did not, as would be predicted by antagonistic pleiotropy, accumulate in a random, non-directed fashion in various species over evolutionary time. Rather, everything we know about these genes suggests they were present in eukaryotic founder cells shortly after, or even congruent with, the emergence of eukaryotes from their prokaryotic ancestors, and have been stringently conserved ever since. Complicated explanations of how so-called "death genes" may have evolved in eukaryotes are thus not required. It is suggested that the evolutionary theory of senescence should be focused on those evolutionary principles that have been validated experimentally, and that the notion of antagonistic pleiotropy--which cannot be experimentally validated--be dropped from our thinking about the evolution of senescence.
Aging↗
Handedness, origin of life and evolution.
Biological polymers have a preferred chirality ond can replicate themselves. Physical arguments provide insight into which of these unique and apparently related properties evolved first, and by what mechanism.
Alanine↗
Conservation biology. Rapid evolution can foil even the best-laid plans.
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Animals↗
DNA display II. Genetic manipulation of combinatorial chemistry libraries for small-molecule evolution.
Biological in vitro selection techniques, such as RNA aptamer methods and mRNA display, have proven to be powerful approaches for engineering molecules with novel functions. These techniques are based on iterative amplification of biopolymer libraries, interposed by selection for a desired functional property. Rare, promising compounds are enriched over multiple generations of a constantly replicating molecular population, and subsequently identified. The restriction of such methods to DNA, RNA, and polypeptides precludes their use for small-molecule discovery. To overcome this limitation, we have directed the synthesis of combinatorial chemistry libraries with DNA "genes," making possible iterative amplification of a nonbiological molecular species. By differential hybridization during the course of a traditional split-and-pool combinatorial synthesis, the DNA sequence of each gene is read out and translated into a unique small-molecule structure. This "chemical translation" provides practical access to synthetic compound populations 1 million-fold more complex than state-of-the-art combinatorial libraries. We carried out an in vitro selection experiment (iterated chemical translation, selection, and amplification) on a library of 10(6) nonnatural peptides. The library converged over three generations to a high-affinity protein ligand. The ability to genetically encode diverse classes of synthetic transformations enables the in vitro selection and potential evolution of an essentially limitless collection of compound families, opening new avenues to drug discovery, catalyst design, and the development of a materials science "biology."
Catalysis↗
Pheromone-inducible conjugation in Enterococcus faecalis: a model for the evolution of biological complexity?
Pheromone-inducible transfer of the plasmid pCF10 in Enterococcus faecalis is regulated using a complicated network of proteins and RNAs. The plasmid itself has been assembled from parts garnered from a variety of sources, and many aspects of the system resemble a biological kluge. Recently several new functions of various pCF10 gene products that participate in regulation of plasmid transfer have been identified. The results indicate that selective pressures controlling the evolution of the plasmid have produced a highly complex regulatory network with multiple biological functions that may serve well as a model for the evolution of biological complexity.
Bacterial Proteins↗
A hierarchical approach to protein molecular evolution.
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with Monte Carlo simulations. These simulations demonstrate that nonhomologous juxtaposition of encoded structure is the rate-limiting step in the production of new tertiary protein folds. Nonhomologous "swapping" of low-energy secondary structures increased the binding constant of a simulated protein by approximately 10(7) relative to base substitution alone. Applications of our approach include the generation of new protein folds and modeling the molecular evolution of disease.
Animals↗
Spontaneous evolution of nuclear size and DNA content of non-small-cell-lung cancers grafted onto nude mice.
We monitored the biological evolution of four human non-small-cell lung cancers labeled KLX6, KLX7, KLX9, and KLX14 that had been grafted onto nude mice. This monitoring was carried out by means of digital cell image analysis which assessed morphometric (nuclear area, NA) and densitometric (nuclear DNA content, DI) features on Feulgen-stained nuclei from imprint smears. In each of the four models, the biological evolution of the NA and DI was characterized through their progression during serial passaging onto nude mice. The results show that of the four lung cancer models analyzed, one (KLX6) remained definitively stable with respect to its DNA content (DI assessments), while the other three, i.e., KLX7, KLX9, and KLX14, varied significantly. As assessed by the morphometric parameter, i.e., the NA, the four xenografted lines also varied significantly over serial passaging. In conclusion, we show that digital cell image analyses of Feulgen-stained cell nuclei including morphometric and densitometric parameters are a powerful tool for monitoring the biological evolution of human lung cancers grafted onto nude mice. We think therefore that the ploidy level of a tumor might be dependent upon its age and/or its related clinical stage.
Animals↗
The biology and evolution of lungfishes. Based on proceedings of a symposium. Denver, Colorado, December 27, 1984.
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Animals↗
Molecular biology and evolution of the grass endophytes.
