The perils of misunderstood and incomplete information. A reply to Johnson and Johnson

This article challenges the methodology and conclusions of a 1991 article by Steven B. Johnson and Ronald C. Johnson (Ethology and Sociobiology 12: 211-220) regarding “Support and Conflict of Kinsmen in Norse Earldoms, Icelandic Families, and the English Royalty.” It replies to specific points raised by Johnson and Johnson and also presents general methodological guidance for nonhistorians seeking to use historical sources. The authors conclude that while the approach of Johnson and Johnson is a worthwhile one, their case is considerably weakened by failure to use sources properly with a full understanding of the cultural, social, and historical realities that these sources represent.     

The integrated Michaelis-Menten rate equation: déjà vu or vu jàdé?

A recent article of Johnson and Goody (Biochemistry, 2011;50:8264–8269) described the almost-100-years-old paper of Michaelis and Menten. Johnson and Goody translated this classic article and presented the historical perspective to one of incipient enzyme-reaction data analysis, including a pioneering global fit of the integrated rate equation in its implicit form to the experimental time-course data. They reanalyzed these data, although only numerical techniques were used to solve the model equations. However, there is also the still little known algebraic rate-integration equation in a closed form that enables direct fitting of the data. Therefore, in this commentary, I briefly present the integral solution of the Michaelis-Menten rate equation, which has been largely overlooked for three decades. This solution is expressed in terms of the Lambert W function, and I demonstrate here its use for global nonlinear regression curve fitting, as carried out with the original time-course dataset of Michaelis and Menten.     

Naturalism, evidence and creationism: The case of Phillip Johnson

Phillip Johnson claims that Creationism is a better explanation of the existence and characteristics of biological species than is evolutionary theory. He argues that the only reason biologists do not recognize that Creationist's negative arguments against Darwinism have proven this is that they are wedded to a biased ideological philosophy —Naturalism — which dogmatically denies the possibility of an intervening creative god. However, Johnson fails to distinguish Ontological Naturalism from Methodological Naturalism. Science makes use of the latter and I show how it is not dogmatic but follows from sound requirements for empirical evidential testing. Furthermore, Johnson has no serious alternative type of positive evidence to offer for Creationism, and purely negative argumentation, despite his attempt to legitimate it, will not suffice.     

The chemical control of Shorgum halepense (Johnson grass) in soybean culture in the Danube meadow

Soybean cultures, especially those from the Danube Meadow, are very strongly infested with Johnson grass, which causes big damages, by the reduction of production with 40-85%, depending on the infestation degree. Before the synthesis of special herbicides for Johnson grass control, this species was controlled by practicing deep tilling, repeated operations with the disk, and, after the sprouting of soy plants, by mechanical and manual hoeings. In the Danube Waterside, the lack of labour force for the manual hoeing is very sharp. For this reason, it was generalized the enlarged use of herbicides for annual weed control (monocotyledonous and dicotyledonous), including Johnson grass. For the control of Johnson grass species, in the conditions of the Danube Meadow, the best results were obtained with the herbicides Fusilade Super, Targa Super, Agil and Select, and for the control of annual dicotyledonous species, with the herbicide Pivot 100LC.     

Free energy couplings between ligand binding and subunit association in hemoglobin are of first order

The calculations presented in a recent paper [Johnson, M. L. (1986) Biochemistry 25, 791-797] to the effect that the free energy couplings between oxygen binding and subunit association in hemoglobin A can be of either first or second order are examined. The fitting of the experimental data to a system with second-order couplings carried out by Johnson belongs to a tetramer in which, in contradistinction to hemoglobin A, oxygen binding promotes subunit association.     

Artefacts, biology and bias in museum collection research

Museum collections are increasingly subjected to scientific scrutiny, including molecular, isotopic and trace-element analyses. Recent advances have extended analyses from natural history specimens to historical artefacts. We highlight three areas of concern that can influence interpretation of data derived from museum collections: sampling issues associated with museum collection use, methods of analysis, and the value of cross-referencing data with historical documents and data sets. We use a case study that focuses on kiwi (Apteryx spp.) feather samples from valuable 19th century Māori cloaks in New Zealand to show how sampling and analysis challenges need to be minimized by careful design. We argue that aligning historical records with scientific data generated from museum collections significantly improves data interpretation.     

