Rational versus anti-rational interpretations of science: an ape-language case-study

Robert Nola (2003) has argued that anti-rationalist interpretations of science fail to adequately explain the process of science, since objective reasons can be causal factors in belief formation. While I agree with Nola that objective reasons can be a cause of belief, in this paper I present a version of the strong programme in the sociology of knowledge, the Interests Thesis, and argue that the Interests Thesis provides a plausible explanation of an episode in the history of ape-language research. Specifically, I examine Terrace, Petitto, Sandess, & Bever (1979, 1980) illegitimate comparison of the signing of their chimpanzee, Nim, with data from human early childhood language development, and argue that Terrace et al.'s interests played a causal role in determining their sceptical beliefs concerning ape linguistic abilities. However, I go on to argue that Terrace et al.'s interests are not the only causal factors in determining their beliefs: objective reasons, associated with the institution of new methodologies, were also causally determinative of Terrace et al.'s sceptical beliefs. Consequently, I argue that belief formation in science is a multi-factorial affair wherein both interests and objective reasons have causal roles. I finish the paper with two conjectures concerning the proper locus of scientific rationality.     

Intermodal transfer from a visual to an auditory discrimination using an errorless learning procedure

Errorless learning is a technique developed by Terrace [Terrace, H.S., 1963a. Discrimination training with and without “errors”. J. Exp. Anal. Behav. 6, 1-27] to train stimulus discriminations with few or no errors. In the first replication of the original findings, errorless learning was also shown to transfer successfully between two visual discriminations without errors [Terrace, H.S., 1963b. Errorless transfer of a discrimination across two continua. J. Exp. Anal. Behav. 6, 223-232]. In the present experiment, we extended the errorless learning procedure to an intermodal transfer, from a discrimination between red and green colors to a discrimination between high and low tones. The pigeons were divided into two groups: an Experimental Group, which learned both discriminations through errorless learning, and a Control Group, which learned them through trial-and-error. Results showed that pigeons from the Experimental Group learned the red-green discrimination with significantly fewer errors than the Control Group and that errorless learning is effective in transferring from a visual to an auditory discrimination.     

Characterization of all human male synaptonemal complexes by subtelomere multiplex-FISH

During meiotic prophase I, homologous chromosomes synapse and recombine. Both events are of vital importance for the success of meiosis. When homologous chromosomes synapse, a proteinaceous structure called synaptonemal complex (SC) appears along the pairing axis and meiotic recombination takes place. The existence of immunolabeling techniques for SC proteins (SCP1, SCP2 and SCP3) and for DNA mismatch repair proteins present in late recombination nodules (MLH1) allow analyses of both synapsis and meiotic recombination in the gametocyte I. In situ hybridization methods can be applied afterwards because chromatin is preserved during cell fixation for immunoanalysis. The combination of both methodologies allows the analysis of synapsis and the creation of recombination maps for each bivalent. In this work we apply the seven-fluorochrome subtelomere-specific multiplex FISH assay (stM-FISH) to human male meiotic cells previously labeled by immunofluorescence (SCP1, SCP3, MLH1, CENP) to assess its utility for human SC karyotyping. This FISH method consists of microdissected subtelomeric probes labeled combinatorially with seven different fluorochromes. Results prove its usefulness for the identification of all human SCs. Furthermore, by labeling subtelomeric regions this one-single-step method enables the characterization of interstitial and terminal SC fragments and SC delineation even if superposition is present in pachytene spreads.     

联会复合体——原发无精症发病中的重要角色

联会复合体(synaptonemal complex,SC)是一种减数分裂特异性超分子蛋白质结构,与减数分裂I(改罗文)中同源染色体的凝缩、配对、重组和分离密切相关。近年来,联会复合体的研究取得了一系列重要的进展,包括在其组成成分和功能上的一些新发现。在小鼠不育模型中联会复合体及其编码基因的异常可引起精子发生障碍。更重要的是,联会复合体编码基因之一SCP3单个碱基缺失导致的无精症已在人类原发不育患者中得到证实。对联会复合体基因SCP1的进一步研究也正在进行之中。      

