Current Problems In The Psychology Of Understanding And The Creation Of "Understanding Systems"

In the Resolution of the CPSU Central Committee entitled "On the journal Kommunist," the creation of "artificial intelligence" is pinpointed as one of the most important sociophilosophical and methodological problems of scientific and technical progress ([Resolution…]. P. 5). The psychological aspects of "artificial intelligence" have been studied fruitfully for a long time in our domestic psychology (see, for example, [Artificial intelligence…]), but the steady refinement of computer technology imposes upon scientists the task of deeper study of the interaction between man and computers.     

HAPSIMU: a genetic simulation platform for population-based association studies

Background

The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices.

Results

To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis.

Conclusion

Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.     

Wie viele Arten? Der Stand der Forschung gegen Ende des Jahrhunderts

How many species have emerged in the whole history of life? We trace the various attempts to answer this question. After reviewing the existing calculations and demonstrating the method we look at the debate about species richness in the Phanerozoic. Finally we present a recalculation of the total number of animals based upon new estimates of the Recent species richness. It is suggested that up to 10 billion animal species might have emerged in the whole history of life, with 200 million being a more conservative estimate. According to the last figure and other data, man has “successfully” eliminated not less than 0,3% of all the animal species that ever existed.     

基于“五位一体”新工科智能信息化教学理念的微生物学线上线下混合式教学改革及实践

近年来,在教育部提出的“一流课程”建设背景下,涌现出了大量的混合式课程。作者团队通过近10年的本科生持续课程培养研究及分析,结合理工科院校背景及信息工程领域优势,初步建立起一套适用于当今“互联网+”背景下的“五位一体”微生物学课程混合式教学体系。课程基于新工科特色内容重构,有效打通了生命科学和工科类课程的联系;随后基于多维度信息化资源,为学生提供分层级和多元化的选择方式;线下开展的高阶性教学活动,为学生科研创新能力打下基础;课程中有效融合系统性育人要素,正确树立学生的价值导向;最后利用大数据开展形成性教学评价,为学生的全过程个性化学习质量保驾护航。该课程基于上述内容持续开展的改革和实践,在不断实践探索中取得了较好的成效。     

The edges of understanding

A culture's icons are a window onto its soul. Few would disagree that, in the culture of molecular biology that dominated much of the life sciences for the last third of the 20th century, the dominant icon was the double helix. In the present, post-modern, 'systems biology' era, however, it is, arguably, the hairball.     

Eric Michaels: An appreciation

… I got into media studies, as an anthropologist, because I believed the media were the belly of the beast, and because I thought television was central to the creation of the extraordinary contradictions that plagued the contemporary world. [Michaels 1983]

It would seem that Malinowski's stricture that the function of the ethnographer was to see the native's culture from the native's own point of view could at last be achieved—literally, and not metaphorically.

What would such a world be like, and more importantly, what problems have we to set before our students now that will, at the least, not hinder them from coming to an understanding of an age in which man presents himself not in person but through the mediation of visual symbolic forms… It is now no longer possible for the student of culture to ignore the fact that people all over the world have learned, and will continue in great numbers to learn, how to use the visual symbolic mode. Anthropologists must begin to articulate the problems that will face us in trying to understand others when their point of view is known to us primarily through movies distributed by broadcast television and cable. [Worth 1981: 94–95]     

The relation of plants to public health

In addition to furnishing clothing, food and shelter—the basic necessities of life—plants, in their utilization by man, have also furnished problems of public health in their production of alcohol, narcotics, allergies, poisons and specific human diseases.     

Advances in theranostic biomarkers for tumor immunotherapy

Cancer treatment has known a revolution with the emergence of immune checkpoint inhibitors. However, accurate theranostic biomarkers are lacking. In this review, we discuss different types of biomarkers currently under investigation. First, we focus on tissue biomarkers including PD-L1 expression by immunohistochemistry—the first Food and Drug Administration—approved biomarker—despite conflicting results. In addition, we report on novel biomarkers, including protein-based, molecular (tumor mutational load, immune signature…), circulating (neutrophil-to-lymphocyte ratio, serum cytokines…), and imaging-based biomarkers (radiomic signatures and positron-emission tomography using radiolabeled antibodies). We highlight the limitations of each candidate biomarker and finally discuss combinatorial approaches for their use and the opportunity to switch from a predictive strategy of biomarker research to an adaptive one in the field of cancer immunotherapy.     

Concept of the "physiological age" of animals and its application to ixodid ticks

The definition "physiological age" of animals has been revised. A new definition has been formulated on the basis of V. N. Beklemishev's (1962) and Ju. S. Balashov's (1962) theses as follows: physiological age of animals (= biological) is an extent of general irreversible morphophysiological change of organism during its whole life and determined by the accumulation of irreversible changes as a result of its normal vital activity. This definition is equivalent to that of "biological ages" of man. The contents of this definition is enlarged and the possibility of its use for different animals including their males is unified. On the basis of the general concept this definition is specified in regard to ixodid ticks: physiological age of hungry ixodid tick is an extent of general irreversible morpholophysiological change of its organism during the whole life and determined by the state of reserve nutrient and excretory substances. According to the amount of reserve and excretory substances in the organism of ixodid tick we distinguish 4 main physiological ages: new-born, young, mature and old which reflect general biological regularity of age development of animals.     

