Essentialism and typological thinking in biological systematics

In biological literature, essentialism and typological thinking are believed to be incompatible with evolutionary ideas. At present, the same considerations underlay the claims to abandon the Linnaean hierarchy, or the fundamental classificatory structure rooted in essentialism. This paper suggests to reconsider the negative views of Plato's typology and Aristotle's essentialism following the narrow interpretations that have nothing to do with the classification of living beings. Plato's theory of 'ideas' (or 'forms') is the basis of classificatory theory; it provided such concepts as 'species', 'genus', 'essence', 'dichotomous division' but the development of this theory in the framework of moral and esthetic values could not be beneficial to biology. Aristotle's essentialism is more complicated and exists in two forms; one of these, or classificatory essentialism, is a modification of Plato's typology; another one, or organismal essentialism, represents the shift of 'essence' from the world of relations between objects to the realm of particular things, where the concept of essence lost its basic meaning. It is senseless to look for unreal 'type of an organism' ('essence of a thing') but precisely this kind of essentialism is attractive for biologists and philosophers. Organismal essentialism is the underlying basis of so-called 'individuality thesis' that is used as a weapon against classificatory essentialism. The same thesis is associated with an extensional vision of taxa that also explains the criticism of Linnaean hierarchy, while the latter is the intentional structure and the first tool suggested for the rank coordination of many unequal taxa.     

The epiglottis in antiquity in medicine and philosophy

In Antiquity, the epiglottis and the related question whether drink enters the lung is a problem embracing both differently organized philosophical strategies and differently developed medical competences. Over the centuries, the history of a physiological question gradually turns into a debate where we find philosophers disagreeing with philosophers and physicians with physicians. A peculiar feature of this debate is that from a certain time on it involves a division between those who defend Plato's view on the subject and those who (philosophers as well as physicians) criticize it. Plato, Aristotle and Chrysippus, the Hippocratic authors and Erasistratus in the testimony of Aulus Gellius, Plutarch and indirectly also of Cicero, and then Galen and Macrobius have a special place in the development of this topic.     

Courses of C-line in schizophrenia

The terminations of the Main Line—C on the plams of 390 schizophrenic male patients were analysed and classified into four modal types according to the direction of their path following Plato's classification (1970). Schizophrenic patients classified into three major sub-categories namely Paranoid (256 palms) Hebephrenic (256 palms), Catatonic (202 palms) and Undifferentiated (66 palms), were taken from the same ethnic group from Yerawada Mental Hospital, Pune and Sassoon General Hospital, Pune (India). Comparisons were made with the respective normal caste control. The frequency of these four model types exhibit strong variations among themselves and between the patients belonging to the sub-categories of schizophrenia. Considerable increase has been observed on the Left Palm of the Paranoid and Catatonic patients for the incidence of Radial and Proximal types. The incidence of Ulnar type showed consistent decrease bilaterally, among all the sub-categories. Absent types showed a steep increase in all the sub-categories of Schizophrenic.     

ONTOGENY AND THE HIERARCHY OF TYPES

Abstract— The long history of belief in a parallelism between ontogeny and a hierarchical order of natural things is reviewed. The meaning of von Baerian recapitulation is analyzed and its implications for cladistic methodology are discussed at two levels: ontogeny and homology. The basic problem inherent in the purported parallelism is that the order of natural things (i.e., the taxic approach to homology) is part of the "world of being" of Platonic ideas, whereas ontogeny and phylogeny (i.e., the transformational approach to homology) belong to Plato's "world of becoming." These two "genera of existence," as Plato put it, being and becoming, are incompatible but complementary views of nature.     

A study of relationship between pulmonary tuberculosis and palmar dermatoglyphic traits

Bilateral inked palmar impressions of 150 male tubercular patients and those of 150 normal controls (males) have been studied comparatively. Patients and controls show deviation from each other with respect to 1. biological concordance-disconcordance in line C and hypothenar patterns, 2. bilateral and left-homolateral (not right) differences in Plato's modal types of line C and 3. occurrence of hypothenar (R + L only) and III interdigital patterns (L-homolateral only). It is significant that tubercular patients do not show any difference with the normal controls in a reliable measure like main-line-index and by and large in occurrence of patterns also (with two exceptions only). Natural selection does not seem to be operative on palmar dermatoglyphic traits.     

