A problem formulation framework for the application of in silico toxicology methods in chemical risk assessment.

The first step in the hazard or risk assessment of chemicals should be to formulate the problem through a systematic and iterative process aimed at identifying and defining factors critical to the assessment. However, no general agreement exists on what components an in silico toxicology problem formulation (PF) should include. The present work aims to develop a PF framework relevant to the application of in silico models for chemical toxicity prediction. We modified and applied a PF framework from the general risk assessment literature to peer reviewed papers describing PFs associated with in silico toxicology models. Important gaps between the general risk assessment literature and the analyzed PF literature associated with in silico toxicology methods were identified. While the former emphasizes the need for PFs to address higher-level conceptual questions, the latter does not. There is also little consistency in the latter regarding the PF components addressed, reinforcing the need for a PF framework that enable users of in silico toxicology models to answer the central conceptual questions aimed at defining components critical to the model application. Using the developed framework, we highlight potential areas of uncertainty manifestation in in silico toxicology PF in instances where particular components are missing or implicitly described. The framework represents the next step in standardizing in silico toxicology PF component. The framework can also be used to improve the understanding of how uncertainty is apparent in an in silico toxicology PF, thus facilitating ways to address uncertainty.

Conflicts of Interest in the Assessment of Chemicals, Waste, and Pollution.

Pollution by chemicals and waste impacts human and ecosystem health on regional, national, and global scales, resulting, together with climate change and biodiversity loss, in a triple planetary crisis. Consequently, in 2022, countries agreed to establish an intergovernmental science-policy panel (SPP) on chemicals, waste, and pollution prevention, complementary to the existing intergovernmental science-policy bodies on climate change and biodiversity. To ensure the SPP's success, it is imperative to protect it from conflicts of interest (COI). Here, we (i) define and review the implications of COI, and its relevance for the management of chemicals, waste, and pollution; (ii) summarize established tactics to manufacture doubt in favor of vested interests, i.e., to counter scientific evidence and/or to promote misleading narratives favorable to financial interests; and (iii) illustrate these with selected examples. This analysis leads to a review of arguments for and against chemical industry representation in the SPP's work. We further (iv) rebut an assertion voiced by some that the chemical industry should be directly involved in the panel's work because it possesses data on chemicals essential for the panel's activities. Finally, (v) we present steps that should be taken to prevent the detrimental impacts of COI in the work of the SPP. In particular, we propose to include an independent auditor's role in the SPP to ensure that participation and processes follow clear COI rules. Among others, the auditor should evaluate the content of the assessments produced to ensure unbiased representation of information that underpins the SPP's activities.

Exploring Scientists' Values by Analyzing How They Frame Nature and Uncertainty.

Several scholars have proposed that values embedded in science are a central reason why more research does not necessarily resolve scientific controversies around complex environmental issues. In the Capital Regional District, British Columbia, Canada, scientists have positioned themselves for and against the construction of a wastewater treatment plant in a debate framed as purely technical. This study explores the link between the scientists' positions in the debate and the way they, in their scientific publications, portray nature and environmental risks. We performed a qualitative content analysis of peer-reviewed publications by scientists who have publicly taken opposing positions in the controversy. We found that scientists against treatment predominantly frame nature as tolerant, up to a limit, to disturbances and potential risks, and they seem to embrace a view of science as capable of reducing uncertainties. In contrast, scientists in favor of treatment predominantly portray nature as fragile, particularly toward human-mobilized environmental risks and they commonly present scientific uncertainty as worrisome based on potentially harmful consequences. Our study suggests that value-laden perspectives impact scientists' positions even in a seemingly technical controversy.

Science for Policy: A Case Study of Scientific Polarization, Values, and the Framing of Risk and Uncertainty.

It is well documented that more research can lead to hardened positions, particularly when dealing with complex, controversial, and value-laden issues. This study is an attempt to unveil underlying values in a contemporary debate, where both sides use scientific evidence to support their argument. We analyze the problem framing, vocabulary, interpretation of evidence, and policy recommendations, with particular attention to the framing of nature and technology. We find clear differences between the two arguments. One side stress that there is no evidence that the present approach is causing harm to humans or the environment, does not ruminate on uncertainties to that end, references nature's ability to handle the problem, and indicates distrust in technological solutions. In contrast, the other side focuses on uncertainties, particularly the lack of knowledge about potential environmental effects and signals trust in technological development and human intervention as the solution. Our study suggests that the two sides' diverging interpretations are tied to their perception of nature: vulnerable to human activities versus robust and able to handle human impacts. The two sides also seem to hold diverging views of technology, but there are indications that this might be rooted in their perception of governance and economy rather than about technology per se. We conclude that there is a need to further investigate how scientific arguments are related to worldviews, to see how (if at all) worldview typologies can help us to understand how value-based judgments are embedded in science advice, and the impact these have on policy preferences.

