Two faces of the prokaryote concept.

Bacteria had remained undefined when, in 1962, Roger Y. Stanier and C.B. van Niel published their famed paper 'The concept of a bacterium.' The articulation of the prokaryote-eukaryote dichotomy was a vital moment in the history of biology. This article provides a brief overview of the context in which the prokaryote concept was successfully launched in the 1960s, and what it was meant to connote. Two concepts were initially distinguished within the prokaryote-eukaryote dichotomy at that time. One was organizational and referred to comparative cell structure; the other was phylogenetic and referred to a 'natural' classification. Here, I examine how the two concepts became inseparable; how the prokaryotes came to signify a monophyletic group that preceded the eukaryotes, and how this view remained unquestioned for 15 years, until the birth of molecular evolutionary biology and coherent methods for bacteria phylogenetics based on 16S rRNA. Today, while microbial phylogeneticists generally agree that the prokaryote is a polyphyletic group, there is no agreement on whether the term should be maintained in an organizational sense.     

The hidden side of the prokaryotic cell: rediscovering the microbial world.

How many different forms of life exist and how they are evolutionarily related is one of the most challenging problems in biology. In 1962, Roger Y. Stanier and Cornelis B. van Niel proposed "the concept of a bacterium" and thus allowed (micro)biologists to divide living organisms into two primary groups: prokaryotes and eukaryotes. Initially, prokaryotes were believed to be devoid of any internal organization or other characteristics typical of eukaryotes, due to their minute size and deceptively simple appearance. However, the last few decades have demonstrated that the structure and function of the prokaryotic cell are much more intricate than initially thought. We will discuss here two characteristics of prokaryotic cells that were not known to Stanier and van Niel but which now allow us to understand the basis of many characteristics that are fully developed in eukaryotic cells: First, it has recently become clear that bacteria contain all of the cytoskeletal elements present in eukaryotic cells, demonstrating that the cytoskeleton was not a eukaryotic invention; on the contrary, it evolved early in evolution. Essential processes of the prokaryotic cell, such as the maintenance of cell shape, DNA segregation, and cell division, rely on the cytoskeleton. Second, the accumulation of intracellular storage polymers, such as polyhydroxyalkanoates (a property studied in detail by Stanier and colleagues), provides a clear evolutionary advantage to bacteria. These compounds act as a "time-binding" mechanism, one of several prokaryotic strategies to increases survival in the Earth's everchanging environments.     

The concept of mechanism in biology

The concept of mechanism in biology has three distinct meanings. It may refer to a philosophical thesis about the nature of life and biology ('mechanicism'), to the internal workings of a machine-like structure ('machine mechanism'), or to the causal explanation of a particular phenomenon ('causal mechanism'). In this paper I trace the conceptual evolution of 'mechanism' in the history of biology, and I examine how the three meanings of this term have come to be featured in the philosophy of biology, situating the new 'mechanismic program' in this context. I argue that the leading advocates of the mechanismic program (i.e., Craver, Darden, Bechtel, etc.) inadvertently conflate the different senses of 'mechanism'. Specifically, they all inappropriately endow causal mechanisms with the ontic status of machine mechanisms, and this invariably results in problematic accounts of the role played by mechanism-talk in scientific practice. I suggest that for effective analyses of the concept of mechanism, causal mechanisms need to be distinguished from machine mechanisms, and the new mechanismic program in the philosophy of biology needs to be demarcated from the traditional concerns of mechanistic biology.     

Screening,Identification and Distribution of Endophytic Associative Diazotrophs Isolated from Rice Plants

29 strains of endophyte associated diazotrophs isolated from rice ( Oryza sutiva L. ) "Yuefu" plant were selected by in vitro acetylene reduced activity and 15 N2-flxing activity determination. They were identificated into 14 species of 9 genera: Agrobacterium tumefaciens (Smith et Townsend) Conn, A. radiobacter (Beijerinck et van Delden) Conn; Alcaligenes piechaudii Kiredjian et al., Al. denitrificans (Leifson et Hagh) Ruger et Tan; Bacillus sphaericus Meyer et Neide, B. licheniforrnis Weigmann Chester, B. cereus Frankland et Frankland; Chryseomonas luteola (Kodama, Kinnura et Komagata) Holmes et al.; Enterobacter cloacae ( Jordan ) Honnaeche et Edwards, E. sakazakii Famer et al.; E. agglomeraus (Beijerinck) Ewing et Fife; Pseudomonas pseudoalcaligenes Stanier, P. alcaligeaes Monias, P. putida Biotype A Evans and Aeromonas Kluyver et van Niel, Serratia Bizio, Staphyloccocus Rosenbach, Xanthomonas Dowson. Among them C. luteola, E. sakazakii, E. agglomeraus, P. pseudoalcaligenes have not been previously reported as diazotrophs. Studying on the distribution of endophytic dizoatrophs in rice seeds and rice plants has demonstrated that the diversity of endophytic associated diazotrophs in roots was more than that in other organs of rice plant. Endophytic associative diazotroph E. cloacae not only occurred on the surface but also occurred intercellularly in R48 rice roots as observed with scanning electron microscopy and transmission microscopy.     

