Reports from the high table

David Sepkoski and Michael Ruse’s edited collection The Peolobiological Revolution covers the changes in paleontological science in the last half-century. The collection should be of interest to philosophers of science (particularly those interested in non-reductive unity) as well as historians. I give an overview of the content and major themes of the volume and draw some lessons for the philosophy of science along the way. In particular, I argue that the history of paleontology demands a new approach to philosophical delineation of sciences.     

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.     

地点覆盖度、集合群落、地质时期动物群:联接古生物学和现代种群生物学的概念

在古生物群落中新近出现的地点覆盖度或发生率的概念,以及对生物集合种群的空间动态学的深入了解,使古生物学和现代生物学的联系更加紧密。集合群落的概念以及地质时期动物群的古生物学认识显示,将古生物学和生态学结合在一起是大有希望的。评述了目前对这些概念的理解,并以欧亚大陆大型食草动物群落的发育作为范例,介绍了运用这些理论来研究化石记录的方法。研究结果表明,化石记录中种群覆盖度的研究可以在以化石为基础的进化研究和以现生有机体为基础的进化研究之间架起一座桥梁。地点覆盖度最大的类群,像现代生态学中发生率最大的类群一样,往往是地理分布最广泛、在当地最丰富的类群。     

Gram-Chromotrope: a New Technique that Enhances Detection of Microsporidial Spores in Clinical Samples

We have developed a new staining procedure that combines the traditional Gram staining for bacteria and the Weber's chromotrope staining method, the standard technique for the detection of microsporidia spores in clinical Specimens. This “Gram-chromotrope” staining technique enhances the staining characteristics of microsporidia spores and facilitates the easy detection and differentiation of spores from other microorganisms that are found in clinical specimens, especially stool samples. This new technique is fast, reliable, and simple to perform, and can be easily adapted for use in clinical laboratories.     

Minimal Erythema Dose (MED) Testing

Ultraviolet radiation (UV) therapy is sometimes used as a treatment for various common skin conditions, including psoriasis, acne, and eczema. The dosage of UV light is prescribed according to an individual''s skin sensitivity. Thus, to establish the proper dosage of UV light to administer to a patient, the patient is sometimes screened to determine a minimal erythema dose (MED), which is the amount of UV radiation that will produce minimal erythema (sunburn or redness caused by engorgement of capillaries) of an individual''s skin within a few hours following exposure. This article describes how to conduct minimal erythema dose (MED) testing. There is currently no easy way to determine an appropriate UV dose for clinical or research purposes without conducting formal MED testing, requiring observation hours after testing, or informal trial and error testing with the risks of under- or over-dosing. However, some alternative methods are discussed.     

Le rôle des exploitations minières de la région d’Autun dans la constitution des collections paléontologiques

The birth of the oil shale industry, in the Autun basin (Saône-et-Loire, department in Burgundy), at the beginning of the 1830s, corresponded to a time during which the scientific progress in geology and paleontology was quite fast-paced. The development of the schist industry happened at a time when landmark works were published such as those by Louis Agassiz or Adolphe Brongniart. These scientists relied upon the on-going findings in the Autunois area. An outstanding dynamics was on its way. It brought about the updating of many samples sparking off important paleontological studies. A remarkable coordination set up between the industrial workers of the schist industry, the local scholars on the one hand and the National Museum of Natural History in Paris on the other hand. There resulted from it a frequent if not constant interest in the discovery of the fossils that the layers of schists – exploited with the aim of obtaining oil used as a quaffing product – can contain. This dynamics kept going on till the beginning of the 19th century. It was carried out by outstanding personalities such as Bernard Renault or Auguste Roche who were at the origin of the first collections gathered by the Society of Natural History in Autun, founded in 1886. But then, the findings were made rare. The mechanization of the chopping down and crushing of the schist did not any more offer the suitable conditions to discover new specimens. Anyway, the accumulated collections are already considerable and make of the Autunois one of the major places of great French paleontological progress in the years 1870 and 1880.     

