Public access for teaching genomics,proteomics, and bioinformatics

When the human genome project was conceived, its leaders wanted all researchers to have equal access to the data and associated research tools. Their vision of equal access provides an unprecedented teaching opportunity. Teachers and students have free access to the same databases that researchers are using. Furthermore, the recent movement to deliver scientific publications freely has presented a second source of current information for teaching. I have developed a genomics course that incorporates many of the public-domain databases, research tools, and peer-reviewed journals. These online resources provide students with exciting entree into the new fields of genomics, proteomics, and bioinformatics. In this essay, I outline how these fields are especially well suited for inclusion in the undergraduate curriculum. Assessment data indicate that my students were able to utilize online information to achieve the educational goals of the course and that the experience positively influenced their perceptions of how they might contribute to biology.     

The how and why of societal publications for citizen science projects and scientists

In the scientific community, the importance of communication to society is often underestimated. Scientists and scientific organisations often lack the skills to organise such communication effectively. The Dutch citizen science phenology network Nature’s Calendar has been successful in communicating to the general public via numerous newspaper articles, television appearances, presentations, websites and social media. We refer to these publications as societal publications. Due to active communication to mass media, we frequently reach millions of people. This communication helped us to involve thousands of volunteers in recording the timing of phenological events like the start of flowering, leaf unfolding and bird migration, but also several health-related events like hay fever symptoms and tick bites. In this paper, we analyse and present our experiences with the Nature’s Calendar project regarding societal publications. Based on this analysis, we explain the importance of societal publications for citizen science projects and scientists in general, and we show how scientists can increase the newsworthiness of scientific information and what factors and activities can increase the chances of media paying attention to this news. We show that societal publications help phenological networks by facilitating the recruitment, retention and instruction of observers. Furthermore, they stimulate the generation of new ideas and partners that lead to an increase in knowledge, awareness and behavioural change of the general public or specific stakeholders. They make projects, and scientists involved, better known to the public and increase their credibility and authority. Societal publications can catalyse the production of new publications, thereby enforcing the previous mentioned points.     

The library in the digital age

Electronic publication is an increasingly popular forum within the scientific community, and many are talking about the possibility of dispensing with paper publications entirely in years to come. How likely is this to happen, and if so how quickly? What will be its impact on the way we use and contribute to the scientific knowledge base? This article discusses the elements of today's digital library and how they might evolve as we confront the online world.     

How citation boosts promote scientific paradigm shifts and nobel prizes

Nobel Prizes are commonly seen to be among the most prestigious achievements of our times. Based on mining several million citations, we quantitatively analyze the processes driving paradigm shifts in science. We find that groundbreaking discoveries of Nobel Prize Laureates and other famous scientists are not only acknowledged by many citations of their landmark papers. Surprisingly, they also boost the citation rates of their previous publications. Given that innovations must outcompete the rich-gets-richer effect for scientific citations, it turns out that they can make their way only through citation cascades. A quantitative analysis reveals how and why they happen. Science appears to behave like a self-organized critical system, in which citation cascades of all sizes occur, from continuous scientific progress all the way up to scientific revolutions, which change the way we see our world. Measuring the "boosting effect" of landmark papers, our analysis reveals how new ideas and new players can make their way and finally triumph in a world dominated by established paradigms. The underlying "boost factor" is also useful to discover scientific breakthroughs and talents much earlier than through classical citation analysis, which by now has become a widespread method to measure scientific excellence, influencing scientific careers and the distribution of research funds. Our findings reveal patterns of collective social behavior, which are also interesting from an attention economics perspective. Understanding the origin of scientific authority may therefore ultimately help to explain how social influence comes about and why the value of goods depends so strongly on the attention they attract.     

Full publication of papers presented at the 1995 through 1999 European Association of Plastic Surgeons annual scientific meetings: a systemic bibliometric analysis

