Mis en avant

Who i am? my digital researcher profile(s)

Olivier Pourret, Geochemist of Open Access

I received my PhD in Earth Sciences in 2006 from Université de Rennes 1 (France). I am now an associate professor of geochemistry at UniLaSalle, Beauvais (France) and co-head of the research group AGHYLE (Agroecology and Hydrogeochemistry). In 2013, i received my Habilitation in Earth Sciences from Université Picardie Jules Verne (France).

I am a Fellow member of the Society of Economic Geologists and a member of the Geochemical Society, European Association of Geochemistry, American Geophysical Union and American Chemical Society.

My research interests include trace metal fractionation and particularly critical elements (rare earth elements, cobalt, vanadium) in low-temperature aqueous systems, a better understanding of trace metal cycles in natural waters, and an improved knowledge of trace metals mobility from rock to soils and vegetation in the critical zone.

Below, you will have access to my digital research profile(s).

First, i want to acknowledge Jon Tennant for sharing his presentation on How to develop your online researcher profile!

Let’s start with my universal identifier: my ORCID (Open Researcher and Contributor ID).

My publications are available in Open Access on the French repository HAL or preprint repository EarthArXiv.

You can check my metrics on Google Scholar, Publons or Impactstory.

You can also keep in touch with me on Linkedin, Twitter or ResearchGate.

Eventually, some miscalleneous stuff (posters, abstracts, presentations…) are available on Zenodo or Figshare.

Ten years of research on the effects of rare earth elements on plant growth and nutrient acquisition strategies

Olivier Pourret (04/05/2024)

Ten years ago, I started working on Rare Earth Elements (REEs) and plants, here is a lay summary of my major results.

Understanding the Impact of REE on Plant Growth

Rare earth elements are chemical elements that naturally occur in soils and are important for various industrial applications. However, their effects on plants, especially crops like rice, are not well understood. In our studies, we investigated how REEs influence the growth of rice plants. We found that when rice plants were exposed to certain concentrations of REEs, their root and overall plant growth were significantly reduced. Interestingly, the presence of iron oxides in the soil seemed to lessen the harmful effects of REEs on the plants to some extent. Our research sheds light on the complex interactions between REEs and plant growth, providing valuable insights for agricultural practices.

Exploring the Relationship Between Soil Chemistry and REE Accumulation in Plants

We conducted a study to understand how REEs behave in the soil and accumulate in plants. By examining soil and plant samples from different environments, we found that certain soil factors, like pH and organic matter content, influence the uptake of REEs by plants. Interestingly, plants tend to accumulate REEs in their shoots in patterns that reflect the composition of the surrounding soil. Our findings highlight the importance of soil chemistry in determining the distribution of REEs in plants, which has implications for ecosystem health and nutrient cycling.

Uncovering the Role of Root Traits in REE Availability to Plants

Rare earth elements are also essential nutrients for plants, but their availability in the soil can be influenced by various factors, including root traits. In our research, we investigated how below-ground traits, such as root exudation and nutrient acquisition strategies, affect the uptake of REEs by plants. We found that plants with different nutrient acquisition strategies show distinct patterns of REE accumulation in their leaves. Additionally, we observed that root exudates released under nutrient deficiency conditions can mobilize REEs in the soil, making them more accessible to plants. These findings enhance our understanding of plant-soil interactions and have implications for sustainable agriculture practices.

Using REEs as Indicators of Plant Nutrient Acquisition Strategies

Phosphorus and iron are other essential nutrients for plant growth, and their availability in the soil depends on root traits and soil chemistry. In our research, we proposed using REEs as indicators of plant nutrient acquisition strategies. We found that plants with different P-acquisition strategies accumulate REEs differently in their tissues. By analyzing REE concentrations in plant material, we can evaluate the efficiency of nutrient acquisition strategies in plants. This approach provides a valuable tool for assessing soil fertility and optimizing agricultural practices for improved nutrient uptake by crops.

