Science education and popularization of science in the biomedical area: its role for the future of science and of society

This paper presents the main subjects discussed in the round-table: "Educational Base for Biomedical Research", during the International Symposium on Biomedical Research in the 21st century; two main aspects will be focused: (1) the importance of popularizing science in order to stimulate comprehension of the scientific process and progress, their critical thinking, citizenship and social commitment, mainly in the biomedical area, considering the new advances of knowledge and the resulting technology; (2) the importance to stimulate genuine scientific vocation among young people, by giving them opportunity to early experience scientific environment, through the hands of well prepared master in a humanistic atmosphere.     

A lost generation

The funding policies of the NIH have made it increasingly difficult for young researchers to procure research funds. This threatens to drive a whole generation of young people away from careers in basic biomedical research.     

Online tools to support literature-based discovery in the life sciences

In biomedical research, the amount of experimental data and published scientific information is overwhelming and ever increasing, which may inhibit rather than stimulate scientific progress. Not only are text-mining and information extraction tools needed to render the biomedical literature accessible but the results of these tools can also assist researchers in the formulation and evaluation of novel hypotheses. This requires an additional set of technological approaches that are defined here as literature-based discovery (LBD) tools. Recently, several LBD tools have been developed for this purpose and a few well-motivated, specific and directly testable hypotheses have been published, some of which have even been validated experimentally. This paper presents an overview of recent LBD research and discusses methodology, results and online tools that are available to the scientific community.     

On the impoverishment of scientific education

Hannah Arendt, one of the foremost political philosophers of the twentieth century, has argued that it is the responsibility of educators not to leave children in their own world but instead to bring them into the adult world so that, as adults, they can carry civilization forward to whatever challenges it will face by bringing to bear the learning of the past. In the same collection of essays, she discusses the recognition by modern science that Nature is inconceivable in terms of ordinary human conceptual categories - as she writes, ‘unthinkable in terms of pure reason’. Together, these views on scientific education lead to an educational process that transforms children into adults, with a scientific adult being one who has the ability to conceptualize scientific systems independent of ordinary physical intuition. This article begins with Arendt’s basic educational and scientific points and develops from them a critique of current scientific education in conjunction with an appeal to educate young scientists in a manner that allows them to fulfill their potential ‘on the shoulders of giants’. While the article takes a general philosophical perspective, its specifics tend to be directed at biomedical education, in particular, how such education pertains to translational science.     

Computer simulation studies and the scientific method

The scientific method is the formal procedure for all acceptable scientific endeavors. With this methodology, there is a continual interaction between theory, in the form of an hypothesis, and objective, experimental analysis. There is a new step in the scientific method that involves the use of computer models and simulation studies. When computer models are incorporated into hypothesis formulation, they can be used in simulation studies to test ideas before they are tried experimentally. An iterative feedback between these tests and current ideas allows for a preliminary refinement of hypotheses and development of more intelligent research protocols. In this way, computer simulation studies can serve as an intermediate step in the scientific method, reducing the number of animals used in biomedical experimentation. In this article we also explore other ways that computer simulation studies could limit the use of animals in biomedical research and education.     

Issues on research integrity: a perspective

This paper discusses several key issues that are relevant to the integrity and success of the biomedical research enterprise. Attention to these issues will improve research outcomes and reduce negative consequences in research. Subjects addressed include normative practices in research; the importance of quality data; mentoring of young scientists; how to proceed when a member of the scientific community discovers misconduct or other breaches of integrity; and the level of harm to public confidence in research due to misconduct and lack of transparency in research findings.     

Report on 2nd Royan Institute International Summer School on Developmental Biology and Stem Cells Tehran,Iran, 17–22nd July 2011

The 2nd Royan Institute International Summer School was built around the topic of stem cells and grounding in the discipline of developmental biology. The meeting provided not only direct transfer of technical and intellectual information, the normal process in scientific meetings, but was also a forum for the exchange of personal ideas of science as a creative pursuit. This summer school introduced aspiring young Iranian scientists to international researchers and exposed the latter to a rich culture that highly values learning and education, attested by the confident, intelligent young men and women who asked probing questions and who were eager to participate in the workshops. Hossein Baharvand's dedication and passion for science have led to an impressive record of national and international peer-reviewed publications and an increasing number of students who pursue science in Iran, and shows how the right people can create an environment where good science, good science education and motivation will flourish. This report summarizes some of the activities of the workshop in the Royan Institute and the impressions of the visiting scientists in the wider context of the scientific and cultural heritage of Iran.     

