Saving our science from ourselves: the plight of biological classification

Saving our science from ourselves: the plight of biological classification. Biological classification ( nomenclature, taxonomy, and systematics) is being sold short. The desire for new technologies, faster and cheaper taxonomic descriptions, identifications, and revisions is symptomatic of a lack of appreciation and understanding of classification. The problem of gadget-driven science, a lack of best practice and the inability to accept classification as a descriptive and empirical science are discussed. The worst cases scenario is a future in which classifications are purely artificial and uninformative.

Taxonomy and nomenclature of the bronzed cowbird, currently called Tangavius aeneus [by] Kenneth C. Parkes and Emmet R. Blake.

v.44:no.22(1964)

Saving our science from ourselves: the plight of biological classification

Saving our science from ourselves: the plight of biological classification. Biological classification ( nomenclature, taxonomy, and systematics) is being sold short. The desire for new technologies, faster and cheaper taxonomic descriptions, identifications, and revisions is symptomatic of a lack of appreciation and understanding of classification. The problem of gadget-driven science, a lack of best practice and the inability to accept classification as a descriptive and empirical science are discussed. The worst cases scenario is a future in which classifications are purely artificial and uninformative.

Lithological studies : a description and classification of the rocks of the Cordilleras / by M.E. Wadsworth. With eight plates.

v.11:no.1 (1884)

New Strategies on Molecular Biology Applied to Microbial Systematics

Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50’s and 60’s. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint

Revisio generum plantarum:vascularium omnium atque cellularium multarum secundum leges nomenclaturae internationales cum enumeratione plantarum exoticarum in itinere mundi collectarum ... /mit erläuterungen von Dr. Otto Kuntze.

v.3 pt. 1-3

Revisio generum plantarum:vascularium omnium atque cellularium multarum secundum leges nomenclaturae internationales cum enumeratione plantarum exoticarum in itinere mundi collectarum ... /mit erläuterungen von Dr. Otto Kuntze.

v.2

Revisio generum plantarum:vascularium omnium atque cellularium multarum secundum leges nomenclaturae internationales cum enumeratione plantarum exoticarum in itinere mundi collectarum ... /mit erläuterungen von Dr. Otto Kuntze.

v.1

Human Endogenous Retrovirus (HERV) Insertional Polymorphisms

Human endogenous retroviruses (HERVs) are the result of ancient germ cell infections of human germ cells by exogenous retroviruses. HERVs belong to the long terminal repeat (LTR) group of retrotransposons that comprise ~8% of the human genome. The majority of the HERVs documented have been truncated and/or incurred lethal mutations and no longer encode functional genes; however a very small number of HERVs seem to maintain functional in making new copies by retrotranspositon as suggested by the identification of a handful of polymorphic HERV insertions in human populations. The objectives of this study were to identify novel insertion of HERVs via analysis of personal genomic data and survey the polymorphism levels of new and known HERV insertions in the human genome. Specifically, this study involves the experimental validation of polymorphic HERV insertion candidates predicted by personal genome-based computation prediction and survey the polymorphism level within the human population based on a set of 30 diverse human DNA samples. Based on computational analysis of a limited number of personal genome sequences, PCR genotyping aided in the identification of 15 dimorphic, 2 trimorphic and 5 fixed full-length HERV-K insertions not previously investigated. These results suggest that the proliferation rate of HERVKs, perhaps also other ERVs, in the human genome may be much higher than we previously appreciated and the recently inserted HERVs exhibit a high level of instability. Throughout this study we have observed the frequent presence of additional forms of genotypes for these HERV insertions, and we propose for the first time the establishment of new genotype reporting nomenclature to reflect all possible combinations of the pre-integration site, solo-LTR and full-length HERV alleles.

Post-collisional lamprophyric event in Sierra Norte, Cordoba, Argentina: Mineralogical, geochemical and isotopic characteristics

