Comment on “The role of scaling laws in upscaling” by B.D. Wood

Comment on the article "The role of scaling laws in upscaling" by B.D. Woo

Peer review: beyond the call of duty?

The number of manuscripts submitted to most scholarly journals has increased tremendously over the last few decades, and shows no sign of leveling off. Increasingly, a key challenge faced by editors of scientific journals like the International Journal of Nursing Studies (IJNS) is to secure peer reviews in a timely fashion for the manuscripts they handle. We hear from editors of some journals that it is not uncommon to have to issue 10–15 invitations before one can secure the peer reviews needed to assess a given manuscript and although the IJNS generally fares better than this it is certainly true that a high proportion, probably a majority, of review invitations are declined.\ud \ud Most often, researchers declining invitations to review invoke the fact that they are too busy to add yet another item to their already overcommitted schedule. Some reviewers respond that administrators at their university or research center are actively discouraging them from engaging in an activity that seems to bear no tangible benefits. Yet, however one looks at it, peer reviewing is a crucial component of the publishing process. Nobody has yet come up with a viable alternative. Therefore, we need to find a way to convince our colleagues to peer review manuscripts more often. This can be done with a stick or with various types of carrots.\ud \ud One “stick”, occasionally envisaged by editors (e.g., Anon., 2009), is straightforward, at least to explain. For the peer-reviewing enterprise to function well, each researcher should be reviewing every year as many manuscripts as the number of reviews he or she is getting for his/her own papers. So, someone submitting 10 manuscripts in a given year should be willing to review 20 or 30 manuscripts during the same timeframe (assuming that each manuscript is reviewed by 2 or 3 individuals, as is commonly the case). If this person does not meet the required quota of reviews, there would be some restrictions imposed on the submission of any new manuscript for publication. Boehlert et al. (2009) have advocated such a “stick” in the case of the submission of grant proposals.\ud \ud However, the implementation of such an automatic accounting of reviewing activities is fraught with difficulties. For one thing, it would not prevent reviewers from defeating the system by writing short, useless reviews just to make the number. To eliminate that loophole, someone would have to assess whether reviews meet minimal standards of quality before they can be counted in the annual or running total. There would need to be allowances, for example to allow young researchers to get established in their career. This raises the prospect of a complex and potentially expensive system somewhat akin to carbon trading where credits for reviewing are granted and then traded with a verification system to ensure that no one cheats.\ud \ud An alternative approach, instead of sanctioning bad reviewing practices, would be to reward good ones. Currently the IJNS publishes the names of all reviewers annually. Other journals go a step further for example by giving awards to outstanding reviewers (Baveye et al., 2009). The lucky few who are so singled out by such awards see their reviewing efforts validated. But fundamentally, these awards do not change the unsupportive atmosphere in which researchers review manuscripts. The problem has to be attacked at its root, in the current culture of universities and research centers, where administrators tend to equate research productivity with the number of articles published and the amount of extramural funding brought in. Annual activity reports occasionally require individuals to mention the number of manuscripts or grant proposals reviewed, but these data are currently unverifiable, and therefore, are generally assumed not to matter at all for promotions or salary adjustments.