Report on 2nd Royan Institute International Summer School on developmental biology and stem cells Tehran, Iran, 17-22nd July 2011

The 2nd Royan Institute International Summer School was built around the topic of stem cells and grounding in the discipline of developmental biology. The meeting provided not only direct transfer of technical and intellectual information, the normal process in scientific meetings, but was also a forum for the exchange of personal ideas of science as a creative pursuit. This summer school introduced aspiring young Iranian scientists to international researchers and exposed the latter to a rich culture that highly values learning and education, attested by the confident, intelligent young men and women who asked probing questions and who were eager to participate in the workshops. Hossein Baharvand's dedication and passion for science have led to an impressive record of national and international peer-reviewed publications and an increasing number of students who pursue science in Iran, and shows how the right people can create an environment where good science, good science education and motivation will flourish. This report summarizes some of the activities of the workshop in the Royan Institute and the impressions of the visiting scientists in the wider context of the scientific and cultural heritage of Iran.     

Emergence of norms for biomedical research. At the origin of the Huriet law (1975-1988)

The French law for the Protection of persons involved in biomedical research, known as "Loi Huriet", defines the frame in which biomedical experimentations on human subjects can take place. Insisting on the emergent character of the norms (laws, scientific standards...) for clinical research in France, this paper presents the general context in which such a law was promulgated. It gives an historical focus on its principal dispositions and underlines the conceptual issues raised by the public acknowledgment of the existence of scientific investigations on humans. This paper contributes to the debate on the meaning of the main notions of the French normative system applying to biomedical researches (protection of the person, individual direct benefice...)     

The Dynamic Interest in Topics within the Biomedical Scientific Community

The increase in the size of the scientific community created an explosion in scientific production. We have analyzed the dynamics of biomedical scientific output during 1957–2007 by applying a bibliometric analysis of the PubMed database using different keywords representing specific biomedical topics. With the assumption that increased scientific interest will result in increased scientific output, we compared the output of specific topics to that of all scientific output. This analysis resulted in three broad categories of topics; those that follow the general trend of all scientific output, those that show highly variable output, and attractive topics which are new and grow explosively. The analysis of the citation impact of the scientific output resulted in a typical longtail distribution: the majority of journals and articles are of very low impact. This distribution has remained unchanged since 1957, although the interests of scientists must have shifted in this period. We therefore analyzed the distribution of articles in top journals and lower impact journals over time for the attractive topics. Novelty is rewarded by publication in top journals. Over time more articles are published in low impact journals progressively creating the longtail distribution, signifying acceptance of the topic by the community. There can be a gap of years between novelty and acceptance. Within topics temporary novelty is created with new subtopics. In conclusion, the longtail distribution is the foundation of the scientific output of the scientific community and can be used to examine different aspects of science practice.     

The Crisis of Reproducibility,the Denominator Problem and the Scientific Role of Multi-scale Modeling

The “Crisis of Reproducibility” has received considerable attention both within the scientific community and without. While factors associated with scientific culture and practical practice are most often invoked, I propose that the Crisis of Reproducibility is ultimately a failure of generalization with a fundamental scientific basis in the methods used for biomedical research. The Denominator Problem describes how limitations intrinsic to the two primary approaches of biomedical research, clinical studies and preclinical experimental biology, lead to an inability to effectively characterize the full extent of biological heterogeneity, which compromises the task of generalizing acquired knowledge. Drawing on the example of the unifying role of theory in the physical sciences, I propose that multi-scale mathematical and dynamic computational models, when mapped to the modular structure of biological systems, can serve a unifying role as formal representations of what is conserved and similar from one biological context to another. This ability to explicitly describe the generation of heterogeneity from similarity addresses the Denominator Problem and provides a scientific response to the Crisis of Reproducibility.     

