Towards “A Natural History of Data”: Evolving Practices and Epistemologies of Data in Paleontology, 1800–2000

The fossil record is paleontology’s great resource, telling us virtually everything we know about the past history of life. This record, which has been accumulating since the beginning of paleontology as a professional discipline in the early nineteenth century, is a collection of objects. The fossil record exists literally, in the specimen drawers where fossils are kept, and figuratively, in the illustrations and records of fossils compiled in paleontological atlases and compendia. However, as has become increasingly clear since the later twentieth century, the fossil record is also a record of data. Paleontologists now routinely abstract information from the physical fossil record to construct databases that serve as the basis for quantitative analysis of patterns in the history of life. What is the significance of this distinction? While it is often assumed that the orientation towards treating the fossil record as a record of data is an innovation of the computer age, it turns out that nineteenth century paleontology was substantially “data driven.” This paper traces the evolution of data practices and analyses in paleontology, primarily through examination of the compendia in which the fossil record has been recorded over the past 200 years. I argue that the transition towards conceptualizing the fossil record as a record of data began long before the emergence of the technologies associated with modern databases (such as digital computers and modern statistical methods). I will also argue that this history reveals how new forms of visual representation were associated with the transition from seeing the fossil record as a record of objects to one of data or information, which allowed paleontologists to make new visual arguments about their data. While these practices and techniques have become increasingly sophisticated in recent decades, I will show that their basic methodology was in place over a century ago, and that, in a sense, paleontology has always been a “data driven” science.     

Ulisse Aldrovandi (1522–1605): The Study of Trace Fossils During the Renaissance

The Renaissance was a time of flourishing for literature, art and science. A prominent figure in Renaissance science was the Italian naturalist Ulisse Aldrovandi, considered today to be one of the founding fathers of modern paleontology. Aldrovandi is known to have widely studied body fossils, but his work on trace fossils has yet to be explored by science historians. This paper proposes to critically analyze Aldrovandi's approach to trace fossils, based on his writings (most of which are still unpublished) and on the illustrations that accompany them. In his studies, the Bologna-born naturalist accurately describes such ichnological celebrities as Gastrochaenolites and Cosmorhaphe and discusses a few theoretic principles on the trace-making process. The study of the works of Aldrovandi brings to light a fascinating and little-known source of the history of ichnology.     

Bigeneric nomina: A proposal for modification of the rules of nomenclature

It is difficult to name fossils which are intermediate between chronospecies or chronogenera in general paleontology. A possible solution is proposed for discussion: namely, to utilize bigeneric nomina to designate a group of fossils which are intermediate between two consecutive genera, and bispecific nomina to designate fossils which are intermediate between two consecutive species.     

Epistemic values in the Burgess Shale debate

Focusing primarily on papers and books discussing the evolutionary and systematic interpretation of the Cambrian animal fossils from the Burgess Shale fauna, this paper explores the role of epistemic values in the context of a discipline (paleontology) striving to establish scientific authority within a larger domain of epistemic problems and issues (evolutionary biology). The focal point of this analysis is the repeated claims by paleontologists that the study of fossils gives their discipline a unique ‘historical dimension’ that makes it possible for them to unravel important aspects of evolution invisible to scientists who study the extant biosphere. The first part of the paper explores the shifting of emphasis in the writings of paleontologists between two strategies that employ opposing views on the classical positivist and physicalist ideal of science. The second part analyzes paleontologists’ claims of privileged access to life’s historical dimension in a situation where a theoretical upheaval occurring independent of the epistemical problem at hand completely shifts the standards for evaluating the legitimacy of various knowledge claims. Though the various strategies employed in defending the privileged historical perspective of paleontology have been disparate and, to an extent contradictory, each impinges on the acceptance of a specific epistemic ideal or set of values and success or failure of each depends on the compatibility of this ideal with the surrounding community of scientists.     

