Papers by Philippe Baveye
Using an R program to "scrape over" 68,000 user-generated comments from multiple Reddit communiti... more Using an R program to "scrape over" 68,000 user-generated comments from multiple Reddit communities, and the software Leximancer to identify the internet domains which these comments cite, Charles Areni addresses the question of whether climate sceptics are more likely to post links to unreliable sources whereas climate change 'believers' are more likely to post links to peer-reviewed science and solid news sources. The results that Areni obtains are interesting in more than one respect, and in particular what I find most revealing about them is something that Areni does not mention. But before I get to these positive aspects of Areni's text, I would like to raise two different points. The first concerns the expressions of climate change "deniers" and "believers" that the author uses throughout the text. As a scientist, trying as much as possible to define precisely the terms I refer to, I find those two expressions very fuzzy, in the sense that they can conceivably encompass all kinds of nuances. Someone (against all available experimental evidence to the contrary) may not believe that the global climate is changing, or may not believe that the changing climate is due to anthropic influences. Both perspectives seem to be lumped together indiscriminately under the heading of climate change "deniers". The same goes for climate change "believers", who can be very heterogeneous as well with regard to the viewpoints they adopt. It may be that for the Reddit comments that Areni consulted, it is not possible to determine to which category of denier or believer their authors belong. In that case, it would be helpful to add a discussion about how confusing the terminology potentially is. If, on the other hand, it is possible to tease apart the deniers and believers into subcategories, that would be very useful, and may prove enlightening. A second criticism is related to the belief Areni seems to hold that blogs and social media are necessarily of "low credibility", whereas news media and academic journals (especially Nature) are "credible, unbiased sources" (page 3 of the preprint). It would be nice if things were as simple as that… But unfortunately, there are plenty of reasons to think that they are not. For starters, one could legitimately argue that the objectivity of scholarly journals is largely a myth, in the sense that journal editors, through the choice they make of several anonymous reviewers, pretty much can dictate a priori if a manuscript will or will not eventually be published in their journal (e.g., discussion in Baveye, 2021c). Experience shows that editors of scholarly journals are routinely under intense pressure by publishers to raise the impact factor of their journal, for example by favouring manuscripts that have a high chance of getting numerous citations, regardless of the soundness of that they contain. Solutions exist to make the peer-review process less subjective and more resilient to misuse, but none has been implemented so far.
HAL (Le Centre pour la Communication Scientifique Directe), 2003
When oocysts of the protozoan Cryptosporidium parvum contaminate drinking water supplies, they ca... more When oocysts of the protozoan Cryptosporidium parvum contaminate drinking water supplies, they can cause outbreaks of Cryptosporidiosis, a common waterborne disease. Of the different pathways by which oocysts can wind up in drinking water, one has received little attention to date; that is, because soils are often considered to be perfect filters, the transport of oocysts through the subsoil to groundwater is generally ignored. To evaluate the significance of this pathway, a series of laboratory experiments investigated subsurface transport of oocysts. Experiment 1 was carried out in a vertical 18-cm-long column filled either with glass beads or silica sand, under conditions known to foster fingered flow. Experiment 2 involved undisturbed, macroporous soil columns subjected to macropore flow. Experiment 3 aimed to study the lateral flow on an undisturbed soil block. The columns and soil samples were subjected to artificial rainfall and were allowed to reach steady state. At that point, feces of contaminated calves were applied at the surface along with a known amount of potassium chloride to serve as a tracer, and rainfall was continued at the same rate. The breakthrough of oocysts and chloride, monitored in the effluent, demonstrate the importance of preferential flow on the transport of oocysts. Compared with chloride, peak oocyst concentrations were not appreciably delayed and, in some cases, occurred even before the chloride peak. Recovery rates for oocysts were low, ranging from 0.1 to 10.4% of the oocysts originally applied on the columns. However, the numbers of oocysts present in the effluents were still orders of magnitude higher than 10 oocysts, the infectious dose considered by the U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, to be sufficient to cause Cryptosporidiosis in healthy adults. These results suggest that the transport of oocysts in the subsurface via preferential flow may create a significant risk of groundwater contamination in some situations. Water Environ. Res., 75, 113 (2003).
