Providing the requested historical consultation: Hekala and Buell's rebuttal to Johnsons' reply

Hekala and Buell provide a detailed example of the use of historical data to answer the original question posed by Johnson and Johnson concerning possible links between genetic kinsmen in support or conflict situations in Northern Europe during the Middle Ages. The authors affirm the viability of sociobiological principles when coupled with an appropriate use of historical data. In brief, the article confirms the findings of Daly and Wilson on homicide and cultural perceptions of kinship, refutes the final conclusions of Johnson and Johnson, and provides a clear, step-by-step instructional model of historical methodology for non-historians.     

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.     

New class of Johnson distributions and its associated regression model for rates and proportions

By starting from the Johnson distribution pioneered by Johnson ( 1949 ), we propose a broad class of distributions with bounded support on the basis of the symmetric family of distributions. The new class of distributions provides a rich source of alternative distributions for analyzing univariate bounded data. A comprehensive account of the mathematical properties of the new family is provided. We briefly discuss estimation of the model parameters of the new class of distributions based on two estimation methods. Additionally, a new regression model is introduced by considering the distribution proposed in this article, which is useful for situations where the response is restricted to the standard unit interval and the regression structure involves regressors and unknown parameters. The regression model allows to model both location and dispersion effects. We define two residuals for the proposed regression model to assess departures from model assumptions as well as to detect outlying observations, and discuss some influence methods such as the local influence and generalized leverage. Finally, an application to real data is presented to show the usefulness of the new regression model.     

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.     

The Use and Economic Value of Manna grass (Glyceria) in Poland from the Middle Ages to the Twentieth Century

Manna grass (mainly but not exclusively G. fluitans) used to be widely gathered in most lowland areas of the present territory of Poland and western and southern Belarus. It had an important function as a component of tribute paid to local landowners by villagers, which led to the persistence of manna gathering even when this was not sustainable for peasants themselves. Manna grass was always an expensive food due to its time consuming gathering, but appreciated for its sweet taste and often served as dessert. In the nineteenth century marshes shrank significantly and the payment of tribute disappeared from the local economy, which gradually led to the total abandonment of Glyceria use around 1914. This article provides a detailed overview of Glyceria use as food within the borders of the former Polish-Lithuanian Kingdom (now Poland, Lithuania, western Belarus and western Ukraine) based on archaeobotanical, historical and ethnographic sources. The evidence for the continued use of manna since at least medieval times is abundant in historical accounts and ethnographic studies, but little has been reported in archaeobotanical findings due to the relatively small amounts of Glyceria consumed.     

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.     

What hypothesis tests are not: a reply to Johnson

We are sorry that Johnson's pleasure at reading our recent paper(Colegrave and Ruxton, 2003) was so short-lived. Johnson (2005)is correct that the definition of the P value that we use inthe paper is incorrect, and we are grateful     

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.     

Application of Johnson et al.'s speciation threshold model to apparent colonization times of island biotas

Understanding patterns of diversity can be furthered by analysis of the dynamics of colonization, speciation, and extinction on islands using historical information provided by molecular phylogeography. The land birds of the Lesser Antilles are one of the most thoroughly described regional faunas in this context. In an analysis of colonization times, Ricklefs and Bermingham (2001) found that the cumulative distribution of lineages with respect to increasing time since colonization exhibits a striking change in slope at a genetic distance of about 2% mitochondrial DNA sequence divergence (about one million years). They further showed how this heterogeneity could be explained by either an abrupt increase in colonization rates or a mass extinction event. Cherry et al. (2002), referring to a model developed by Johnson et al. (2000), argued instead that the pattern resulted from a speciation threshold for reproductive isolation of island populations from their continental source populations. Prior to this threshold, genetic divergence is slowed by migration from the source, and species of varying age accumulate at a low genetic distance. After the threshold is reached, source and island populations diverge more rapidly, creating heterogeneity in the distribution of apparent ages of island taxa. We simulated of Johnson et al.'s speciation-threshold model, incorporating genetic divergence at rate k and fixation at rate M of genes that have migrated between the source and the island population. Fixation resets the divergence clock to zero. The speciation-threshold model fits the distribution of divergence times of Lesser Antillean birds well with biologically plausible parameter estimates. Application of the model to the Hawaiian avifauna, which does not exhibit marked heterogeneity of genetic divergence, and the West Indian herpetofauna, which does, required unreasonably high migration-fixation rates, several orders of magnitude greater than the colonization rate. However, the plausibility of the speciation-divergence model for Lesser Antillean birds emphasizes the importance of further investigation of historical biogeography on a regional scale for whole biotas, as well as the migration of genes between populations on long time scales and the achievement of reproductive isolation.     

The feeding ecology of Axiothella rubrocincta (Johnson) (Polychaeta: Maldanidae)

The feeding ecology of Axiothella rubrocincta (Johnson) from Tomales Bay, California, is described. This worm inhabits a U-shaped tube of agglutinated sand grains and mucus. Morphological adaptations such as nuchal and anal plaques prevent the tube from becoming clogged. Foreign debris entering the tube is either consumed or incorporated into the tube wall. The proboscis and notosetae are probably used to clean the tube wall. A. rubrocincta combines feeding and burrowing activities to form the funnel and complete the tube: it does not ingest sediment while burrowing. Organic matter deposited into the funnel is buried there by sand slides originating at the rim of the funnel. The concentration of organic matter within the funnel is significantly higher than for non-funnel sediments. A. rubrocincta consumes food from the upper 2 cm of the substratum and is 4.6% efficient as a depositfeeder. It also feeds within the funnel and can ingest large quantities of food. This feeding process is described. A. rubrocincta irrigates its tube at a rate of 5.1 ml sea water/g/h while feeding, and briefly reverses this current to a rate of 0.1 ml/g/h when defaecating. The rhythmic activity patterns are integrated: the mean defaecation and inverse pumping time is 14.4 min at 15 ± 1 C.     

