Rehabilitating Reductionism

SYNOPSIS: Reductionism has become the object of a great dealof criticism from a variety of quarters within evolutionarybiology in recent years. Many contemporary anti-reductionistsargue that reductionism is inappropriate in biological inquirygiven the prevalence of hierarchies, scales of complexity andlevels of organization in the organic world. They further contendthat a commitment to reductionism has led evolutionary theoriststo make a large number of methodological blunders and conceptualerrors in constructing explanations of biological evolution. The contemporary critics of reductionism have not made a persuasivecase for the ontological peculiarity of the organic world. Muchof their argument concerning hierarchy and levels appears torest on assertion rather than metaphysical necessity or ontologicalpeculiarity. Moreover, the interpretations of reductionism attackedby contemporary critics in biology are narrow and overly simplistic. The modern synthetic theory of evolution may well have explanatoryinadequacies that demand the attention of biologists workingin many fields. But attempts to motivate theoretical alternativesto this theory based solely on ontological grounds appear toplace the ontological cart before the theoretical horse. Theoriesdictate ontological commitments and, as a result, it is at thelevel of theoretical rather than ontological adequacy that theassessment of the modern synthetic theory ought to proceed.     

Teaching Evolution with Historical Narratives

This paper focuses on evolution as a unifying theme in biology education. Our aim is to argue that the different topics taught in secondary school biology classes should be enriched with and linked together by means of accounts of the history of life. We named this approach a “natural history perspective” on biology education. An essential aspect of the natural history perspective is the claim that evolutionary history forms the context for the development of an understanding of evolutionary processes. While there are some indications that a natural history perspective can function as a context for understanding micro-evolutionary processes, more research is called for.

Structure And Evolution Of Calcium-Modulated Protein

Abstract

The question posed by the science of analytical histology is how the properties and interactions of the components of the tissues determine their organization in the organs. The relevant components of the tissues are the cells and the extracellular matrix. The ability of cohering populations of cells to self-assemble structured tissues by cell sorting out offers an important opportunity for the experimental study of the mechanisms by which the cells and extracellular matrix interact to determine structure. The investigator can manipulate the initial organization and the cellular composition of the system and, in favorable situations, the composition of the extracellular matrix and the activities of candidate adhesive molecules.     

Historical Burden In Systematics And The Interrelationships Of 'Parareptiles'

The interrelationships within the clade comprised of turtles, pareiasaurs, and procolophonid-like taxa are investigated via a cladistic analysis incorporating 56 characters. A single most parsimonious tree was found (80 steps, c. i. = 0·8) in which the successive outgroups to turtles are: pareiasaurs, Sclerosaurus, lanthanosuchids, procolophonoids (=Owenetta, Barasaurus and procolophonids), and nyctiphruretians (= nycteroleterids). Thus, as suggested recently by other workers (Reisz, in Fischman, 1993) turtles are the highly modified survivors of a radiation of poorly-known reptiles commonly called ‘parareptiles’. Pareiasaurs are united with turtles on the basis of twenty unambiguous derived features which are absent in other basal amniotes (=‘primitive reptiles’) and reptiliomorph amphibians: for example, the medially located choana, enlarged foramina palatinum posterius, blunt cultriform process, fully ossified medial wall of the prootic, opisthotic-squamosal suture, lateral flange of exoccipital, loss of ventral cranial fissure, thickened braincase floor, ‘pleurosphenoid’ ossification, reduced presacral count, acromion process, trochanter major, reduced fifth pedal digit, and presence of transverse processes on most caudals. Recent phylogenetic proposals linking turtles with captorhinids, with dicynodonts, and with procolophonoids are evaluated. None of the proposed traits supporting the first two hypotheses is compelling. The procolophonoid hypotheses is supported by only one synapomorphy (the slender stapes). All other synapomorphies proposed in favour of the above groupings either occur in many other primitive amniotes, or are not primitive for turtles, or are not primitive for the proposed chelonian sister-group. Nyctiphruretus and Lanthanosuchids and nycteroleterids, often considered to be seymouriamorph amphibians, are demonstrated unequivocally to be amniotes. The ‘rhipaeosaurs’, currently considered to be pareiasaur relatives, are shown to be a heterogenous assemblage of seymouriamorphs, therapsids and nycteroleterids. The phylogeny proposed here indicates that many of the traits of the earliest known turtle, Proganochelys, previously interpreted as unique specialisations, also occur in pareiasaurs and other near outgroups of turtles, and must instead represent the primitive chelonian condition: for example, the wide parietals and the short quadrate flange of the pterygoid. The sequence of acquisition of chelonian traits is discussed: many features once thought to be diagnostic of turtles actually characterize larger groupings of procolophonomorphs, and must have evolved long before the chelonian shell appeared. These traits include most of the chelonian-pareiasaur synapomorphies listed above, and many others which characterize more inclusive groupings found in this analysis. In putting Proganochelys much closer to the main line of chelonian evolution, in elucidating the sequence of acquisition of chelonian traits, and in reducing greatly the number of differences between turtles and their nearest relatives, this study helps bridge one of the major gaps in the fossil record. The failure of previous cladistic analyses to identify correctly the nearest relatives of turtles is attributed to biased character selection, caused by an over-reliance on cranial characters deemed ‘important’ by earlier workers, and by a tendency to shoehorn ‘parareptile’ taxa into phylogenies derived from analyses restricted to ‘mainstream’ groups such as synapsids, diapsids, turtles, and ‘captorhinomorphs’. Many of the synapomorphies that resolve turtle origins are postcranial, and the three nearest outgroups to turtles are all highly bizarre groups which were dismissed as ‘too specialized’ by early workers and continued to be inadequately assessed even by workers using a cladistic framework.     