The Gold-Plated Leucotomy Standard and Deep Brain Stimulation

Walter Freeman, the self styled neurosurgeon, became famous (or infamous) for psychosurgery. The operation of frontal leucotomy swept through the world (with Freeman himself performing something like 18,000 cases) but it has tainted the whole idea of psychosurgery down to the present era. Modes of psychosurgery such as Deep Brain Stimulation and other highly selective neurosurgical procedures for neurological and psychiatric conditions are in ever-increasing use in current practice. The new, more exciting techniques are based in a widely held philosophical position on the relationship between the mind, brain and soul, which is the key to ethical debates in this area. Psychosurgery has always posed questions of responsibility, personality, character, identity, spirit, relationship, integrity, and human flourishing and they do not go away when we enter the brave new world of neuroethics and Deep Brain Stimulation.     

Double coned inverse sandwich complexes [M-(η4-C4H4)-M′] of Gr-IA and Gr-IIA Metals: theoretical study of electronic of structure and second hyperpolarizability

Molecular interaction between dioxane and methanol involves certain polar and nonpolar bonding to form a one to one complex. Interatomic distances between hydrogen and oxygen within 3 Å have been considered as hydrogen bonding. Optimizations of the structures of dioxane-methanol complexes were carried out considering any spatial orientation of a methanol molecule around a chair/boat/twisted-boat conformation of dioxane. From 45 different orientations of dioxane and water, 23 different structures with different local minima were obtained and the structural characteristics like interatomic distances, bond angles, dihedral angles, dipole moment of each complex were discussed. The most stable structure, i.e., with minimum heat of formation is found to have a chair form dioxane, one O-H…O, and two C-H…O hydrogen bonds. In general, the O-H…O hydrogen bonds have an average distance of 1.8 Å while C-H…O bonds have 2.6 Å. The binding energy of the dioxane-methanol complex is found to be a linear function of number of O-H…O and C-H…O bonds, and hydrogen bond length. Graphical Abstract

Sixteen orientations of methanol around dioxane converge to six local minima including the global minima with one H-O…H and two C-H…O hydrogen bonds.     

« Biology/medicine 2.0 »: an overview

In the last decade, the applications known as "web 2.0" (Facebook, Youtube, Twitter…) have changed our daily life and gradually influence the field of research. This article aims at proposing a critical overview of these new services, and emphasizes the changes induced for researchers (practice of scientific publication, sharing and mutualization of research data and discussion between researchers…) especially in the field of biology/medicine. A focus is done on the limitations that prevent most of scientists from using these services in their common practice (lack of knowledge about these tools, time-consuming, fear of sharing data and ideas). Despite these restrictions, some mutations affecting researcher's information uses are unavoidable, and these new tools may rapidly contribute to scientific advances.     

A new method to characterize saturation functions by their first four moments

The calculation of the first four moments of saturation functions is proposed as a method to describe the properties of enzymes or receptors models. The values of these moments in the case of the Langmuir or Michaelis-Menten equation and the Hill equation are reviewed. They have been calculated for the second degree Adair equation and in the case of binding site heterogeneity. A method for generalization to cases of greater complexity is also proposed. The advantage of this method over the classical ones—graphical representations and derivation of coefficients like n_H, $\text{[L]0.9}\text{[L]0.1}$…—is essentially that the moments are defined by one single value independently of any particular model for the whole of the saturation curve.     