Over 20 lamprophyre dykes, varying in width between a few centimeters and several meters, have been identified in central Sierra Norte - Eastern Pampean Ranges, Cordoba, Argentina. Their mineralogy and chemistry indicate that they are part of the calc-alkaline lamprophyres clan (CAL). They contain phenocrysts of magnesiohomblende +/- augite set in a groundmass of magnesiohornblende, calcic-plagioclase, alkali feldspar, and opaque minerals, which designate them as spessartite-type lamprophyres. Alteration products include chlorite, calcite and iron oxides after malfic phenocrysts, though some are partially replaced by actinolite. Feldspars are replaced by carbonate and clay minerals. The dykes are relatively primitive, and show restricted major element variation (SiO(2) 51.1-55.3 wt.%, Al(2)O(3) 12-16.6 wt.%, total alkalies 1.5-4.7 wt.%), high Mg# (55-77), high Cr contents (27-988 ppm) and moderate to high Ni contents (60-190 ppm). Lamprophyre LILE (e.g. Rb averages 110 ppm, Sr 211-387 ppm, Ba 203-452 ppm) are high relative to HFSE (e.g., Ta 0.2-1.6 ppm, Nb 4-11 ppm, Y 17-21 ppm), and are enriched in LREE (30-70 times chondrite). They are characterized by relatively high (208)Pb/(204)Pb (38.8-39.9), (207)Pb/(204)Pb(similar to 15.7), and (206)Pb/(204)Pb (18.7-20.1), combined with low (epsilon)epsilon(Nd) (-4.69 to -1.52) and a relative moderately high ((87)Sr/(86)Sr)(i) of 0.7055-0.7074. The Rb-Sr whole rock isochron indicates an Early Ordovician age of 485 +/- 25 Ma. The calculated T(DM) (1.7 Ga) suggests that these rocks appear to have originated from a reservoir that was created during a mantle metasomatism event related to the Pampean orogeny. The Sierra Norte lamprophyres show affinities with a subduction-related magma in an active continental margin. Their geochemical and isotopic features suggest a multicomponent source, composed of enriched mantle material variably contaminated by crustal components. The lamprophyric suite emplacement occurred at the dawning stage of the Pampean orogeny, in a regional post-collisional extensional setting developed in the Sierra Norte-Ambargasta batholith (SNAB) in Early Ordovician times. (C) 2008 Published by Elsevier Ltd.

Revised nomenclature and classification of inherited ichthyoses: results of the First Ichthyosis Consensus Conference in Sorèze 2009.

BACKGROUND: Inherited ichthyoses belong to a large, clinically and etiologically heterogeneous group of mendelian disorders of cornification, typically involving the entire integument. Over the recent years, much progress has been made defining their molecular causes. However, there is no internationally accepted classification and terminology. OBJECTIVE: We sought to establish a consensus for the nomenclature and classification of inherited ichthyoses. METHODS: The classification project started at the First World Conference on Ichthyosis in 2007. A large international network of expert clinicians, skin pathologists, and geneticists entertained an interactive dialogue over 2 years, eventually leading to the First Ichthyosis Consensus Conference held in Sorèze, France, on January 23 and 24, 2009, where subcommittees on different issues proposed terminology that was debated until consensus was reached. RESULTS: It was agreed that currently the nosology should remain clinically based. "Syndromic" versus "nonsyndromic" forms provide a useful major subdivision. Several clinical terms and controversial disease names have been redefined: eg, the group caused by keratin mutations is referred to by the umbrella term, "keratinopathic ichthyosis"-under which are included epidermolytic ichthyosis, superficial epidermolytic ichthyosis, and ichthyosis Curth-Macklin. "Autosomal recessive congenital ichthyosis" is proposed as an umbrella term for the harlequin ichthyosis, lamellar ichthyosis, and the congenital ichthyosiform erythroderma group. LIMITATIONS: As more becomes known about these diseases in the future, modifications will be needed. CONCLUSION: We have achieved an international consensus for the classification of inherited ichthyosis that should be useful for all clinicians and can serve as reference point for future research.

Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009

Different types of cell death are often defined by morphological criteria, without a clear reference to precise biochemical mechanisms. The Nomenclature Committee on Cell Death (NCCD) proposes unified criteria for the definition of cell death and of its different morphologies, while formulating several caveats against the misuse of words and concepts that slow down progress in the area of cell death research. Authors, reviewers and editors of scientific periodicals are invited to abandon expressions like 'percentage apoptosis' and to replace them with more accurate descriptions of the biochemical and cellular parameters that are actually measured. Moreover, at the present stage, it should be accepted that caspase-independent mechanisms can cooperate with (or substitute for) caspases in the execution of lethal signaling pathways and that 'autophagic cell death' is a type of cell death occurring together with (but not necessarily by) autophagic vacuolization. This study details the 2009 recommendations of the NCCD on the use of cell death-related terminology including 'entosis', 'mitotic catastrophe', 'necrosis', 'necroptosis' and 'pyroptosis'.

Allergic reactions following contrast material administration: nomenclature, classification, and mechanisms

In forensic pathology routine, fatal cases of contrast agent exposure can be occasionally encountered. In such situations, beyond the difficulties inherent in establishing the cause of death due to nonspecific or absent autopsy and histology findings as well as limited laboratory investigations, pathologists may face other problems in formulating exhaustive, complete reports, and conclusions that are scientifically accurate. Indeed, terminology concerning adverse drug reactions and allergy nomenclature is confusing. Some terms, still utilized in forensic and radiological reports, are outdated and should be avoided. Additionally, not all forensic pathologists master contrast material classification and pathogenesis of contrast agent reactions. We present a review of the literature covering allergic reactions to contrast material exposure in order to update used terminology, explain the pathophysiology, and list currently available laboratory investigations for diagnosis in the forensic setting.