The tempo of avian diversification: a comment on Johnson and Cicero

Johnson and Cicero (2004) claimed that inspection of a distribution of uncorrected mitochondrial DNA avian sister-taxon distances illustrated that the late Pleistocene was an important time for avian speciation. They believed this finding to be at odds with conclusions of Klicka and Zink (1997). However, both studies document recent speciation events. More germane to the discussion is what is meant by an "important" time for speciation, which we take to mean above some baseline diversification rate. We constructed a null distribution of sister-taxon distances based on a model of constant speciation and extinction rates. The empirical distribution of sister-taxon distances in Johnson and Cicero (2004) did not differ from the null model. Therefore, our analysis of Johnson and Cicero's data suggests that the late Pleistocene was no more important for avian speciation than any other time during this time period.     

Comparison of lithium chloride-phenylethanol-moxalactam and modified Vogel Johnson agars for detection of Listeria spp. in retail-level meats, poultry, and seafood

The effectiveness of Modified Vogel Johnson agar and lithium chloride-phenylethanol-moxalactam agar for detection of Listeria spp. in foods was compared by using the media to analyze retail-level meat, poultry, and seafood both by direct plating and in conjunction with a three-tube most-probable-number enrichment. The most-probable-number protocol detected Listeria species, including Listeria monocytogenes, in a substantial portion of the fresh meat and seafood samples. In most instances the Listeria levels were less than 2 CFU/g, which precluded detection by direct plating. Modified Vogel Johnson agar performed as well as did lithium chloride-phenylethanol-moxalactam agar and was considerably easier to use because of its ability to differentiate Listeria spp. from other microorganisms.     

Comparison of lithium chloride-phenylethanol-moxalactam and modified Vogel Johnson agars for detection of Listeria spp. in retail-level meats, poultry, and seafood.

The effectiveness of Modified Vogel Johnson agar and lithium chloride-phenylethanol-moxalactam agar for detection of Listeria spp. in foods was compared by using the media to analyze retail-level meat, poultry, and seafood both by direct plating and in conjunction with a three-tube most-probable-number enrichment. The most-probable-number protocol detected Listeria species, including Listeria monocytogenes, in a substantial portion of the fresh meat and seafood samples. In most instances the Listeria levels were less than 2 CFU/g, which precluded detection by direct plating. Modified Vogel Johnson agar performed as well as did lithium chloride-phenylethanol-moxalactam agar and was considerably easier to use because of its ability to differentiate Listeria spp. from other microorganisms.     

Historical Land Use Explains Current Distribution of Calcareous Grassland Species

In this study we analyzed if characteristic calcareous grassland species persist in forest habitats after land use change. Furthermore, we investigated whether the current distribution of such species is related to historical land use of the mid-19th century. Current distributions of nine calcareous grassland species were recorded in a region of Upper Franconia, Germany. Historical (up to 1850) and current land-use data were analyzed using historical maps and aerial photographs. To study the effects of historical land use in current species distributions, we used Generalized Estimating Equations (GEE) and ANOVA, accounting for spatial autocorrelation. Variance partitioning was applied to separate the influence of historical versus current land use. On average 26% of the recorded grassland species occurrences are located in sub-optimal forest habitats. Grassland populations are likely to persist in forest for at least 50 years. Even though current land use explains a higher proportion of the variation in species distribution than historical land use alone, model fit could be significantly improved (P?<?0.001) considering the historical component. We conclude that consideration of historical land use is essential to understand the current grassland species distributions and may be of general importance for perennial species of temperate grasslands. In addition, historical legacy has far-reaching implications for conservation biology in terms of realistic assessments of species threat status in present landscapes.     