Further reading

Articles

Monei, N., Hitch, M., Heim, J. et al. Effect of substrate properties and phosphorus supply on facilitating the uptake of rare earth elements (REE) in mixed culture cropping systems of Hordeum vulgare, Lupinus albus and Lupinus angustifolius. Environ Sci Pollut Res 29, 57172–57189 (2022). https://doi.org/10.1007/s11356-022-19775-x

Pourret, O., van der Ent, A., Hursthouse, A. et al. The ‘europium anomaly’ in plants: facts and fiction. Plant Soil 476, 721–728 (2022). https://doi.org/10.1007/s11104-021-05210-6

Wiche, O., Pourret, O. The role of root carboxylate release on rare earth element (hyper)accumulation in plants – a biogeochemical perspective on rhizosphere chemistry. Plant Soil 492, 79–90 (2023). https://doi.org/10.1007/s11104-023-06177-2

Wiche, O., Dittrich, C., Pourret, O. et al. Relationships between carboxylate-based nutrient-acquisition strategies, phosphorus-nutritional status and rare earth element accumulation in plants. Plant Soil 489, 645–666 (2023). https://doi.org/10.1007/s11104-023-06049-9

Preprint

Pourret, O., Lange, B., Martinez, R.E. et al. Relationships between soil chemical properties and rare earth element concentrations in the aboveground biomass of a tropical herbaceous plant. EarthArXiv (2019) https://doi.org/10.31223/osf.io/w4hgs

Conference proceedings

Wiche, O., Pourret, O., and Lambers, H.: Rare earth elements as potential tracers of carboxylate-based plant nutrition strategies , EGU General Assembly 2022, Vienna, Austria, 23–27 May 2022, EGU22-3674, (2022).  https://doi.org/10.5194/egusphere-egu22-3674Wiche, O., Heilmeier, H., and Pourret, O.: Below-ground functional traits during nutrient-acquisition affect the availability of rare earth elements to plants , EGU General Assembly 2020, Online, 4–8 May 2020, EGU2020-5831,(2020). https://doi.org/10.5194/egusphere-egu2020-5831

Still time to reconsider the use of « Heavy Metal » terminology in science

Olivier Pourret (January 10th 2024)

New Year, but still time to advocate for the correct use of the terms « Heavy Metal ». If I ask ChatGPT for a definition of « Heavy Metal », it answers something like that:

« Heavy metal is a genre of rock music characterized by its aggressive sound, amplified distortion, and emphatic beats. It typically features strong rhythms, electric guitar riffs, and powerful vocals. Lyrically, it often explores themes of rebellion, power, and sometimes fantasy or mythology. Bands like Black Sabbath, Iron Maiden, Metallica, and Judas Priest are considered pioneers and influential figures within the genre. »

I totally agree with artificial intelligence.

Cartoon illustrating the misused term “heavy metal” (artwork from Dr. Justin Larrouzée) https://doi.org/10.1007/s11356-019-06835-y

However, « heavy metal » is a term used in science as well. In chemistry and environmental science, « heavy metals » refer to a group of metallic elements that have a high atomic weight and density. Some common examples include lead, mercury, cadmium, arsenic, and chromium, among others. These elements can be toxic to living organisms in high concentrations and can have detrimental effects on the environment and human health when they accumulate. They’re often a concern in pollution and industrial contamination due to their persistence and potential for bioaccumulation in the food chain…

It is a big mistake!

See all i wrote in my previous articles:

Heavy metal: a misused term?

It’s time to replace the term “heavy metals” with “potentially toxic elements” when reporting environmental research

On the Necessity of Banning the Term “Heavy Metal” from the Scientific Literature

“Heavy metal” – What to do now: To use or not to use?

Except where otherwise noted, content on this personal blog is licensed under a Creative Commons Attribution 4.0 International license.

Diamond Open Access Journals are not an emerging solution to APC journals, they have existed for several decades

Olivier Pourret and Dasapta Erwin Irawan

11/19/2023

This is an opinion submitted as a Correspondence to Nature but not considered for publication.

In her News Features, Katharine Sanderson presents Diamond Open Access Journals as an emerging solution to article processing charges (APC) in scientific publishing.

This is a simplified representation of non-APC models, referring to them as ’emerging’, when in fact they have been established by humanities and social science presses, scholar-led publishers (e.g. in Indonesia), high-energy physicists, Latin American institutions (e.g. Scielo and Redalyc), and many others, for quite some time.