The serine carboxypeptidase like gene family of rice (Oryza sativa L. ssp. japonica)

Serine carboxypeptidases (SCPs) comprise a large family of protein hydrolyzing enzymes and have roles ranging from protein turnover and C-terminal processing to wound responses and xenobiotic metabolism. The proteins can be classified into three groups, namely carboxypeptidase I, II and III, based on their coding protein sequences and the fact that each family is characterized by a central catalytic domain of unique topology designated as the “α/β hydrolase fold”. The available SCP protein sequences have been utilized as datasets to build a HMM (hidden Markov model) profile, which is used to search the rice (Oryza sativa L. ssp. japonica) proteome. A total of 71 SCP and serine carboxypeptidase-like (SCPL) protein-coding genes exist in rice. The intron-exon structure, chromosome localization, expression and characteristics of encoded protein sequences of the 71 putative genes are reviewed.     

The interaction between the major capsid protein and the smallest capsid protein of human cytomegalovirus is dependent on two linear sequences in the smallest capsid protein

The assembly of human cytomegalovirus (HCMV) with recombinant systems has not been accomplished. An understanding of specific interactions between individual capsid proteins could point to unique characteristics of the assembly process of HCMV capsids. Similar to its herpes simplex virus counterpart, VP26 (UL35), the HCMV smallest capsid protein (SCP; UL48/49) decorates hexons in the mature capsid. In contrast to VP26, the HCMV SCP is essential for virus assembly. In this study we have shown that the major capsid protein (MCP) and the SCP interact in the cytoplasm of transfected cells and can be coprecipitated from insect cells expressing the MCP and the SCP. Using a two-hybrid reporter assay, we demonstrated that two linear sequences within the SCP are sufficient for SCP and MCP interactions.     

Using a course-long theme for inquiry-based laboratories in a comparative physiology course

I developed an inquiry-based laboratory model that uses a central theme throughout the semester to develop in undergraduate biology majors the skills required for conducting science while introducing them to modern and classical physiological techniques. The physiology laboratory uses a goal-oriented approach, with students working cooperatively in small groups to answer basic biological questions. The student teams work to develop skills associated with experimental design, data analysis, written and oral communication, science literacy, and critical thinking. The laboratory curriculum is a research-based model that offers the advantage of students asking open-ended questions by use of a variety of techniques. For the students and instructor alike, this presents an exciting and challenging approach for learning physiology and basic biological principles. Another advantage of this laboratory model is that it is flexible and adaptable; the central theme can be any that the instructor chooses, and the goals and techniques developed are based on student and instructor needs and interests. Students who have completed this model at Loyola College in Maryland have become equipped with the skills essential for any area of the biological sciences and, most importantly, showed elevated excitement and commitment to learning.     

Structure of Semliki Forest virus core protein

Alphaviruses are enveloped, insect-borne viruses, which contain a positive-sense RNA genome. The protein capsid is surrounded by a lipid membrane, which is penetrated by glycoprotein spikes. The structure of the Sindbis virus (SINV) (the type virus) core protein (SCP) was previously determined and found to have a chymotrypsin-like structure. SCP is a serine proteinase which cleaves itself from a polyprotein. Semliki Forest virus (SFV) is among the most distantly related alphaviruses to SINV. Similar to SCP, autocatalysis is inhibited in SFCP after cleavage of the polyprotein by leaving the carboxy-terminal tryptophan in the specificity pocket. The structures of two different crystal forms (I and II) of SFV core protein (SFCP) have been determined to 3.0 Å and 3.3 Å resolution, respectively. The SFCP monomer backbone structure is very similar to that of SCP. The dimeric association between monomers, A and B, found in two different crystal forms of SCP is also present in both crystal forms of SFCP. However, a third monomer, C, occurs in SFCP crystal form I. While monomers A and B make a tail-to-tail dimer contact, monomers B and C make a head-to-head dimer contact. A hydrophobic pocket on the surface of the capsid protein, the proposed site of binding of the E2 glycoprotein, has large conformational differences with respect to SCP and, in contrast to SCP, is found devoid of bound peptide. In particular, Tyr184 is pointing out of the hydrophobic pocket in SFCP, whereas the equivalent tyrosine in SCP is pointing into the pocket. The conformation of Tyr184, found in SFCP, is consistent with its availability for iodination, as observed in the homologous SINV cores. This suggests, by comparison with SCP, that E2 binding to cores causes major conformational changes, including the burial of Tyr184, which would stabilize the intact virus on budding from an infected cell. The head-to-tail contacts found in the pentameric and hexameric associations within the virion utilize the same monomer surface regions as found in the crystalline dimer interfaces. Proteins 27:345–359, 1997. © 1997 Wiley-Liss, Inc.     