Spanish Journal of Soil Science, Jul 4, 2017
European Journal of Soil Science, May 18, 2020
For over a half a century, researchers have been aware of the fact that the physical and chemical... more For over a half a century, researchers have been aware of the fact that the physical and chemical characteristics of microenvironments in soils strongly influence the activity, growth and metabolism of microorganisms. However, many aspects of the effect of soil physical characteristics, such as the pore geometry, remain poorly understood. Therefore, the objective of the present research was to determine the influence of soil pore characteristics on the spread of bacteria, observed at the scale relevant to microbes. Pseudomonas fluorescens was introduced in columns filled with 1-2 mm soil aggregates, packed at different bulk densities. Soil microcosms were scanned at 10.87 μm voxel resolution using X-ray computed tomography (CT) to characterize the geometry of pores. Thin sections were prepared to determine the spread and colonization of bacteria. The results showed that average bacterial cell density was 174 cells mm −2 in soil with bulk density of 1.3 g cm −3 and 99 cells mm −2 in soil with bulk density of 1.5 g cm −3. Soil porosity and solid-pore interfaces influence the spread of bacteria and their colonization of the pore space at lower bulk density, resulting in relatively higher bacterial densities in larger pore spaces. The study also demonstrates that thin sectioning of resinimpregnated soil samples can be combined with X-ray CT to visualize bacterial colonization of a 3D pore volume. This research therefore represents a significant step towards understanding how environmental change and soil management impact bacterial diversity in soils. Highlights • We used a quantitative approach to study bacterial spread in soil at scales relevant to microbes. • The rate of pseudomonas spread decreased with increased bulk density of soil. • Soil porosity and soil-pore interface influence Pseudomonas in lower bulk density soil. • Soil structure with different pore characteristics effects spread and activity of bacteria in soil.
Resources Conservation and Recycling, May 1, 2023
Outlook on Agriculture, Aug 8, 2022
In recent years, the need for profound changes in agricultural practices has become increasingly ... more In recent years, the need for profound changes in agricultural practices has become increasingly acknowledged, and it has given rise to an intense, and rapidly intensifying, debate among experts and in the media. Before the general framework under which this debate currently unfolds become too set in stone, it would seem useful to devote some time to a reflexion on how discussions should be approached in order to have the best chance to result in practically workable, sustainable solutions. In a recent, provocative article, Amundson (2022) voiced very strong opinions in this respect. In particular, he criticizes the emergence in the general public of “we” visions about alternate forms of agriculture, he argues that key current stakeholders (i.e. farmers) imperatively have to be included in the discussions, and he opines that the debate should not attempt to solve “social wicked problems”, which tend to remain long-standing because no one can manage to solve them. In the present article, I propose an in-depth reflexion on these three aspects of the debate, and adopt very different perspectives than Amundson’s (2022). After decades of laboriously trying to get members of the general public engaged with soils and agricultural issues, “we” visions with which members of the public may come up need to be resolutely welcomed, carefully analyzed, and responded to, soon after they emerge. Furthermore, I argue that stakeholders who are currently in the agricultural sector may not necessarily be the most likely to eventually implement changes and therefore should not be allowed to sway the debate in a direction that suits them in the short run. Finally, I contend that the lack of willingness, or the reluctance, of decision-makers and the private sector to envisage fundamental changes, thereby giving the impression that some problems cannot be readily solved, should not constrain in any way the scope of the reflexion.
Science & public policy, Sep 26, 2022
Over the last two decades, there has been a documented decline in public trust toward science. Th... more Over the last two decades, there has been a documented decline in public trust toward science. This evolution has often been attributed to the fast expansion of Internet, making it very easy to spread alternate viewpoints. In the present perspective piece, it is argued that the unethical behavior of some researchers also has fueled the public distrust toward science. In this context, a solution could come from creating publicly accessible registries that would provide all the information needed by the public to determine whether a given researcher could safely be presumed to be an ‘honest broker’, i.e. to act in a disinterested manner about particular issues being debated. In the development of such registries, academies would be particularly suited to provide oversight, since some of their senior members, by virtue of their retirement from active duty, meet many of the conditions to effectively be honest brokers.
Soil Science Society of America Journal, Sep 1, 1988
Abstract Mass spectrometric procedures for determination of dinitrogen (N 2) and nitrous oxide (N... more Abstract Mass spectrometric procedures for determination of dinitrogen (N 2) and nitrous oxide (N 2 O) evolved during denitrification in soil treated with 15 N-labeled fertilizer are based on the hypothesis that the nitrate (NO− 3) undergoing denitrification can be ...