Authors have the option to publish their work for free in Diamond Open Access (OA) journals. According to the Directory of Open Access Journals, in 2023, 67% of fully OA journals do not charge APCs (the oldest was indexed in 2002). Interestingly, 69% of articles published OA are published in journals that require APCs (Crawford, 2023). This seeming contradiction can be explained by two factors that are closely related to career advancement: publication in certain journals and citations. However, it is important to note that this perspective is limited. Like many authors, Katharine Sanderson highlights a common misconception that OA limits author choice through APCs.

Overall, Diamond Open Access Journals have gained prominence since 2022 due to new national and international policies. These include the UNESCO recommendation on open science and the Action Plan for Diamond Open Access promoted by cOAlition S, which aim to support the growth of non-commercial or community-driven forms of OA publishing.

Except where otherwise noted, content on this personnal blog is licensed under a Creative Commons Attribution 4.0 International licence.

EU council ‘no pay’ publishing model is realistic

Olivier Pourret, Dasapta Erwin Irawan and Jessica Polka

09/09/2023

This is an opinion submitted as a Correspondence to Nature but not considered for publication.

According to Katharine Sanderson, “publishing-industry representatives warn” that May’s EU Council call for a “no pay” academic publishing model is “unrealistic and lack[ing] detail”. However, the proposal is already being implemented via several approaches: 

(i) Authors can publish their work for free in ‘Diamond’ Open Access (OA) journals. According to the Directory of Open Access Journals, in 2023 67.5% of fully OA journals do not levy article processing charges, and most of them are published by university press.

(ii) The European Commission has launched a publishing platform, Open Research Europe, an OA publishing platform for the publication of research stemming from Horizon 2020, Horizon Europe and/or Euratom funding.  

(iii) Preprints are rising in many disciplines and several new initiatives (such as Peer Community In, Review Commons, and RR\ID) organize peer review on preprints at no cost to authors or readers.

(iv) New publishing models such as Subscribe to Open enable journals to flip to OA while retaining library support. 

Many of these are already supported directly by institutions, governments, or private funders, and they are here to stay. 

It is up to us, researchers and policy makers, to make sure we support “no pay” solutions where they exist. Scientific knowledge is a public good, and it should be treated as such.

Except where otherwise noted, content on this personnal blog is licensed under a Creative Commons Attribution 4.0 International licence.

A discussion with ChatGPT on predatory journals

Many people are speaking about AI, i decided to test ChatGPT on a subject i am working on, predatory journals, with a little bit fun at the end.

Me: What is a predatory scientific journal?

Screenshot from the first answer of my discussion with ChatGPT

The answer:

A predatory scientific journal is a publication that claims to be a legitimate academic journal but operates solely for profit, rather than to advance scientific knowledge. These journals use deceptive and unethical practices to lure authors to submit their work, often by falsely claiming to have high impact factors or editorial boards comprised of reputable academics.

Predatory journals usually charge authors high fees for publication without providing any quality control or peer-review process. As a result, they frequently publish low-quality, pseudoscientific or even fraudulent research. In some cases, predatory journals may publish articles without the author’s knowledge or consent, or recycle content from previously published articles.

Predatory journals can harm scientific progress by disseminating misinformation and compromising the integrity of the research process. It is important for authors and readers to be aware of these journals and to carefully evaluate the legitimacy of any publication before submitting or citing it as a source of scientific knowledge.

Me: Could you give me an example of predatory journal?

The answer:

I cannot provide you with a specific example of a predatory journal as I am an AI language model and do not have access to real-time information on the current state of scientific journals. However, there are several characteristics that can be used to identify predatory journals:

  1. They have a very short review time, often as little as a few days, which suggests that little or no peer review is being conducted.
  2. They claim to have a high impact factor, despite not being indexed in major databases like Web of Science or Scopus.
  3. They send unsolicited emails to academics and researchers, inviting them to submit articles or serve on editorial boards.
  4. They have little or no editorial oversight or quality control.
  5. They charge high publication fees without providing any value-added services like editing, proofreading, or formatting.
  6. They have a broad scope of research topics and publish papers on a wide range of topics that are not closely related, suggesting that they are willing to publish anything for a fee.