Willi Hennig’s dichotomization of nature

Two formal assumptions implied in Willi Hennig’s “phylogenetic systematics” were repeatedly criticized for not being biologically grounded. The first is that speciation is always dichotomous; the second is that the stem‐species always goes extinct when its lineage splits into two daughter species. This paper traces the theoretical roots of Hennig’s “principle of dichotomy”. While often considered merely a methodological principle, Hennig’s realist perspective required him to ground the “principle of dichotomy” ontologically in speciation. As a methodological principle, the adherence to a strictly dichotomously structured phylogenetic system allowed Hennig to be unequivocal in character analysis and precise in the rendition of phylogenetic relationships. The ontological grounding of the “principle of dichotomy” in speciation remains controversial, however. This has implications for the application of techniques of phylogeny reconstruction to populations of bisexually reproducing organisms (phylogeography). Beyond that, the “principle of dichotomy” has triggered an intensive debate with respect to phylogeny reconstruction at the prokaryote level. © The Willi Hennig Society 2010.     

TRIBUTE: In Goethe's Wake: Marvalee Wake's conceptual contributions to the development and evolution of a science of morphology

Decrying the typological approach in much of the teaching of morphology, from the outset of her career Marvalee Wake advocated a synthetic, mechanistic and pluralistic developmental and evolutionary morphology. In this short essay, I do not evaluate Wake's contributions to our knowledge of the morphology of caecilians, nor her contributions to viviparity, both of which are seminal and substantive, nor do I examine her role as mentor, supervisor and collaborator, but assess her broader conceptual contributions to the development and evolution of morphology as a science. One of the earliest morphologists to take on board the concept of constraint, she viewed constraint explicitly in relation to adaptation and diversity. Her approach to morphology as a science was hierarchical – measure form and function in a phylogenetic context; seek explanations at developmental, functional, ecological, evolutionary levels of the biological hierarchy; integrate those explanations to the other levels. The explanatory power of morphology thus practised allows morphology to inform evolutionary biology and evolutionary theory, and paves the way for the integrative biology Wake has long championed.     

Biodiversity Realism: Preserving the tree of life

Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’.     

Phylogenetic inertia and Darwin's higher law

The concept of 'phylogenetic inertia' is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of 'phylogenetic inertia' and its relationship to selection are far from clear. After tracing the history of the concept of 'inertia' in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because phylogenetic inertia is, from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss 'phylogenetic inertia,' he did assert the explanatory priority of selection over descent. An analysis of 'phylogenetic inertia' provides a perspective from which to assess Darwin's view.     

Assessing similarity: on homology,characters and the need for a semantic approach to non‐evolutionary comparative homology

The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of “characters” as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre‐Darwinian comparative homology concepts and their problem of invoking non‐material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer‐parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.     

The interaction between developmental bias and natural selection: from centipede segments to a general hypothesis

Do limitations to the ways in which mutations can alter developmental processes help to determine the direction of phenotypic evolution? In the early days of neo-Darwinism, the answer given to this question was an emphatic 'no'. However, recent work, both theoretical and empirical, argues that the answer should at least be 'sometimes', and possibly even a straightforward 'yes'. Here, I examine the key concept of developmental bias, which encompasses both developmental constraint and developmental drive. I review the case of centipede segment number, which is a particularly clear example of developmental bias, but also a rather unusual one. I then consider how, in general terms, developmental bias and natural selection might interact, with the result that it is their interaction, rather than either process on its own, that determines evolutionary direction. Essentially, the whole argument is about the extent to which phenotypic variation is developmentally structured as opposed to amorphous or random. This issue can be traced back to the very beginning of evolutionary biology, and in particular to a difference of opinion between Darwin and Wallace, who emphasized, respectively, character correlation and character independence.     