Classification of organisms and structuralism in biology

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.     

Perfecting people: selective breeding at the Oneida Community (1869-1879) and the eugenics movement

The paper describes the selective breeding experiment which took place in the Bible Communist Oneida Community in New York State. The Community was founded in 1848 by John Humphrey Noyes and grew to some three hundred members. It disbanded in 1880 and became a joint stock company, Oneida Ltd., which today is a multinational cutlery manufacturer. Between 1869 and 1880 there was a selective breeding programme ("stirpiculture") with parents chosen for intellectual, physical and spiritual characteristics. Fifty-eight children were born. The programme was inspired by Noyes' theology of Perfectionism, Plato's Republic, agricultural selective breeding and concerns about human heredity. It was later justified by Noyes with the writings of Darwin and Galton. The children were followed up and deemed to be superior in physique, intellect, health and other characteristics. Though it attracted attention in its day, the experiment had little influence on the later eugenic movements in the USA and the UK. It is argued that this was because the Community's system of "complex marriage" and the arranged matings were an unacceptably radical challenge to the conventional notions of love and marriage which dominated these later eugenics movements. The first generation of descendants' attempts to bury aspects of the history of the Community also contributed a lack of knowledge of the experiment and its outcome.     

Plato on kinds of animals

Some biologists and philosophers of biology have seen in Plato an especially objectionable version of essentialism or topology. Although kinds of animals are mentioned in almost all of Plato's dialogues, in none of them is there an explicity stated doctrine of animal kinds. An examination of the dialogues has, moreover, failed to reveal some implicit but consistent and unambiguous view of kinds that Plato might have held.     

Thomism and science education: history informs a modern debate

There is no debate over the Theory of Evolution. Among biologiststhe Theory of Evolution is a settled principle. Yet, the issueis far from settled in the larger context of society; betweensectors of lay society and biological scientists in the UnitedStates there is evidence of a deep divide. Faith and reason,religion, and science at odds—that is hardly a recentdivide. It is the premise of the author that the origin of thecurrent conflict over the teaching of evolution stems from afundamental philosophical divide that began long before Darwinfirst proposed his Theory of Evolution. It predates the inclusionof physical and biological sciences in the curriculum of westernuniversities. It is older than either Islam or Christianity.The conflict goes back to Plato's Academy in 385 BC where theschools of Idealism and Realism first emerged as two distinctphilosophical systems. Idealism and Realism diverged over essentialissues of philosophy: What are we, what is true, and how dowe know? Answers to these questions about the natural orderare framed within philosophical constructs, themselves basedupon essential assumptions about the essence of being, the essenceof truth, and the nature of learning. Idealism and Realism developedindependently for over 1500 years into two competing schools:the Augustinians (fundamentally Idealists) and the Latin Averroists(fundamentally Realists). It was over the place of natural philosophyin the curriculum that these two competing schools collidedviolently at the University of Paris in 1252. It was ThomasAquinas who brokered a ceasefire between two embattled schools.Aquinas forged a philosophical system, called Thomism, thatallowed the two schools to agree to disagree to the extent thatin the graduate curriculum of the University Natural Philosophycould be taught apart from theology. This separation of secularor natural philosophy from theology opened the way for the developmentof the empirical sciences, the effects of which are evidenttoday. All but forgotten, however, is that Thomism provideda system for resolving the disparities between these two separateways of knowing, not by compartmentalizing them into separatedomains, but by proving the domains to be philosophically complementary,creating a holistic framework in which to reconcile apparentconflicts between theology (religion) and natural philosophy(science). The essence of this historic compromise and its implicationsfor the teaching of the Theory of Evolution form the core ofthis article.     

Tributyltin-resistant bacteria from estuarine and freshwater sediments.