If you come across a journal that exhibits one or more of these characteristics, it may be a predatory journal. It is important to carefully evaluate any journal before submitting your work or citing it as a source of scientific knowledge.

Me: Thank you, could you recommend me a few real literature references?

The answer:

Certainly! Here are a few references that provide more information on predatory journals:

  1. Beall, J. (2012). Predatory publishers are corrupting open access. Nature, 489(7415), 179. doi: 10.1038/489179a
  2. Shamseer, L., Moher, D., Maduekwe, O., Turner, L., Barbour, V., Burch, R., … & Shea, B. J. (2017). Potential predatory and legitimate biomedical journals: can you tell the difference? A cross-sectional comparison. BMC medicine, 15(1), 28. doi: 10.1186/s12916-017-0785-9
  3. Grudniewicz, A., Moher, D., Cobey, K. D., Bryson, G. L., Cukier, S., Allen, K., … & Straus, S. E. (2019). Predatory journals: no definition, no defence. Nature, 576(7786), 210-212. doi: 10.1038/d41586-019-03759-y
  4. Crawford, W., & Wouters, P. (2018). Predatory publishing in academic psychology and the broader social sciences. Frontiers in psychology, 9, 2261. doi: 10.3389/fpsyg.2018.02261

I hope you find these references helpful in learning more about predatory journals.

NDLR: these are real references.

Me: What do you think about the article entitled « mitochondria: structure, functions and clinical relavance »?

NDLR: i am refering here to a false article published in a predatory journals, dealing on midichlorians.

The answer:

As an AI language model, I don’t have access to real-time information on specific articles or journals. Therefore, I cannot provide an opinion on the article you mentioned, « Mitochondria: structure, functions, and clinical relevance. » However, in general, articles on mitochondria are important as they are crucial organelles involved in energy production and have a role in many cellular processes. It is important to note that the quality of an article should be evaluated based on the scientific merit of the research, the methodology used, and the soundness of the conclusions drawn, rather than on the title or topic of the article alone.

Me: I understand, thank you. So do you think midichlorian may exist?

The answer: Midichlorians are a fictional concept from the Star Wars universe and do not exist in the real world. They are portrayed as microscopic, intelligent life-forms that reside within the cells of living beings and are capable of communicating with the Force, a mystical energy that permeates the Star Wars universe.

It is important to note that while the concept of midichlorians is not based in scientific fact, the Star Wars franchise has helped to popularize and generate interest in science, particularly in fields like astronomy, physics, and robotics. However, it is always important to distinguish between science fiction and actual scientific knowledge.

Me (as abig Star Wars fan): May the force be with you!

The answer: Thank you! May the force be with you too!

Ten years of research on cobalt

Cobalt does not get a ton of press, it is indeed a pretty important metal in this day and age.

Cobalt (chemical symbol, Co) is a d-block transition metal, bluish-white. It appears in the first long period of the Periodic Table between iron and nickel. Cobalt shares many chemical and physical properties with these two elements.

Cobalt is economically considered as a critical metal

Cobalt is often associated with Ni, Ag, Pb, Cu and Fe-Mn ores, from which it is most frequently obtained as by-product. The main known ore deposits are found in Katanga (Democratic Republic of Congo) whereas some recent discoveries evidenced that central Pacific Ocean may have Co-rich deposits (i.e., manganese nodules and Co-rich ferromanganese crusts) at relatively shallow depths. Almost 50% of the world’s cobalt supply in 2020 was mined in the Democratic Republic of Congo. Mining and smelter activities in Katanga have contaminated soil, water and urban environments.

Cobalt is an essential trace element in life and plays an important role in biochemical reactions essential for life, notably in the coenzyme cobalamin (Co chelated to four N atoms at the center of a porphyrin- like structure).

Some plant species, also called metallophytes, have adapted to natural and contaminated Co-rich soils. Among these metallophytes, some are able to hyperaccumulate Co in plant shoots (>300 mg/kg, without toxicity symptoms and growth inhibition). Eventually, we have highlighted the potential of a Co accumulator in agromining, and have defined perspectives for Co agromining by designing multi-functions and services of agroecosystems by a functional plant traits approach.