‘The vain speculation disillusioned by the sense’: the Italian painter Agostino Scilla (1629–1700) called ‘The Discoloured’, and the correct interpretation of fossils as ‘lithified organisms’ that once lived in the sea

The search for the true nature and origin of fossils gave rise, starting about the beginning of the sixteenth century and throughout the seventeenth century, to a heated debate between the supporters of the inorganic nature of these objects and proponents of an interpretation of fossils as ex-vivi. Among the latter, a key figure is the Italian painter Agostino Scilla (1629–1700), who represents one of the first naturalists who was able to accumulate substantial evidence to support the interpretation of fossils as once-living marine organisms. The world view of Scilla and his real contribution to paleontology are here analysed and contextualised, taking into account the state of knowledge characterising the time of his activities. Scilla was not only a pioneer in the field of paleontology, but he prepared the groundwork for the achievement of milestone geological concepts such as actualism, taphonomy and recognition of internal and external moulds (in the instance of non-representation of original hard parts); Scilla deserves further recognition as one of the first to attempt sedimentological interpretation of rocky bodies observed directly in the field.     

A Multifaceted Approach to Ichnology

Trace fossils link paleontology and sedimentology in ways that most body fossils cannot achieve. A multifaceted approach to ichnology helps to bridge the gap the biologic and geologic standpoints, to connect different levels of analysis (conceptual framework, explanatory schemata and applications), and to reconcile dichotomic views (e.g., adaptationist vs. interactionist approaches, time's arrow vs, time's cycle perspectives) by integrating the multiple aspects of the science of animal-substrate interactions. In this context, ichnologic investigations provide important links among numerous different fields. Analysis of specific ichnofaunas using this integrated approach may result in important and meaningful contributions to our understanding of paleoecology, sedimentology, sequence stratigraphy, reservoir characterization, biostratigraphy, evolutionary paleoecology, paleoceanography, and paleoclimatology.     

Evolutionary Theory and the Florence Paleontological Collections

Florence has a tradition of Natural Philosophy, and since as early as the sixteenth century fossils were collected by the Granduke. The Museum of Natural History of the University of Florence houses today collections that belonged to Nicolas Steno, when fossils were for the first time used as documents to reconstruct Earth history. Natural philosophers and geologists, both Italian and foreigners, continued to study fossils collected in Tertiary strata of Tuscany until the nineteenth century, when the first speculations on the origin of species were proposed. Charles Darwin himself mentions fossil vertebrates that are today on show in our museum. In the last years, this part of the history of science has been proposed to the public. The aim was to foster an understanding of the centrality of fossils in two cultural revolutions, the discovery of deep time and the birth of evolutionary theory–connected among themselves and with the emergence of geology. Dedicated volumes, public conferences, guided visits to the collections, and field trips to paleontological sites have attracted an attentive and responsive public, showing that the history of science can help deliver modern evolutionary thinking. Other activities aimed at students of all ages have also shown that the interaction between schools, university teachers, and museum personnel is vital to form the mind of future generations on the reality of the evolution of natural systems.     

两种微体化石三维无损成像技术的对比

近年来,各种X射线三维无损成像技术在古生物学领域的应用越来越广泛。但是,不同的X射线三维无损成像技术针对不同保存类型和尺寸的化石标本在成像效果上各有利弊。本文以埃迪卡拉纪陡山沱组磷酸盐化的动物胚胎化石为研究对象,将目前应用最广的两种X射线三维无损成像方法,即基于实验室X光源的吸收衬度显微断层成像技术和基于同步辐射光源的相位衬度显微断层成像技术进行了对比分析。通过对两种技术的原理、效率、空间分辨率和图像衬度的对比,认为基于同步辐射光源的相位衬度显微断层成像技术是目前对于均一矿化的微体化石最佳的三维无损成像解决方案。     

Shifting public values and what they mean for increasing democracy in wildlife management decisions

Over the last century, changing public attitudes about the value of wildlife have triggered substantial changes in species management that have both benefited and hindered conservation efforts. Understanding and integrating contemporary public values is therefore critical for effective conservation outcomes. Using historic and contemporary examples, we highlight how public attitudes—expressed through the media and campaigns—are shaping the management of introduced and native species, as values shift towards animal welfare and mutualism. We focus on the issue of deliberate human-caused killing of wildlife, because protests against such management have disrupted traditional political and management structures that favoured eradication of wildlife across many jurisdictions and ecological contexts. In doing so, we show that it is essential to work with multiple stakeholder interest groups to ensure that wildlife management is informed by science, while also supported by public values. Achieving this hinges on appropriate science communication to build a better-informed public because management decisions are becoming increasingly democratised.     