Accessibility maps as a tool to predict sampling bias in historical biodiversity occurrence records

Historical biodiversity occurrence records are often discarded in spatial modeling analyses because of a lack of a method to quantify their sampling bias. Here we propose a new approach for predicting sampling bias in historical written records of occurrence, using a South African example as proof of concept. We modelled and mapped accessibility of the study area as the mean of proximity to freshwater and European settlements. We tested the model's ability to predict the location of historical biodiversity records from a dataset of 2612 large mammal occurrence records collected from historical written sources in South Africa in the period 1497–1920. We investigated temporal, spatial and environmental biases in these historical records and examined if the model prediction and occurrence dataset share similar environmental bias. We find a good agreement between the accessibility map and the distribution of sampling effort in the early historical period in South Africa. Environmental biases in the empirical data are identified, showing a preference for lower maximum temperature of the warmest month, higher mean monthly precipitation, higher net primary productivity and less arid biomes than expected by a uniform use of the study area. We find that the model prediction shares similar environmental bias as the empirical data. Accessibility maps, built with very simple statistical rules and in the absence of empirical data, can thus predict the spatial and environmental biases observed in historical biodiversity occurrence records. We recommend that this approach be used as a tool to estimate sampling bias in small datasets of occurrence and to improve the use of these data in spatial analyses in ecological and conservation studies.     

Confidence intervals for the similarity between algal communities

While researchers commonly use similarity measures to compare algal communities, very few researchers have considered the variability of these estimated measures. This paper discusses a recent method for estimating the variance of and confidence intervals for similarity measures proposed by Johnson & Millie (1982, Hydrobiologia 89: 3–8). Applications of this method to data have produced confidence intervals that are too narrow. Two alternative methods, the jackknife method and the bootstrap, are shown to provide superior estimates of the variability.     

Can whole-drawer images measure up? A reply to Johnson et al. (2013)?

Johnson et al. (2013) found that morphometric measurements of dragonfly wings taken from actual specimens and measurements taken from whole-drawer images of those specimens were equally accurate. We do not believe that their conclusions are justified by their data and analysis. Our reasons are, first, that their study was constrained in ways that restrict the generalisability of their results, but second, and of far greater significance, their statistical approach was entirely unsuited to their data and their results misled them to erroneous conclusions. We offer an alternative analysis of their data as published. Our reanalysis demonstrates, contra Johnson et al., that measurements from scanned images are not a reliable substitute for direct measurement.     

Variable selection method improves the prediction of protein secondary structure from circular dichroism spectra

A new procedure based on the statistical method of "variable selection" is used to predict the secondary structure of proteins from circular dichroism spectra. Variable selection adds the flexibility found in the Provencher and Gl?ckner method (S. W. Provencher and J. Gl?ckner, 1981, Biochemistry 20, 33-37) to the method of Hennessey and Johnson (J. P. Hennessey and W. C. Johnson, 1981, Biochemistry 20, 1085-1094). Two analytical methods are presented for choosing a solution from the series generated by the Provencher and Gl?ckner method, and this improves the technique. All three methods are compared and it is shown that both the variable selection method and the improved Provencher and Gl?ckner methods have equivalent reliability superior to the original Hennessey and Johnson method. For the new variable selection method, correlation coefficients calculated between X-ray structure and predicted secondary structures for data measured to 178 nm are: 0.97 for alpha-helix, 0.75 for beta-sheet, 0.50 for beta-turn, and 0.89 for other structures. Although the variable selection method improves the analysis of circular dichroism data truncated at 190 nm, data measured to 178 nm gives superior results. It is shown that improving the fit to the measured CD beyond the accuracy of the data can result in poorer analyses.     

Using a historical map as a baseline in a land-cover change study of northeast Tanzania

Vegetation data in an early 20th century map from northern Tanzania are presented and discussed for its potential of expanding the analytical time-frame in studies of land-use and land-cover change. The starting point is that much research on land-use and land-cover change suffers from a time-frame bias, caused by limitations in remote sensing data. At the same time, the use of historical maps as a complementary data-set is rather insignificant. Can information in historical maps be used to extend the baseline in land-use and land-cover change studies? The historical context of the vegetation data is evaluated, and as an illustration of its potential for interdisciplinary research on land-cover and ecosystems change, a section of the map is juxtaposed with a recent pollen record specifically addressing the impact of a 'large infrequent disturbance' (LID) event at the end of the 19th century. It is concluded that the vegetation data in the map are not likely to be reflecting an extreme situation due to the LID event. Finally, the historical vegetation data were visually compared with a national 1995 land-cover data set, illustrating the possibility of using the map data as a baseline in land-cover change studies.     