\ud \ud There may be ways out of this difficulty. All the major publishers have information on who reviews what, how long reviewers take to respond to invitations, how long it takes them to send in their reviews. All it would take, in addition, would be for editors or associate editors who receive reviews to assess and record their usefulness, and one would have a very rich data set, which, if it were made available to universities and research centers in a way that preserves the anonymity of the peer-review process, could be used fruitfully to evaluate individuals’ reviewing performance and impact. Of course, one would have to agree on what constitutes a “useful” review. Pointing out typos and syntax errors in a manuscript is useful, but not hugely so. Identifying problems and offering ways to overcome them, proposing advice on how to analyze data better, or editing the text to increase its readability are all ways to make more substantial contributions. Generally, one might consider that there is a usefulness gradation from reviews focused on finding flaws in a manuscript to those focused on helping authors improve their text. Debate among scientists could result in a reliable set of guidelines on how to evaluate peer reviews.\ud \ud Beyond making statistics available to decision makers, other options are also available to raise the level of visibility and recognition of peer reviews (Baveye, 2010). Right or wrong, universities and research centers worldwide now rely more and more on some type of scientometric index, like the h-index (Hirsch, 2005), to evaluate the “impact” of their researchers. In other cases, such as the UK, the basis on which institutions are funded is linked to schemes which have measures such as the impact factor at their core (Nolan et al., 2008 M. Nolan, C. Ingleton and M. Hayter, The research excellence framework (REF): a major impediment to free and informed debate?, International Journal of Nursing Studies 45 (4) (2008), pp. 487–488. Article | PDF (202 K) | View Record in Scopus | Cited By in Scopus (4)Nolan et al., 2008). While many researchers see bibliometric analysis as a legitimate tool to explore discipline's activities and knowledge sources (see for example [Beckstead and Beckstead, 2006], [Oermann et al., 2008] and [Urquhart, 2006]), previous editorials in the IJNS have noted this trend and expressed disquiet at the distorting effect it could have on academic practice when used to pass judgments on quality ([Ketefian and Freda, 2009] and [Nolan et al., 2008]).\ud \ud Many of these indices implicitly encourage researchers to publish more articles, which in turn may detract researchers from engaging in peer reviewing. Certainly, none of the current indices encompass in any way the significant impact individuals can have on a discipline via their peer reviewing. But one could conceive of scientometric indexes that would include some measure of peer-reviewing impact, calculated on the basis of some of the data mentioned earlier. Clearly, such developments will not happen overnight. Before any of them can materialize, a necessary first step is for researchers to discuss with their campus administration, or the managers of their research institution, the crucial importance of peer reviewing and the need to have this activity valued in the same way that research, teaching, and outreach are. A debate along these lines is long overdue.\ud \ud Academic peer review is a necessary part of the publication process but while publication is recognised and valued, peer review is not. Even without the pressures of reward based on publication-based measures there is a potential for those less civic-minded authors to benefit from, but not contribute to, the peer-review system. Current scientometrics actively encourage and reward such behavior in a way that is, ultimately, not sustainable. Once administrators perceive that there is a need in this respect, are convinced that it will not cost a fortune to give peer reviewing more attention, and formulate a clear demand to librarians and publishers to help move things forward, there is hope that this perverse incentive in the current system can be removed. Otherwise the future of the current model of peer review looks bleak and we may indeed have to look forward to a complex bureaucratic system in which review credits are traded.\ud \ud For now, although the IJNS can count itself lucky because the problem affects this journal less than many others, in common with other journals we must thank our peer reviewers who are acting above and beyond the call of duty as it is perceived by many institutions. Without their efforts, journals like this cannot maintain their high standards. It is time for us to lend our weight to calls for a wide-ranging debate in order to ensure that these efforts are properly acknowledged and rewarded when judging the extent and quality of an academic's scientific contribution

