Again on language of biology]

Some time ago I proposed in an Editorial in this journal some considerations on the language of biology. I concluded that, to realize an autonomy of such a language (and therefore of biology), we have to develop a valid language for biology. In such a context, it seemed to me that the term "metaphors" referred to the concepts concerning the information carried by genetic code, was a reasonable one. However, Barbieri's article in this issue of Rivista di Biologia / Biology Forum calls for a reply. Of course, we do not know very much in this field, even if we have some evidence that a sequence of bases on a DNA is not determined only by chance. In any case we can exclude that nature in this occasion has "invented" a code. Nature doesn't "invent" anything: it only follows its rules, that we name "laws of nature". Barbieri quotes the Morse code, but forgets to say that such a code is "conventional" in the sense that it is valid only because it is the result of an "agreement" between Morse and the users of that code. There is nothing more unnatural than a "code": with whom nature should actually have to "reach an agreement"? As a matter of fact, we interpret as "information" what happens by law of nature. Also Barbieri's thesis that genes and proteins are molecular artifacts, assembled by external agents, whereas generally molecules are determined by their bonds, i.e. by internal factors, is a disputable one. It is examined how much an external structure plays a role in ordinary chemical reactions. The "information" of physics is not a semantic information. For such information we can refer to history of literature, telegraphic offices, genetics or biochemistry.     

青海省三江源自然保护区生态移民补偿标准

生态补偿是目前生态学研究的热点,生态补偿的关键问题是补偿标准的确定.将三江源自然保护区的生态移民作为对象,结合确定补偿标准的方法的特点,针对研究区域的实际情况以及我国生态补偿存在的主要问题,运用不同的方法提出了生态移民补偿标准的不同方案,所采用的方法分别是:牲畜机会成本法、草场机会成本法、以果洛新村和河源新村两个移民新村为例的地区发展差异法.结果表明:3种方法的侧重点各不相同,所确定的平均生态补偿标准也稍有不同,分别为1.39万元·户-1·a-1;1.03万元·户-1·a-1;1.1万元·户-1·a-1.研究为确定三江源自然保护区生态补偿的标准提供了科学依据,也为其他地区提供一定的借鉴.     

Increased complexity of radiation-induced chromosome aberrations consistent with a mechanism of sequential formation

Complex chromosome aberrations (any exchange involving three or more breaks in two or more chromosomes) are effectively induced in peripheral blood lymphocytes (PBL) after exposure to low doses (mostly single particles) of densely ionising high-linear energy transfer (LET) alpha-particle radiation. The complexity, when observed by multiplex fluorescence in situ hybridisation (m-FISH), shows that commonly four but up to eight different chromosomes can be involved in each rearrangement. Given the territorial organisation of chromosomes in interphase and that only a very small fraction of the nucleus is irradiated by each alpha-particle traversal, the aim of this study is to address how aberrations of such complexity can be formed. To do this, we applied theoretical "cycle" analyses using m-FISH paint detail of PBL in their first cell division after exposure to high-LET alpha-particles. In brief, "cycle" analysis deconstructs the aberration "observed" by m-FISH to make predictions as to how it could have been formed in interphase. We propose from this that individual high-LET alpha-particle-induced complex aberrations may be formed by the misrepair of damaged chromatin in single physical "sites" within the nucleus, where each "site" is consistent with an "area" corresponding to the interface of two to three different chromosome territories. Limited migration of damaged chromatin is "allowed" within this "area". Complex aberrations of increased size, reflecting the path of alpha-particle nuclear intersection, are formed through the sequential linking of these individual sites by the involvement of common chromosomes.     

A mechanism and its metaphysics: An evolutionary account of the social and conceptual development of science

The claim that conceptual systems change is a platitude. That our conceptual systems are theory-laden is no less platitudinous. Given evolutionary theory, biologists are led to divide up the living world into genes, organisms, species, etc. in a particular way. No theory-neutral individuation of individuals or partitioning of these individuals into natural kinds is possible. Parallel observations should hold for philosophical theories about scientific theories. In this paper I summarize a theory of scientific change which I set out in considerable detail in a book that I shall publish in the near future. Just as few scientists were willing to entertain the view that species evolve in the absence of a mechanism capable of explaining this change, so philosophers should be just as reticent about accepting a parallel view of conceptual systems in science evolving in the absence of a mechanism to explain this evolution. In this paper I set out such a mechanism. One reason that this task has seemed so formidable in the past is that we have all construed conceptual systems inappropriately. If we are to understand the evolution of conceptual systems in science, we must interpret them as forming lineages related by descent. In my theory, the notion of a family resemblance is taken literally, not metaphorically. In my book, I set out data to show that the mechanism which I propose is actually operative. In this paper, such data is assumed.I wish to thank both Michael Ruse and Ronald Giere for suggesting improvements in an early draft of this paper. This paper is an abstract of a very long book. The number of people who helped me in developing the ideas set out in this book is extremely large, so large that I decided to defer expressing my gratitude to them until its appearance.     