Estimating age‐dependent survival from age‐aggregated ringing data—extending the use of historical records

Bird ring‐recovery data have been widely used to estimate demographic parameters such as survival probabilities since the mid‐20th century. However, while the total number of birds ringed each year is usually known, historical information on age at ringing is often not available. A standard ring‐recovery model, for which information on age at ringing is required, cannot be used when historical data are incomplete. We develop a new model to estimate age‐dependent survival probabilities from such historical data when age at ringing is not recorded; we call this the historical data model. This new model provides an extension to the model of Robinson, 2010, Ibis, 152, 651–795 by estimating the proportion of the ringed birds marked as juveniles as an additional parameter. We conduct a simulation study to examine the performance of the historical data model and compare it with other models including the standard and conditional ring‐recovery models. Simulation studies show that the approach of Robinson, 2010, Ibis, 152, 651–795 can cause bias in parameter estimates. In contrast, the historical data model yields similar parameter estimates to the standard model. Parameter redundancy results show that the newly developed historical data model is comparable to the standard ring‐recovery model, in terms of which parameters can be estimated, and has fewer identifiability issues than the conditional model. We illustrate the new proposed model using Blackbird and Sandwich Tern data. The new historical data model allows us to make full use of historical data and estimate the same parameters as the standard model with incomplete data, and in doing so, detect potential changes in demographic parameters further back in time.     

Power priors based on multiple historical studies for binary outcomes

Incorporating historical information into the design and analysis of a new clinical trial has been the subject of much recent discussion. For example, in the context of clinical trials of antibiotics for drug resistant infections, where patients with specific infections can be difficult to recruit, there is often only limited and heterogeneous information available from the historical trials. To make the best use of the combined information at hand, we consider an approach based on the multiple power prior that allows the prior weight of each historical study to be chosen adaptively by empirical Bayes. This choice of weight has advantages in that it varies commensurably with differences in the historical and current data and can choose weights near 1 if the data from the corresponding historical study are similar enough to the data from the current study. Fully Bayesian approaches are also considered. The methods are applied to data from antibiotics trials. An analysis of the operating characteristics in a binomial setting shows that the proposed empirical Bayes adaptive method works well, compared to several alternative approaches, including the meta‐analytic prior.     

Compilation and use of genetic toxicity historical control data

The optimal use of historical control data for the interpretation of genotoxicity results was discussed at the 2009 International Workshop on Genotoxicity Testing (IWGT) in Basel, Switzerland. The historical control working group focused mainly on negative control data although positive control data were also considered to be important. Historical control data are typically used for comparison with the concurrent control data as part of the assay acceptance criteria. Historical control data are also important for providing evidence of the technical competence and familiarization of the assay at any given laboratory. Moreover, historical control data are increasingly being used to aid in the interpretation of genetic toxicity assay results. The objective of the working group was to provide generic advice for historical control data that could be applied to all assays rather than to give assay-specific recommendations. In brief, the recommendations include:     

Ideology,democracy and the national front

This article uses ethnographic and historical data on certain pastoral and agro-pastoral communities in Jammu and Kashmir to illustrate the simultaneous or consecutive use of a variety of cultural features in the construction, maintenance and manipulation of identity. It describes and analyses the context specific uses of religion, language and so on to include as much as to exclude in various economic and political settings. The data exemplify the floating nature of identity, which enables adaptation, assimilation and accommodation to a range of historical contexts within broader regional systems of power.     

Approximating Nature's Variation: Selecting and Using Reference Information in Restoration Ecology

Restoration ecologists use reference information to define restoration goals, determine the restoration potential of sites, and evaluate the success of restoration efforts. Basic to the selection and use of reference information is the need to understand temporal and spatial variation in nature. This is a challenging task: variation is likely to be scale dependent; ecosystems vary in complex ways at several spatial and temporal scales; and there is an important interaction between spatial and temporal variation. The two most common forms of reference information are historical data from the site to be restored and contemporary data from reference sites (sites chosen as good analogs of the site to be restored). Among the problems of historical data are unmeasured factors that confound the interpretation of historical changes observed. Among the problems of individual reference sites is the difficulty of finding or proving a close match in all relevant ecological dimensions. Approximating and understanding ecological variation will require multiple sources of information. Restoration, by its inherently experimental nature, can further the understanding of the distribution, causes, and functions of nature's variation.