Analysis of chromatin in limited numbers of cells: a PCR-SSCP based assay of allele-specific nuclease sensitivity.

Chromatin can be analysed by assaying its sensitivity to DNase I or other nucleases in purified nuclei. Usually, this is performed by Southern analysis of genomic DNA extracted from nuclease-treated nuclei, a methodology that requires many cells. Applying restriction fragment length polymorphisms (RFLPs), this methodology has been used for parental allele-specific chromatin studies on imprinted mammalian genes. However, such allelic studies are limited by the availability of suitable RFLPs. We therefore developed an alternative, PCR and single strand conformation polymorphism (SSCP)-based assay with which allelic sensitivity to nucleases can be determined in virtually all localised regions that have nucleotide polymorphisms. We also demonstrate that analysis of DNase I sensitivity can be performed on permeabilised cells. Combining the two approaches, in the imprinted mouse U2af1-rs1 gene we analysed parental allele-specific chromatin conformation in limited numbers of cultured cells. We also applied the PCR-SSCP approach to assay allelic DNA methylation at specific restriction enzyme sites. In summary, we developed an allele-specific assay that should be useful for biochemical and developmental investigation of chromatin, in particular for studies on genomic imprinting and X-chromosome inactivation.     

Substrate specificity of the streptococcal cysteine protease.

The streptococcal pyrogenic exotoxin B (SpeB) is an important factor in mediating Streptococcus pyogenes infections. SpeB is the zymogen of the streptococcal cysteine protease (SCP), of which relatively little is known regarding substrate specificity. To investigate this aspect of SCP function, a series of internally quenched fluorescent substrates was designed based on the cleavage sites identified in the autocatalytic processing of SpeB to mature SCP. The best substrates for SCP contain three amino acids in the nonprimed position (i.e. AIK in P(3)-P(2)-P(1)). Varying the length of the substrate on the primed side of the scissile bond has a relatively lower effect on activity. The highest activity (k(cat)/K(M) = 2.8 +/- 0.6 (10(5) x m(-1)s(-1)) is observed for the pentamer 3-aminobenzoic acid-AIKAG-3-nitrotyrosine, which spans subsites S(3) to S(2)' on the enzyme. High pressure liquid chromatography and mass spectrometry analyses show that the substrates are cleaved at the site predicted from the autoprocessing experiments. These results show that SCP can display an important level of endopeptidase activity. Substitutions at position P(2) of the substrate clearly indicate that the S(2) subsite of SCP can readily accommodate substrates containing a hydrophobic residue at that position and that some topological preference exists for that subsite. Substitutions in positions P(3), P(1), and P(1)' had little or no effect on SCP activity. The substrate specificity outlined in this work further supports the similarity between SCP and the cysteine proteases of the papain family. From the data regarding the identified or proposed natural substrates for SCP, it appears that this substrate specificity profile may also apply to the processing of mammalian and streptococcal protein targets by SCP.     