Hilgendorf’s (1863) dissertation on the steinheim planorbids (Gastropoda; Miocene): The development of a phylogenetic research program for paleontology

Hilgendorf’s (1866) publication on the phylogenyof Planorbis multiformis from Steinheim, Swabian Mountains, is one of the most important contributions of paleontology to early Darwinism. At the same time it helped to lay the foundation for paleontological phylogenetics. Hilgendorf’s unpublished dissertation of 1863, the newly rediscovered collection to his dissertation and the document-file ofHilgendorf’s graduation from Tübingen University help to trace back the origin of Hilgendorf’s ideas.Hilgendorf’s collection contains the oldest phylogenetic tree, which is known so far.     

Photoelectron imaging of cells: photoconductivity extends the range of applicability.

Photoelectron imaging is a sensitive surface technique in which photons are used to excite electron emission. This novel method has been applied successfully in studies of relatively flat cultured cells, viruses, and protein-DNA complexes. However, rounded-up cell types such as tumor cells frequently are more difficult to image. By comparing photoelectron images of uncoated and metal-coated MCF-7 human breast carcinoma cells, it is shown that the problem is specimen charging rather than a fundamental limitation of the electron imaging process. This is confirmed by emission current measurements on uncoated monolayers of MCF-7 carcinoma cells and flatter, normal Wi-38 fibroblasts. We report here that sample charging in photoelectron microscopy can be eliminated in most specimens by simultaneous use of two light sources--the standard UV excitation source (e.g., 254 nm) and a longer wavelength light source (e.g., 325 nm). The reduction in sample charging results largely from enhanced photoconduction in the bulk sample and greatly extends the range of cells that can be examined by photoelectron imaging. The contributions of photoconductivity, the electric field of the imaging system, and the short escape depths of the photoelectrons combine to make photoelectron imaging a uniquely sensitive technique for the study of biological surfaces.     

Damage to Biological Samples Caused by the Electron Beam during Electron Microscopy

A new method has been developed which measures directly the beam damage suffered by biological specimens in the electron microscope. This method involves the use of radioautography to measure specific radioactivity of labeled specimens, either exposed or unexposed to the beam. Using this technique, it has been found that macromolecular samples such as ribosomes and R17 virions are severely damaged during standard electron microscopic operations: from 15 to 40% of the mass of the sample may be lost in a 30 sec exposure to the beam.     

Information in morphological characters

The construction of morphological character matrices is central to paleontological systematic study, which extracts paleontological information from fossils. Although the word information has been repeatedly mentioned in a wide array of paleontological systematic studies, its meaning has rarely been clarified nor specifically defined. It is important, however, to establish a standard to measure paleontological information because fossils are hardly complete, rendering the recognition of homologous and homoplastic structures difficult. Here, based on information theory, we show the deep connections between paleontological systematic study and communication system engineering. Information is defined as the decrease of uncertainty and it is the information in morphological characters that allows distinguishing operational taxonomic units (OTUs) and reconstructing evolutionary history. We propose that concepts in communication system engineering such as source coding and channel coding, correspond to the construction of diagnostic features and the entire character matrices in paleontological studies. The two coding strategies should be distinguished following typical communication system engineering, because they serve dual purposes. With character matrices from six different vertebrate groups, we analyzed their information properties including source entropy, mutual information, and channel capacity. Estimation of channel capacity shows character saturation of all matrices in transmitting paleontological information, indicating that, due to the presence of noise, oversampling characters not only increases the burden in character scoring, but also may decrease quality of matrices. We further test the use of information entropy, which measures how informative a variable is, as a character weighting criterion in parsimony‐based systematic studies. The results show high consistency with existing knowledge with both good resolution and interpretability.     

