“Trees Live on Soil and Sunshine!”- Coexistence of Scientific and Alternative Conception of Tree Assimilation

Successful learning is the integration of new knowledge into existing schemes, leading to an integrated and correct scientific conception. By contrast, the co-existence of scientific and alternative conceptions may indicate a fragmented knowledge profile. Every learner is unique and thus carries an individual set of preconceptions before classroom engagement due to prior experiences. Hence, instructors and teachers have to consider the heterogeneous knowledge profiles of their class when teaching. However, determinants of fragmented knowledge profiles are not well understood yet, which may hamper a development of adapted teaching schemes. We used a questionnaire-based approach to assess conceptual knowledge of tree assimilation and wood synthesis surveying 885 students of four educational levels: 6^th graders, 10^th graders, natural science freshmen and other academic studies freshmen. We analysed the influence of learner’s characteristics such as educational level, age and sex on the coexistence of scientific and alternative conceptions. Within all subsamples well-known alternative conceptions regarding tree assimilation and wood synthesis coexisted with correct scientific ones. For example, students describe trees to be living on “soil and sunshine”, representing scientific knowledge of photosynthesis mingled with an alternative conception of trees eating like animals. Fragmented knowledge profiles occurred in all subsamples, but our models showed that improved education and age foster knowledge integration. Sex had almost no influence on the existing scientific conceptions and evolution of knowledge integration. Consequently, complex biological issues such as tree assimilation and wood synthesis need specific support e.g. through repeated learning units in class- and seminar-rooms in order to help especially young students to handle and overcome common alternative conceptions and appropriately integrate scientific conceptions into their knowledge profile.     

Deep space and hidden depths: understanding the evolution and ecology of fungal entomopathogens

Entomopathogens are important natural enemies of many insect and mite species and as such have been recognised as providing an important ecosystem service. Indeed, fungal entomopathogens have been widely investigated as biological control agents of pest insects in attempts to improve the sustainability of crop protection. However, even though our understanding of the ecology of fungal entomopathogens has vastly increased since the early 1800s, we still require in-depth ecological research that can expand our scientific horizons in a manner that facilitates widespread adoption of these organisms as efficient biological control agents. Fungal entomopathogens have evolved some intricate interactions with arthropods, plants and other microorganisms. The full importance and complexity of these relationships is only just becoming apparent. It is important to shift our thinking from conventional biological control, to an understanding of an as yet unknown “deep space”. The use of molecular techniques and phylogenetic analyses have helped us move in this direction, and have provided important insights on fungal relationships. Nevertheless, new techniques such as the PhyloChip and pyrosequencing might help us see beyond the familiar fields, into areas that could help us forge a new understanding of the ecology of fungal entomopathogens.     

Still More “Fancy” and “Myth” than “Fact” in Students’ Conceptions of Evolution

College students do not come to biological sciences classes, including biological anthropology, as “blank slates.” Rather, these students have complex and strongly held scientific misconceptions that often interfere with their ability to understand accurate explanations that are presented in class. Research indicates that a scientific misconception cannot be corrected by simply presenting accurate information; the misconception must be made explicit, and the student must decide for him or herself that it is inaccurate. The first step in helping to facilitate such conceptual change among college students is to understand the nature of the scientific misconceptions. We surveyed 547 undergraduate students at the University of Missouri-Columbia on their understanding of the nature and language of science, the mechanisms of evolution, and their support for both Lamarckian inheritance and teleological evolution. We found few significant sex differences among the respondents and identified some common themes in the students’ misconceptions. Our survey results show that student understanding of evolutionary processes is limited, even among students who accept the validity of biological evolution. We also found that confidence in one’s knowledge of science is not related to actual understanding. We advise instructors in biological anthropology courses to survey their students in order to identify the class-specific scientific misconceptions, and we urge faculty members to incorporate active learning strategies in their courses in order to facilitate conceptual change among the students.     