European Journal of Soil Science, 2023
Terrestrial enhanced rock weathering (ERW) is a carbon dioxide removal technology that aims at ac... more Terrestrial enhanced rock weathering (ERW) is a carbon dioxide removal technology that aims at accelerating one of the most powerful negative feedbacks on Earth's climate, the chemical weathering of silicates. To achieve this, ERW proposes to spread ground silicate rock on agricultural soils. According to many models, global application rates of 40 tonnes of ground basaltic rock per hectare and per year would be necessary to sequester a significant amount of CO2, representing up to 24% of the current net annual increase in atmospheric CO2. When assessing the viability of ERW as a global geo‐engineering strategy, a pivotal but overlooked question to address is whether ERW may lead to toxic trace element accumulation in soils at unauthorized and potentially harmful levels. This study evaluates the legal sustainability of ERW with regard to trace element contents in soils. We compare different trace element accumulation scenarios considering a range of rock sources, application rates and national regulatory limits. The results indicate that, at the suggested annual application rate of 40 tonnes per hectare, the first regulatory limits would be exceeded after 6 and 10 years for copper and nickel, respectively. This study argues in favour of close tailoring of ERW deployment to local conditions in order to tap into its climate mitigation potential while preserving long‐term soil uses.Highlights Terrestrial enhanced rock weathering (ERW) is a carbon sequestration technology that consists in applying rock powder to soils. This study evaluates whether rock powder application can lead to trace metals accumulation in soils beyond regulatory limits. ERW can lead to the overrun of some environmental regulatory limits within less than a decade. Specific site and rock selection will be necessary for this method to preserve long‐term soil uses.
Soil Biology & Biochemistry, Sep 1, 2023
European Journal of Soil Science, Oct 24, 2021
Over the last decade, the adoption of new sensing techniques, producing vast amounts of data, and... more Over the last decade, the adoption of new sensing techniques, producing vast amounts of data, and the ease of storing and processing these data, have changed appreciably the general conditions under which at least some of the soil research is carried out. To try to extract knowledge and relevant information from increasingly large, diverse, and complex soil-related data sets, researchers in sizeable numbers have turned with increasing frequency to techniques like “data mining” (e.g., Bui, Henderson, & Viergever, 2006, 2009; Mohammadifar, Gholami, Comino, & Collins, 2021) and “machine learning” (e.g., Dong, Wang, Liu, Xie, & Han, 2021; Wadoux, Samuel-Rosa, Poggio, & Mulder, 2019). Some authors (e.g., Bui, 2016) have argued that the use of these sophisticated statistical and algorithmic tools constitutes a paradigm shift in soil research, from the traditional “hypothesis-driven” science to one that is instead “data-driven,” that is, where rather than starting with a hypothesis (i.e., a tentative, testable answer to a question), one focuses from the onset on “finding patterns, correlations, and order in data.” In an insightful review article published recently in this journal, Wadoux, Dobarco, and McBratney (2021) provide a balanced analysis of the various benefits that could arguably be derived from data-driven research, as well as of a number of significant concerns associated with that approach. These authors readily acknowledge that the scope of their analysis is restricted largely to the field of pedometrics, with which they are most familiar. Given the significance that the possible paradigm shift they review would have for other subdisciplines in soil science, it seems opportune to complement the analysis of Wadoux et al. (2021) and to broaden its scope, so that a healthy debate can ensue where all the subdisciplines of soil science ideally would participate. This is what this letter aims to foster. There is no doubt, as shown by Wadoux et al. (2021), that over the last few decades, even before the topic became the object of significant hype in science in general, large-scale spatial information about soil characteristics has ventured into the realm of what is now often referred to as “big data.” Interestingly, however, there is another area in soil science where researchers have had to manipulate extremely large data sets for a while, but where one has traditionally refrained from using expressions like “big data” and resisted any compulsion to switch to a “data-driven” approach in any way. On the contrary, for practical reasons, the size of the data sets has been seen more as a curse than as a blessing. This other area is associated with the three-dimensional, nondestructive characterization of the architecture of soil samples, achieved by using either computed tomography (CT) or nuclear magnetic resonance (NMR) equipment. A typical X-ray CT image of a soil sample, for example, may encompass 500 500 500, or 125,000,000 grey level values associated with individual voxels, and many CT images are larger still. To identify the pore space in these images, one needs to threshold them, that is, transform them to black and white versions. For that specific purpose, machine-learning methods have occasionally been adopted (e.g., Lavrukhin, Gerke, Romanenko, Abrosimov, & Karsanina, 2021), but aside from this limited context, data-mining or machine-learning techniques have not been used at all to “discover knowledge” from CT or NMR