A rapid rabies enzyme immuno-diagnosis (RREID): a useful and simple technique for the routine diagnosis of rabies

A Rapid Rabies Enzyme Immuno-Diagnosis (RREID) technique has been developed. This technique for the diagnosis of rabies was performed in microplates which had been previously sensitized with IgG to purified antinucleocapsids. Suspensions of homogenized material were incubated in the plate and the specific binding of rabies antigen was revealed by the use of the same IgG conjugated with peroxidase. With the RREID technique it was possible to detect rabies antigens in brain specimens with the same specificity and sensitivity as that of the direct immunofluorescence test or the neuroblastoma cell inoculation technique regardless of the species of animal from which the specimen was derived. Moreover, RREID was performed with fox salivary gland specimens with the same results as were obtained with brain specimens. RREID does not require an UV light microscope and a photometer is not essential. It is a useful and simple technique for the routine laboratory diagnosis of rabies.     

Methodological innovations for the study of irreplaceable samples reveal giardiasis in extinct animals (Nothrotherium maquinense and Palaeolama maior)

The use of diagnostic methods that prevent irreplaceable samples (from museum collections, archaeological and paleontological samples) of being consumed or that increase their yield is relevant. For museum collections, archaeological and paleontological samples it is essential to conserve samples, subsamples or portions for future research. We are addressing methods for conservation of irreplaceable samples that could be fully consumed. Innovations in methodologies that are used in studies of Paleoparasitology and Paleomicrobiology will contribute to the preservation of collections. Therefore, to the development of archaeology and paleontology in the future, we evaluated whether the discarded material of the immunochromatography test could be used for molecular diagnosis and vice versa. We used a genotyped experimental coprolite positive for Giardia duodenalis. The diagnosis was positive for giardiasis in both cases. This methodology can be corroborated with the coprolite of a Paleolama maior (extinct llama) previously diagnosed for G. duodenalis with an immunoenzymatic test. The residue of the pre-digestion step of the DNA extraction before adding Proteinase K was confirmed positive with the immunochromatographic test. Also, the DNA extraction residue from a coprolite of Nothrotherium maquinense (ground sloth) was tested positive with immunochromatographic test for G. duodenalis. These are the oldest findings for G. duodenalis confirming that this intestinal parasite occurred among Northeastern Brazilian Megafauna animals from the late Pleistocene period, correlated to human occupation. The relevance of these results will allow the study by different methodological approaches from a small amount of material, reusing discarded materials.     

Determining landscape use of Holocene mammals using strontium isotopes

The use of the landscape by animals is predicted to be a function of their body size. However, empirical data relating these two variables from an array of body sizes within a single mammalian community are scarce. We tested this prediction by assessing landscape use of mammals by analyzing strontium (Sr) isotope signatures found in mammalian hard tissues representing a 3,000-year record. We examined: (1) the Sr-determined landscape area of small (∼100 g), medium (∼1,500 g) and large (∼100,000 g) mammals, and; (2) whether the area used by these mammals varied during periods of environmental change. Strontium isotope values were obtained from 46 specimens from the Holocene paleontological deposits of Lamar Cave and Waterfall Locality in Wyoming, USA, as well as from 13 modern ungulate specimens from the same area. Our data indicate that medium- and large-sized species use larger percentages of the landscape than do species of small body size. The isotope values for specimens from each of the paleontological sites are similar across all stratigraphic levels, suggesting no change in home range over the last 3,000 years, even though climate is known to have fluctuated at these sites over this time period. Further, our study verifies that the fossil localities represent the local community. Where bedrock geology is appropriate, the use of strontium isotope analyses provides a valuable tool for discerning landscape use by vertebrate communities, an important though generally difficult aspect of an ancient species niche to identify. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular paleobiology — Progress and perspectives

Molecular paleobiology is a subfield of paleontology that uses molecular biological methods on extant organisms to address geoscientifically relevant questions. Progress in the field was last reviewed in 2007, and here we highlight some of the more recent developments, with a focus on ancient animal evolution, in areas such as the application of molecular clocks to estimate clade ages, the evolution of biomineralization, and the evolution of key traits. We argue that molecular paleobiology has much to offer and will be central to paleontological research and evolutionary biology in general, but we also discuss some remaining challenges and future directions of the discipline.     