God and natural selection: The Darwinian idea of design

Conclusion If we arrange in chronological order the various statements Darwin made about God, creation, design, plan, law, and so forth, that I have discussed, there emerges a picture of a consistent development in Darwin's religious views from the orthodoxy of his youth to the agnosticism of his later years. Numerous sources attest that at the beginning of the Beagle voyage Darwin was more or less orthodox in religion and science alike.⁷⁸ After he became a transmutationist early in 1837, he concluded that the doctrine of secondary causes must be extented even to the history of life and that after the first forms of life were created, there was no further need for divine intervention, except where man was concerned. Man's body, he thought, was produced by the process of transmutation, but he believed for a time that man's soul was superadded. By mid-1838 he had become convinced that nothing, after the creation of life, was due to miracles. God works only through laws, which are capable of producing every effect of evey kind which surrounds us. The existence of man, the idea of God in man's mind, and the harmony of the whole system were in his eyes prearranged goals of deterministic laws imposed by God. Such a conception excludes the miracles on which Christianity depends; but it is not possible to say whether Darwin's loss of Christian faith, which occurred at about this same time, preceded and made possible his materialism or was rather caused or hastened by it.⁷⁹ In the weeks after his reading of Malthus, Darwin's belief in a plan of creation gave way to the belief that God created matter and life and designed their laws, leaving the details, however, to the workings of chance. This remained his view until the 1860s.There is no exact parallel between this development of Darwin's religious views and the development of his ideas on evolution, but there is a general correspondence. When he believed in a plan of creation, Darwin's theory of transmutation did not depend on struggle or the selection of chance variations. Adaptation was, for him, an automatic response to environmental chance. From late 1838 to 1859 he believed in designed laws and chance, and this belief, too, has its parallel in his theory. The element of chance in natural selection meant that there could be no detailed plan,in which even man's idea of God would be a necessary outcome of nature's laws (man himself is not a necessary outcome of the working of natural selection).⁸⁰ But Darwin still believed nature was programmed to achieve certain general ends. We might say that he believed in a general, though not a special, teleology. Natural selection was for him a law to maximize utility, creating useful organs, retaining vestiges for future use. For many years it was a law designed to produce organisms perfectly adapted to their environments. Only later did Darwin come to doubt even this sort of design in nature.⁸¹ One way of describing the development of Darwin's evolutionary thought is to say that it shows a gradual abandoning of his theistic assumptions, so that by the late 1860s his theory was informed to a slighter extent by notions of purpose and design than it was in 1838 or 1844 or 1859.     

Discrimination in resolving systems II: Ephedrine-substituted mandelic acids

Binary diastereomeric (-) (1R,2S)-ephedrine salts of various mandelic acids obtained from 95% ethanol show considerable differences in solubility. Structures and some properties of the less-soluble (L) and more-soluble (M) solid phases of (-)-ephedrine with unsubstituted mandelic acid, 2-, 3-, and 4-monosubstituted halo (F, Cl, Br) mandelic acids, and 3- and 4-methylmandelic acids have been determined. Salts were found to be binary, without solvent of crystallization, and composed of double-layered arrays of alternating anions and cations linked by H-bonds normal to the layers. H-bonding links charged donors and acceptors usually along a crystallographic 2-fold screw axis. A striking discrimination is evident in that the (2R)-mandelate salts typically display a compact four-atom chain as the H-bonding repeating unit [⁺N—H…O(—C^?—O)…H-N′, C₂¹(4)] while the (2S)-mandelate salts adopt a more dimensionally variable six-atom chain repeating unit [⁺N—H…O—C^?—O…H—N′, C₂²(6)]. Two distinct packing schemes display the shorter H-bonding chain of the (2R)-mandelates which always occurs with ephedrinium ions in the fully extended conformation. Slightly greater packing efficiency and H-bonding energies of the (2R)-mandelate salts correlates with increased fusion points, lower solubilities (95% ethanol), and higher heats of fusion relative to the phase adopted by their diastereoisomers. In contrast, (2S)-mandelate salts exhibit considerably more structural variability involving all three major ephedrinium conformations, and at least four distinct packing motifs. Mandelates with larger 3′-substituents (Cl, Br, methyl) show similar property discriminations, but these occur with an opposing trend, that is, between phases in which the less-soluble salts contain (2S)-mandelates. Salts with 2-bromomandelate do not show property disparities and their structures are dissimilar to the other phases. © 1995 Wiley-Liss, Inc.     

Toolbox for retrovectorologists

Retroviral vectors have actively contributed to the advent of gene therapy as a realistic approach in human therapeutics. At the beginning, the use of retroviral vectors was thought to be as simple as the collection of a viral supernatant that was applied to the desired cell. Rapidly, target resistance to transduction appeared in various conditions, ex vivo as well as in vivo. At that time, retrovectorologists entered an active "back to the bench" era. This phase was thought to have reached its conclusion with the generation of theoretically safe lentiviral vectors and when, in 2000, a first clinical trial using retroviral vectors proved to be successful. Unfortunately, recent developments have shown that we still need to improve our knowledge of several steps in the retroviral life cycle before we can accurately adapt vectors to target specific cells. In this review we will first briefly detail key features of the life cycle of wild-type retroviruses. Thereafter, an overview of the minimal requirements needed to generate retroviral vectors will be followed by the relevant developments in this rapidly moving field. Of note, we have highlighted the crucial biosafety issues in a specific section.     

植物蛋白质组学面临的挑战和前景

目前功能基因组研究开展得如火如荼 ,蛋白质组研究是阐明基因组所表达的真正执行生命活动的全部蛋白质的表达规律和生物功能 ,而植物蛋白质组研究是 2 1世纪整体细胞生物学最重要的内容 ,将为医药、农业和工业的革新提供崭新的思路。当前主要的研究手段为双向凝胶电泳、双向高效柱层析、质谱分析和生物信息学     

Low temperature infrared spectra of polyglycines and C--H...O==C hydrogen bonding in polyglycine II

Infrared spectra of polyglycines I and II obtained at ?170°C. have been compared with those obtained at room temperature. The changes in frequency of some of the C—H stretching bands are consistent with the earlier suggestion that C—H …? O?C hydrogen bonds are present in the structure of polyglycine II.