Coppice Harvesting of Fuelwood Species on a South African Common: Utilizing Scientific and Indigenous Knowledge in Community Based Natural Resource Management

The limitations of Community Based Natural Resource Management (CBNRM) with respect to the difficulties of comparing local versus scientific knowledge categories within a bounded definition of ‘community’ were investigated by means of a study exploring local indigenous knowledge pertaining to harvesting technique, and the impact of soil and species type on the post-harvest coppice response of popular savanna fuelwood species, among rural inhabitants of the Bushbuckridge region of the Limpopo Province, South Africa. Soils and plants were evaluated chiefly in terms of their perceived ability to retain precipitation, making rainfall a driving force in local understanding of environmental productivity. Some indigenous knowledge showed an agreement with biological data, but overall the variability in responses, as well as the diverse scales at which indigenous and scientific knowledge is directed, were too great to allow for simplistic parallels between local ecological indices to be made. Indigenous environmental knowledge was underscored by the perceived symbolic link between environmental and social degradation. It is recommended that environmental managers incorporate indigenous knowledge as a component of a systems-level approach to natural resource management, where biological, cultural, economic, and symbolic aspects of natural resource use are nested within a broader ecosocial system. This approach to indigenous knowledge is offered as an alternative to the simple scientific evaluation that so often characterizes environmental management.     

Is There Any Possible Genotoxic Effect in Exfoliated Bladder Cells of Rat Under the Exposure of 1800 MHz GSM-Like Modulated Radio Frequency Radiation (RFR)?

People are exposed to many carcinogenic and mutagenic chemicals in their everyday lives. These include antineoplastic drugs, Polycyclic aromatic hydrocarbons (PAH)s, aromatic amines, nitrosamines, metals, and electromagnetic radiation. Based on the state of knowledge acquired during the last 50 years of research on possible biological effects of electromagnetic fields (EMF), the majority of the scientific community is convinced that exposure to EMF below the existing security limits does not cause a risk to the health of the general public. However, this position is questioned by others, who are of the opinion that the available research data are contradictory or inconsistent and, therefore, unreliable.

In this study, we aimed to investigate if there is any effect of 1800?MHz GSM modulated radio frequency radiation (RFR) on the number of micronucleus in exfoliated bladder cells of rat which will be informative about the genotoxic damage. Exposure period was 20?min/day, 5 days/week during a month. Six female Wistar rats were used for two groups: Group I (n=6): controls; Group II (n=6): 1.8?GHz exposed animals. 1800?MHz RFR did not showed a significant MN frequencies in rat bladder cells when compared with the control group (p>0.05). 1800?MHz RFR-exposed animals did not produce any genotoxic effect when compared with the control group ( p>0.05). Kinetic studies are important for any biomarker, especially those in which tissue differentiation and maturation processes will heavily influence the time between induction of damage and collection of damaged cells for micronucleus analysis.     

Science in the age of mechanical reproduction: moral and epistemic relations between diagrams and photographs

Sociologists, philosophers and historians of science are gradually recognizing the importance of visual representation. This is part of a more general movement away from a theory-centric view of science and towards an interest in practical aspects of observation and experimentation. Rather than treating science as a matter of demonstrating the logical connection between theoretical and empirical statements, an increasing number of investigations are examining how scientists compose and use diagrams, graphs, photographs, micrographs, maps, charts, and related visual displays. This paper focuses on diagrams in biology, and tries to demonstrate how diagrams are an integral part of the production of scientific knowledge. In order to disclose some of the distinctive practical and analytical uses of diagrams, the paper contrasts the way diagrams and photographs are used in biological texts. Both diagrams and photographs are shown to be “constructions” that separately and together mediate the investigation of scientific phenoman.     