计算流体力学在古生物学中的应用——以寒武纪始海百合在COMSOL软件中的模拟为例

提要关于古生物生态位和功能形态学方面的研究通常是推测性的,而定量分析工作较少。此外由于缺少现生生物做对比等诸多因素,使得有些假说存在争议。计算流体力学CFD (computational fluid dynamics)在验证这些推测性假说上具有极大的潜力,并为了解古生物的生活环境以及解释生物在进化过程中的形态变化提供了新的契机。COMSOL Multiphysics作为一款多物理场仿真软件,适用于对古生物的CFD模拟,本文以凯里组始海百合Globoeocrinus模型在COMSOL中的流体实验为案例,来论证关于Globoeocrinus螺旋的腕会使附近的水体形成湍性流动进而帮助滤食这一假说的可能性。流体模拟结果表明在水流流速0.01–0.5 m/s的范围内,Globoeocrinus腕周围并没有出现湍性流动的涡,而是形成了低流速域。低流速域的形成有利于增加始海百合滤取食物的概率。同时文章详细介绍了在COMSOL中进行案例研究的操作步骤,以期望帮助更多的古生物研究者理解和应用CFD技术。     

Cladistics and the hominid fossil record

Cladistic methodology has become common in phylogenetic analyses of the hominid fossil record. Even though it has correctly placed emphasis on morphology for the primary determination of affinities between groups and on explicit statements regarding traits and methods employed in making phylogenetic assessments, cladistics nonetheless has limitations when applied to the hominid fossil record. These include 1) the uncritical assumption of parsimony, 2) uncertainties in the identification of homoplasies, 3) difficulties in the appropriate delimitation of samples for analysis, 4) failure to account for normal patterns of variation, 5) methodological problems with the appropriate identification of morphological traits involving issues of biological relevance, intercorrelation, primary versus secondary characters, and the use of continuous variables, 6) issues of polarity identification, and 7) problems in hypothesis testing. While cladistics has focused attention on alternative phylogenetic reconstructions in hominid paleontology and on explicit statements regarding their morphological and methodological underpinnings, its biological limitations are too abundant for it to be more than a heuristic device for the preliminary ordering of complex human paleontological and neonatological data.     

Marcellin Boule et les types du Prodrome d'Alcide d'Orbigny

During its thirty first years, from 1906 to 1937, the Annales de Paléontologie included, at the instigation of Marcellin Boule, many articles apparently anonymous, devolved to the d'Orbigny's types of the Prodrome. In these articles, not easy to cite because the most part not signed and for some even not titled, are rediscribed and illustrated the species established by d'Orbigny in 1850 and 1852 in his Prodrome de Paléontologie stratigraphique universelle, but then briefly characterized and not figured. It is in fact a collective work, widely remained unfinished but which however totalizes 510 text pages and 139 photographic plates, in the course of which the authors, Armand Thévenin, Ferdinand Canu and Jean Cottreau, redefined more than one thousand species (molluscs, brachiopods, echinoderms, bryozoans, madreporaria and porifers) disposed from the Lower Silurian to the Neocomian, according to the stratigraphic levels then established by d'Orbigny. This redefinition of the d'Orbigny's types of the Prodrome makes up a comprehensive work, the interest of which being possibly evaluated by the numerous quotations referring to it in the former and also recent publications on invertebrate paleontology, this in spite of the questionable choice of some of the type specimens then proposed.     

