The gene and the genon concept: a functional and information‐theoretic analysis

Scherrer, Klaus; Jost, Jürgen

doi:10.1038/msb4100123

Cited by 44 publications

(20 citation statements)

References 63 publications

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“…As a result, the delimitation and definition of different types of genes is not as straightforward as it is for molecules at the lower molecular level (e.g. Gerstein et al., 2007; Scherrer and Jost, 2007a,b; Prohaska and Stadler, 2008), because it is not reasonable or practical to use overall compositional and structural identity as a criterion. This explains why the annotation and classification of genes is more difficult and controversial than the description of DNA sequence data.…”

Section: The Linguistic Problem Of Morphologymentioning

confidence: 99%

The linguistic problem of morphology: structure versus homology and the standardization of morphological data

2010

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The present article discusses the need for standardization in morphology in order to increase comparability and communicability of morphological data. We analyse why only morphological descriptions and not character matrices represent morphological data and why morphological terminology must be free of homology assumptions. We discuss why images only support and substantiate data but are not data themselves. By comparing morphological traits and DNA sequence data we reveal fundamental conceptual shortcomings of the former that result from their high average degree of individuality. We argue that the delimitation of morphological units, of datum units, and of evidence units must be distinguished, each of which involves its own specific problems. We conclude that morphology suffers from the linguistic problem of morphology that results from the lack of (i) a commonly accepted standardized morphological terminology, (ii) a commonly accepted standardized and formalized method of description, and (iii) a rationale for the delimitation of morphological traits. Although this is not problematic for standardizing metadata, it hinders standardizing morphological data. We provide the foundation for a solution to the linguistic problem of morphology, which is based on a morphological structure concept. We argue that this structure concept can be represented with knowledge representation languages such as the resource description framework (RDF) and that it can be applied for morphological descriptions. We conclude with a discussion of how online databases can improve morphological data documentation and how a controlled and formalized morphological vocabulary, i.e. a morphological RDF ontology, if it is based on a structure concept, can provide a possible solution to the linguistic problem of morphology.Ó The Willi Hennig Society 2009.Due to the fact that biology has to deal with a continuum of highly complex forms and structures, in which usually no two organisms are completely identical, the comparative approach takes a central role in biological methodology. Although the comparative approach originated in morphology and classification, today it is used in various biological disciplines, among others for the inference of function of very similar structures, thereby saving resources associated with expensive and time-consuming experiments. The comparative approach thus represents one of the most important approaches in biological research. Comparison requires data to be comparable. Moreover, in order to allow the sharing of data and the cooperation of biologists (collective empiricism), data must also be communicable. Communicability of data represents an indication of its objectivity-if a specific observation relies less on the particular scientist who described it than another observation, it is considered to be more objective (aperspectival objectivity sensu Daston, 1992Daston, , 1998Daston and Galison, 1992; procedural objectivity sensu Heintz, 2000).In order to guarantee comparability and communicability of data, each...

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Section: The Linguistic Problem Of Morphologymentioning

confidence: 99%

The linguistic problem of morphology: structure versus homology and the standardization of morphological data

2010

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“…As a result of the unrelenting progress in biology, a lively discussion has now ensued as to what a gene really is [261][262][263][264]. There were times when the notion of a gene was simple.…”

Section: Resultsmentioning

confidence: 99%

Evolvability and Speed of Evolutionary Algorithms in Light of Recent Developments in Biology

Banzhaf

2010

Journal of Artificial Evolution and Applications

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Biological and artificial evolutionary systems exhibit varying degrees of evolvability and different rates of evolution. Such quantities can be affected by various factors. Here, we review some evolutionary mechanisms and discuss new developments in biology that can potentially improve evolvability or accelerate evolution in artificial systems. Biological notions are discussed to the degree they correspond to notions in Evolutionary Computation. We hope that the findings put forward here can be used to design computational models of evolution that produce significant gains in evolvability and evolutionary speed.

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“…For instance on the morphological level biologists have to deal with the linguistic problem of morphology, causing fundamental ambiguities regarding morphological terminology and resulting in a serious slowdown of scientiWc progress in morphology . But also on the genetic level, biologists had to deal with a lack of standards regarding gene names and spellings (Brazma 2001;Stein 2003), not to speak of the conceptual problems of agreeing on a common gene concept (e.g., Beurton et al 2000;Wilson 2005;Gerstein et al 2007;GriYths and Stotz 2007;Scherrer and Jost 2007;Prohaska and Stadler 2008). As a consequence, communication of data is not trivial and comparing data sometimes even impossible, which considerably hampers co-operations between biologists.…”

Section: Introductionmentioning

confidence: 98%

The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology

Vogt

2008

Zoomorphology

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Due to lack of common data standards, the communicability and comparability of biological data across various levels of organization and taxonomic groups is continuously decreasing. However, the interdependence between molecular and higher levels of organization is of growing interest and calls for co-operations between biologists from diVerent methodological and theoretical backgrounds. A general data standard in biology would greatly facilitate such co-operations. This article examines the role that deWned and formalized vocabularies (i.e., ontologies) could have in developing such a data standard. I suggest basic criteria for developing data standards on grounds of distinguishing content, concept, nomenclatural, and format standards and discuss the role of data bases and their use of bio-ontologies in current activities for data standardization in biology. General principles of ontology development are introduced, including foundational ontology properties (e.g. class-subclass, parthood), and how concepts are deWned. After addressing problems that are speciWc to morphological data, the notion of a general structure concept for morphology is introduced and why it is required for developing a morphological ontology. The necessity for a general morphological ontology to be taxon-independent and free of homology assumptions is discussed and how it can solve the problems of morphology. The article concludes with an outlook on how the use of ontologies will likely establish some sort of general data standard in biology and why the development of a set of commonly used foundational ontology properties and the use of globally unique identiWers for all classes deWned in ontologies is crucial for its success.

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The gene and the genon concept: a functional and information‐theoretic analysis

Cited by 44 publications

References 63 publications

The linguistic problem of morphology: structure versus homology and the standardization of morphological data

The linguistic problem of morphology: structure versus homology and the standardization of morphological data

Evolvability and Speed of Evolutionary Algorithms in Light of Recent Developments in Biology

The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology

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