Reductionism Redux: Computing the Embryo

This paper argues that the consensus physicalist antireductionism in the philosophy of biology cannot accommodate the research strategy or indeed the recent findings of molecular developmental biology. After describing Wolperts programmatic claims on its behalf, and recent work by Gehring and others to identify the molecular determinants of development, the paper attempts to identify the relationship between evolutionary and developmental biology by reconciling two apparently conflicting accounts of bio-function – Wrights and Nagels (as elaborated by Cummins). Finally, the paper seeks a way of defending the two central theses of physicalist antireductionism in the light of the research program of molecular developmental biology, by sharply reducing their metaphysical force.     

Historical Biogeography: Evolution in Time and Space

Biogeography is the discipline of biology that studies the present and past distribution patterns of biological diversity and their underlying environmental and historical causes. For most of its history, biogeography has been divided into proponents of vicariance explanations, who defend that distribution patterns can mainly be explained by geological, tectonic-isolating events; and dispersalists, who argue that current distribution patterns are largely the result of recent migration events. This paper provides an overview of the evolution of the discipline from methods focused on finding general patterns of distribution (cladistic biogeography), to those that integrate biogeographic processes (event-based biogeography), to modern probabilistic approaches (parametric biogeography). The latter allows incorporating into biogeographic inference estimates of the divergence time between lineages (usually based on DNA sequences) and external sources of evidence, such as information on past climate and geography, the organism fossil record, or its ecological tolerance. This has revolutionized the discipline, allowing it to escape the dispersal versus vicariance dilemma and to address a wider range of evolutionary questions, including the role of ecological and historical factors in the construction of biomes or the existence of contrasting patterns of range evolution in animals and plants.     

ABA信号通路的起源与进化

植物激素脱落酸（abscisic acid,ABA）在植物的生长、发育和胁迫反应方面起重要的调控作用,其信号转导通路由4个核心组分共同组成一个双重负调控系统（PYR/PYL/RCAR—| PP2C—| SnRK2—ABF/AREB）,调控ABA应答反应。本文在综述和分析ABA信号通路4个核心组分的起源与进化的基础上,初步提出ABA信号通路的起源与进化路径：A类PP2C、第Ⅲ亚类SnRK2以及转录因子AREB/ABF在水生植物轮藻中已经进化产生,当陆生植物进化产生ABA受体PYR/PYL/RCAR后,即与其它3个组分形成完整的ABA信号通路。在植物进化过程中,ABA信号通路4个核心组分各家族成员的数量（亚类）呈递增趋势。     

Functional Cerebral Asymmetry and Its Possible Evolution in Historical Times

The paper addresses problems of the development of visual spatial functions of the right hemisphere of the human brain in ontogeny and phylogeny. The problem is being treated as an interdisciplinary one, and its potential as evidence of significant changes in cerebral asymmetry in historical times is discussed. Data from evolutionary physiology, anthropology, neuropsychology, and visual art history beginning with the Paleolithic are considered together. The authors pay special attention to such functions as perception of volume of objects and depth of three-dimensional visual scenery as well as perception of the face and emotional expressiveness both in clinical pathology and in normal subjects at different stages of ontogeny, and the appearance of these features in the history of art.     