images. A key reason the data-driven approach has manifestly not had much appeal in this field may be that prior to acquiring a CT or NMR image of a soil sample, an observer necessarily has to determine what question needs to be addressed, because that question unequivocally determines at what resolution and over what size of a sample (the two being intimately linked), the image should be obtained. If the question one is interested in relates to the movement of earthworms in soil columns, the columns have to be big enough to comfortably host one or more earthworms, and the resolution of the images can safely be in the tens or even hundreds of microns. Contrastedly, attempts to understand how the geometry and connectivity of pores in soils affects the propagation of fungi should ideally be based on CT images with a resolution of a few microns, which enables the visualization of pores that are large enough to allow the penetration of hyphae. A similar research focusing on bacterial-, and, a fortiori, viral movement in soils, or on the microscale structure of organo-mineral complexes, requires resolutions that are considerably higher, which practically can be obtained only with correspondingly minute samples. This primacy of “questions” over “data” in soil research is not unique to the use of CT or NMR images, far from it. Received: 20 July 2021 Accepted: 6 August 2021
Thinking with Soils: Material Politics and Social Theory Salazar, J.F., Granjou, C., Kearnes, M., Krzywoszynska, A., and Tironi, M. (eds) Bloomsbury Academic, London, UK, 2020. xv + 220 pp. £85, hardback. <scp>ISBN</scp> 978‐1‐3501‐0957‐5 European Journal of Soil Science, Dec 28, 2020
Springer eBooks, 2003
Softcover reprint of the hardcover 1st edition 2003 No part of this work may be reproduced, store... more Softcover reprint of the hardcover 1st edition 2003 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work.
SSSA special publication series, Oct 26, 2015
European Journal of Soil Science
Terrestrial enhanced rock weathering (ERW) is a carbon dioxide removal technology that aims at ac... more Terrestrial enhanced rock weathering (ERW) is a carbon dioxide removal technology that aims at accelerating one of the most powerful negative feedbacks on Earth's climate, the chemical weathering of silicates. To achieve this, ERW proposes to spread ground silicate rock on agricultural soils. According to many models, global application rates of 40 tonnes of ground basaltic rock per hectare and per year would be necessary to sequester a significant amount of CO2, representing up to 24% of the current net annual increase in atmospheric CO2. When assessing the viability of ERW as a global geo‐engineering strategy, a pivotal but overlooked question to address is whether ERW may lead to toxic trace element accumulation in soils at unauthorized and potentially harmful levels. This study evaluates the legal sustainability of ERW with regard to trace element contents in soils. We compare different trace element accumulation scenarios considering a range of rock sources, application rat...
European Journal of Soil Science
Over the last decades, a new generation of microscale models have been developed to simulate soil... more Over the last decades, a new generation of microscale models have been developed to simulate soil microbial activity. An earlier article (Pot et al., 2021) presented a detailed review of the description of soil architecture and microbial dynamics in these models. In the present article, we summarize the main results obtained by these models according to six model outputs: growth and spatial organization of microbial colonies, soil hydraulic conductivity, coexistence and trophic interactions of microorganisms, temporal dynamics of the amount of solid and dissolved organic matter in soil and, microbial production of CO 2. For each of these outputs, we draw particular attention to the respective roles of soil architecture and microbial dynamics, and we report how microscale models allow for disentangling and quantifying them. We finally discuss limitations and future directions of microscale models in combination with the ongoing development of high-performance imaging tools revealing the spatial heterogeneity of the actors of soil microbial activity. Highlights • We review the insights on soil functions derived from microscale models of soil microbial processes • Microscale models disentangle the complex interactions between soil architecture and microbial dynamics
European Journal of Soil Science, 2021
Macroscopic models of soil organic matter (SOM) turnover have faced difficulties in reproducing S... more Macroscopic models of soil organic matter (SOM) turnover have faced difficulties in reproducing SOM dynamics or in predicting the spatial distribution of carbon stocks. These models are based on a largely inadequate linear response of soil microorganisms to bulk concentrations of nutrients and it is clear that a new approach to SOM modelling is required. Introducing explicit microbial activity and organic matter (OM) reactivity in macroscopic models represents a challenge because of the fine spatial scales at which the processes occur. To get a better grasp on interactions that take place at the microscale, a new generation of SOM models have been developed at the spatial scale of the soil microenvironments where microorganisms evolve. These models are well adapted to challenge traditional hypotheses about the influence of soil architecture on soil microbial activity. Soil architecture provides the stage for a dynamic spatial accessibility of resources to microbes and the emergence ...
Uploads
Papers by Philippe Baveye