Resistance to tributyltin (TBT) was examined in populations from TBT-polluted sediments and nonpolluted sediments from an estuary and from fresh water as well as in pure cultures isolated from those sediments. The 50% effective concentrations (EC50s) for populations were higher at a TBT-polluted freshwater site than at a site without TBT, suggesting that TBT selected for a TBT-resistant population. In contrast, EC50s were significantly lower for populations from a TBT-contaminated estuarine site than for those from a site without TBT, suggesting that other factors in addition to TBT determine whether populations become resistant. EC50s for populations from TBT-contaminated freshwater sediments were nearly 30 times higher than those for populations from TBT-contaminated estuarine sediments. We defined a TBT-resistant bacterium as one which grows on trypticase soy agar containing 8.4 microM TBT, a concentration which prevented the growth of 90% of the culturable bacteria from these sediments. The toxicity of TBT in laboratory media was influenced markedly by the composition of the medium and whether it was liquid or solid. Ten TBT-resistant isolates from estuarine sediments and 19 from freshwater sediments were identified to the genus level. Two isolates, each a Bacillus sp., may be the first gram-positive bacteria isolated from fresh water in the presence of a high concentration of TBT. There was a high incidence of resistance to heavy metals: metal resistance indices were 0.76 for estuarine isolates and 0.68 for freshwater isolates.(ABSTRACT TRUNCATED AT 250 WORDS)     

Tributyltin-resistant bacteria from estuarine and freshwater sediments.

Resistance to tributyltin (TBT) was examined in populations from TBT-polluted sediments and nonpolluted sediments from an estuary and from fresh water as well as in pure cultures isolated from those sediments. The 50% effective concentrations (EC50s) for populations were higher at a TBT-polluted freshwater site than at a site without TBT, suggesting that TBT selected for a TBT-resistant population. In contrast, EC50s were significantly lower for populations from a TBT-contaminated estuarine site than for those from a site without TBT, suggesting that other factors in addition to TBT determine whether populations become resistant. EC50s for populations from TBT-contaminated freshwater sediments were nearly 30 times higher than those for populations from TBT-contaminated estuarine sediments. We defined a TBT-resistant bacterium as one which grows on trypticase soy agar containing 8.4 microM TBT, a concentration which prevented the growth of 90% of the culturable bacteria from these sediments. The toxicity of TBT in laboratory media was influenced markedly by the composition of the medium and whether it was liquid or solid. Ten TBT-resistant isolates from estuarine sediments and 19 from freshwater sediments were identified to the genus level. Two isolates, each a Bacillus sp., may be the first gram-positive bacteria isolated from fresh water in the presence of a high concentration of TBT. There was a high incidence of resistance to heavy metals: metal resistance indices were 0.76 for estuarine isolates and 0.68 for freshwater isolates.(ABSTRACT TRUNCATED AT 250 WORDS)     

Taxonomic significance of yeast sphaeroplast release after enzymatic treatment of intact cells.

Treatment of whole yeast cells with a mixture of a reducing agent and 1,3-beta-glucanase isolated from Basidiomycete QM806 led to the production of sphaeroplasts from ascomycetes, from some fungi imperfecti, but not from basidiomycetes. Association of 1,3-beta-glucanase with a second enzyme, 1,4-alpha-glucanase, from Trichoderma viride, was required for sphaeroplast release from some, but not all, basidiomycetes and fungi imperfecti. The ability of yeast cells to liberate sphaeroplasts following appropriate enzymic treatment is proposed as a taxonomic criterion for differentiating basidiomycetous from ascomycetous yeasts and for classifying fungi imperfecti yeasts.     