Further reading

Back to basic or … definitely maybe: mafic

Last Monday I saw this poll on twitter on how to describe igneous rocks either basic/acidic or mafic/felsic.

https://twitter.com/lithospheric/status/1543696729060564992

My first reaction was to ask this question: 

Why so many people still used « mafic/felsic » while IUGS recommends the use of « basic/acid »? 

That is not simple, the debate is there.

Yes, IUGS recommends “basic/acid” but… the use is different. I just pick a few textbooks on my shelves.

Best (2003) in his Igneous Petrology textbook said:

Mafic is a mnemonic adjective derived from the words magnesium and ferrous/ferric. Mafic is a less cumbersome term than the synonymous ferromagnesian. It refers to major rock-forming biotite, amphibole, pyroxene, olivine, and Fe-Ti oxide solid solutions as well as rocks that contain large proportions of them, such as basalt.

Moreover Klein and Dutrow (2007) in their classic Mineral Science textbook further said:

When the magma is low in SiO2, the resulting rocks will contain mainly silica-poor minerals, such as olivine, pyroxene, hornblende, or biotite and little or no free SiO2 (i.e., quartz, cristobalite, tridymite). These rocks, which tend to be dark because of high percentage of ferromagnesians minerals, are known as mafic rock types.

Both are petrology and mineralogy references, what about geochemistry? I am a geochemist after all!

If we check the entry “acide-base” in the latest Encyclopedia of Geochemistry we can read:

The more common recent trend is to reserve acidic and basic for descriptions of reactivity and to use terms like silicic, felsic, or mafic to describe the composition of rocks.

I very much like this vision; I learn everyday and will update my use of “felsic/mafic”!

Thanks to the community for highlighting this debate to me.

Are narrative CVs really fairer?

The Swiss National Science Foundation’s ‘narrative’ template seeks evidence of applicants’ wider contributions to science1. Narrative CVs are on the front of the scene for several months now and are here to replace more quantitative usual CVs2. Indeed, narrative CVs are among the alternatives implemented in research evaluation and assessment these last months, being more descriptive and detailed. As a DORA signatories myself, I agree that we should avoid using some metrics like journal impact factors and h-index. But are narrative Cvs really fairer, more objective and inclusive?

This subject was discussed at the latest European Geosciences Union General Assembly held in May in a Great Debate on research assessment. I do agree that we need to change and improve the way scientists are hired, granted, awarded and rewarded.

However, given difficulties of some researchers in creating one, the main concern is that part of the community (e.g., caretakers, some disabled people…) may be unable to do so. They will have to find extra time that they may or may not have, as writing a proposal or application is already a difficult task; this appears to add to the scientists’ load.

This is another of those well-intentioned interventions that appears to have only one goal: to make panels’ judgments simpler rather than to remove barriers to individuals who are already marginalized. Those who can best manipulate the system, who can write or say exactly what the panels want to hear, will profit the most.

References

1 Chawla D.S. 2022. Swiss funder unveils new CV format to make grant evaluation fairer. Nature https://doi.org/10.1038/d41586-022-01599-x

2 Woolston, C., 2022. Time to rethink the scientific CV. Nature, 604, 203-205.  https://doi.org/10.1038/d41586-022-00928-4

Modernisation des publications en géoscience

Cet article de blog est une traduction du point de vue Modern geoscience publishing.

Une prépublication (ou preprint en anglais) est la version initiale d’un article de recherche, souvent (mais pas toujours) avant la soumission à une revue et avant l’évaluation formelle par les pairs. Les prépublications contribuent à moderniser les géosciences en supprimant les obstacles qui entravent une large participation au processus scientifique et qui ralentissent les progrès vers une culture de la recherche plus ouverte et transparente.

Les prépublications ne sont pas nouvelles ; elles existent depuis les années 1960. En août 1991, un réseau Web centralisé, arXiv (arxiv.org/, prononcé « är kīv », de la lettre grecque « chi »), a été créé pour partager les prépublications de physique. arXiv soutient les domaines de la physique, des mathématiques et de l’informatique depuis plus de 30 ans, période au cours de laquelle le rythme de diffusion de l’information scientifique s’est accéléré. Ces dernières années, davantage de disciplines – y compris les géosciences, via EarthArXiv (eartharxiv.org/; Narock et al., 2019) et ESSOAr (essoar.org) – ont commencé à tirer parti des prépublications.