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.     

Theory of Threshold Fluctuations in Nerves: II. Analysis of Various Sources of Membrane Noise

Threshold fluctuations in axon firing can arise as a result of electrical noise in the excitable membrane. A general theoretical expression for the fluctuations is applied to the analysis of three sources of membrane noise: Johnson noise, excess 1/f noise, and sodium conductance fluctuations. Analytical expressions for the width of the firing probability curve are derived for each of these noise sources. Specific calculations are performed for the node of Ranvier of the frog, and attention is given to the manner in which threshold fluctuations are affected by variations of temperature, ion concentrations, and the application of various drugs. Comparison with existing data suggests that threshold fluctuations can best be explained by sodium conductance fluctuations. Additional experiments directed at distinguishing among the various noise sources are proposed.     

Comparison and Evaluation of Three Methods of Estimation of the Johnson Sb Distribution

Thre methods of estimating the parameters of the Johnson S₆ distribution were tested by simulation. The maximum likelihood method, the method based on percentiles of a sample and the method based on moments of a transformed random variable were taken into consideration. Many sets of samples were generated differing in sizes and in the actual values of parameters, whereupon the parameters were estimated by the three methods. It was proved that if the sample is small or the skewness of the distribution is considerable, the maximum likelihood estimates can assume preposterous values. The method based on moments is recommended due to its simplicity and to the fact that the estimates, though usually biased, never assume absurd values.     

Phenotypic variations of haptoglobin Johnson types

Summary Sera from four individuals with haptoglobin Johnson phenotypes were examined. Polyacrylamide gel electrophoresis revealed minor phenotypic variations between the Johnson types of two members from a Czechoslovakian family and of two unrelated Caucasians from the USA. The subtyping procedure after haptoglobin isolation and reductive cleavage showed Hp J-polypeptide chains with identical electrophoretic mobilities in the four individuals analyzed. In addition to the Hp J chain two persons had a Hp 1 S chain and two persons had a Hp 1 F chain. The two members of the Czechoslovakian family had, furthermore, a third component with an electrophoretic migration rate intermediate between a common Hp 2 and a common Hp 1 S chain.Supported by U.S.P.H.S. Grant AM 11796-02 and aided by a grant from the Deutsche Forschungsgemeinschaft, Bad Godesberg.     

Cyanogenic polymorphism in Eucalyptus polyanthemos Schauer subsp. vestita L. Johnson and K. Hill (Myrtaceae)

Plant cyanogenesis, the release of cyanide from endogenous cyanide-containing compounds, is an effective herbivore deterrent. This paper characterises cyanogenesis in the Australian tree Eucalyptus polyanthemos Schauer subsp. vestita L. Johnson and K. Hill for the first time. The cyanogenic glucoside prunasin ((R)-mandelonitrile β-D-glucoside) was determined to be the only cyanogenic compound in E. polyanthemos foliage. Two natural populations of E. polyanthemos showed quantitative variation in foliar prunasin concentration, varying from zero (i.e. acyanogenic) to 2.07 mg CN g^-1 dry weight in one population and from 0.17 to 1.98 mg CN g^-1 dry weight in the other. No significant difference was detected between the populations with respect to the mean prunasin concentration or the degree of variation in foliar prunasin, despite significant differences in foliar nitrogen. Variation between individuals was also observed with respect to the capacity of foliage to catabolise prunasin to form cyanide. Moreover, variation in this capacity generally correlated with the amount of prunasin in the tissue, suggesting genetic linkage between prunasin and β-glucosidase.     

Molecular evidence of triplication in the haptoglobin Johnson variant gene

Summary The protein and gene structure of the Hp Johnson variant (Hp3) were analyzed in two related heterozygous individuals. The molecular weight (23kd) and amino acid composition of Hp3 alpha chain were in agreement with the triplicated structure first suggested by Smithies in 1964. Direct gene analysis by Southern blotting showed a three-fold tandem repeat of the same 1.7 kb DNA segment implicated in the Hp2 gene duplication. On the basis of these data a nine exon model for the Hp3 gene is proposed.     

Brown trout population structure highly affected by multiple stocking and river diversion in a high mountain national park

Stocking is a widely applied practice for enhancement of fish populations exploited for recreational and commercial uses. In the present study, we investigate the genetic consequences of stocking and river diversion by analyzing 18 microsatellites in 440 brown trout (Salmo trutta L.) from three historical and ten contemporary populations from two river systems in a national park in Norway. Eight sources have been recorded for stocking in this area, but not concurrently. These stocking events took place after historical sampling and river diversion by construction of a barrier and a channel. A complete shift in the genetic structure between historical and contemporary populations was revealed. The genetic differentiation can be explained by stocking with just four non-native sources. The constructed barrier has helped to maintain a fraction of the historical genetic profile. Stocking success is discussed in relation to population exploitation, variation in natural recruitment, and reduced discharge due to river diversion. Our study demonstrates a high vulnerability of natural populations to stocking with non-native fish, of particular importance for fishery management and preservation of native fish.