Performance of pairwise shape dissimilarity morphometrics on nonmammalian taxa (Insecta: Neuroptera: Mantispidae)

Morphometric dissimilarity metrics aim to quantify the variation between compared specimens such that inferences about their relatedness and alpha taxonomy can be made. Recently, the technique has developed metrics that purport to quantify shape dissimilarity between specimens—employing the use of least squares regression analysis. These metrics have been well applied by studies in the hominin fossil record with an arguably unsubstantiated backing for the technique. Originally postulated was the log₁₀ se_m metric which subsequently led to the standard error test of the null hypothesis metric. Following this, the standard deviation of logged ratios (S_LR) metric arose as a pairwise dissimilarity metric that constrains the regression to a zero‐intercept, that is, a significant development in the robustness of the technique. This metric was tested on extant primates in order to evaluate its effectiveness alongside the two other metrics. It was shown to be the most reliable for comparisons between specimens of primates, but was unable to discriminate between heterospecific and conspecific comparisons. Arguably, an alternative model organism with which to compare the technique is lacking. This study considers shape dissimilarity metrics with respect to a group of nonmammalian organisms (mantidflies) and tests the metrics against three lines of evidence (morphology, CO1‐DNA, and geographic distribution) that can delimit the species‐level taxonomy for the group. It is shown that the metrics are unable to discriminate between pairwise comparisons of closely related species, resulting in biologically erroneous groupings, and contradicting the groupings derived from morphological, CO1‐DNA, and distributional comparisons. It is thus asserted that the technique is unsuitable for use in alpha taxonomy as an additional line of evidence in mantidflies. It is further supposed that morphometrics in general should be employed with caution in studies of evolutionary history as phylogeny is not the only information contained within morphometric data. J. Morphol. 276:1482–1494, 2015. © 2015 Wiley Periodicals, Inc.     

Virtual Fossils: a New Resource for Science Communication in Paleontology

Computer-aided 3-D reconstruction of fossils, or virtual paleontology, is an increasingly common and powerful technique. It is now regularly used for research in paleontology, yet to date has impacted little on public outreach and science communication; however, it is ideally suited for these purposes, being increasingly cheap and available, dynamic and exciting, and applicable to a range of topics. Here, we provide an introduction to the field, and a case study of its use for a public engagement event. The steps involved in creating such an educational resource are outlined, and include computed tomography scanning, digital visualization, and 3-D printing of fossils. We emphasize the value of virtual fossils for science communication; they allow for diverse learning styles in a variety of topics. In the future, we hope that virtual paleontology will become a mainstay of communicating the history of life, thereby promoting accurate understanding of evolution.     

Predicting body mass of bonobos (Pan paniscus) with human-based morphometric equations

A primate's body mass covaries with numerous ecological, physiological, and behavioral characteristics. This versatility and potential to provide insight into an animal's life has made body mass prediction a frequent and important objective in paleoanthropology. In hominin paleontology, the most commonly employed body mass prediction equations (BMPEs) are “mechanical” and “morphometric”: uni- or multivariate linear regressions incorporating dimensions of load-bearing skeletal elements and stature and living bi-iliac breadth as predictor variables, respectively. The precision and accuracy of BMPEs are contingent on multiple factors, however, one of the most notable and pervasive potential sources of error is extrapolation beyond the limits of the reference sample. In this study, we use a test sample requiring extrapolation—56 bonobos (Pan paniscus) from the Lola ya Bonobo sanctuary in Kinshasa, Democratic Republic of the Congo—to evaluate the predictive accuracy of human-based morphometric BMPEs. We first assess systemic differences in stature and bi-iliac breadth between humans and bonobos. Due to significant differences in the scaling relationships of body mass and stature between bonobos and humans, we use panel regression to generate a novel BMPE based on living bi-iliac breadth. We then compare the predictive accuracy of two previously published morphometric equations with the novel equation and find that the novel equation predicts bonobo body mass most accurately overall (41 of 56 bonobos predicted within 20% of their observed body mass). The novel BMPE is particularly accurate between 25 and 45 kg. Given differences in limb proportions, pelvic morphology, and body tissue composition between the human reference and bonobo test samples, we find these results promising and evaluate the novel BMPE's potential application to fossil hominins.