Les prépublications présentent de nombreux avantages bien documentés pour les chercheurs et le public (par exemple, Bourne et al., 2017 ; Sarabipour et al., 2019 ; Pourret et al., 2020). Par exemple, les prépublications permettent :

• Le partage rapide des résultats de recherche, qui peut être essentiel pour les études urgentes (comme après des catastrophes), ainsi que pour les chercheurs en début de carrière postulant à un emploi, ou tout universitaire postulant pour des subventions ou une promotion, étant donné que l’évaluation par les pairs des articles peut prendre plusieurs mois à plusieurs années ;

• Une plus grande visibilité et accessibilité pour les résultats de la recherche, étant donné qu’il n’y a pas de frais pour publier ou lire une prépublication, en particulier pour ceux qui n’ont pas accès à des revues payantes, ou un accès limité en raison du travail à distance (comme pendant les confinements) ;

• Un retour d’information supplémentaire par les pairs au-delà de celui fourni par l’évaluation par les pairs lors des soumissions aux revues scientifiques, améliorant la possibilité de collaboration via la contribution et la discussion de la communauté ;

• Les chercheurs établissent une priorité (ou un précédent) sur leurs résultats, atténuant ainsi le risque d’être « pillés » ;

• L’éclatement des silos que maintiennent les revues traditionnelles, en nous exposant à une recherche plus large que celle que nous pourrions rencontrer autrement, et en accueillant des travaux qui n’ont pas de destination claire dans une publication traditionnelle ;

• La recherche doit être plus ouverte et transparente, dans le but d’améliorer la qualité globale, l’intégrité et la reproductibilité des résultats.

Pendant la pandémie, la communauté médicale et scientifique au sens large, ainsi que le public, ont vu le rôle des prépublications dans l’accélération du processus scientifique au profit de l’humanité (Besançon et al., 2021). Les prépublications font désormais partie intégrante du processus de publication scientifique et sont là pour rester (Lanati et al., 2021).

Les prépublications contribuent à moderniser les géosciences en supprimant les barrières structurelles qui rendent la science et les connaissances moins accessibles à ceux qui financent souvent la création de connaissances – les contribuables – ainsi qu’en rendant les résultats de la recherche rapidement accessibles à tous ceux qui pourraient en bénéficier.

Références 

Besançon, L. et al. (2021) Open science saves lives: lessons from the COVID-19 pandemic. BMC Med Res Methodol 21, 117; https://doi.org/10.1186/s12874-021-01304-y.

Bourne, P.E. et al. (2017) Ten simple rules to consider regarding preprint submission. PLoS Comput Biol 13, e1005473; https://doi.org/10.1371/journal.pcbi.1005473.

Lanati, A. et al. (2021) Research Funding Bodies Need to Follow Scientific Evidence: Preprints Are Here to Stay. OSF Preprint; doi:10.31219/osf.io/k54pe.

Narock, T. et al. (2019) Earth science is ready for preprints. Eos 100; https://doi.org/10.1029/2019EO121347. 

Pourret, O. et al. (2020) On the Potential of Preprints in Geochemistry: The Good, the Bad, and the Ugly. Sustainability 12, 3360; https://doi.org/10.3390/su12083360.

Sarabipour, S. et al. (2019) On the value of preprints: An early career researcher perspective. PLoS Biology 17; https://doi.org/10.1371/journal.pbio.3000151.

Inclusive terminology in isotope geochemistry

Our short comment on gender issues with isotope terminology is now published. The terms « parent »/ »daughter » should be avoided in favor of the more descriptive « precursor ion » and « product ion » terms.

Notre bref commentaire sur les questions de genre avec la terminologie isotopique vient d’être publié. Les termes « père»/« fils » doivent être évités au profit des termes plus descriptifs « ion précurseur » et « ion produit ».

Our viewpoint is also translated in Chinese and available on WeeChat thanks to Zimeng Wang.
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