Acremonium coenophialum Morgan-Jones et W. Gams is a maternally transmitted fungal symbiont (endophyte) of the important forage grass Festuca arundinacea Schreb. (tall fescue), and provides biological protection and enhanced fitness to its host, but its anti-mammalian ergot alkaloids detract from the usefulness of tall fescue as forage for livestock. Molecular genetic techniques and materials are being developed in order to specifically eliminate the gene(s) encoding the first enzyme in ergot alkaloid biosynthesis. These techniques will also facilitate basic studies, such as host-fungus compatibility or biosynthesis of insecticidal alkaloids. Molecular phylogenetics indicate that endophytes related to A. coenophialum have evolved on multiple occasions from strains of Epichloë typhina (Ascomycotina, Clavicipitaceae), for which the sexual cycle is known. These studies also reveal significant diversity among seedborne endophytes in individual grass species. Thus, the endophytes are an important source of biochemical potential and genetic diversity in grass-fungus symbiota.
Acremonium↗
Spontaneous evolution of modularity and network motifs.
Biological networks have an inherent simplicity: they are modular with a design that can be separated into units that perform almost independently. Furthermore, they show reuse of recurring patterns termed network motifs. Little is known about the evolutionary origin of these properties. Current models of biological evolution typically produce networks that are highly nonmodular and lack understandable motifs. Here, we suggest a possible explanation for the origin of modularity and network motifs in biology. We use standard evolutionary algorithms to evolve networks. A key feature in this study is evolution under an environment (evolutionary goal) that changes in a modular fashion. That is, we repeatedly switch between several goals, each made of a different combination of subgoals. We find that such "modularly varying goals" lead to the spontaneous evolution of modular network structure and network motifs. The resulting networks rapidly evolve to satisfy each of the different goals. Such switching between related goals may represent biological evolution in a changing environment that requires different combinations of a set of basic biological functions. The present study may shed light on the evolutionary forces that promote structural simplicity in biological networks and offers ways to improve the evolutionary design of engineered systems.
Algorithms↗
Vasopressin and oxytocin: molecular biology and evolution of the peptide hormones and their receptors.
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Amino Acid Sequence↗
Thermodynamics of terrestrial evolution.
The causal element of biological evolution and development can be understood in terms of a potential function which is generalized from the variational principles of irreversible thermodynamics. This potential function is approximated by the rate of entropy production in a configuration space which admits of macroscopic excursions by fluctuation and regression as well as microscopic ones. Analogously to Onsager's dissipation function, the potential takes the form of a saddle surface in this configuration space. The path of evolution following from an initial high dissipation state within the fixed constraint provided by the invariant energy flux from the sun tends toward the stable saddle point by a series of spontaneous regressions which lower the entropy production rate and by an alternating series of spontaneous fluctuations which introduce new internal constraints and lead to a higher entropy production rate. The potential thus rationalizes the system's observed tendency toward "chemical imperialism" (high dissipation) while simultaneously accommodating the development of "dynamic efficiency" and complication (low dissipation).
Biological Evolution↗
Multistability: a major means of differentiation and evolution in biological systems.
Very simple biochemical systems regulated at the level of gene expression or protein function are capable of complex dynamic behaviour. Among the various patterns of regulation associated with non-linear kinetics, multistability, which corresponds to a true switch between alternate steady states, allows a graded signal to be turned into a discontinuous evolution of the system along several possible distinct pathways, which can be either reversible or irreversible. Multistability plays a significant role in some of the basic processes of life. It might account for maintenance of phenotypic differences in the absence of genetic or environmental differences, as has been demonstrated experimentally for the regulation of the lactose operon in Escherichia coli. Cell differentiation might also be explained as multistability.
Biological Evolution↗
Biology and evolution of cervical squamous intraepithelial lesions: a hypothesis with diagnostic prognostic implications.
Recent advances in the understanding of HPV-associated cervical squamous intraepithelial lesions, specifically with respect to HPV DNA integration into basal cervical epithelial cells, need to be incorporated into strategies for diagnosing and classifying these lesions. The biology and evolution of HPV-associated cervical squamous intraepithelial lesions is reviewed, along with recent developments using tyramide-based in situ hybridization and MIB-1 immunoreactivity. It is proposed that HPV DNA integration into the basal cells of cervical squamous epithelium precedes the transformation of low-into high-grade lesions. The HPV DNA tyramide-based in situ hybridization system may prove to be a powerful diagnostic/prognostic tool in this regard. It is also proposed that the presence of mitoses (especially atypical forms) in the upper layers may be a discriminatory hallmark in the morphologic distinction between low- and high-grade lesions. Further, since the biologic changes manifest between these two lesions are reflected in their respective phenotype, it appears plausible to adopt the Bethesda System two-tiered/binary classification of LGSIL and HGSIL for histopathologic diagnoses.
DNA, Neoplasm↗
A general account of selection: biology, immunology, and behavior.