Relative male and female contributions to the supercooling point of their offspring in Microvelia reticulata (Heteroptera: Veliidae)

Cold hardiness is a key life history trait in temperate and polar ectothermic species, as it affects survival during overwintering, but its evolution is poorly understood. While many studies of cold hardiness in insects have shown differences between species, populations or developmental stages, data on the relative contribution of individual genotypes to cold hardiness are scarce and mainly limited to drosophilid fly species. We used a sib‐analysis (paternal half‐sib/full‐sib breeding design) to estimate the relative contributions of parental generation to the supercooling point (SCP) of the offspring of a heteropteran non‐model insect species, Microvelia reticulata (Heteroptera: Gerromorpha: Veliidae). We found that parent identity affected significantly SCP values of their offspring. Magnitudes of estimated sire and dam variance components were similar but the distributions of individual contributions to SCP differed between sires and dams, which points to sex‐specific genetic or parental effects on SCP in this species. The animal model failed to find a realistic estimate of heritability (h²) of SCP, suggesting that the underlying genetics of SCP in M. reticulata can not be characterized by purely additive effects.     

Warning signals, receiver psychology and predator memory

This review identifies four receiver psychology perspectives that are likely to be important in the design and evolution of warning signals. Three of these perspectives (phobia, learning and prey recognition) have been studied in detail, and I include a brief review of recent work. The fourth, a memory perspective, has received little attention and is developed here. A memory perspective asks, 'how might warning signals function to reduce forgetting of avoidances between encounters?'. To answer this question I review data from psychology literature that describe important features of animal long-term memory. These data suggest that components of warning signals may function to reduce forgetting (and therefore increase memorability) by (1) preventing forgetting of learnt prey discriminations; (2) jogging the memories of forgetful predators; and (3) biasing forgetting in favour of prey avoidance when the warning signal of a defended aposematic species is copied by an edible Batesian mimic. A combination of a learning and a memory perspective suggests that the features of aposematic prey that accelerate avoidance learning may also be the features that decelerate forgetting processes. If correct, this would have important implications for the comprehension of signal design. Finally, I suggest that the cryptic appearance of an edible prey may decelerate predator learning and accelerate predator forgetting, to the benefit of the prey. In terms of learning and memory, crypsis may be an antisignal. Copyright 2000 The Association for the Study of Animal Behaviour.     

Electrostatic effects in proteins: comparison of dielectric and charge models.

Two approaches for calculating electrostatic effects in proteins are compared and ana analysis is presented of the dependence of calculated properties on the model used to define the charge distribution. Changes in electrostatic free energy have been calculated using a screened Coulomb potential (SCP) with a distance-dependent effective dielectric permittivity to model bulk solvent effects and a finite difference approach to solve the Poisson-Boltzmann (FDPB) equation. The properties calculated include shifts in dissociation constants of ionizable groups, the effect of annihilating surface charges on the binding of metals, and shifts in redox potentials due to changes in the charge of ionizable groups. In the proteins considered the charged sites are separated by 3.5-12 A. It is shown that for the systems studied in this distance range the SCP yields calculated values which are at least as accurate as those obtained from solution of the FDPB equation. In addition, in the distance range 3-5 A the SCP gives substantially better results than the FDPB equation. Possible sources of this difference between the two methods are discussed. Shifts in binding constants and redox potentials were calculated with several standard charge sets, and the resulting values show a variation of 20-40% between the 'best' and 'worst' cases. From this study it is concluded that in most applications, changes in electrostatic free energies can be calculated economically and reliably using an SCP approach with a single functional form of the screening function.     

Spheroidal carbonaceous particles as a marker for recent sediment distribution

We have tested the hypothesis that spheroidal carbonaceous particles (SCP), emitted from oil and coal combustion, can be used as a marker for recent sediment distribution in lake basins. Sediment traps have been used to study when and how the particles are introduced into a lake, a laboratory experiment has been made to study the depositional behaviour of the particles in relation to other sedimentary constituents, and spatial SCP distributions have been surveyed in three lakes. The results support the hypothesis that SCP can be used as a marker, and also indicate that acidification can change sediment distribution in lakes.     