A priority paper for the societal and ethical aspects of synthetic biology

As synthetic biology develops into a promising science and engineering field, we need to have clear ideas and priorities regarding its safety, security, ethical and public dialogue implications. Based on an extensive literature search, interviews with scientists, social scientists, a 4 week long public e-forum, and consultation with several stakeholders from science, industry and civil society organisations, we compiled a list of priority topics regarding societal issues of synthetic biology for the years ahead. The points presented here are intended to encourage all stakeholders to engage in the prioritisation of these issues and to participate in a continuous dialogue, with the ultimate goal of providing a basis for a multi-stakeholder governance in synthetic biology. Here we show possible ways to solve the challenges to synthetic biology in the field of safety, security, ethics and the science–public interface.     

Gedanken zu Ibn Sinas (Avicennas) Fossil-Interpretation

Especially in the German literature on the history of paleontology it is said since more than 200 years, that Ibn Sina explained fossils as result of the so-called “vis plastica”. Actually Ibn Sina thought many fossils to be petrified organisms. Vis plastica is a term that comprises different genetic opinions. Some remarks about the influence of ancient Greek and Roman authors (including philosophers) on the interpretation of fossils in medieval and Renaissance times.     

Bioethics,politics and the moral economy of human embryonic stem cell science: the case of the European Union's Sixth Framework Programme

Public communication of science is still largely conceptualized within a ‘transfer’ paradigm that describes it as a displacement of results and ideas from the specialists to the lay public, problematizing the public, the media, (sometimes) science, but very rarely the notion of communication itself. This paper is a preliminary attempt to see if the discourse about genes and the genome can help us to problematize the concept of communication in relation to science, rethink our models of public communication of science and, more generally, the metaphors we employ to describe communication. It is suggested that the relationship between science and the public could be understood better by viewing communication through metaphors drawn from contemporary biology, e.g. as ‘cross‐talk’ between the specialist and public discourse or as a ‘double helix’ coupling the two dimensions under certain conditions.     

What's next for science communication? Promising directions and lingering distractions

In this essay, we review research from the social sciences on how the public makes sense of and participates in societal decisions about science and technology. We specifically highlight the role of the media and public communication in this process, challenging the still dominant assumption that science literacy is both the problem and the solution to societal conflicts. After reviewing the cases of evolution, climate change, food biotechnology, and nanotechnology, we offer a set of detailed recommendations for improved public engagement efforts on the part of scientists and their organizations. We emphasize the need for science communication initiatives that are guided by careful formative research; that span a diversity of media platforms and audiences; and that facilitate conversations with the public that recognize, respect, and incorporate differences in knowledge, values, perspectives, and goals.     

Analysis of the Capacity of Google Trends to Measure Interest in Conservation Topics and the Role of Online News

With the continuous growth of internet usage, Google Trends has emerged as a source of information to investigate how social trends evolve over time. Knowing how the level of interest in conservation topics—approximated using Google search volume—varies over time can help support targeted conservation science communication. However, the evolution of search volume over time and the mechanisms that drive peaks in searches are poorly understood. We conducted time series analyses on Google search data from 2004 to 2013 to investigate: (i) whether interests in selected conservation topics have declined and (ii) the effect of news reporting and academic publishing on search volume. Although trends were sensitive to the term used as benchmark, we did not find that public interest towards conservation topics such as climate change, ecosystem services, deforestation, orangutan, invasive species and habitat loss was declining. We found, however, a robust downward trend for endangered species and an upward trend for ecosystem services. The quantity of news articles was related to patterns in Google search volume, whereas the number of research articles was not a good predictor but lagged behind Google search volume, indicating the role of news in the transfer of conservation science to the public.     

On the eve of animal radiation: phylogeny, ecology and evolution of the Ediacara biota

Ediacara fossils document an important evolutionary episode just before the Cambrian explosion and hold critical information about the early evolution of macroscopic and complex multicellular life. They also represent an enduring controversy in paleontology. How are the Ediacara fossils related to living animals? How did they live? Do they share any evolutionary patterns with other life forms? Recent developments indicate that Ediacara fossils epitomize a phylogenetically diverse biosphere, probably including animals, protists, algae, fungi and others. Their simple ecology is dominated by epibenthic osmotrophs, deposit feeders and grazers, but few if any predators. Their evolution started with an early morphospace expansion followed by taxonomic diversification within confined morphospace, and concluded by extinction of many taxa at the Ediacaran-Cambrian boundary.     