Socio-environmental consideration of phosphorus flows in the urban sanitation chain of contrasting cities.

Understanding how cities can transform organic waste into a valuable resource is critical to urban sustainability. The capture and recycling of phosphorus (P), and other essential nutrients, from human excreta is particularly important as an alternative organic fertilizer source for agriculture. However, the complex set of socio-environmental factors influencing urban human excreta management is not yet sufficiently integrated into sustainable P research. Here, we synthesize information about the pathways P can take through urban sanitation systems along with barriers and facilitators to P recycling across cities. We examine five case study cities by using a sanitation chains approach: Accra, Ghana; Buenos Aires, Argentina; Beijing, China; Baltimore, USA; and London, England. Our cross-city comparison shows that London and Baltimore recycle a larger percentage of P from human excreta back to agricultural lands than other cities, and that there is a large diversity in socio-environmental factors that affect the patterns of recycling observed across cities. Our research highlights conditions that may be "necessary but not sufficient" for P recycling, including access to capital resources. Path dependencies of large sanitation infrastructure investments in the Global North contrast with rapidly urbanizing cities in the Global South, which present opportunities for alternative sanitation development pathways. Understanding such city-specific social and environmental barriers to P recycling options could help address multiple interacting societal objectives related to sanitation and provide options for satisfying global agricultural nutrient demand.

Removal and Re-use of Tar-contaminated Sediment by Freeze-dredging at a Coking Plant Luleå, Sweden.

Submerged tar-contaminated sediment are generally very loose, which makes remediation challenging. We tested if a modified version of freeze-dredging could be used to remove and dewater such sediment in a canal down-stream a coking plant. PVC hoses carrying a heat medium were placed horizontally in the submerged sediment. Five days of freezing allowed straightforward removal of most of the sediment. Flat freeze cells were placed side by side in the canal to remove the rest. The freeze-thaw process increased the dry substance content from approximately 50 to 80%. Outdoors storage under rainy conditions did not re-wet the dried sediment. The material was successfully used as feed-stock in the coking plant, with the double cost-benefit of avoided transportation to deposit and reduced use of coal. The study demonstrates that freeze-dredging can facilitate removal, storage and beneficial re-use of submerged tar-contaminated sediment.

Possible roles of reactive chlorine II: assessing biotic chlorination as a way for organisms to handle oxygen stress.

Natural formation of organically bound chlorine is extensive in many environments. The enzymes associated with the formation of chlorinated organic matter are produced by a large variety of organisms. Little is known about the ecological role of the process, the key question being: why do microorganisms promote chlorination of organic matter? In a recent paper we discuss whether organic matter chlorination may be a result of antagonistic interactions among microorganisms. In the present paper we evaluate whether extracellular microbial formation of reactive chlorine may be used as a defence against oxygen stress, and we discuss whether this process is likely to contribute to the formation of chlorinated organic matter. Our analysis suggests that periodic exposure to elevated concentrations of reactive oxygen species is a common denominator among the multitude of organisms that are able to enzymatically catalyse formation of reactive chlorine. There is also some evidence suggesting that the production of such enzymes in algae and bacteria is induced by oxygen stress. The relative contribution from this process to the extensive formation of chlorinated organic matter in natural environments remains to be empirically assessed.

Portable chamber system for measuring chloroform fluxes from terrestrial environments--methodological challenges.

This study describes a system designed to measure chloroform flux from terrestrial systems, providing a reliable first assessment of the spatial variability of flux over an area. The study takes into account that the variability of ambient air concentrations is unknown. It includes quality assurance procedures, sensitivity assessments, and testing of materials used to ensure that the flux equation used to extrapolate from concentrations to fluxes is sound and that the system does not act as a sink or a source of chloroform. The results show that many materials and components commonly used in sampling systems designed for CO2, CH4, and N2O emit chloroform and other volatile chlorinated compounds (VOCls) and are thus unsuitable in systems designed for studies of such compounds. To handle the above-mentioned challenges, we designed a system with a non-steady-state chamber and a closed-loop air-circulation unit returning scrubbed air to the chamber. Based on empirical observations, the concentration increase during a deployment was assumed to be linear. Four samples were collected consecutively and a line was fitted to the measured concentrations. The slope of the fitted line and the y-axis intercept were input variables in the equation used to transform concentration change data to flux estimates. The soundness of the flux equation and the underlying assumptions were tested and found to be reliable by comparing modeled and measured concentrations. Fluxes of chloroform in a forest clear-cut on the east coast of Vancouver Island, BC, during the year were found to vary from -130 to 620 ng m(-2) h(-1). The study shows that the method can reliably detect differences of approximately 50 ng m(-2) h(-1) in chloroform fluxes. The statistical power of the method is still comparatively strong down to differences of 35 ng m(-2) h(-1), but for smaller differences, the results should be interpreted with caution.