Intersession reliability of vertical jump height in women and men

The purpose of the present study was to investigate the intersession reliability of vertical jump height in women and men recorded from a contact mat. Thirty-five women and 35 men performed four testing sessions across a 4-week period, with each session separated by 1 week. Within each testing session, subjects completed three countermovement vertical jumps (CMJs) for maximum height. Reliability statistics were calculated using the highest jump (HIGH) and also from the mean of all three jumps (3 MEAN) during each session. Reliability was calculated as a change in the mean, coefficients of variation (CVs), and intraclass correlations coefficients (ICCs) between testing sessions. For women, jump heights were not substantially different between sessions for either the HIGH or 3 MEAN data. The CVs for women ranged from 4.4 to 6.6% for HIGH and 4.1 to 6.0% for 3 MEAN, with the corresponding ICCs ranging from 0.87 to 0.94 for HIGH and 0.90 to 0.95 for 3 MEAN. For men, jump heights were not substantially different between sessions for HIGH. However, jump heights during session 1 were substantially greater than those during session 2 when using the 3 MEAN data. CVs between sessions for HIGH ranged from 4.0 to 5.6%, and those for 3 MEAN ranged from 4.2 to 5.2%. The ICCs ranged from 0.87 to 0.93 for HIGH and from 0.89 to 0.93 for 3 MEAN. Given the maximal nature of vertical jump tests, it seems appropriate to use the highest jump from a number of trials for women and men when using a contact mat. Practitioners and researchers can use the data to identify the range in which the true value of an athlete's score lies and calculate sample sizes for studies assessing height during CMJs recorded from a contact mat.     

An affinity-column procedure for the purification of veratrate O-demethylase from fungi.

An affinity column procedure is reported for purifying veratrate O-demethylase from higher fungi. The procedure is based on the affinity of the fungal demethylases for veratrate, which was coupled to AH-Sepharose 4B. An over 300-fold purification of the enzyme from an Ascomycete (Chaetomium piluliferum), and a lower degree of purification (20-fold) from a Basidiomycete (Xerocomus badius), were obtained. The O-demethylases from higher fungi require NADH and oxygen. The enzyme activity is sensitive to exposure to oxygen. The pH optima are 5 for enzyme from Chaetomium, and 7 for demethylase from Xerocomus, respectively. The enzymes are not specific for veratrate. They also demethylate p- and m-anisate and 3,4-dimethoxycinnamate, but to a lower degree.     

An architecture for biological information extraction and representation

Motivations: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data. RESULTS: In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation. CONTACT: aditya_vailaya@agilent.com.     

Simultaneous detection and identification of Bacillus cereus group bacteria using multiplex PCR

Bacillus cereus group bacteria share a significant degree of genetic similarity. Thus, to differentiate and identify the Bacillus cereus group efficiently, a multiplex PCR method using the gyrB and groEL genes as diagnostic markers is suggested for simultaneous detection. The assay yielded a 400 bp amplicon for the groEL gene from all the B. cereus group bacteria, and a 253 bp amplicon from B. anthracis, 475 bp amplicon from B. cereus, 299 bp amplicon from B. thuringiensis, and 604 bp amplicon from B. mycoides for the gyrB gene. No nonspecific amplicons were observed with the DNA from 29 other pathogenic bacteria. The specificity and sensitivity of the B. cereus group identification using this multiplex PCR assay were evaluated with different kinds of food samples. In conclusion, the proposed multiplex PCR is a reliable, simple, rapid, and efficient method for the simultaneous identification of B. cereus group bacteria from food samples in a single tube.     

Seasonal variation in white spot syndrome virus-positive samples in broodstock and post-larvae of Penaeus monodon in Thailand

Records of PCR test results for white spot syndrome virus (WSSV) were reviewed in Thailand from 1998 to 2000 for wild Penaeus monodon broodstock purchased by hatcheries and for post-larvae (PL) brought by farmers to diagnostic laboratories for testing. Samples for PCR comprised DNA extracts from the last pleopod dissected from broodstock females after the first spawning and DNA extracts from whole, homogenized PL. There was a consistent pattern of fluctuation in percentage of WSSV-positive broodstock and PL. In broodstock, the fluctuation pattern was similar each year, with a low percentage (0 to 6%) from January to May and a higher percentage (6 to 18%) for the rest of the year, with a peak from September to November. The fluctuation pattern for PL was similar but offset with peaks and troughs occurring approximately 2 mo after those for the broodstock. The peak percentages of broodstock-positive samples were roughly constant from year to year, but those for PL decreased progressively in magnitude from 1998 to 2000. Examination of a small number of hatcheries in 2000 revealed that the percentage of WSSV-positive PL samples was significantly lower for hatcheries that routinely discarded WSSV-PCR-positive wild broodstock when compared to hatcheries that did not.     