Ancient evolution of stress-regulating peptides in vertebrates

Recent studies on genomic sequences have led to the discovery of novel corticotropin-releasing factor (CRF) type 2 receptor-selective agonists, stresscopin (SCP)/urocortin III (UcnIII), and stresscopin-related peptide (SRP)/urocortin II (UcnII). In addition, analyses of vertebrate genomes showed that the CRF peptide family includes four distinct genes, CRF, urocortin/urotensin I, SCP/UcnIII, and SRP/UcnII. Each of these four genes is highly conserved during evolution and the identity between mammalian and teleost orthologs ranges from >96% for CRF to >55% for SCP. Phylogenetic studies showed that the origin of each of these peptides predates the evolution of tetrapods and teleosts, and that this family of peptide hormones evolved from an ancestor gene that developed the CRF/urocortin and SCP/SRP branches through an early gene duplication event. These two ancestral branches then gave rise to additional paralogs through a second round of gene duplication. Consequently, each of these peptides participates in the regulation of stress responses over the 550 million years of vertebrate evolution. The study also suggested that the fight-or-flight and stress-coping responses mediated mainly by CRF types 1 and 2 receptors evolved early in chordate evolution. In addition, we hypothesize that the CRF/CRF receptor signaling evolved from the same ancestors that also gave rise to the diuretic hormone/diuretic hormone receptors in insects. Thus, a complete inventory of CRF family ligands and their receptors in the genomes of different organisms provides an opportunity to reveal an integrated view of the physiology and pathophysiology of the CRF/SCP family peptides, and offers new insights into the evolution of stress regulation in vertebrates.     

Impaired passive avoidance acquisition in Wistar rats after restraint/cold stress and/or stresscopin administration

Stresscopin (SCP) and related peptides are new members of the corticotropin-releasing factor (CRF) peptide family that are selective ligands for CRF type 2 receptor; these ligands are essential for maintaining homeostasis after stress. SCP (i.p. injections) was tested on the passive avoidance learning task in stressed Wistar rats; it impaired the formation of memory trace. The retention performance deficit induced by SCP was comparable with the deficit induced by the stressor of restraint/cold. More profound impairment of avoidance response occurred following combined application of SCP and stressor. More specific actions of SCP can be expected from its studies with targeted intracerebral applications.     

An Automated System for Skeletal Maturity Assessment by Extreme Learning Machines

Assessing skeletal age is a subjective and tedious examination process. Hence, automated assessment methods have been developed to replace manual evaluation in medical applications. In this study, a new fully automated method based on content-based image retrieval and using extreme learning machines (ELM) is designed and adapted to assess skeletal maturity. The main novelty of this approach is it overcomes the segmentation problem as suffered by existing systems. The estimation results of ELM models are compared with those of genetic programming (GP) and artificial neural networks (ANNs) models. The experimental results signify improvement in assessment accuracy over GP and ANN, while generalization capability is possible with the ELM approach. Moreover, the results are indicated that the ELM model developed can be used confidently in further work on formulating novel models of skeletal age assessment strategies. According to the experimental results, the new presented method has the capacity to learn many hundreds of times faster than traditional learning methods and it has sufficient overall performance in many aspects. It has conclusively been found that applying ELM is particularly promising as an alternative method for evaluating skeletal age.     

The Synaptonemal Complex Protein SCP3 Can Form Multistranded, Cross-striated Fibers In Vivo

The synaptonemal complex protein SCP3 is part of the lateral element of the synaptonemal complex, a meiosis-specific protein structure essential for synapsis of homologous chromosomes. We have investigated the fiber-forming properties of SCP3 to elucidate its role in the synaptonemal complex. By synthesis of SCP3 in cultured somatic cells, it has been shown that SCP3 can self-assemble into thick fibers and that this process requires the COOH-terminal coiled coil domain of SCP3, as well as the NH₂-terminal nonhelical domain. We have further analyzed the thick SCP3 fibers by transmission electron microscopy and immunoelectron microscopy. We found that the fibers display a transversal striation with a periodicity of ~20 nm and consist of a large number of closely associated, thin fibers, 5–10 nm in diameter. These features suggest that the SCP3 fibers are structurally related to intermediate filaments. It is known that in some species the lateral elements of the synaptonemal complex show a highly ordered striated structure resembling that of the SCP3 fibers. We propose that SCP3 fibers constitute the core of the lateral elements of the synaptonemal complex and function as a molecular framework to which other proteins attach, regulating DNA binding to the chromatid axis, sister chromatid cohesion, synapsis, and recombination.