Natural immunoglobulins (contribution to a debate on biomedical education)

Immunology has contributed to biomedical education in many important ways since the creation of scientific medicine in the last quarter of the 19th century. Today, immunology is a major area of biomedical research. Nevertheless, there are many basic problems unresolved in immunological activities and phenomena. Solving these problems is probably necessary to devise predictable and safe ways to produce new vaccines, treat allergy and autoimmune diseases and perform safe transplants. This challenge involves not only technical developments but also changes in attitude, of which the most fundamental is to abandon the traditional stimulus-response perspective in favor of more "systemic" views. Describing immunological activities as the operation of a complex multi connected network, raises biological and epistemological issues not usually dealt with in biomedical education. Here we point to one example of systemic approaches. A new form of immunoblot (Panama blot), by which the reaction of natural immunoglobulins with complex protein mixtures may be analyzed by a special software and multivariate statistics, has been recently used to characterize human autoimmune diseases. Our preliminary data show that Panama blots can also be used to characterize global (systemic) immunological changes in chronic human parasitic diseases, such as malaria and schistosomiasis mansoni, that correlate with the clinical status.     

On the persistence of supplementary resources in biomedical publications

Background  

Providing for long-term and consistent public access to scientific data is a growing concern in biomedical research. One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers.     

Blood Collection Procedure of Laboratory Primates: A Neglected Variable in Biomedical Research

A survey of 75 biomedical articles dealing with stress-dependent blood parameters in caged primates revealed that the conditions under which blood collection occurred were in most cases described either not at all or so haphazardly that it would be impossible to determine if humane handling procedures were used and basic principles of scientific methodology applied. These findings were unexpected because there is ample scientific evidence not only that stress-sensitive research data are influenced by traditional blood sampling procedures, but also that those data-biasing effects can be avoided. If dependent variables of the blood collection procedure are not controlled, data variability will increase, automatically increasing the number of animals needed for statistical analysis. For ethical and scientific reasons, it was recommended that editors of biomedical journals require authors to provide sufficient information of the blood collection--and, when applicable, the sedative injection--procedure to ensure that the experiment was done with the smallest number of animals possible to achieve statistical significance and that the investigation can be replicated reliably in another laboratory and the research data interpreted with reasonable accuracy.     

The acid drops project: pollution monitoring by young people

The spectrum of research at the Field Studies Council spans generations of scientists, from fully qualified and experienced staff to quite young children engaged in serious environmental monitoring. Pollution monitoring networks run by young people have a proven history, starting in 1971 with the Advisory Centre for Education air and water surveys, up to the present day with the Watch/Field Studies Council acid rain projects. Each project has demonstrated how a well coordinated network of unqualified volunteers, using inexpensive kits and simple techniques, can produce data worthy of scientific attention.     

Improving Validity of Informed Consent for Biomedical Research in Zambia Using a Laboratory Exposure Intervention

Background

Complex biomedical research can lead to disquiet in communities with limited exposure to scientific discussions, leading to rumours or to high drop-out rates. We set out to test an intervention designed to address apprehensions commonly encountered in a community where literacy is uncommon, and where complex biomedical research has been conducted for over a decade. We aimed to determine if it could improve the validity of consent.

Methods

Data were collected using focus group discussions, key informant interviews and observations. We designed an intervention that exposed participants to a detailed demonstration of laboratory processes. Each group was interviewed twice in a day, before and after exposure to the intervention in order to assess changes in their views.

Results

Factors that motivated people to participate in invasive biomedical research included a desire to stay healthy because of the screening during the recruitment process, regular advice from doctors, free medical services, and trust in the researchers. Inhibiting factors were limited knowledge about samples taken from their bodies during endoscopic procedures, the impact of endoscopy on the function of internal organs, and concerns about the use of biomedical samples. The belief that blood can be used for Satanic practices also created insecurities about drawing of blood samples. Further inhibiting factors included a fear of being labelled as HIV positive if known to consult heath workers repeatedly, and gender inequality. Concerns about the use and storage of blood and tissue samples were overcome by a laboratory exposure intervention.

Conclusion

Selecting a group of members from target community and engaging them in a laboratory exposure intervention could be a useful tool for enhancing specific aspects of consent for biomedical research. Further work is needed to determine the extent to which improved understanding permeates beyond the immediate group participating in the intervention.     