Organic matter chlorination rates in different boreal soils: the role of soil organic matter content.

Transformation of chloride (Cl(-)) to organic chlorine (Cl(org)) occurs naturally in soil but it is poorly understood how and why transformation rates vary among environments. There are still few measurements of chlorination rates in soils, even though formation of Cl(org) has been known for two decades. In the present study, we compare organic matter (OM) chlorination rates, measured by (36)Cl tracer experiments, in soils from eleven different locations (coniferous forest soils, pasture soils and agricultural soils) and discuss how various environmental factors effect chlorination. Chlorination rates were highest in the forest soils and strong correlations were seen with environmental variables such as soil OM content and Cl(-) concentration. Data presented support the hypothesis that OM levels give the framework for the soil chlorine cycling and that chlorination in more organic soils over time leads to a larger Cl(org) pool and in turn to a high internal supply of Cl(-) upon dechlorination. This provides unexpected indications that pore water Cl(-) levels may be controlled by supply from dechlorination processes and can explain why soil Cl(-) locally can be more closely related to soil OM content and the amount organically bound chlorine than to Cl(-) deposition.

Mechanism of antibacterial activity of the white-rot fungus Hypholoma fasciculare colonizing wood.

In a previous study it was shown that the number of wood-inhabiting bacteria was drastically reduced after colonization of beech (Fagus sylvatica) wood blocks by the white-rot fungus Hypholoma fasciculare, or sulfur tuft (Folman et al. 2008). Here we report on the mechanisms of this fungal-induced antibacterial activity. Hypholoma fasciculare was allowed to invade beech and pine (Pinus sylvestris) wood blocks that had been precolonized by microorganisms from forest soil. The changes in the number of bacteria, fungal biomass, and fungal-related wood properties were followed for 23 weeks. Colonization by the fungus resulted in a rapid and large reduction in the number of bacteria (colony-forming units), which was already apparent after 4 weeks of incubation. The reduction in the number of bacteria coincided with fungal-induced acidification in both beech and pine wood blocks. No evidence was found for the involvement of toxic secondary metabolites or reactive oxygen species in the reduction of the number of bacteria. Additional experiments showed that the dominant bacteria present in the wood blocks were not able to grow under the acidic conditions (pH 3.5) created by the fungus. Hence our research pointed at rapid acidification as the major factor causing reduction of wood-inhabiting bacteria upon colonization of wood by H. fasciculare.

Reframing human excreta management as part of food and farming systems.

Recognition of human excreta as a resource, rather than as waste, has led to the emergence of a range of new and innovative nutrient recovery solutions. Nevertheless, the management of human excreta remains largely rooted in current sanitation and wastewater management approaches, which often makes nutrient recovery an add-on to existing infrastructures. In this paper, we argue that framing human excreta management as a resource recovery challenge within waste management obscures important trade-offs. We explore the factors that would be brought to the fore by reframing human excreta management as part of food and farming systems. We find that such a reframing would accentuate (at least) six aspects of critical importance that are currently largely overlooked. Recognizing that the proposed framing may also have its limitations, we argue that it has the potential to better guide human excreta management towards long-term global food, soil, and nutrient security while reducing the risk of compromising other priorities related to human and environmental health.

Possible role of reactive chlorine in microbial antagonism and organic matter chlorination in terrestrial environments.

Several studies have demonstrated that extensive formation of organically bound chlorine occurs both in soil and in decaying plant material. Previous studies suggest that enzymatic formation of reactive chlorine outside cells is a major source. However, the ecological role of microbial-induced extracellular chlorination processes remains unclear. In the present paper, we assess whether or not the literature supports the hypothesis that extracellular chlorination is involved in direct antagonism against competitors for the same resources. Our review shows that it is by no means rare that biotic processes create conditions that render biocidal concentrations of reactive chlorine compounds, which suggest that extracellular production of reactive chlorine may have an important role in antagonistic microbial interactions. To test the validity, we searched the UniprotPK database for microorganisms that are known to produce haloperoxidases. It appeared that many of the identified haloperoxidases from terrestrial environments are originating from organisms that are associated with living plants or decomposing plant material. The results of the in silico screening were supported by various field and laboratory studies on natural chlorination. Hence, the ability to produce reactive chlorine seems to be especially common in environments that are known for antibiotic-mediated competition for resources (interference competition). Yet, the ability to produce haloperoxidases is also recorded, for example, for plant endosymbionts and parasites, and there is little or no empirical evidence that suggests that these organisms are antagonistic.

On the role of review papers in the face of escalating publication rates - a case study of research on contaminants of emerging concern (CECs).