From the multitude of oral presentations at major medical meetings, the most informative and highest-quality studies make it to full publication in peer-reviewed journals. The rate of publication may be regarded as an indicator of the scientific level of the meeting. Study of the publication rates of consecutive annual meetings allows for the evaluation of the consistency of the scientific level of these meetings and for comparison with publication rates of other meetings in the same field of interest. To grade how useful any publication is to other authors, one can furthermore measure how frequently they cite it in their own publications. Finally, the time lag between oral presentation and full publication is of importance to both its authors and the audience at the meeting. The main objectives of this study were to determine the publication rate of papers of various fields of interest as presented at five consecutive annual meetings of the European Association of Plastic Surgeons (EURAPS) and the time lag between these presentations and their publication. The authors compared their overall findings to those reported for other surgical specialties. Moreover, they identified and classified the journals in which the full publications appeared as an indicator of the scientific value of the meeting. They conclude that a greater than average number of papers presented at the 1995 through 1999 annual EURAPS meetings went on to full publication in peer-reviewed journals. Among these journals, Plastic and Reconstructive Surgery was the best source for information presented at the meetings. Although approximately 90 percent of the publications appeared before 3 years had passed after a meeting, additional publications may be expected to appear even more than 6 years after the meeting. Given the high publication rate and the high average normalized impact factor of the journals in which the presentations appeared, the five studied EURAPS meetings overall had high scientific value.     

Island ecology and contingent theory: the role of spatial scale and taxonomic bias

Scale, the scale dependency of patterns and processes, and the ways that organisms scale their responses to these patterns and processes are central to island and landscape ecology. Here, we take a database of studies in island ecology and investigate how studies have changed over a 40-year period with respect to spatial scale and organisms studied. We demonstrate that there have been changes in the spatial scale of islands studied and that there is taxonomic bias in favour of vertebrates in island ecological studies when compared to scientific publications as a whole. We discuss how such taxonomic bias may have arisen and discuss the implications for ecology and biogeography.     

Political advocacy by the American Society for Cell Biology and its partners

I trace how the American Society for Cell Biology became a strong political advocate for the scientific community. I celebrate how good leadership and an effective staff enabled its energetic volunteer organization to have an impact, but I also ask how the effort can be made more successful.Many scientists take for granted that their scientific societies advocate for the well being of their individual members and the health of science. However, advocacy is a relatively recent development that emerged over the past two decades. Advocacy is essential in a democracy because science competes for taxpayer dollars with every other activity supported by the federal government. Advocacy is also important to ensure that lawmakers adopt sensible policies. I review how the American Society for Cell Biology (ASCB) and its allies learned how to fulfill this obligation, and I ask the reader to join the effort. The objective of these advocacy efforts is to influence political decisions through education and information, but the efforts by scientific societies are completely nonpartisan. Support from both political parties is essential to meet our goals.During the 1970s and 1980s biomedical scientists discussed federal funding and public policies that affected our science. Each year the public policy staff of the Federation of Societies of Experimental Biology (FASEB) helped member societies reach a consensus recommendation on the level of federal funding for the biosciences. However, we tended to talk to ourselves because we lacked effective ways to communicate with politicians or the outside world. For the most part we relegated the responsibility for advocacy to medical school deans and presidents of research universities. Their professional associations—the American Association of Medical Colleges (AAMC) and the Association of American Universities (AAU)—generally did a reasonable job of representing the interests of the scientists who worked at their schools.     

Robustness in crossover regulation during meiosis

Meiotic recombination produces physical linkages between homologous chromosomes that enable their segregation to opposite poles during meiosis I. In the absence of recombination, chromosomes mis-segregate, resulting in aneuploidy associated with severe birth defects. A recent study provides exciting insights into how recombination is fine-tuned to enforce a robust meiotic program.     

Harmonic Allocation of Authorship Credit: Source-Level Correction of Bibliometric Bias Assures Accurate Publication and Citation Analysis

Authorship credit for multi-authored scientific publications is routinely allocated either by issuing full publication credit repeatedly to all coauthors, or by dividing one credit equally among all coauthors. The ensuing inflationary and equalizing biases distort derived bibliometric measures of merit by systematically benefiting secondary authors at the expense of primary authors. Here I show how harmonic counting, which allocates credit according to authorship rank and the number of coauthors, provides simultaneous source-level correction for both biases as well as accommodating further decoding of byline information. I also demonstrate large and erratic effects of counting bias on the original h-index, and show how the harmonic version of the h-index provides unbiased bibliometric ranking of scientific merit while retaining the original''s essential simplicity, transparency and intended fairness. Harmonic decoding of byline information resolves the conundrum of authorship credit allocation by providing a simple recipe for source-level correction of inflationary and equalizing bias. Harmonic counting could also offer unrivalled accuracy in automated assessments of scientific productivity, impact and achievement.     