双歧杆菌属天然质粒系统分类

【背景】以往双歧杆菌质粒分类学研究较少,双歧杆菌属质粒系统分类方法缺失。【目的】建立双歧杆菌属天然质粒系统分类和鉴定方法,促进质粒在双歧杆菌生物学研究中的理解和应用。【方法】利用质粒复制起始蛋白进化树和基因组共线性分析方法,对目前所有已测序的双歧杆菌属天然质粒进行系统分类研究。【结果】双歧杆菌所有已知天然质粒可以划分为6个不同类型的质粒家族和3个独特的复合质粒,家族Ⅲ和家族Ⅵ质粒可进一步划分为不同的亚型类群。家族Ⅲ质粒是双歧杆菌属天然质粒的主要类型和优势家族。家族Ⅵ质粒成员亚型分类最丰富。在质粒家族水平,2种方法的分类结果完全一致。【结论】本文揭示了所有分析质粒之间的系统分类关系,建立了双歧杆菌属天然质粒系统的分类标准、方法和体系,可为今后双歧杆菌天然质粒分类和鉴定提供重要的理论参考和分类依据。     

What, Exactly, is Cladistics? Re-writing the History of Systematics and Biogeography

The development of comparative biology (systematics) has been of interest to philosophers and historians. Particular attention has been placed on the 'war' of the 1970s and 1980s, the apparent dispute among those who preferred this or that methodology. In this contribution we examine the history of comparative biology from the perspective of fundamentals rather than methodologies. Our examination is framed within the artificial-natural classification dichotomy, a viewpoint currently lost from view but worth resurrecting.     

Proper names in twin worlds: Monophyly, paraphyly, and the world around us

This paper addresses the theoretical relevance of monophyletic, paraphyletic and polyphyletic groups under the paradigm of sophisticated scientific realism. The doctrine of metaphysical realism is introduced using the philosophy of Karl Popper as an example, which is then contrasted with scientific realism. A discussion of the nature of causal relations presents an account of counterfactual conditionals. The current state of art casts the theory of phylogenetic systematics in a stark contrast of classes (universals) and individuals (particulars). In practice, however, individuals piggyback on classes, or sets. Natural kinds are introduced in order to overcome this deep dichotomy. The theoretical relevance of natural kinds lies in their explanatory value, and that may change with changing context. It is for this reason that non-monophyletic groups can have explanatory value (their members can function as tokens of causally relevant kinds) within certain domains of evolutionary biology. Explanatory value is maximized by integration of the genealogical hierarchy of species and monophyletic taxa with other areas of evolutionary biology.     

Sequence heterochrony and the evolution of development

One of the most persistent questions in comparative developmental biology concerns whether there are general rules by which ontogeny and phylogeny are related. Answering this question requires conceptual and analytic approaches that allow biologists to examine a wide range of developmental events in well-structured phylogenetic contexts. For evolutionary biologists, one of the most dominant approaches to comparative developmental biology has centered around the concept of heterochrony. However, in recent years the focus of studies of heterochrony largely has been limited to one aspect, changes in size and shape. I argue that this focus has restricted the kinds of questions that have been asked about the patterns of developmental change in phylogeny, which has narrowed our ability to address some of the most fundamental questions about development and evolution. Here I contrast the approaches of growth heterochrony with a broader view of heterochrony that concentrates on changes in developmental sequence. I discuss a general approach to sequence heterochrony and summarize newly emerging methods to analyze a variety of kinds of developmental change in explicit phylogenetic contexts. Finally, I summarize a series of studies on the evolution of development in mammals that use these new approaches.     

The randomness of life: A philosophical approach inspired by the Enlightenment

Did the Enlightenment anticipate modern reflections about the role of chance within cells or in living beings? No, especially if one pays attention to the very different scientific context of that periods and takes care to distrust the concept of "precursors". Nonetheless, several thinkers of the Enlightenment, scientists or philosophers, have constructed an opposition between the random and order that shares some links with modern concerns. More precisely, philosophers like Diderot and some physicians, chemists or naturalists, have articulated the necessity and contingency in opposition to the idea of an absolute natural order and to any preformed "germ" explaining the development of animals. But I will argue that this subtle concept also diverges from the idea of a universal determinism developed by Laplace. There is a way to deal with natural necessity and the universal interdependence of phenomena without excluding the random, going beyond the classical - though posterior to the eighteenth century - opposition between determinism and indeterminism. Particularly with Diderot, the Enlightenment presents an epistemology of the random loosely attached to the natural sciences, producing a philosophical reflection that can be linked with some modern issues of biology. I examine two examples: the criticism of the explanation of order by order, and the thesis that probability can tell us something about natural productions through the idea of randomized "expression," e.g., stochastic expression of genes for modern molecular biology and expressions of natural forms for Diderot.     