Book Review: Pedometrics: How Relevant Is It to the Research on Soil Processes?

Over the last three decades, hundreds of articles, quite a few books, and several international meetings (e.g., Vanwalleghem et al., 2018) have been devoted to the field of “pedometrics.” The aims that are pursued in this field, and the achievements accomplished to date, may not be familiar to researchers working on the description of physical, (bio)chemical, or microbiological processes in soils. The recent publication by Springer of a comprehensive treatise on the topic affords an opportunity to gain some understanding of what the field is about, and, perhaps of more direct interest to readers of our section of the journal, to assess to what extent the content of the book is relevant to the research on soil processes.The field covered by the term “pedometrics”, used analogously to other words such as biometrics, psychometrics, or econometrics (Webster, 1994), has evolved over the years, from “the use of quantitative methods for the study of soil distribution and genesis and as a sustainable resource” when the neologism was first coined in 1986, to “the development and application of statistical and mathematical methods applicable to data analysis problems in soil science” in the book reviewed here. An additional meaning, due to Webster (1994) is “soil science under uncertainty,” implying that pedometrics deals with uncertainty in soil models that is due to deterministic or stochastic variation, vagueness, and lack of knowledge of soil properties and processes. Thus, from the narrow focus of pedometrics in 1986 on quantitative aspects of soil distribution, there has been an intent, at least, to broaden the scope to include pretty much any application of statistics and mathematics to soil science. Indeed, according to this broader intent, any quantitative research on soils could in principle fall within the purview of pedometrics. With this understanding, one might assume a priori that the field could be of direct relevance to the research on soil processes. However, this warrants further scrutiny.The Pedometrics book comprises 23 chapters, written by 44 different authors and organized according to 7 parts: Introduction: What is pedometrics? (Part I, 1 chapter, 45 pages), Statistical footings (Part II, 3 chapters, 71 pages), Soil measurements and properties (Part III, 3 chapters, 107 pages), Soil materials, horizons and profiles (Part IV, 2 chapters, 67 pages), Soil variation in space and time (Part V, 3 chapters, 71 pages), Soil genesis (Part VI, 2 chapters, 47 pages), and Application of pedometrics (Part VII, 4 chapters, 123 pages). Judging from the dates of the references cited and in particular the fact that only 3 chapters contain any reference to work published in 2017, most of the contributed texts appear to have been completed in 2016, a relatively long time before the publication of the book, and therefore do not present the most up-to-date material in some areas. Chapter 22, on broad-scale soil monitoring schemes, is even a reprinted version of a Pedosphere article published in 2012. To some extent, it is unavoidable for edited books, which can be published only when all contributions are in, to have chapters with a range of completion dates. One could probably argue that virtual special issues of electronic journals (like the “Research Topics” at Frontiers), in which articles are published as soon as they are accepted, and from which e-books can emanate if there is a demand for them, constitute more efficient venues to disseminate up-to-date information in a timely manner. As an additional advantage, journal articles are perhaps reviewed more carefully than is the case with book chapters, and in particular more attention tends to be placed on whether or not they provide an appropriate coverage of previous work.A word count analysis of the book, using the search feature associated with the e-book version, provides a fittingly quantitative perspective on its content. Words like “variogram,” “geostatistic,” “variability,” “mapping,” or “model” are found with great frequency in the text and cited references, respectively 539, 232, 259, and 319, 1552 times. Words like “normality” or “non-parametric,” which provide a counterpoint to the traditional Gaussian foundation of geostatistics, are seldom mentioned, respectively 12 and 16 times, even though practical experience with non-normally distributed soil data suggests that they should be paid significantly more attention. Terms that relate to topical areas in the spatial analysis of soils, such as “Bayesian” (21) or “machine learning” (25), make few appearances, which is surprising, in view of the enthusiasm with which researchers have adopted the associated perspectives in recent years (e.g., Douaik et al., 2004; Chammartin et al., 2013; Keskin et al., 2019; Sergeev et al., 2019). Insofar as words typically used in the description of specific soil processes are concerned, very rare to virtually inexistent in the book are mentions of “tomography” (19 occurrences), “leaching” (17), “macropore” (18), “bacteria (7)”, “fungal” (4), “preferential” (3), “swelling” (1), “earthworm” (1), or “macrofauna” (0).In many ways, these occurrence statistics convey the strong impression, confirmed upon reading through the text, that the book, and by extension, the field of pedometrics, are still predominantly focused on a very classical presentation of geostatistics and of its application to the description of spatially varying, largely static, characteristics of soils, with the specific objective of producing maps. Pedostransfer functions are advocated as a way to translate the information contained in or associated with these maps into parameters that may be useful to describe other soil features, and several applications presented in the book illustrate their use. Nevertheless, the bulk of the text is a description of parametric geostatistical methods available to