Homology and the hierarchy of biological systems

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.     

Function without purpose

Philosophers of evolutionary biology favor the so-called etiological concept of function according to which the function of a trait is its evolutionary purpose, defined as the effect for which that trait was favored by natural selection. We term this the selected effect (SE) analysis of function. An alternative account of function was introduced by Robert Cummins in a non-evolutionary and non-purposive context. Cummins's account has received attention but little support from philosophers of biology. This paper will show that a similar non-purposive concept of function, which we term causal role (CR) function, is crucial to certain research programs in evolutionary biology, and that philosophical criticisms of Cummins's concept are ineffective in this scientific context. Specifically, we demonstrate that CR functions are a vital and ineliminable part of research in comparative and functional anatomy, and that biological categories used by anatomists are not defined by the application of SE functional analysis. Causal role functions are non-historically defined, but may themselves be used in an historical analysis. Furthermore, we show that a philosophical insistence on the primary of SE functions places practicing biologists in an untenable position, as such functions can rarely be demonstrated (in contrast to CR functions). Biologists who study the form and function of organismal design recognize that it is virtually impossible to identify the past action of selection on any particular structure retrospectively, a requirement for recognizing SE functions.     

Modularity: a new perspective in biology

Several decades of research in biochemistry and molecular biology have been devoted for studies on isolated enzymes and proteins. Recent high throughput technologies in genomics and proteomics have resulted in avalanche of information about several genes, proteins and enzymes in variety of living systems. Though these efforts have greatly contributed to the detailed understanding of a large number of individual genes and proteins, this explosion of information has simultaneously brought out the limitations of reductionism in understanding complex biological processes. The genes or gene products do not function in isolation in vivo. A delicate and dynamic molecular architecture is required for precision of the chemical reactions associated with "life". In future, a paradigm shift is, therefore, envisaged, in biology leading to exploration of molecular organizations in physical and genomic context, a subtle transition from conventional molecular biology to modular biology. A module can be defined as an organization of macromolecules performing a synchronous function in a given metabolic pathway. In modular biology, the biological processes of interest are explored as complex systems of functionally interacting macromolecules. The present article describes the perceptions of the concept of modularity, in terms of associations among genes and proteins, presenting a link between reductionist approach and system biology.     

Social responsibility in human genetics – a survey

The potential for molecular biological manipulation of human beings is a challenge to the social responsibility of human geneticists. The concept of individual healthcare is compromised by a reductionist approach to human biology which defines health solely in terms of genetics. The ability of professionals working in the fields of molecular biology and human genetics to understand the wider social context of their work and the effects it may have on individual health is rarely discussed. This is a report of a survey of social attitudes and awareness carried out among molecular biologists and human geneticists in Germany. The results reveal differences in the understanding of health and these perceptions are shown to depend on the age and gender of the professionals involved.     

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.     

The prokaryote-eukaryote dichotomy: meanings and mythology.

Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the "prokaryote," in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology.     

Conceptual assessment in the biological sciences: a National Science Foundation-sponsored workshop

Twenty-one biology teachers from a variety of disciplines (genetics, ecology, physiology, biochemistry, etc.) met at the University of Colorado to begin discussions about approaches to assessing students' conceptual understanding of biology. We considered what is meant by a "concept" in biology, what the important biological concepts might be, and how to go about developing assessment items about these concepts. We also began the task of creating a community of biologists interested in facilitating meaningful learning in biology. Input from the physiology education community is essential in the process of developing conceptual assessments for physiology.     

At the dawn of a new revolution in life sciences

In a recently published article Sydney Brenner argued that the most relevant scientific revolution in biology at his time was the breakthrough of the role of "information" in biology.The fundamental concept that integrates this new biological "information" with matter and energy is the universal Turing machine and von Neumann's self-reproducing machines.In this article we demonstrate that in contrast to Turing/von Neumann machines living cells can really reproduce themselves.Additionally current knowledge on the roles of noncoding RNAs indicates a radical violation of the central dogma of molecular biology and opens the way to a new revolution in life sciences.     

Endosymbiosis as a compact ecosystem with material cycling: parasitism or mutualism?