The William Allan Memorial Award. Presented to Elizabeth F. Neufeld, Ph. D., at the annual meeting of the American Society of Human Genetics Detroit, September 29-October 2, 1982

The opportunity for this presentation provides me with three gratifications. The first and most important is that the scientist being honored is Elizabeth Neufeld. The second is the honor bestowed upon me by being selected to introduce Dr. Neufeld. Finally, the preparation of this introduction has provided me with the opportunity to reconstruct a scientific career from its beginnings to its present exciting momentum, an exercise in which I was helped with great enthusiasm by a number of people who have known Liz during the various phases of her scientific life. I am particularly pleased to note that our awardee is the product of that unique breeding ground of success stories, the special New York education system. After arriving in New York in 1940 at the age of 12 from Paris, a refugee from Nazi persecutions in Europe, Liz Neufeld, like so many other young refugees at the time, qualified for one of the specialized schools in New York--the Hunter College High School. From there she went to Queens College, one of the major high-quality free institutions of higher learning of the New York City college system, and graduated with a Bachelor of Science degree in 1948. Obviously turned on to a scientific career, she successfully applied for a research assistantship at the Jackson Laboratory in Bar Harbor, Maine, where she worked with the first of her mentors, Dr. Elizabeth Russell, to this day her good friend and enthusiastic admirer. Her first publications are derived from that experience and are concerned with hematologic genetics of mice.(ABSTRACT TRUNCATED AT 250 WORDS)     

The Citation Wake of Publications Detects Nobel Laureates' Papers

For several decades, a leading paradigm of how to quantitatively assess scientific research has been the analysis of the aggregated citation information in a set of scientific publications. Although the representation of this information as a citation network has already been coined in the 1960s, it needed the systematic indexing of scientific literature to allow for impact metrics that actually made use of this network as a whole, improving on the then prevailing metrics that were almost exclusively based on the number of direct citations. However, besides focusing on the assignment of credit, the paper citation network can also be studied in terms of the proliferation of scientific ideas. Here we introduce a simple measure based on the shortest-paths in the paper''s in-component or, simply speaking, on the shape and size of the wake of a paper within the citation network. Applied to a citation network containing Physical Review publications from more than a century, our approach is able to detect seminal articles which have introduced concepts of obvious importance to the further development of physics. We observe a large fraction of papers co-authored by Nobel Prize laureates in physics among the top-ranked publications.     

Validating concepts of mental disorder: precedents from the history of science

A fundamental issue in any branch of the natural sciences is validating the basic concepts for use in that branch. In psychiatry, this issue has not yet been resolved, and indeed, the proper nature of the problem has scarcely been recognised. As a result, psychiatry (or at least those parts of the discipline which aspire to scientific status) still cannot claim to be a part of scientific medicine, or to be incorporated within the common language of the natural sciences. While this creates difficulties within the discipline, and its standing in relation to other branches of medicine, it makes it an exciting place for “frontiersmen” (and women). This is one of the key growing points in the natural science tradition. In this essay, which moves from the early history of that tradition to today’s debates in scientific psychiatry, I give my views about how these fundamental issues can move towards resolution.     

Retos y oportunidades en el estudio de vesículas extracelulares: contexto institucional a nivel mundial y situación actual en Colombia

In the last decade, the number of studies and publications on extracellular vesicles (EV) and exosomes has boomed. Colombia has displayed interest and progress in their study as shown in the increase of research project publications and products. However, this research field is still developing and has its own analytical challenges and technical limitations. For planning research projects and developing EV studies it is necessary to consider what is the state of the scientific field worldwide concerning EV nomenclature and classification, available techniques, resources, requirements and quality specifications, and the institutions that regulate the field. Answering this question will elicit EV studies that comply with international standards and respond to institutional demands and recommendations. However, the scientific information available is scattered and not all the aspects are considered in full.In this update, the available information is condensed and the official terms and currently defined nomenclature is presented, as well as the evolution of the field, the homogenization of the experimental parameters, the establishment of scientific authorities, institutions, and resources, and the recommendations generated worldwide for their development and research including their isolation, characterization, and functional studies. Finally, I analyzed the national context in a critical way, considering institutional strengths, common mistakes, and available analytical techniques and technologies.     