manipulate spatial data related to soils, in line largely with the 1986 definition of pedometrics mentioned earlier. In that context, the level of the text is that of a treatise, meant mostly for specialists, and may not be ideally suited for researchers with little background knowledge, who might want to learn not just about geostatistics, but more broadly about the quantitative analysis of spatial and spatio-temporal data. From that standpoint, books like those of Bivand et al. (2013), Chun and Griffith (2013), or Cressie (2015), might be more suitable introductions to the field. Anyone who is keen to transition to the Bayesian perspective, or is interested in the analysis of spatio-temporal data, both of which in my view are steps in the right direction, may want to turn to books written by Cressie and Wikle (2011) or Blangiardo and Cameletti (2015).From a process-oriented viewpoint, an aspect of the Pedometrics book that is likely to surprise readers is the fact that, aside from the production of maps and more recently of digital maps, little is said in the book about possible purposes pursued by pedometrics, as if the development of geostatistical methods and their application to mapping were, in and of themselves, satisfactory objectives. One could make in this context the same comments that were made decades ago by, e.g., De Bakker (1970) or Schelling (1970) with respect to soil classification. De Bakker (1970), in particular, wrote that “from an extensive survey of recent literature it appears that much is said about principles of soil classification, whereas there is often a lack of definite statements about purposes. As the character of any system of soil classification is partly defined by the ultimate purposes which the drafters had in mind, it is very important to know these purposes.” Indeed, a soil map made for fishermen, with only two classes (soils with- and soils without earthworms), would in all likelihood not be very useful for a wide range of other applications. In a rational approach to the spatial (and temporal) heterogeneity of soils, and to avoid putting the cart before the horse, it would seem that the first step should be to state clearly what question needs to be addressed and at what scale. From there should follow the gathering of appropriate data and the selection of the method(s) to be used for their analysis. One could argue that this crucial issue of the ultimate purposes of data gathering and analysis has not been sufficiently discussed so far in the soil science literature, even in the latest massive effort to produce a global digital map, in spite of vivid illustration that purpose matters (e.g., Basu et al., 2010; Baveye and Laba, 2015). In this respect, by avoiding to bring up the issue, the Pedometrics book regrettably adheres to a long tradition1.Nevertheless, several of the chapters may in principle be of interest to researchers working on soil processes. Chapters 18 and 19 in Part VI deal with the genesis of soils, and involve many “pedogenetic” processes whose study over the years have produced a number of mathematical models, with which researchers in any discipline of soil science should probably be acquainted. Chapter 18, on mysterious-sounding, so-called “Clorpt” functions (standing for “climate, organisms, topography, parent material, and time”), is very short. Chapter 19 is significantly longer and covers some of the relevant literature, but not all of it. In particular, the text ignores all the very interesting research carried out in the last decade on the short-term evolution of soils, e.g., in response to anthropic effects (Cornu et al., 2009, 2012a,b; Montagne and Cornu, 2010; Montagne et al., 2013, 2016; Keyvanshokouhi et al., 2016; van Oort et al., 2017; Bakker et al., 2018).Two other chapters are particularly relevant to the research on soil processes. Chapter 6 (Tarquis et al., 2018) deals with the scaling characteristics of soil structure, and presents in detail some of the measurement techniques (e.g., X-ray computed tomography) and mathematical tools (fractal geometry, multifractal measures, Minkowski functionals) that have been used in the past two decades to characterize the geometry and connectivity of the pore space in soils, as well as the architecture (formerly referred to as the “structure”) of the solid phase. These different topics, as well as the upscaling of soil characteristics to the macroscopic scale, remain extremely challenging at the moment (e.g., Baveye et al., 2018), and researchers who are confronted with them in the study of a wide range of soil processes will find this chapter an especially valuable source of information. Another chapter, Chapter 17 (Rossiter et al., 2018) also presents material that readers of this section of our journal are likely to find particularly interesting. The chapter provides a very good coverage of the literature dealing with the valuation of the various ecosystem services delivered by soils to human populations. The literature has expanded greatly in this very topical area since mid-2016, when this chapter was completed, but nevertheless the very lucid discussion by Rossiter et al. (2018) of the limitations of the economic valuation and of its use for decision making, even when envisaged in an ecological economics context, is well worth reading.Given the prohibitively high cost of this book, even at discount book sellers, it is unlikely that many soil scientists, especially if they are interested predominantly in the dynamics of soil processes, will have much incentive in purchasing a copy of it for their own library. The table of contents of the book can be consulted on the Springer web site, or on the site of Google books (where a preview of some of the pages is also available). From there on, the best option may be to do what we used to do with journal articles in the “good old days”, i.e., ask the authors of chapters of interest for a (now electronic) reprint of their wor