Authors frequently refer to gene-based selection in biological evolution, the reaction of the immune system to antigens, and operant learning as exemplifying selection processes in the same sense of this term. However, as obvious as this claim may seem on the surface, setting out an account of "selection" that is general enough to incorporate all three of these processes without becoming so general as to be vacuous is far from easy. In this target article, we set out such a general account of selection to see how well it accommodates these very different sorts of selection. The three fundamental elements of this account are replication, variation, and environmental interaction. For selection to occur, these three processes must be related in a very specific way. In particular, replication must alternate with environmental interaction so that any changes that occur in replication are passed on differentially because of environmental interaction. One of the main differences among the three sorts of selection that we investigate concerns the role of organisms. In traditional biological evolution, organisms play a central role with respect to environmental interaction. Although environmental interaction can occur at other levels of the organizational hierarchy, organisms are the primary focus of environmental interaction. In the functioning of the immune system, organisms function as containers. The interactions that result in selection of antibodies during a lifetime are between entities (antibodies and antigens) contained within the organism. Resulting changes in the immune system of one organism are not passed on to later organisms. Nor are changes in operant behavior resulting from behavioral selection passed on to later organisms. But operant behavior is not contained in the organism because most of the interactions that lead to differential replication include parts of the world outside the organism. Changes in the organism's nervous system are the effects of those interactions. The role of genes also varies in these three systems. Biological evolution is gene-based (i.e., genes are the primary replicators). Genes play very different roles in operant behavior and the immune system. However, in all three systems, iteration is central. All three selection processes are also incredibly wasteful and inefficient. They can generate complexity and novelty primarily because they are so wasteful and inefficient.
Behaviorism↗
Genetic variation: molecular mechanisms and impact on microbial evolution.
On the basis of established knowledge of microbial genetics one can distinguish three major natural strategies in the spontaneous generation of genetic variations in bacteria. These strategies are: (1) small local changes in the nucleotide sequence of the genome, (2) intragenomic reshuffling of segments of genomic sequences and (3) the acquisition of DNA sequences from another organism. The three general strategies differ in the quality of their contribution to microbial evolution. Besides a number of non-genetic factors, various specific gene products are involved in the generation of genetic variation and in the modulation of the frequency of genetic variation. The underlying genes are called evolution genes. They act for the benefit of the biological evolution of populations as opposed to the action of housekeeping genes and accessory genes which are for the benefit of individuals. Examples of evolution genes acting as variation generators are found in the transposition of mobile genetic elements and in so-called site-specific recombination systems. DNA repair systems and restriction-modification systems are examples of modulators of the frequency of genetic variation. The involvement of bacterial viruses and of plasmids in DNA reshuffling and in horizontal gene transfer is a hint for their evolutionary functions. Evolution genes are thought to undergo biological evolution themselves, but natural selection for their functions is indirect, at the level of populations, and is called second-order selection. In spite of an involvement of gene products in the generation of genetic variations, evolution genes do not programmatically direct evolution towards a specific goal. Rather, a steady interplay between natural selection and mixed populations of genetic variants gives microbial evolution its direction.
Bacteria↗
Creativity in biology and in the human mind (manifestation of concepts).
The article is based on the widely held notion that creativity is a phenomenon studied in two branches of the science of life: psychology (in a wide sense) on one side, and evolutionary biology on the other. Therefore, an analysis of creativity of the mind should contribute to the solution of problems in biological evolution, problems which cannot be fully explained by the orthodox assumption of small steps of mutation and selection. This analysis is restricted to three classes of creativity, which are: a) organismal creativity, as exemplified by the creation of organs such as "eye" and "heart". b) mental-scientific creativity, exemplified by Newton's notion of "gravity" between planets and stars. c) mental-technological creativity, exemplified by Gutenberg's invention of "printing by movable types". The analysis of these classes is based on concepts, which are interrelated structurally by means of propositions. Two types of propositions are distinguished: factual ones named "cognita", and hypothetical ones named "hypothetical episodes". A further basis of the analysis is the assumption that creativity consists of several phases, of which incubation and insight are the essential ones. In carrying out the analysis, the writer shows that incubation functions on two or three lines of thought, one of which can be expressed by factual cognita, and the other ones predominantly by hypothetical episodes. Those several lines are integrated by means of logical implication, by which insight into a novel concept is obtained. In a second method of analysis, the several lines of incubation are represented by networks. In this method, the novel concept is obtained by integrating the individual networks into a common structure. It is proved that the methods of analysis described above can be applied to all three classes of creativity definined previously. Drawing conclusions from the analysis, the writer points out that the organismal concepts were manifested in biological evolution many millions of years prior to the appearance of man and his brain on earth. The writer, therefore, argues that a great number of concepts are not a creation of man's mind, but are entities which pre-existed man and were manifested to him. Such concepts may be conceived as forming a time-independent "conceptual universe" external to the "material universe" of galaxies, stars and organisms. Thus, for example, the concept of an "eye" was manifested in biological evolution as the organ "eye" of many organisms. Much later, this concept was manifested to man, when he invented the optical camera.(ABSTRACT TRUNCATED AT 400 WORDS)
Animals↗