Dynamics of the interaction of polyreactive immunoglobulins with immobilized antigens]

The kinetic of polyreactive immunoglobulins (PRIG) and immobilized antigen interaction was examined at different temperatures. It was shown that this process can be described by the so-called "competitive" model, and the relatively simple method for the rate constant determination for this process was developed. According to the "competitive" model PRIG molecule could be either in "active" or in "inactive" state and dynamic equilibrium exist between "active" and "inactive" molecules which strongly depend on incubation temperature. Only "active" PRIG can interact with antigens, and this is the reason of strong temperature dependence of PRIG-antigen interaction. The data also show that the mechanism of PRIG-antigen interaction differ from that of antibody-antigen interaction.     

Implementing noncollective parallel I/O in cluster environments using Active Message communication

A costeffective secondary storage architecture for parallel computers is to distribute storage across all processors, which then engage in either computation or I/O, depending on the demands of the moment. A difficulty associated with this architecture is that access to storage on another processor typically requires the cooperation of that processor, which can be hard to arrange if the processor is engaged in other computation. One partial solution to this problem is to require that remote I/O operations occur only via collective calls. In this paper, we describe an alternative approach based on the use of singlesided communication operations such as Active Messages. We present an implementation of this basic approach called Distant I/O and present experimental results that quantify the lowlevel performance of DIO mechanisms. This technique is exploited to support noncollective parallel shared file model for a large outofcore scientific application with very high I/O bandwidth requirements. The achieved performance exceeds by a wide margin the performance of a well equipped PIOFS parallel filesystem on the IBM SP.     

Induction of ?2 frameshift mutations within alternating GC sequences by carcinogens that bind to the C8 position of guanine residues Development of a specific mutation assay

Summary Using a forward mutation assay we have previously found that N-2-acetylaminofluorene (AAF), a strong chemical carcinogen, induces a majority of frameshift mutations located at specific sequences called mutation hot spots. Among these hot spot sequences, the NarI sequence (GGCGCC), is specific for –2 frameshifts (GGCGCC) GGCC). Interestingly, these frameshift mutations occur independently of a functional umuDC locus. Being interested in elucidating this mutation pathway we have developed a reversion assay that is specific for this class of mutations. The assay is based on the reversion of a +2 frameshift mutant of plasmid pBR322 from tetracycline sensitivity to tetracycline resistance. It is shown that only true reversion events lead to tetracycline resistance. The carcinogen AAF induces this reversion event at a frequency that is increased four- to fivefold over the background frequency. A series of chemical carcinogens which, like AAF, bind covalently to the C8 position of guanine, are compared for their efficiency to induce this specific mutation event. Large variations in the mutagenic efficiency of these chemicals are observed and discussed in terms of the anti/syn conformation of the carcinogen-modified guanine residue. Based on this test, we describe a convenient spot assay that this presently used in our laboratory to isolate Escherichia coli mutants affected in this mutation pathway.     

Persistent spatial patterns for semi-discrete models of excitable media

Excitable media have the property that in the spatially homogeneous configuration there is a globally asymptotically stable equilibrium, and no sustained non-decaying oscillations are possible. If diffusion effects are present, however, experiments seem to indicate the possibility of persistent oscillations. In more than one space dimension this may occur, apparently, even if the initial disturbance is restricted to a compact subset of an open domain in the medium. In this paper we discuss a mathematical model of this phenomenon. The model consists of a doubly infinite coupled system of ordinary differential equations, and therefore is intended to represent a spatially discrete network of interconnected cells.     

Levels of organization in biology: on the nature and nomenclature of ecology's fourth level

Viewing the universe as being composed of hierarchically arranged systems is widely accepted as a useful model of reality. In ecology, three levels of organization are generally recognized: organisms, populations, and communities (biocoenoses). For half a century increasing numbers of ecologists have concluded that recognition of a fourth level would facilitate increased understanding of ecological phenomena. Sometimes the word "ecosystem" is used for this level, but this is arguably inappropriate. Since 1986, I and others have argued that the term "landscape" would be a suitable term for a level of organization defined as an ecological system containing more than one community type. However, "landscape" and "landscape level" continue to be used extensively by ecologists in the popular sense of a large expanse of space. I therefore now propose that the term "ecoscape" be used instead for this fourth level of organization. A clearly defined fourth level for ecology would focus attention on the emergent properties of this level, and maintain the spatial and temporal scale-free nature inherent in this hierarchy of organizational levels for living entities.     