Visualizing 3D data obtained from microscopy on the Internet

The Internet is a powerful communication medium increasingly exploited by business and science alike, especially in structural biology and bioinformatics. The traditional presentation of static two-dimensional images of real-world objects on the limited medium of paper can now be shown interactively in three dimensions. Many facets of this new capability have already been developed, particularly in the form of VRML (virtual reality modeling language), but there is a need to extend this capability for visualizing scientific data. Here we introduce a real-time isosurfacing node for VRML, based on the marching cube approach, allowing interactive isosurfacing. A second node does three-dimensional (3D) texture-based volume-rendering for a variety of representations. The use of computers in the microscopic and structural biosciences is extensive, and many scientific file formats exist. To overcome the problem of accessing such data from VRML and other tools, we implemented extensions to SGI's IFL (image format library). IFL is a file format abstraction layer defining communication between a program and a data file. These technologies are developed in support of the BioImage project, aiming to establish a database prototype for multidimensional microscopic data with the ability to view the data within a 3D interactive environment.     

The Unbearable Lightness of Health Science Reporting: A Week Examining Italian Print Media

Background

Although being an important source of science news information to the public, print news media have often been criticized in their credibility. Health-related content of press media articles has been examined by many studies underlining that information about benefits, risks and costs are often incomplete or inadequate and financial conflicts of interest are rarely reported. However, these studies have focused their analysis on very selected science articles. The present research aimed at adopting a wider explorative approach, by analysing all types of health science information appearing on the Italian national press in one-week period. Moreover, we attempted to score the balance of the articles.

Methodology/Principal Findings

We collected 146 health science communication articles defined as articles aiming at improving the reader''s knowledge on health from a scientific perspective. Articles were evaluated by 3 independent physicians with respect to different divulgation parameters: benefits, costs, risks, sources of information, disclosure of financial conflicts of interest and balance. Balance was evaluated with regard to exaggerated or non correct claims. The selected articles appeared on 41 Italian national daily newspapers and 41 weekly magazines, representing 89% of national circulation copies: 97 articles (66%) covered common medical treatments or basic scientific research and 49 (34%) were about new medical treatments, procedures, tests or products. We found that only 6/49 (12%) articles on new treatments, procedures, tests or products mentioned costs or risks to patients. Moreover, benefits were always maximized and in 16/49 cases (33%) they were presented in relative rather than absolute terms. The majority of stories (133/146, 91%) did not report any financial conflict of interest. Among these, 15 were shown to underreport them (15/146, 9.5%), as we demonstrated that conflicts of interest did actually exist. Unbalanced articles were 27/146 (18%). Specifically, the probability of unbalanced reporting was significantly increased in stories about a new treatment, procedure, test or product (22/49, 45%), compared to stories covering common treatments or basic scientific research (5/97, 5%) (risk ratio, 8.72).

Conclusions/Significance

Consistent with prior research on health science communication in other countries, we report undisclosed costs and risks, emphasized benefits, unrevealed financial conflicts of interest and exaggerated claims in Italian print media. In addition, we show that the risk for a story about a new medical approach to be unbalanced is almost 9 times higher with respect to stories about any other kind of health science-related topics. These findings raise again the fundamental issue whether popular media is detrimental rather than useful to public health.     

Scientists’ Prioritization of Communication Objectives for Public Engagement

Amid calls from scientific leaders for their colleagues to become more effective public communicators, this study examines the objectives that scientists’ report drive their public engagement behaviors. We explore how scientists evaluate five specific communication objectives, which include informing the public about science, exciting the public about science, strengthening the public’s trust in science, tailoring messages about science, and defending science from misinformation. We use insights from extant research, the theory of planned behavior, and procedural justice theory to identify likely predictors of scientists'' views about these communication objectives. Results show that scientists most prioritize communication designed to defend science from misinformation and educate the public about science, and least prioritize communication that seeks to build trust and establish resonance with the public. Regression analyses reveal factors associated with scientists who prioritize each of the five specific communication objectives. Our findings highlight the need for communication trainers to help scientists select specific communication objectives for particular contexts and audiences.     

Functional morphology and evolutionary ecology

Functional morphology studies physico-chemical properties and biological roles of organs. If applied to fossils this approach is connected with specific methodological problems. The fields of application of functional morphology in paleontology are illustrated with examples. In a working concept it is shown how the results of functional morphology can be integrated into an account of the evolutionary ecology of fossil taxa.