A case for more curiosity-driven basic research

Having been selected to be among the exquisitely talented scientists who won the Sandra K. Masur Senior Leadership Award is a tremendous honor. I would like to take this opportunity to make the case for a conviction of mine that I think many will consider outdated. I am convinced that we need more curiosity-driven basic research aimed at understanding the principles governing life. The reasons are simple: 1) we need to learn more about the world around us; and 2) a robust and diverse basic research enterprise will bring ideas and approaches essential for developing new medicines and improving the lives of humankind.When I was a graduate student, curiosity-driven basic research ruled. Studying mating-type switching in budding yeast, for example, was exciting because it was an interesting problem: How can you make two different cells from a single cell in the absence of any external cues? We did not have to justify why it is important to study what many would now consider a baroque question. Scientists and funding agencies alike agreed that this was an exciting biological problem that needed to be solved. I am certain that all scientists of my generation can come up with similar examples.Open in a separate windowAngelika AmonSince the time I was a graduate student, the field of biological research has experienced a revolution. We can now determine the genetic makeup of every species in a week or so and have an unprecedented ability to manipulate any genome. This revolution has led to a sense that we understand the principles governing life and that it is now time to apply this knowledge to cure diseases and make the world a better place. While applying knowledge to improve lives and treat diseases is certainly a worthwhile endeavor, it is important to realize that we are far from having a mechanistic understanding of even the basic principles of biology. What the genomic revolution brought us are lists, some better than others. We now know how many coding genes define a given species and how many protein kinases, GTPases, and so forth there are in the various genomes we sequenced. This knowledge, however, does not even scratch the surface of understanding their function. When I browse the Saccharomyces cerevisiae genome database (my second-favorite website), I am still amazed how many genes there are that have not even been given a name.To me the most important achievement the new genome-sequencing and genome-editing technologies brought us is that nearly every organism can be a model organism now. We can study and manipulate the processes that most fascinate us in the organisms in which they occur, with the exception, of course, of humans. Thus, I believe that the golden era of basic biological research is not behind us but in front of us, and we need more people who will take advantage of the tools that have been developed in the past three decades. I am therefore hoping that many young people will chose a career in basic research and find an exciting question to study. The more of us there are, the more knowledge we will acquire, and the higher the likelihood we will discover something amazing and important. There is so much interesting biology out there that we should strive to understand. Some of my favorite unanswered questions are: What are the biological principles underlying symbiosis and how did it evolve? Why is sleep essential? Why do plants, despite an enormous regenerative potential, never die of cancer? Why do brown bears, despite inactivity, obesity, and high levels of cholesterol, exhibit no signs of atherosclerosis? How do sharks continuously produce teeth?One could, of course, argue that the knowledge we have accumulated over the past 50 years provides a reasonable framework, and it is now time to leave basic science and model organisms behind and focus on what matters—curing diseases, developing methods to produce energy, cleaning up the oceans, preventing global warming, building biological computers, designing organisms, or engineering whatever the current buzz is about. Like David Botstein, who eloquently discussed the importance of basic research in these pages in 2012 (Botstein, 2012 ), I believe that the notion that we already know enough is wrong and the current application-centric view of biology is misguided. Experience has taught us over and over that we cannot predict where the next important breakthrough will be emerge. Many of the discoveries that we consider groundbreaking and that have brought us new medicines or improved our lives in other ways are the result of curiosity-driven basic research. My favorite example is the discovery of penicillin. Alexander Fleming, through the careful study of his (contaminated) bacterial plates, enabled humankind to escape natural selection. More recent success stories such as new cures for hepatitis C, the human papillomavirus vaccine, the HIV-containment regimens, or treatments for BCR-ABL induced chronic myelogenous leukemia have also only been possible because of decades of basic research in model organisms that taught us the principles of life and enabled us to acquire the methodologies critical to develop these treatments. Although work from my own lab on the causes and consequences of chromosome mis-segregation in budding yeast has not led to the development of new treatments, it has taught us a lot about how an imbalanced karyotype, a hallmark of cancer, affects the physiology of cancer cells and creates vulnerabilities in cancer cells that could represent new therapeutic targets.These are but a few examples for why it is important that we scientists must dedicate ourselves to the pursuit of basic knowledge and why we as a society must make funding basic research a priority. Achieving the latter requires that we scientists tell the public about the importance of what we are doing and explain the potential implications of basic research for human health. At the same time, it will be important to manage expectations. We must explain that not every research project will lead to the development of new medicines and that we cannot predict where the next big breakthroughs will materialize. We must further make it clear that this means we have to fund a broad range of basic research at a healthy level. Perhaps a website that collects examples of how basic research has led to breakthroughs in medicine could serve as a showcase for such success stories, bringing the importance of what we do to the public.While conducting research to improve the lives of others is certainly a worthy motivation, it is not the main reason why I get up very early every morning to go to the lab. To me, gaining an understanding of a basic principle in the purest Faustian terms is what I find most rewarding and exciting. Designing and conducting experiments, pondering the results, and developing hypotheses as to how something may work is most exciting, the idea that I, or nowadays the people in my lab, may be (hopefully) the first to discover a new aspect of biology is the best feeling. It is these rare eureka moments, when you first realize how a process works or when you discover something that opens up a new research direction, that make up for all the woes and frustrations that come with being an experimental scientist in an expensive discipline.For me, having a career in curiosity-driven basic research has been immensely rewarding. It is my hope that basic research remains one of the pillars of the American scientific enterprise, attracting the brightest young minds for generations to come. We as a community can help to make this a reality by telling people what we do and highlighting the importance of our work to their lives.     