Emergent behavior of soil fungal dynamics:influence of soil architecture and water distribution

Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a "looped" configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass

Control of pore geometry in soil microcosms and its effect on the growth and spread of <i>Pseudomonas </i>and <i>Bacillus</i> sp.

Simplified experimental systems, often referred to as microcosms, have played a central role in the development of modern ecological thinking on issues ranging from competitive exclusion to examination of spatial resources and competition mechanisms, with important model-driven insights to the field. It is widely recognized that soil architecture is the key driver of biological and physical processes underpinning ecosystem services, and the role of soil architecture and soil physical conditions is receiving growing interest. The difficulty to capture the architectural heterogeneity in microcosms means that we typically disrupt physical architecture when collecting soils. We then use surrogate measures of soil architecture such as aggregate size distribution and bulk-density, in an attempt to recreate conditions encountered in the field. These bulk-measures are too crude and do not describe the heterogeneity at microscopic scales where microorganisms operate. In the current paper we therefore ask the following questions: (i) To what extent can we control the pore geometry at microscopic scales in microcosm studies through manipulation of common variables such as density and aggregate size?; (ii) What is the effect of pore geometry on the growth and spread dynamics of bacteria following introduction into soil? To answer these questions, we focus on Pseudomonas sp. and Bacillus sp. We study the growth of populations introduced in replicated microcosms packed at densities ranging from 1.2 – 1.6 g cm-3, as well as packed with different aggregate sizes at identical bulk-density. We use X-ray CT and show how pore geometrical properties at microbial scales such as connectivity and solid-pore interface area, are affected by the way we prepare microcosms. At a bulk-density of 1.6 g cm-3 the average number of Pseudomonas was 63% lower than at a bulk-density of 1.3 g cm-3. For Bacillus this reduction was 66 %. Depending on the physical conditions, bacteria in half the samples took between 1.62 and 9.22 days to spread 1.5 cm. Bacillus did spread faster than Pseudomonas and both did spread faster at a lower bulk-density. Our results highlight the importance that soil physical properties be considered in greater detail in soil microbiological studies than is currently the case

Movement of Cryptosporidium parvum Oocysts through Soils without Preferential Pathways: Exploratory Test

Groundwater contamination by oocysts of the waterborne pathogen Cryptosporidium parvum is a significant cause of animal and human disease worldwide. Although research has been undertaken in the past to determine how specific physical and chemical properties of soils affect the risk of groundwater contamination by C. parvum, there is as yet no clear conclusion concerning the range of mobility of C. parvum that one should expect in field soils. In this context, the key objective of this research was to determine the magnitude of C. parvum transport in a number of soils, under conditions in which fast and preferential transport has been successfully prevented. C. parvum oocysts were applied at the surface of different soils and subjected to artificial rainfall. Apparently for the first time, quantitative PCR was used to detect and enumerate oocysts in the soil columns and in the leachates. The transport of oocysts by infiltrating water, and the considerable retention of oocysts in soil was demonstrated for all soils, although differences in the degree of transport were observed with soils of different types. More oocysts were found in leachates from sandy loam soils than in leachates from loamy sand soils and the retention of oocysts in different soils did not significantly differ. The interaction of various processes of the hydrologic system and biogeochemical mechanisms contributed to the transport of oocysts through the soil matrix. Results suggest that the interplay of clay, organic matter, and Ca2+ facilitates and mediates the transfer of organic matter from mineral surfaces to oocysts surface, resulting in the enhanced breakthrough of oocysts through matrices of sandy loam soils compared to those of loamy sand soils. Although the number of occysts that penetrate the soil matrix account for only a small percentage of initial inputs, they still pose a significant threat to human health, especially in groundwater systems with a water table not too distant from the soil surface. The results of the research demonstrate a critical need for the simultaneous study of the interaction of various processes affecting oocysts transport in the subsurface, and for its expansion into complex systems, in order to obtain a coherent picture of the behavior of C. parvum oocysts in soils

Combining X-ray CT and 3D printing technology to produce microcosms with replicable, complex pore geometries

Measurements in soils have been traditionally used to demonstrate that soil architecture is one of the key drivers of soil processes. Major advances in the use of X-ray Computed Tomography (CT) afford significant insight into the pore geometry of soils, but until recently no experimental techniques were available to reproduce this complexity in microcosms. This article describes a 3D additive manufacturing technology that can print physical structures with pore geometries reflecting those of soils. The process enables printing of replicated structures, and the printing materials are suitable to study fungal growth. This technology is argued to open up a wealth of opportunities for soil biological studies