In the past few decades, there has been a dramatic increase in scientific publications dealing with contaminants of emerging concern (CECs) and the escalating publication rate makes it close to impossible for individual researchers to get an overview of the field. Assuring the relevance and quality of the research conducted in any research field is a crucially important task. The rapidly increasing publication rates imply that review papers will play a progressively more central role to that end. The aim of the present paper is to critically assess whether reviews dealing with contaminants of emerging concern (CECs) are effective vehicles for a healthy dialogue about methodological weaknesses, uncertainties, research gaps and the future direction of the field. We carried out a tiered content-analysis of CEC review papers. Relevant papers were identified through searches in Web of Science (Clarivate), leading to the identification of 6391 original research papers of which 193 are review papers. We find that the majority of CEC reviews are written as if they are comprehensive, even though this clearly is not the case. A minority (~20%) take a critical-analytical approach to the reviewing task and identify weaknesses and research gaps. The following widespread tendencies in CEC research papers are commonly noted as concerning: to equate removal of CECs to 'decreased concentrations in the effluent'; to focus on parent substances and not concern oneself with degradation products; to focus on most commonly studied substances rather than those of most concern; to not deal with the corollary of our inability to detect or assess the risk for all substances, and to give insufficient attention to uncertainties and the unknown. Several critical-analytical reviews are among the highest cited, which suggests that they have the potential to function as effective vehicles for a healthy dialogue on these topics. On the other hand, it would appear that the concerns expressed in these reviews have a limited impact, as the same concerns are repeated over time. This might be due to a tendency among review authors to express their concerns implicitly, instead of clearly spelling them out. Our study suggests that CEC reviews presently fail to provide adequate and reliable guidance regarding the relevance and quality of research in the field. We argue that the overwhelming number of publications in combination with a lack of quality criteria for review papers are reasons to this failure: it is well documented that choices made during the reviewing process have a major impact on the outcome of a review. These choices include: search engine; the criteria used to include or exclude papers; the criteria used to assess the quality of the data generated in the research papers included; the criteria used for the choice of substances/ organisms/ technologies reported on. The lack of transparent procedures makes it very difficult, if not impossible, to assess the quality of the findings presented or to put those findings in context. In this light, it is noteworthy that criteria for a good review paper are rarely spelled out by peer-reviewed journals or included in instructions on scientific writing. The dramatic increase in publications is a challenge for the entire research community, particularly for research fields that are expected to provide policy-relevant data. We argue that only when peer-reviewed journals start specifying quality criteria for review papers, can such papers be relied upon to provide adequate and strategic guidance on the development of CEC research. We anticipate that our findings and conclusions are valid for many other research fields.

Spatial patterns of organic chlorine and chloride in Swedish forest soil.

The concentration of organic carbon, organic chlorine and chloride was determined in Swedish forest soil in the southern part of Sweden and the spatial distribution of the variables were studied. The concentration of organically bound chlorine was positively correlated to the organic carbon content, which is in line with previous studies. However, the spatial distribution patterns strongly indicate that some other variable adds structure to the spatial distribution of organic chlorine. The distribution patterns for chloride strongly resembled the distribution of organic chlorine. The spatial distribution of chloride in soil depends on the deposition pattern which in turn depends on prevailing wind-direction, amount of precipitation and the distance from the sea. This suggests that the occurrence of organic chlorine in soil is influenced by the deposition of chloride or some variable that co-varies with chloride. Two clearly confined strata were found in the area: the concentrations of organic chlorine and chloride in the western area were significantly higher than in the eastern area. No such difference among the two areas was seen regarding the carbon content.

Temperature sensitivity indicates that chlorination of organic matter in forest soil is primarily biotic.

Old assumptions that chloride is inert and that most chlorinated organic matter in soils is anthropogenic have been challenged by findings of naturally formed organochlorines. Such natural chlorination has been recognized for several decades, but there are still very few measurements of chlorination rates or estimates of the quantitative importance of terrestrial chlorine transformations. While much is known about the formation of specific compounds, bulk chlorination remains poorly understood in terms of mechanisms and effects of environmental factors. We quantified bulk chlorination rates in coniferous forest soil using 36Cl-chloride in tracer experiments at different temperatures and with and without molecular oxygen (O2). Chlorination was enhanced by the presence of O2 and had a temperature optimum at 20 degrees C. Minimum rates were found at high temperatures (50 degrees C) or under anoxic conditions. The results indicate (1) that most of the chlorination between 4 and 40 degrees C was biotic and driven by O2 dependent enzymes, and (2) that there is also slower background chlorination occurring under anoxic conditions at 20 degrees C and under oxic conditions at 50 degrees C. Hence, while oxic and biotic chlorination clearly dominated, chlorination by other processes including possible abiotic reactions was also detected.