Theme section on mesophotic coral ecosystems: advances in knowledge and future perspectives

The Second International Mesophotic Coral Ecosystems (MCEs) workshop was held in Eilat, Israel, October 26–31, 2014. Here we provide an account of: (1) advances in our knowledge of MCE ecology, including the central question of the potential vertical connectivity between MCEs and shallow-water reefs (SWRs), and that of the validity of the deep-reef refugia hypothesis (DRRH); (2) the contribution of the 2014 MCE workshop to the central question presented in (1), as well as its contribution to novel MCE studies on corals, sponges, fish, and crabs; and (3) gaps, priorities, and recommendations for future research stemming from the workshop. Despite their close proximity to well-studied SWRs, and the growing evidence of their importance, our scientific knowledge of MCEs is still in its infancy. During the last five years, we have witnessed an ever-increasing scientific interest in MCEs, expressed in the exponential increase in the number of publications studying this unique environment. The emerging consensus is that lower MCE benthic assemblages represent unique communities, either of separate species or genetically distinct individuals within species, and any significant support for the DRRH will be limited to upper MCEs. Determining the health and stability of MCEs, their biodiversity, and the degree of genetic connectivity among SWRs and MCEs, will ultimately indicate the ability of MCEs to contribute to the resilience of SWRs and help to guide future management and conservation strategies. MCEs deserve therefore management consideration in their own right. With the technological advancements taking place in recent years that facilitate access to MCEs, the prospects for exciting and innovative discoveries resulting from MCE research, spanning a wide variety of fields, are immense.     

Graphical integrity issues in open access publications: Detection and patterns of proportional ink violations

Academic graphs are essential for communicating complex scientific ideas and results. To ensure that these graphs truthfully reflect underlying data and relationships, visualization researchers have proposed several principles to guide the graph creation process. However, the extent of violations of these principles in academic publications is unknown. In this work, we develop a deep learning-based method to accurately measure violations of the proportional ink principle (AUC = 0.917), which states that the size of shaded areas in graphs should be consistent with their corresponding quantities. We apply our method to analyze a large sample of bar charts contained in 300K figures from open access publications. Our results estimate that 5% of bar charts contain proportional ink violations. Further analysis reveals that these graphical integrity issues are significantly more prevalent in some research fields, such as psychology and computer science, and some regions of the globe. Additionally, we find no temporal and seniority trends in violations. Finally, apart from openly releasing our large annotated dataset and method, we discuss how computational research integrity could be part of peer-review and the publication processes.     

Is Primatology an Equal-Opportunity Discipline?

The proportion of women occupying academic positions in biological sciences has increased in the past few decades, but women are still under-represented in senior academic ranks compared to their male colleagues. Primatology has been often singled out as a model of “equal-opportunity” discipline because of the common perception that women are more represented in Primatology than in similar fields. But is this indeed true? Here we show that, although in the past 15 years the proportion of female primatologists increased from the 38% of the early 1990s to the 57% of 2008, Primatology is far from being an “equal-opportunity” discipline, and suffers the phenomenon of “glass ceiling” as all the other scientific disciplines examined so far. In fact, even if Primatology does attract more female students than males, at the full professor level male members significantly outnumber females. Moreover, regardless of position, IPS male members publish significantly more than their female colleagues. Furthermore, when analyzing gender difference in scientific productivity in relation to the name order in the publications, it emerged that the scientific achievements of female primatologists (in terms of number and type of publications) do not always match their professional achievements (in terms of academic position). However, the gender difference in the IPS members'' number of publications does not correspond to a similar difference in their scientific impact (as measured by their H index), which may indicate that female primatologists'' fewer articles are of higher impact than those of their male colleagues.