To discover the evolutionary logic of intracellular endosymbiosis, we investigated a theoretical model (simultaneous ordinary differential equations) of a material-cycling system inside a host cell. In the model, we introduced a recently developed cell biology concept called "autophagy", which is a decomposing-recycle process of self-compiled materials found universally among eukaryote cells. Our model is based on traditional simultaneous ODE for natural ecosystems that involve producing, grazing, and decomposing processes in material cycling. In the basic intracellular metabolic system, several enzymes regulate metabolism by synthesizing and converting metabolites into biomolecules that are precursors for enzymes involved in the producing process. Symbionts are involved in grazing processes and autophagosomes that degrade materials are involved in decomposing recycles. We compared and analyzed the local stability of ODE systems in three cases: (1) the independent, free-living cell (the basal state of a cell), (2) the case where symbionts invade and exploit macrobiomaterials as parasites inside a host cell, and (3) the combination where symbionts assist the host's metabolism. We conclude that: (i) as consumers, symbionts are required to have a growth rate that is higher than the rate of autophagosome decomposition, (ii) the host cell with a biomass larger than the threshold size would realize the mutualistic relationship with its symbiont, and (iii) this partnership accelerates the biomaterial turnover flow on the basis of biomaterials.     

Species,sets, and the derivative nature of Philosophy

Concepts and methods originating in one discipline can distort the structure of another when they are applied to the latter. I exemplify this mostly with reference to systematic biology, especially problems which have arisen in relation to the nature of species. Thus the received views of classes, individuals (which term I suggest be replaced by units to avoid misunderstandings), and sets are all inapplicable, but each can be suitably modified. The concept of fuzzy set was developed to deal with species and I defend its applicability. Taxa at all levels are real and participate in biological processes. Analysis of cause and pattern provides the deep structure in which metabiology is grounded; violation of this principle has led to diverse errors in biology.     

A novel terrestrial fish habitat inside emergent logs

Reports of new habitats for a major group of organisms are rare. Fishes display diverse adaptations for temporary (amphibious) existence on land, but to our knowledge, none have ever been reported regularly living inside emergent logs. Here, we show that the mangrove killifish, Kryptolebias marmoratus, a species previously known to emerse (leave the water) regularly, is now known to emerse and aggregate in large numbers inside decaying mangrove logs that have been "galleried" by terrestrial insects. This behavior has now been documented in both Belize, Central America, and Florida, U.S.A., populations and represents the first known case of fishes entering terrestrial woody material. The dense packing of fish in the narrow log galleries may imply a novel social context in which intraspecific aggressive behaviors are reduced, possibly mediated by the physiological limitations imposed within this restrictive habitat.     

Craniofacial development and the evolution of the vertebrates: the old problems on a new background

Based on recent advances in experimental embryology and molecular genetics, the morphogenetic program for the vertebrate cranium is summarized and several unanswered classical problems are reviewed. In particular, the presence of mesodermal segmentation in the head, the homology of the trabecular cartilage, and the origin of the dermal skull roof are discussed. The discovery of the neural-crest-derived ectomesenchyme and the roles of the homeobox genes have allowed the classical concept of head segmentation unchanged since Goethe to be re-interpreted in terms of developmental mechanisms at the molecular and cellular levels. In the context of evolutionary developmental biology, the importance of generative constraints is stressed as the developmental factor that generates the homologous morphological patterns apparent in various groups of vertebrates. Furthermore, a modern version of the germ-layer theory is defined in terms of the conserved differentiation of cell lineages, which is again questioned from the vantage of evolutionary developmental biology.     

Secondary chemical shifts in immobilized peptides and proteins: a qualitative basis for structure refinement under magic angle spinning

Resonance assignments recently obtained on immobilized polypeptides and a membrane protein aggregate under Magic Angle Spinning are compared to random coil values in the liquid state. The resulting chemical shift differences (secondary chemical shifts) are evaluated in light of the backbone torsion angle previously reported using X-ray crystallography. In all cases, a remarkable correlation is found suggesting that the concept of secondary chemical shifts, well established in the liquid state, can be of similar importance in the context of multiple-labelled polypeptides studied under MAS conditions.     

Parallelized shifted‐excitation Raman difference spectroscopy for fluorescence rejection in a temporary varying system

A fluorescence background is one of the common interference factors of the Raman spectroscopic analysis in the biology field. Shifted‐excitation Raman difference spectroscopy (SERDS), in which a slow (typically 1 Hz) modulation to excitation wavelength is coupled with a sequential acquisition of alternating shifted‐excitation spectra, has been used to separate Raman scattering from excitation‐shift insensitive background. This sequential method is susceptible to spectral change and thus is limited only to stable samples. We incorporated a fast laser modulation (200 Hz) and a mechanical streak camera into SERDS to effectively parallelize the SERDS measurement in a single exposure. The developed system expands the scope of SERDS to include temporary varying system. The proof of concept is demonstrated using highly fluorescent samples, including living algae. Quantitative performance in fluorescence rejection and the robustness of the method to the dynamic spectral change during the measurement are manifested.      