基于“管制平衡”的草原生态补偿政策参与式干预发展评价研究

从整体性治理理论视角出发,深入分析了草原生态补偿政策实施过程中的管制与治理维度,认为草原生态补偿政策是一个"管制平衡"导向型政策,进而提出从"参与式干预发展"的角度对该政策的实施效果进行综合性评价。基于内蒙古锡林郭勒典型草原的一个纯牧业嘎查(村庄)的案例研究,将参与式干预发展评价(PADev)方法的应用进行了详细呈现,并获得了兼具"形成性"和"主体间性"的综合性评价结论与发现。为验证PADev的适合性和科学性,从"元评价"的角度,进一步呈现了基于生态调研和抽样社会调查的评价,作为PADev方法的"验证性"评价。案例研究发现,草原生态补偿政策的地位和作用体现在"草-畜-人"历史性(长达35年,从1983年牲畜承包开始)发展变迁的结构关系中,从政策作用的末端来评价生态补偿政策所产生的生态效益,比较难以直接确定其因果关系,但从基于制度变迁的路径依赖及未来发展的角度,政府主导的生态补偿政策将积极地促进牧民们的自主整合和适应市场的发展,以及"生态载畜量"和"实际载畜量"的收敛趋同。     

On the history of nuclear matrix manifestation

The nonchromatin proteinous residue of the cell nucleus was revealed in our laboratory as early as in 1948 and then identified by light and electron microscopy as residual nucleoli,intranuclear network and nuclear envelope before 1960,This structure termed afterwards as “nuclear residue“,“nuclear skeleton“,“nuclear cage“,“nuclear carcass“etc.,was much later(in 1974) isolated,studied and entitled as “nuclear matrix“ by Berezney and Coffey,to whom the discovery of this residual structure is often wronly ascribed.The real history of nuclear matrix manifestation is reported in this paper.     

Quantification of the Impact of Feature Selection on the Variance of Cross-Validation Error Estimation

Given the relatively small number of microarrays typically used in gene-expression-based classification, all of the data must be used to train a classifier and therefore the same training data is used for error estimation. The key issue regarding the quality of an error estimator in the context of small samples is its accuracy, and this is most directly analyzed via the deviation distribution of the estimator, this being the distribution of the difference between the estimated and true errors. Past studies indicate that given a prior set of features, cross-validation does not perform as well in this regard as some other training-data-based error estimators. The purpose of this study is to quantify the degree to which feature selection increases the variation of the deviation distribution in addition to the variation in the absence of feature selection. To this end, we propose the coefficient of relative increase in deviation dispersion (CRIDD), which gives the relative increase in the deviation-distribution variance using feature selection as opposed to using an optimal feature set without feature selection. The contribution of feature selection to the variance of the deviation distribution can be significant, contributing to over half of the variance in many of the cases studied. We consider linear-discriminant analysis, 3-nearest-neighbor, and linear support vector machines for classification; sequential forward selection, sequential forward floating selection, and the -test for feature selection; and -fold and leave-one-out cross-validation for error estimation. We apply these to three feature-label models and patient data from a breast cancer study. In sum, the cross-validation deviation distribution is significantly flatter when there is feature selection, compared with the case when cross-validation is performed on a given feature set. This is reflected by the observed positive values of the CRIDD, which is defined to quantify the contribution of feature selection towards the deviation variance.[1,2,3,4,5,6,7,8,9,10,11,12,13]     

The origin of crop weed communities composed of summer annuals

Summary Evidence for the origin and dating of crop weed communities composed of summer annuals is to be found in palaeobotanical and archaeological data. There is archaeological evidence that around the middle of the first millennium BC fields were taken into permanent cultivation, even on the poorer soils.Fertilization with lime and manure and Plaggenwirtschaft were evidently involved in this early agriculture. In this paper the idea is put forward that Plaggenwirtschaft resulted in a sudden increase in the number of weed species brought together in cornfields and that this practise led to the very first beginning of our modern weed communities.Translated into English by Drs. C. van Driel-Murray.     