Dark extinction: the problem of unknown historical extinctions

The extinction of species before they are discovered and named (dark extinction, DE) is widely inferred as a significant part of species loss in the ‘pre-taxonomic’ period (approx. 1500–1800 CE) and, to some extent, in the ‘taxonomic period’ (approx. 1800–present) as well. The discovery of oceanic islands and other pristine habitats by European navigators and the consequent introduction of destructive mammals, such as rats and goats, started a process of anthropogenic extinction. Much ecosystem change happened before systematic scientific recording, so has led to DE. Statistical methods are available to robustly estimate DE in the ‘taxonomic period’. For the ‘pre-taxonomic period’, simple extrapolation can be used. The application of these techniques to world birds, for example, suggests that approximately 56 DEs occurred in the ‘taxonomic period’ (1800–present) and approximately 180 in the ‘pre-taxonomic period’ (1500–1800). Targeting collection activities in extinction hotspots, to make sure organisms are represented in collections before their extinction, is one way of reducing the number of extinct species without a physical record (providing that collection efforts do not themselves contribute to species extinction).     

Education for science and science for education: more than a play upon words

In the celebration of the Oswaldo Cruz Institute centenary, we wanted to stress our concern with the relationship between two of its missions: research and education. What are the educational bases required for science and technology activities on health sciences for the future years? How can scientists collaborate to promote the popularization of academic knowledge and to improve a basic education for citizenship in an ethic and humanistic view? In this article we pointed out to need of commitment, even in the biomedical post-graduation level, of a more integrated philosophy that would be centered on health education, assuming health as a dynamic biological and social equilibrium and emphasizing the need of scientific popularization of science in a cooperative construction way, instead of direct transfer of knowledge, preserving also macro views of health problems in the development of very specific studies. The contemporary explosion of knowledge, particularly biological knowledge, imposes a need of continuous education to face the growing illiteracy. In order to face this challenge, we think that the Oswaldo Cruz Institute honors his dialectic profile of tradition and transformation, always creating new perspectives to disseminate scientific culture in innovator forms.     

Comprehensive Metabolomic,Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis

Yarrowia lipolytica is an oleaginous ascomycete yeast that accumulates large amounts of lipids and has potential as a biofuel producing organism. Despite a growing scientific literature focused on lipid production by Y. lipolytica, there remain significant knowledge gaps regarding the key biological processes involved. We applied a combination of metabolomic and lipidomic profiling approaches as well as microscopic techniques to identify and characterize the key pathways involved in de novo lipid accumulation from glucose in batch cultured, wild-type Y. lipolytica. We found that lipids accumulated rapidly and peaked at 48 hours during the five day experiment, concurrent with a shift in amino acid metabolism. We also report that exhaustion of extracellular sugars coincided with thickening of the cell wall, suggesting that genes involved in cell wall biogenesis may be a useful target for improving the efficiency of lipid producing yeast strains.     

Gravitational biology within the German Space Program: goals, achievements, and perspectives

Summary. Gravity plays an important role for the evolution, orientation and development of organisms. Most of us, however, tend to overlook its importance because – due to its constant presence from the beginning of evolution some 4 billion years ago – this environmental parameter is almost hardwired into our interpretation of reality. This negligence of gravity is the more surprising as we all have our strong fights with this factor, especially during the very early and again during the late phases of our lives. On the other hand, scientists have been fascinated to observe the effects of gravity especially on plants and microorganisms for more than a hundred years, since Darwin and Sachs demonstrated the role of the root cap for downward growing plants. Different experimental approaches are nowadays available in order to change the influence of gravity and to study the corresponding influences on the physiology of biological systems. With the advent of spaceflight, a long-term nearly nullification of gravity is possible. Utilisation of this so-called “microgravity” condition for research in life sciences thus became an important asset in the space programs of various space agencies around the world. The German Space Life Sciences Program is managed – like all other space programs and activities in Germany – by the German Aerospace Center (DLR) in its role as space agency for Germany. Within the current space program, approved by the German government in May 2001, the overall goal for its life sciences part was defined as to gain scientific knowledge and to disclose new application potential by research under space conditions, especially by utilising the microgravity environment of the International Space Station. Three main scientific fields have been identified in collaboration with the scientific community: integrative human physiology, biotechnological applications of the microgravity environment, and fundamental biology of gravity and radiation responses (i.e., gravitational and radiation biology). In the present contribution, specific goals as well as achievements and perspectives of research in gravitational biology are given. In addition, some information is provided on spaceflight opportunities available. Correspondence and reprints: German Aerospace Center (DLR), Space Agency, P.O. Box 300364, 53183 Bonn, Federal Republic of Germany.     