蜜环菌生物种及鉴定方法研究进展

蜜环菌属真菌是一类重要的大型真菌,在全世界范围广泛分布。该属中有些种是重要的林木病原菌,有些种则具有很高的食药用价值。由于蜜环菌属真菌形态差异并不明显,缺乏分类特征,该属的分类和鉴定一直是大型真菌的研究热点。自从生物种的概念提出之后,蜜环菌的分类鉴定取得了突破性的进展,目前全球范围内已报道的蜜环菌生物种近40种;而对蜜环菌生物种的鉴定方法则包括了最初的形态学鉴定以及近些年发展起来的分子生物学鉴定方法。本文对当前世界范围内已经鉴定的蜜环菌生物种进行了梳理,并对蜜环菌生物种的鉴定方法的研究进展进行了综述,旨在为蜜环菌的研究提供参考。     

Molecular-genetic imaging: a nuclear medicine-based perspective

Molecular imaging is a relatively new discipline, which developed over the past decade, initially driven by in situ reporter imaging technology. Noninvasive in vivo molecular-genetic imaging developed more recently and is based on nuclear (positron emission tomography [PET], gamma camera, autoradiography) imaging as well as magnetic resonance (MR) and in vivo optical imaging. Molecular-genetic imaging has its roots in both molecular biology and cell biology, as well as in new imaging technologies. The focus of this presentation will be nuclear-based molecular-genetic imaging, but it will comment on the value and utility of combining different imaging modalities. Nuclear-based molecular imaging can be viewed in terms of three different imaging strategies: (1) "indirect" reporter gene imaging; (2) "direct" imaging of endogenous molecules; or (3) "surrogate" or "bio-marker" imaging. Examples of each imaging strategy will be presented and discussed. The rapid growth of in vivo molecular imaging is due to the established base of in vivo imaging technologies, the established programs in molecular and cell biology, and the convergence of these disciplines. The development of versatile and sensitive assays that do not require tissue samples will be of considerable value for monitoring molecular-genetic and cellular processes in animal models of human disease, as well as for studies in human subjects in the future. Noninvasive imaging of molecular-genetic and cellular processes will complement established ex vivo molecular-biological assays that require tissue sampling, and will provide a spatial as well as a temporal dimension to our understanding of various diseases and disease processes.     

The phylotypic stage as a boundary of modular memory: non mechanistic perspective

The concept of the phylotypic stage has been strongly integrated into developmental biology, thanks mostly to drawings presented by Haeckel (Anthropogenie oder Entwicklungsgeschichte des Menschen, 1874). They are printed in every textbook as proof of the existence of the phylotypic stage and the fact of its conservation, albeit many times criticized as misleading and simplifying (Richardson in Develop Biol 172:412–421, 1995, Richardson et al. in Anat Embryo 196:91–106, 1997; Bininda-Emons et al. in Proc R Soc Lond 270:341–346, 2003). Although generally accepted by modern biology, doubt still exists concerning the very existence or the usefulness of the concept. What kind of evolutionary and developmental horizons does it open indeed? This article begins with the history of the concept, discusses its validity and draws this into connotation with the idea of a memory activated throughout the development. Barbieri (The organic codes. An introduction to semantic biology, 2003) considers the phylotypic stage to be a crucial boundary when the genetic program ceases to suffice for further development of the embryo, and supracellular memory of the body plan is activated. This moment clearly coincides with the commencing of the modular development of the embryo. In this article the nature of such putative memory will be discussed.     

Modelling biological processes using workflow and Petri Net models

MOTIVATION: Biological processes can be considered at many levels of detail, ranging from atomic mechanism to general processes such as cell division, cell adhesion or cell invasion. The experimental study of protein function and gene regulation typically provides information at many levels. The representation of hierarchical process knowledge in biology is therefore a major challenge for bioinformatics. To represent high-level processes in the context of their component functions, we have developed a graphical knowledge model for biological processes that supports methods for qualitative reasoning. RESULTS: We assessed eleven diverse models that were developed in the fields of software engineering, business, and biology, to evaluate their suitability for representing and simulating biological processes. Based on this assessment, we combined the best aspects of two models: Workflow/Petri Net and a biological concept model. The Workflow model can represent nesting and ordering of processes, the structural components that participate in the processes, and the roles that they play. It also maps to Petri Nets, which allow verification of formal properties and qualitative simulation. The biological concept model, TAMBIS, provides a framework for describing biological entities that can be mapped to the workflow model. We tested our model by representing malaria parasites invading host erythrocytes, and composed queries, in five general classes, to discover relationships among processes and structural components. We used reachability analysis to answer queries about the dynamic aspects of the model. AVAILABILITY: The model is available at http://smi.stanford.edu/projects/helix/pubs/process-model/.