A major clade of prokaryotes with ancient adaptations to life on land

Evolutionary trees of prokaryotes usually define the known classes and phyla but less often agree on the relationships among those groups. This has been attributed to the effects of horizontal gene transfer, biases in sequence change, and large evolutionary distances. Furthermore, higher level clades of prokaryote phyla rarely are supported by information from ecology and cell biology. Nonetheless, common patterns are beginning to emerge as larger numbers of species are analyzed with sophisticated methods. Here, we show how combined evidence from phylogenetic, cytological, and environmental data support the existence of an evolutionary group that appears to have had a common ancestor on land early in Earth's history and includes two-thirds of known prokaryote species. Members of this terrestrial clade (Terrabacteria), which includes Cyanobacteria, the gram-positive phyla (Actinobacteria and Firmicutes), and two phyla with cell walls that differ structurally from typical gram-positive and gram-negative phyla (Chloroflexi and Deinococcus-Thermus), possess important adaptations such as resistance to environmental hazards (e.g., desiccation, ultraviolet radiation, and high salinity) and oxygenic photosynthesis. Moreover, the unique properties of the cell wall in gram-positive taxa, which likely evolved in response to terrestrial conditions, have contributed toward pathogenicity in many species. These results now leave open the possibility that terrestrial adaptations may have played a larger role in prokaryote evolution than currently understood.     

Methodology in Aristotle’s Theory of Spontaneous Generation

Aristotle’s theory of spontaneous generation offers many puzzles to those who wish to understand his theory both within the context of his biology and within the context of his more general philosophy of nature. In this paper, I approach the difficult and vague elements of Aristotle’s account of spontaneous generation not as weaknesses, but as opportunities for an interesting glimpse into the thought of an early scientist struggling to reconcile evidence and theory. The paper has two goals: (1) to give as charitable and full an account as possible of what Aristotle’s theory of spontaneous generation was, and to examine some of its consequences; and (2) to reflect on Aristotle as a scientist, and what his comments reveal about how he approached a difficult problem. In particular, I propose that the well-recognized problem of the incompatibility between Aristotle’s concept of spontaneity and his theory of spontaneous generation presents an opportunity for insight into his scientific methodology when approaching ill-understood phenomena.     

Coherence, correspondence, and the renaissance of morphology in phylogenetic systematics

The decline in morphological phylogenies has become a pronounced trend in contemporary systematics due to a disregard for theoretical, methodological, conceptual, and philosophical approaches. The role and meaning of morphology in phylogenetic reconstruction and classification have been undermined by the following: (i) the ambiguous delineation of morphological characters; (ii) the putative “objectivity” of molecular data; (iii) that morphology has not been included in data matrices; (iv) that morphology has been mapped onto molecular cladograms; and (v) a separation of a paradigmatic relationship among morphology, phylogeny, and classification. Historical/philosophical arguments including the synthesis of coherence (coherentism) and correspondence (foundationalism) theories—i.e. “foundherentism” as a theory of epistemic justification—provide support for a renaissance of morphology in phylogenetic systematics. In the language of systematics, coherence theory corresponds to the logical/operational congruence of character states translated into a hierarchical/relational system of homologues and monophyletic groups as natural kinds. Correspondence theory corresponds to the empirical/causal accommodation of homologues and monophyletic groups as natural kinds grounded in the concept of semaphoront, and in developmental biology, genetics, inheritance, ontogenesis, topology, and connectivity. The role and meaning of morphology are also discussed in the context of separate and combined analyses, palaeontology, natural kinds, character concepts, semaphoront, modularity, and taxonomy. Molecular systematics suffers from tension between coherence and correspondence theories, and fails to provide a pragmatic language for predicates in science and in everyday life. Finally, the renaissance of morphology is not only dependent on a scientific/philosophical perspective but also depends on political, economic, social, and educational reforms in contemporary systematics. © The Willi Hennig Society 2009.     

Towards a historization of aposematism

Aposematism is one of the oldest phenomena in evolutionary biology and still a major puzzle to biologists. Despite its evolutionary nature, most attempts to understand aposematism are devoid of phylogenetic components. In addition, most studies that do take phylogeny into account need to bring the analysis even further. We argue that in order to fully understand aposematism we must have a clear picture of the evolutionary history behind present behaviours. In this paper we frame aposematism in a phylogenetic context and argue that most studies still are wanting in terms of demonstrating aposematism. Aposematism is not an end product but rather evolutionary scenarios including character transformations as well as prey–predator interactions. Finally, we suggest that, regardless how we restrict the concept of aposematism, knowing the directions of events facilitate all kinds of comparisons with a promise of uniting functional and evolutionary aspects into a historization of aposematism.