Mechanistic Approaches to Community Ecology: A New Reductionism

Mechanistic approaches to community ecology are those whichemploy individual— ecological concepts—those ofbehavioral ecology, physiological ecology, and ecomorphology—as theoretical bases for understanding community patterns. Suchapproaches, which began explicitly about a decade ago, are justnow coming into prominence. They stand in contrast to more traditionalapproaches, such as MacArthur and Levins (1967),which interpretcommunity ecology almost strictly in terms of "megaparameters.". Mechanistic approaches can be divided into those which use populationdynamics as a major component of the theory and those whichdo not; examples of the two are about equally common. The firstapproach sacrifices a highly detailed representation of individual—ecological processes; the second sacrifices an explicit representationof the abundance and persistence of populations. Three subdisciplines of ecology—individual, populationand community ecology—form a "perfect" hierarchy in Beckner's(1974) sense. Two other subdisciplines—ecosystem ecologyand evolutionary ecology—lie somewhat laterally to thishierarchy. The modelling of community phenomena using sets ofpopulation-dynamical equations is argued as an attempt at explanationvia the reduction of community to population ecology. Much ofthe debate involving Florida State ecologists is over whetheror not such a relationship is additive (or conjunctive), a verystrong form of reduction. I argue that reduction of communityto individual ecology is plausible via a reduction of populationecology to individual ecology. Approaches that derive the population-dynamicalequations used in population and community ecology from individual-ecologicalconsiderations, and which provide a decomposition of megaparametersinto behavioral and physiological parameters, are cited as illustratinghow the reduction might be done. I argue that "sufficient parameters"generally will not enhance theoretical understanding in communityecology. A major advantage of the mechanistic approach is that variationin population and community patterns can be understood as variationin individual-ecological conditions. In addition to enrichingthe theory, this allows the best functional form to be chosenfor modeling higher-level phenomena, where "best" is definedas biologically most appropriate rather than mathematicallymost convenient. Disadvantages of the mechanistic approach arethat it may portend an overly complex, massive and special theory,and that it naturally tends to avoid many-species phenomenasuch as indirect effects. The paper ends with a scenario fora mechanistic-ecological utopia.     

Historical Contingency Drives Compensatory Evolution and Rare Reversal of Phage Resistance

Bacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, whereas others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each individual mutant in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, whereas others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with the same resistance gene acquired more parallel sets of mutations than populations with different resistance genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria–phage coevolution and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides a new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.     

制度变迁视角下的公立医院编制制度改革的历史演进

分析历史发展脉络是推进制度创新的重要基础,公立医院编制制度改革是公立医院改革的重要内容之一。本研究基于制度变迁的理论和视角,对我国公立医院编制制度改革的历史发展沿革进行梳理,分析制度发展脉络,总结变迁规律,为下一阶段的公立医院编制制度改革提供政策建议。     

Historical Biogeography and Body Form Evolution of Ground Squirrels (Sciuridae: Xerinae)

Xerinae is the most species-rich subfamily of the Sciuridae (Rodentia). This group of animals has a long complex evolutionary history, which witnessed severe environmental changes. In this paper, a comprehensive approach integrating information from fossil records, morphological, molecular and geographical data of extant species, and events of paleoclimate and paleogeography, were used to explore the evolutionary processes in the Xerinae. Xerinae probably originated in Eurasia around the early Oligocene, and dispersed to Africa via the Africa-Eurasia Land Bridge on two occasions during the Miocene, and subsequently evolved into the Protoxerini and African Xerini. The tribe Marmotini derived from a Eurasian ancestor and thrived in North America. Tamias re-occupied Eurasia in the early Miocene, while the distributions of Marmota and ‘Spermophilus’ genus-groups were restricted to North America at least until the late Miocene. Global cooling and the emergence of grass-dominated ecosystems from 15 Ma are likely to be the main causes for the radiation of Marmotini. The body form of Xerinae displays an allometric mode of evolution, with ground-living taxa, such as Marmota, Cynomys and Xerus notably enlarged, while Tamias has remained slim in body form. To cope with the global environmental changes, particularly the global cooling induced forest degradation and grassland expansion in the late Miocene, most Marmotini developed into true ground squirrels with short tails. The slim body adaptation in Tamias may be related to competition from tree squirrels, or their hoarding behavior, the latter helping them to cope with cold winter.