Field homology: a meaningful definition

Field homology refers to populations of cells that derive from evolutionarily conserved regions of embryos but are distributed across sets of adult morphological structures that cannot be placed in one-to-one correspondance. The concept of field homology has proven especially attractive to comparative neurologists because it allows them to deal with the fact that sets of nuclei or nuclear subdivisions often cannot be compared on a one-to-one basis across phyletic groups. However, the concept of field homology has recently come under criticism. It has been argued that field homology is theoretically impossible because it requires sequences of developmental stages to be both evolutionarily conserved and evolutionarily modified. It has also been argued that field homology allows overly vague comparisons of adult morphological structures, fails to account for homologous structures that derive from non-homologous embryonic sources, and establishes overly rigid links between embryonic and adult morphology. All of these criticisms may be adequately addressed by explaining field homology in terms of differentiation. The present paper explains field homology in terms of differentiation using the amniote dorsal thalamus to illustrate major points. It is concluded that field homology is a meaningful concept when defined in terms of differentiation, applied to appropriate cases, and properly limited in its comparisons of adult structures.     

Origins of life: An operational definition

Two very different models are used for the scientific study of life's origins: in the Troland-Muller model, life is molecular and its defining characteristic is gene function; in the Oparin-Haldane model, life is cellular and its defining characteristic is metabolic function. While each of these models implicitly defines the living, neither provides criteria by which theemergence of life could be recognized in the laboratory.Anoperational definition of the living makes explicit the system logic of metabolic self-production: (1) that whatever form it may take, life is a function of its biochemical processes; (2) that no single biochemical process has integrity apart from an entire network of processes; (3) that a network of processes can have continuity only by being enclosed within a boundary structure, i.e., by the selective partition of a microenvironment as a domain for the bioenergetic-biosynthetic network; and (4) that life is a single phenomenon, distinct in its continuity of capture and storage of energy in such networks, driving the processes that produce its material constituents.This paper presentsautopoiesis as life-defining and discusses the utility of its criteria in our search for the origins of life on Earth. Enactment of the autopoietic criteria would result in aminimal cell and would demonstrate the experimental recapitulation of life's Archaean origins.     

Characterization of dose-response relationships inferred by statistically significant trend tests

A method is proposed for classifying various experimental outcomes associated with statistically significant trend tests according to a set of sequential testing within a family of closed (under intersections) one-sided tests. The intent of the procedure is to characterize the general shape of implied dose-response relationships, taking care neither to inflate the false-positive (Type I) error rate by overtesting, nor to sacrifice power by overadjusting for multiple comparisons.     

The concept and operational definition of protein epitopes

The antigenic determinants or epitopes of a protein correspond to those parts of the molecule that are specifically recognized by the binding sites or paratopes of certain immunoglobulin molecules. Epitopes are thus relational entities that require complementary paratopes for their operational recognition. Some authors consider that the concept of epitope necessarily involves the two properties of antigenic reactivity (ability to bind to a paratope) and immunogenicity (ability to induce an immune response). Such a view creates difficulties because it makes the existence of epitopes in a protein depend on immunogenetic and regulatory mechanisms of the immunized host. The delineation of epitopes can be achieved by antigenic cross-reactivity studies or by X-ray crystallography. Both approaches require specific criteria for deciding which residues of the antigen are in contact with the paratope and are functionally part of the epitope. The relative contribution of static accessibility, segmental mobility and induced fit to immune recognition remains controversial. Each of the methods used for analysing antigenic specificity is subject to various operational constraints originating from the type of experimental probe and from the format sensitivity and specificity of the immunoassay used. If a protein is assumed to contain as many epitopes as the number of different monoclonal antibodies that can be raised against it, the delineation of epitopes corresponds to the summation in various hosts of the immune repertoire specific for the antigen. Neutralization epitopes are a special subclass of the epitopes of infectious agents and toxins that are specifically recognized by antibody molecules able to neutralize the biological activity of the antigen. The identification of neutralization epitopes is important for the development of synthetic vaccines because it is this type of epitope that should be mimicked by synthesis and used as a vaccine for eliciting protective immunity. The first demonstration that synthetic peptides could elicit antibodies that neutralized viral infectivity was made by Anderer and his colleagues in the 1960s in their work with tobacco mosaic virus. Nearly 20 years passed before it was shown that antibodies to synthetic peptides were also able to neutralize the infectivity of other viruses such as foot-and-mouth disease, polio and hepatitis B viruses.     

Considerations for operational space definition and optimization of a no-salt flowthrough hydrophobic interaction chromatography purification step

No-salt flowthrough hydrophobic interaction chromatography (HIC) has been shown to effectively remove process and product-related impurities from bioprocess streams. In this publication, a panel of six antibodies has been used to demonstrate operating principles for the application of no-salt flowthrough HIC in antibody purification processes. The results indicate that no-salt flowthrough HIC provides robust aggregate clearance across operating conditions including flow rate, and variations in resin ligand density. Additionally, HMW reduction has an optimal pH range relative to the isoelectric point of each molecule and high molecular weight (HMW) reduction can be improved by altering the total protein load and/or HMW concentration to drive binding of high molecular weight species to the resin.     