Tagging gene and protein names in biomedical text

MOTIVATION: The MEDLINE database of biomedical abstracts contains scientific knowledge about thousands of interacting genes and proteins. Automated text processing can aid in the comprehension and synthesis of this valuable information. The fundamental task of identifying gene and protein names is a necessary first step towards making full use of the information encoded in biomedical text. This remains a challenging task due to the irregularities and ambiguities in gene and protein nomenclature. We propose to approach the detection of gene and protein names in scientific abstracts as part-of-speech tagging, the most basic form of linguistic corpus annotation. RESULTS: We present a method for tagging gene and protein names in biomedical text using a combination of statistical and knowledge-based strategies. This method incorporates automatically generated rules from a transformation-based part-of-speech tagger, and manually generated rules from morphological clues, low frequency trigrams, indicator terms, suffixes and part-of-speech information. Results of an experiment on a test corpus of 56K MEDLINE documents demonstrate that our method to extract gene and protein names can be applied to large sets of MEDLINE abstracts, without the need for special conditions or human experts to predetermine relevant subsets. AVAILABILITY: The programs are available on request from the authors.     

Text mining for literature review and knowledge discovery in cancer risk assessment and research

Research in biomedical text mining is starting to produce technology which can make information in biomedical literature more accessible for bio-scientists. One of the current challenges is to integrate and refine this technology to support real-life scientific tasks in biomedicine, and to evaluate its usefulness in the context of such tasks. We describe CRAB - a fully integrated text mining tool designed to support chemical health risk assessment. This task is complex and time-consuming, requiring a thorough review of existing scientific data on a particular chemical. Covering human, animal, cellular and other mechanistic data from various fields of biomedicine, this is highly varied and therefore difficult to harvest from literature databases via manual means. Our tool automates the process by extracting relevant scientific data in published literature and classifying it according to multiple qualitative dimensions. Developed in close collaboration with risk assessors, the tool allows navigating the classified dataset in various ways and sharing the data with other users. We present a direct and user-based evaluation which shows that the technology integrated in the tool is highly accurate, and report a number of case studies which demonstrate how the tool can be used to support scientific discovery in cancer risk assessment and research. Our work demonstrates the usefulness of a text mining pipeline in facilitating complex research tasks in biomedicine. We discuss further development and application of our technology to other types of chemical risk assessment in the future.     

NetiNeti: discovery of scientific names from text using machine learning methods

ABSTRACT: BACKGROUND: A scientific name for an organism can be associated with almost all biological data. Name identification is an important step in many text mining tasks aiming to extract useful information from biological, biomedical and biodiversity text sources. A scientific name acts as an important metadata element to link biological information. RESULTS: We present NetiNeti (Name Extraction from Textual Information-Name Extraction for Taxonomic Indexing), a machine learning based approach for recognition of scientific names including the discovery of new species names from text that will also handle misspellings, OCR errors and other variations in names. The system generates candidate names using rules for scientific names and applies probabilistic machine learning methods to classify names based on structural features of candidate names and features derived from their contexts. NetiNeti can also disambiguate scientific names from other names using the contextual information. We evaluated NetiNeti on legacy biodiversity texts and biomedical literature (MEDLINE). NetiNeti performs better (precision = 98.9 % and recall = 70.5 %) compared to a popular dictionary based approach (precision = 97.5 % and recall = 54.3 %) on a 600-page biodiversity book that was manually marked by an annotator. On a small set of PubMed Central's full text articles annotated with scientific names, the precision and recall values are 98.5 % and 96.2 % respectively. NetiNeti found more than 190,000 unique binomial and trinomial names in more than 1,880,000 PubMed records when used on the full MEDLINE database. NetiNeti also successfully identifies almost all of the new species names mentioned within web pages. Additionally, we present the comparison results of various machine learning algorithms on our annotated corpus. Naive Bayes and Maximum Entropy with Generalized Iterative Scaling (GIS) parameter estimation are the top two performing algorithms. CONCLUSIONS: We present NetiNeti, a machine learning based approach for identification and discovery of scientific names. The system implementing the approach can be accessed at http://namefinding.ubio.org.     

An October call to arms: We Are Research!

The American Society for Cell Biology is targeting the first week of October 2012 (the week before Nobel Prize winners are announced) to launch the We Are Research initiative. The goal of this initiative is to mobilize practicing junior and senior scientists, including graduate students, postdocs, and other lab members, to make contact with their elected officials and neighbors and explain to them why Federal support and investment in biomedical research is vital to the health and economic welfare of the United States. This initiative is designed to illustrate how important people are to scientific research and to supply our representatives with reliable and accurate information in the form of letters, emails, telephone calls, and personal visits.