Utility of ADL index for partially dependent older people: discriminating the functional level of an older population

In the present study, the ADL index for the partially dependent older people (Demura et al., 1999) was applied to 218 bedridden (BED), 466 partially dependent (PD) and 245 independent living (IL) people in older groups. The purposes of this study were to clarify the meaning of the evaluation of this index and to examine how ADL items are useful in determining each older group. It is suggested that a perfect score with our ADL index means independent living level, and a score of zero means bedridden level. The results of discriminant analysis indicated that four items with low-difficulty, such as "eating," "going to the toilet," "tossing about in bed" and "writing," are useful in determining if the PD is becoming bedridden. While five items with high-difficulty, such as "putting on slacks," "putting on trousers," "standing up from a sitting posture," "going up stairs" and "washing the whole body," are useful in determining if the PD is becoming independent living. Furthermore, it is inferred that the possibility of falling into a bedridden situation increases when the total score is 5 or less, while the functional level is close to independent living when the total score is 13 or more. These findings make clear the meaning of the evaluation of our ADL index. Furthermore, the functional level of older population may be screened using evaluation of total and item scores of this ADL index.     

Systems biology of symmetry breaking during neuronal polarity formation

Polarization, in which a single axon and multiple dendrites are formed, is crucial for neuronal functions, and symmetry breaking is the initial step of this process. Accumulating studies have revealed a number of molecules that act asymmetrically in neurons, and thereby regulate neuronal polarity. Thus, one of the major goals of current research is to understand how asymmetric signals are generated during the symmetry-breaking step. Current models of neuronal symmetry breaking generally involve "local activation" for induction of axon outgrowth and "global inhibition" to suppress formation of multiple axons and can be categorized into "one-takes-all" and "activator-inhibitor" models. Both types of model incorporate a positive feedback loop to execute local activation, but differ in the manner of global inhibition. Quantitative experimentation combined with computational modeling is a powerful strategy in systems biology, and analyses in this direction have begun to yield a more profound understanding of how neurons break their symmetry during polarity formation.     

Ideas in Theoretical Biology - Comment About the Fractality of the Lung

It is generally believed, that when the surface/volume ratio is high, fractal structure is expected to exist. The branched fractal structure of the lung has been cited as a classical example of this statement. In this short paper I would like to demonstrate that an alternative lung structure (namely sponge-like fractal) is at least as good as, or even better than the branched one, concerning this ratio, therefore, the cause of the lung's fractality lies elsewhere.     

Transplasma membrane electron transport in plants

The presence of transplasma membrane electron transport in a variety of plant cells and tissues is reported. It is now agreed that this property of eukaryotic cells is of ubiquitous nature. Studies with highly purified plasma membranes have established the presence of electron transport enzymes. Two types of activities have been identified. One, termed Standard reductase, is of general occurrence. The other, inducible under iron deficiency and relatively more active, is Turbo reductase. However, the true nature of components participating in electron transport and their organization in the plasma membrane is not known. The electron transport is associated with proton release and uses intracellular NAD(P)H as substrate. The electron flow leads to changes in intracellular redox status, pH, and metabolic energy. The responsiveness of this system to growth hormones is also observed. These findings suggest a role for electron flow across the plasma membrane in cell growth and regulation of ion transport. Involvement of this system in many other cellular functions is also argued.     

On dorsal prothoracic appendages in treehoppers (Hemiptera: Membracidae) and the nature of morphological evidence

A spectacular hypothesis was published recently, which suggested that the "helmet" (a dorsal thoracic sclerite that obscures most of the body) of treehoppers (Insecta: Hemiptera: Membracidae) is connected to the 1st thoracic segment (T1; prothorax) via a jointed articulation and therefore was a true appendage. Furthermore, the "helmet" was interpreted to share multiple characteristics with wings, which in extant pterygote insects are present only on the 2nd (T2) and 3rd (T3) thoracic segments. In this context, the "helmet" could be considered an evolutionary novelty. Although multiple lines of morphological evidence putatively supported the "helmet"-wing homology, the relationship of the "helmet" to other thoracic sclerites and muscles remained unclear. Our observations of exemplar thoraces of 10 hemipteran families reveal multiple misinterpretations relevant to the "helmet"-wing homology hypothesis as originally conceived: 1) the "helmet" actually represents T1 (excluding the fore legs); 2) the "T1 tergum" is actually the anterior dorsal area of T2; 3) the putative articulation between the "helmet" and T1 is actually the articulation between T1 and T2. We conclude that there is no dorsal, articulated appendage on the membracid T1. Although the posterior, flattened, cuticular evagination (PFE) of the membracid T1 does share structural and genetic attributes with wings, the PFE is actually widely distributed across Hemiptera. Hence, the presence of this structure in Membracidae is not an evolutionary novelty for this clade. We discuss this new interpretation of the membracid T1 and the challenges of interpreting and representing morphological data more broadly. We acknowledge that the lack of data standards for morphology is a contributing factor to misinterpreted results and offer an example for how one can reduce ambiguity in morphology by referencing anatomical concepts in published ontologies.