One operational definition by population: the need for local evaluations of frailty

Frailty is a health problem that increases the probability of developing adverse health outcomes in the elderly. A frequently used way to operationalize frailty is the construction of a frailty index, which is built from the addition of several health deficits that describe biological aging. However, there is no consensus about the number of health deficits for building a frailty index and about which deficits must be chosen. This lack of a standardized frailty index is assumed to be an obstacle for the advancement of research on frailty. The focus of the present article is to propose a theoretically plausible alternative way of operationalizing frailty by means of frailty indexes composed of deficits selected at a local level. These deficits would therefore be different for each given population. This "anthropological approach" is on the opposite side from current trends in frailty research, which is characterized by the search for a standardized operational definition of frailty. The anthropological approach would generate more reliable data by taking into account the specificity of the population to be studied for selecting frailty deficits. In this approach, emotions, motives, and beliefs are as important to determine individuals' health vulnerability as chronic diseases and physical function. Physiological anthropologists are well positioned to contribute to research on frailty by carrying out studies on the selection of the best deficits to operationalize frailty in different populations, with different socio-cultural determinants of health, and living in different environmental life spaces.     

The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools

The stoichiometric matrix, S, represents a mapping of reaction rate vectors into a space of concentration time derivatives. The left null space of the stoichiometric matrix contains the dynamic invariants: a combination of concentration variables, referred to as metabolic pools, whose total concentration does not change over time. By analogy to the traditional reaction map formed by S, a compound map can be derived from -S(T). The analogy to flux analysis of the (right) null space of S enables us to classify the metabolic pools into three categories: Type A that contains chemical elements and their combinations in the form of certain moieties, Type B that contains such moieties in addition to cofactors carrying such moieties that are internal to the network, and Type C that contains only the cofactors. A convex formulation of the basis for the left null space allows us to directly classify the metabolic pools into these three categories. Type B metabolic pools include conservation pools that form conjugates of moiety-occupied and moiety-vacant concentration states of metabolites and cofactors. Type B metabolic pools thus describe the various states of moiety exchange between the primary substrates and the cofactors that capture properties like energy and redox potential. The convex basis gives clear insight into this exchange for glycolytic pathway in human red blood cell, including the identification of high and low energy pools that form conjugates. Examples suggest that pool maps may be more appropriate for signaling pathways than flux maps. The analysis of the left null space of the stoichiometric matrix allows us to define the achievable states of the cell and their physiological relevance.     

An operational strategy for unstable recombinant DNA cultures

A simple operational strategy is shown to offer a viable means of enhancing plasmid stability in chemostat systems where plasmid loss is a common problem. Feedback control can be used to stabilize coexistence states, which are naturally unstable in the system investigated, and thus gurantee retention of the plasmid-carrying strain. The strategy exploits the normally undesirable characteristics of substrate inhibited growth kinetics, and is illustrated with specific reference to methanolutilizing organisms. Since the methodology may be easily implemented in practice, it offers an alternative to costly environmental methods such as antibiotic addition.     

Toward a definition of diaspora

With the emergence of diaspora studies as a field, scholars from different disciplines have offered diverse definitions of the concept of diaspora. Thus far, scholarly debates about what constitutes a diaspora continue to thrive. In this article, I approach this conceptual divide inductively, by analysing how scholars identify and discuss the defining features of diaspora. I have constructed a database that consists of highly cited articles in the social sciences and the humanities that define diaspora. Using ATLAS.ti, a qualitative data analysis software, I coded and aggregated the most prevalent attributes of diaspora in those definitions. The features that appear in at least half of the definitions are dispersal or immigration, location outside a homeland, community, orientation to a homeland, transnationalism, and group identity. These attributes provided me with the foundation to offer a clear, comprehensive, and workable definition of diaspora.     

An operational heat/health warning system in shanghai

Previous research has noted that high surface temperatures within certain offensive air masses can lead to increased mortality. This study assesses the relationship between daily mortality rates and weather within the city of Shanghai, China, while introducing an operational heat/health warning system for the city. Using numerous meteorological observations, the spatial synoptic classification has been used to classify each summer day from 1989 to 1998 into one of eight air mass types for Shanghai. Through the comparative analysis of the daily air mass type and the corresponding Shanghai mortality rate, moist tropical plus (MT+), an extremely hot and humid air mass, was identified as an offensive air mass with the highest rates of mortality. Using stepwise regression, an algorithm was produced to help predict the number of excess deaths that will occur with each occurence of the MT+ airmass. The heat/health warning system was run experimentally in the summer of 2001 and illustrated that the use of a warning system can alert the citys residents of potentially offensive weather situations that can lead to a deterioration in human health.     

On a formal definition of organization

A mathematic definition is proposed to account for the intuitive features of what is usually meant by organization. To account for both functional and structural aspects of organization the rate at which information content of a system changes in time is examined. It can be shown that Shannon's expression for ambiguity in a channel has two different meanings according to whether one is interested in the information transmitted in the channel or in the information transmitted to the observer from a whole system in which the channel is a part of a redundant communication network. This was applied in a previous work to show that the effects of noise on the information content H of a system result in two kinds of ambiguities, “autonomy-producing” and “destructive” leading to increase and decrease in H, respectively. By making use of this observation and Shannon's definition of redundancy R, a single equation for $\text{d}\text{H}\text{dt}$ is proposed to define organization on the basis of a kinetics of change of information content of a system under the effects of environmental noise-producing factors accumulated in time. It is shown how these factors, obviously responsible for a decrease in H, i.e. a “disorganizing” effect, can be responsible also—under certain conditions and up to a certain time or “dose” of noise—for an initial increase in H interpreted as a process of “self”-organization. The autonomy-producing ambiguity is expressed by a term of decrease in redundancy, while a second term in the equation, of decrease in maximum-non-redundant-information content expresses the destructive ambiguity. A given organization is defined at least by three parameters, which determine the main features of its characteristic function H(t). One of them is the initial information content H₀ and has a structural meaning. A second parameter, with a dimension of time, has the meaning of a functional reliability, related to the overall resistance of the system to noise-producing factors. The third parameter, namely the initial redundancy R₀, is both structural and functional in character, since structural redundancy is known to help insure reliability. Various conditions on these parameters lead to various kinds of organizations, with and without self-organizing properties.