Causality, randomness, intelligibility, and the epistemology of the cell

Because the basic unit of biology is the cell, biological knowledge is rooted in the epistemology of the cell, and because life is the salient characteristic of the cell, its epistemology must be centered on its livingness, not its constituent components. The organization and regulation of these components in the pursuit of life constitute the fundamental nature of the cell. Thus, regulation sits at the heart of biological knowledge of the cell and the extraordinary complexity of this regulation conditions the kind of knowledge that can be obtained, in particular, the representation and intelligibility of that knowledge. This paper is essentially split into two parts. The first part discusses the inadequacy of everyday intelligibility and intuition in science and the consequent need for scientific theories to be expressed mathematically without appeal to commonsense categories of understanding, such as causality. Having set the backdrop, the second part addresses biological knowledge. It briefly reviews modern scientific epistemology from a general perspective and then turns to the epistemology of the cell. In analogy with a multi-faceted factory, the cell utilizes a highly parallel distributed control system to maintain its organization and regulate its dynamical operation in the face of both internal and external changes. Hence, scientific knowledge is constituted by the mathematics of stochastic dynamical systems, which model the overall relational structure of the cell and how these structures evolve over time, stochasticity being a consequence of the need to ignore a large number of factors while modeling relatively few in an extremely complex environment.     

On the Limitations of Biological Knowledge

Scientific knowledge is grounded in a particular epistemology and, owing to the requirements of that epistemology, possesses limitations. Some limitations are intrinsic, in the sense that they depend inherently on the nature of scientific knowledge; others are contingent, depending on the present state of knowledge, including technology. Understanding limitations facilitates scientific research because one can then recognize when one is confronted by a limitation, as opposed to simply being unable to solve a problem within the existing bounds of possibility. In the hope that the role of limiting factors can be brought more clearly into focus and discussed, we consider several sources of limitation as they apply to biological knowledge: mathematical complexity, experimental constraints, validation, knowledge discovery, and human intellectual capacity.     

Molecular and cell models of biological effects of heavy ion radiation

Many quantitative models have been developed for the biological effectiveness of radiation of different quality. They differ substantially in their assumptions, and a lack of firm knowledge remains as to the detailed nature of the critical early molecular damage. Analyses of microscopic features of the stochastic structures of radiation tracks have led to hypotheses on the importance of clustered damage in DNA and associated molecules. Clustered damage of greater complexity or severity is suggested to be less repairable and therefore to dominate the biological consequences.Invited paper presented at the International Symposium on Heavy Ion Research: Space, Radiation Protection and Therapy, Sophia-Antipolis, France, 21–24 March 1994     

A Novel Dictionary Based Computer Vision Method for the Detection of Cell Nuclei

Cell nuclei detection in fluorescent microscopic images is an important and time consuming task in a wide range of biological applications. Blur, clutter, bleed through and partial occlusion of nuclei make individual nuclei detection a challenging task for automated image analysis. This paper proposes a novel and robust detection method based on the active contour framework. Improvement over conventional approaches is achieved by exploiting prior knowledge of the nucleus shape in order to better detect individual nuclei. This prior knowledge is defined using a dictionary based approach which can be formulated as the optimization of a convex energy function. The proposed method shows accurate detection results for dense clusters of nuclei, for example, an F-measure (a measure for detection accuracy) of 0.96 for the detection of cell nuclei in peripheral blood mononuclear cells, compared to an F-measure of 0.90 achieved by state-of-the-art nuclei detection methods.     