Fruit cuticle lipid composition and water loss in a diverse collection of pepper (Capsicum)

Pepper (Capsicum spp.) fruits are covered by a relatively thick coating of cuticle that limits fruit water loss, a trait previously associated with maintenance of postharvest fruit quality during commercial marketing. To shed light on the chemical‐compositional diversity of cuticles in pepper, the fruit cuticles from 50 diverse pepper genotypes from a world collection were screened for both wax and cutin monomer amount and composition. These same genotypes were also screened for fruit water loss rate and this was tested for associations with cuticle composition. Our results revealed an unexpectedly large amount of variation for the fruit cuticle lipids, with a more than 14‐fold range for total wax amounts and a more than 16‐fold range for cutin monomer amounts between the most extreme accessions. Within the major wax constituents fatty acids varied from 1 to 46%, primary alcohols from 2 to 19%, n‐alkanes from 13 to 74% and triterpenoids and sterols from 10 to 77%. Within the cutin monomers, total hexadecanoic acids ranged from 54 to 87%, total octadecanoic acids ranged from 10 to 38% and coumaric acids ranged from 0.2 to 8% of the total. We also observed considerable differences in water loss among the accessions, and unique correlations between water loss and cuticle constituents. The resources described here will be valuable for future studies of the physiological function of fruit cuticle, for the identification of genes and QTLs associated with fruit cuticle synthesis in pepper fruit, and as a starting point for breeding improved fruit quality in pepper.     

The kinetics of drug-membrane interactions in human erythrocytes

The time course of the shape transformations and vesicle release in human erythrocytes caused by lysophosphatidylcholine and chlorpromazine was monitored using a light microscope-video recording technique. The time required for the erythrocytes to reach a stage I echinocytic shape decreased from 4.0 to 2.0 s, when the concentration of the lysophosphatidylcholine solution injected was increased from 1 to 25 microM. The time required to reach stage II decreased from 8.3 to 3.5 s and that required for vesicle release and the formation of stage IV spherocytes decreased from 78.0 to 11.6 s. Correspondingly, the time needed for the formation of stage I stomatocytes decreased from 2.3 to 1.0 s and that for stage II stomatocytes from 3.1 to 2.0 s, when the ambient chlorpromazine concentration was increased from 50 to 200 microM. The kinetics of the shape transformations of the erythrocytes were dependent on the ambient drug concentration. The rate of shape transformations could be predicted from a formula derived for the kinetics of the incorporation of the detergent into the cell membrane, providing that the affinity coefficient and mass transfer coefficient for drugs changed as a function of the free drug concentration. The results give a time scale for the drug-membrane interactions, i.e., the formation of stages I and II for drug-lipid bilayer interactions and the release of vesicles for drug-cytoskeleton interactions.     

A procedure for regenerating Japonica and Indica varieties of rice from protoplasts

Fertile rice plants have been regenerated from protoplasts of two japonica rice varieties (Radon and Baldo) using a protocol initially developed for plant regeneration from protoplasts of an indica rice. Embryogenic calli were developed from immature embryos of Radon and Baldo rice on a callus induction medium, and then used to establish cell suspensions. Protoplasts were isolated from the cell suspensions, and cultured on a Millipore filter placed on a Kao/agarose medium that contained cell clusters from suspensions of IR52 or IR45. The protoplasts grew vigorously on Kao medium and developed into embryogenic calli within two to three weeks. Somatic embryo development occurred during a subsequent transfer of the calli to an LS medium for two to three weeks. The calli were then transferred to MS or N6 plant regeneration medium, and within one to three weeks, plants regenerated from 21 to 32% of the Radon calli, and 33 to 35% of the Baldo calli. Based upon these results and the previous success in regenerating an indica variety from protoplasts, this procedure has great promise for regenerating a range of rice varieties, and probably for regeneration of other monocotyledonous plants from protoplasts