A historical review of research on the weaver ant Oecophylla in biological control

1 Although the weaver ant Oecophylla is the first written record of biological control, dating from 304 ad , there have been fewer than 70 scientific publications on this predator as a biological control agent in Asia, from the early 1970s onwards, and fewer than 25 in Africa. 2 Apart from crop‐specific ecological and perceptual factors, a historical review shows that political and market forces have also determined the extent to which Oecophylla was incorporated into research and development programmes. 3 In Africa, research on weaver ants in biological control concentrated on export crops, such as coconut and cocoa, whereas, in Asia and Australia, research focused on fruit and nut crops, primarily destined for domestic markets. 4 Increased evidence of pesticide inefficiency under tropical smallholder conditions, changing paradigm shifts in participatory research and a growing scientific interest in local knowledge in the early 1990s opened up new avenues for research on conservation biological control. 5 Lobbying and advocacy have been needed to ensure that Oecophylla was recognized as an effective biological control agent. 6 With an increased market demand for organic produce, holistic approaches such as conservation biological control, particularly the use of Oecophylla, are increasing in importance. 7 Multi‐stakeholder strategies for collaborative learning are proposed for a better control of major fruit, nut and timber tree pests in Africa, Asia and Australia.     

Community Intelligence in Knowledge Curation: An Application to Managing Scientific Nomenclature

Harnessing community intelligence in knowledge curation bears significant promise in dealing with communication and education in the flood of scientific knowledge. As knowledge is accumulated at ever-faster rates, scientific nomenclature, a particular kind of knowledge, is concurrently generated in all kinds of fields. Since nomenclature is a system of terms used to name things in a particular discipline, accurate translation of scientific nomenclature in different languages is of critical importance, not only for communications and collaborations with English-speaking people, but also for knowledge dissemination among people in the non-English-speaking world, particularly young students and researchers. However, it lacks of accuracy and standardization when translating scientific nomenclature from English to other languages, especially for those languages that do not belong to the same language family as English. To address this issue, here we propose for the first time the application of community intelligence in scientific nomenclature management, namely, harnessing collective intelligence for translation of scientific nomenclature from English to other languages. As community intelligence applied to knowledge curation is primarily aided by wiki and Chinese is the native language for about one-fifth of the world’s population, we put the proposed application into practice, by developing a wiki-based English-to-Chinese Scientific Nomenclature Dictionary (ESND; http://esnd.big.ac.cn). ESND is a wiki-based, publicly editable and open-content platform, exploiting the whole power of the scientific community in collectively and collaboratively managing scientific nomenclature. Based on community curation, ESND is capable of achieving accurate, standard, and comprehensive scientific nomenclature, demonstrating a valuable application of community intelligence in knowledge curation.     

The conserved genome organisation of non-falciparum malaria species: the need to know more

The current knowledge on genomes of non-falciparum malaria species and the potential of model malaria parasites for functional analyses are reviewed and compared with those of the most pathogenic human parasite, Plasmodium falciparum. There are remarkable similarities in overall genome composition among the different species at the level of chromosome organisation and chromosome number, conserved order of individual genes, and even conserved functions of specific gene domains and regulatory control elements. With the initiative taken to sequence the genome of P. falciparum, a wealth of information is already becoming available to the scientific community. In order to exploit the biological information content of a complete genome sequence, simple storage of the bulk of sequence data will be inadequate. The requirement for functional analyses to determine the biological role of the open reading frames is commonly accepted and knowledge of the genomes of the animal model malaria species will facilitate these analyses. Detailed comparative genome information and sequencing of additional Plasmodium genomes will provide a deeper insight into the evolutionary history of the species, the biology of the parasite, and its interactions with the mammalian host and mosquito vector. Therefore, an extended and integrated approach will enhance our knowledge of malaria and will ultimately lead to a more rational approach that identifies and evaluates new targets for anti-malarial drug and vaccine development.     

Investigation of polyethylenimine‐grafted‐triamcinolone acetonide as nucleus‐targeting gene delivery systems

Background

Nuclear membrane is one of the main barriers in polymer mediated intracellular gene delivery. To improve the transgenic activity and safety of nonviral vector, triamcinolone acetonide (TA) as a nuclear localization signal was conjugated with different molecular weight polyethylenimine (PEI).

Methods

Different molecular weight PEI [600, 1800, 25 000 (25k)] was conjugated with TA to synthesize PEI‐TA by two‐step reaction. Their physicochemical characteristics, in vitro cytotoxicity and transfection efficiency were evaluated. To investigate the difference of transfection efficiency of various molecular weight PEI‐TA, their transfection mechanism was further investigated by confocal microscopy and competition assay. Transgenic expression in vivo was evaluated by injection into hepatic portal vein of mice.

Results

All PEI‐TA could form nanosize polyplexes with DNA and their physicochemical properties resemble each other. Their cytotoxicities were negligible compared to PEI 25k. The order of transfection efficiency was PEI 1800‐TA > PEI 600‐TA > PEI 25k‐TA. A transfection mechanism study displayed that TA could inhibit considerably the transgenic activity of PEI 1800‐TA and PEI 600‐TA, but that of PEI 25k‐TA was not inhibited. It was suggested that PEI 1800‐TA and PEI 600‐TA might translocate into the nucleus. Confocal microscopy investigation verified this suggestion. The data strongly suggested that the transfection efficiency of PEI 1800‐TA in vivo was much higher than that of PEI 25k, which was consistent with the results obtained in vitro.

Conclusions

Low molecular weight PEI‐TA could translocate into the nucleus efficiently. PEI 1800‐TA presented higher transgenic activity and it has a great potential for gene therapy as a nonviral carrier. Copyright © 2010 John Wiley & Sons, Ltd.     

Ontology annotation: mapping genomic regions to biological function

With numerous whole genomes now in hand, and experimental data about genes and biological pathways on the increase, a systems approach to biological research is becoming essential. Ontologies provide a formal representation of knowledge that is amenable to computational as well as human analysis, an obvious underpinning of systems biology. Mapping function to gene products in the genome consists of two, somewhat intertwined enterprises: ontology building and ontology annotation. Ontology building is the formal representation of a domain of knowledge; ontology annotation is association of specific genomic regions (which we refer to simply as 'genes', including genes and their regulatory elements and products such as proteins and functional RNAs) to parts of the ontology. We consider two complementary representations of gene function: the Gene Ontology (GO) and pathway ontologies. GO represents function from the gene's eye view, in relation to a large and growing context of biological knowledge at all levels. Pathway ontologies represent function from the point of view of biochemical reactions and interactions, which are ordered into networks and causal cascades. The more mature GO provides an example of ontology annotation: how conclusions from the scientific literature and from evolutionary relationships are converted into formal statements about gene function. Annotations are made using a variety of different types of evidence, which can be used to estimate the relative reliability of different annotations.     

Coefficient of relationship by isonymy between 14 Sardinian villages in the periods 1800-1824 and 1950-1974

Lasker's coefficient of relationship was calculated between 14 villages in Sardinia in order to estimate biological relationships on the base of common surnames. The data derive from parish marriage registers for the periods 1800-1824 and 1950-1974. Through time, coefficients of relationship between villages are generally higher for neighbouring villages. Moreover, the Ri between values decreases as the geographic distances increase. The negative Pearson product-moment correlation observed between the Ri matrix and the geographic distance matrix is statistically significant (Mantel's test) for the two periods considered. These results suggest that the biological similarity between villages, as shown by isonymy, tends to decrease as the geographic distance increases. In addition, the plots of isonymic relationships obtained by nonmetric multidimensional scaling for 1800-1824 and 1950-1974 show that the biological relationships between neighbouring villages increase in the second period considered.