Blending Geoscience Research with Machine Learning

Who we Are

We are the John Lab, a research group led by Professor Cédric John and hosted in the Digital Environment Research Institute (DERI) at Queen Mary University of London. At DERI, Professor John leads the Data Science for the Environment and Sustainability Research Platform, one of four key research directions for the institute. Before joining DERI, the group was based for nearly 16 years in the Department of Earth Science and Engineering at Imperial College London.

Our research approach blends machine learning and AI with cutting edge field and experimental methods in Earth and Planetary Sciences. The Digital Environment Research Institute is the centre of digital, data science, and AI research at Queen Mary and it underpins the university’s vision for its research Strategy 2030. For us, DERI is the perfect home for an interdisciplinary team working on scientific machine learning applied to environmental and Earth Science problems.

DERI and Queen Mary University of London are affiliated with the Alan Turing Institute.

Testimonials

Hear what former members of the lab have to say about their time with us.

Niranjana Sundararajan (MSc Student, 2022)

Niranjana Sundararajan (MSc Student, 2022)

“Working on my MSc thesis with Cedric as my supervisor was the most interesting, productive and challenging part of my academic experience at Imperial. Cedric is an excellent supervisor-  providing constant support, direction and the encouragement necessary to reach research goals.”
Marta Marchegiano(Postdoc, 2019-2021)

Marta Marchegiano(Postdoc, 2019-2021)

“I did my first postdoc at John lab where I learnt about the clumped isotope technique. Cédric is a very thoughtful and knowledgeable supervisor, he always took the time to teaching me about this exciting thermometer. Thanks to his enthusiasm I became very passionate about carbonate geochemistry and this experience was an important stepping stone for my future career. “
Sarah Robinson (PhD Student, 2019-2022)

Sarah Robinson (PhD Student, 2019-2022)

“Over the course of my time with John’s Lab I have benefited from a strong and diverse group of peers. I have gained knowledge in not only my own field, but the fields of my peers through discussions in bi-weekly lab meetings. I will miss working within John’s lab as I move onto my next chapter.”
Tobias Kluge (Postdoc, 2012-2015)

Tobias Kluge (Postdoc, 2012-2015)

Research topics in the John lab are at the cutting edge of the respective field and provided me a fascinating insight in current scientific developments. They were a strong motivation for my own research. A vibrant and motivated research group inspired exciting project ideas and enabled thorough scientific discussions.”
John MacDonald (Postdoc, 2013-2015)

John MacDonald (Postdoc, 2013-2015)

“I had a great time working in the John Lab. Cedric was a fantastic mentor to me as a postdoc, and he really helped me in getting to my current career stage as a Senior Lecturer in Earth Sciences at the University of Glasgow.”
Annabel Dale (PhD Student, 2011-2015)

Annabel Dale (PhD Student, 2011-2015)

“Cedric was great to work with as a supervisor for my PhD and afterwards whilst co-supervising a PhD student. His enthusiasm and good instinct for interesting science, means that working in the John lab is an excellent place to learn and develop research skills.”
Qi Adlan (PhD Student, 2019-2022)

Qi Adlan (PhD Student, 2019-2022)

“Working in John Lab makes me feel engaged and valued. Cedric is very knowledgeable and kind — he helped me reach my full potential to become an independent researcher.”
Adhipa Herlambang (PhD Student, 2018-2021)

Adhipa Herlambang (PhD Student, 2018-2021)

“It was a great honor to be part of the amazing John Lab. Participating in the clumped isotope lab during my Ph.D. was an immensely satisfying experience in many ways. It allowed me to develop a series of learning experiences in a very friendly atmosphere.”

research Highlights

We have two main research themes: Applied Artificial Intelligence for Earth and Space Sciences (we call it Earth-Centric AI) and Carbonate Research. You can also find about our publications and the software and data stemming from our research.

AI Research

Our group applies data-centric machine learning techniques to Earth and planetary sciences, leading to innovative approaches for analyzing and interpreting data in these fields.

Carbonate Research

Our research in carbonates focuses on the processes involved in their formation and alteration, and how these processes impact the geochemistry and stratigraphy of carbonate rocks.

Publications

Our group has published over 100 peer-reviewed papers in a variety of fields, including clumped isotopes, carbonate diagenesis, climate change, stratigraphy, AI and machine learning.

Software and Data

Our research has led to the development of free software tools that have been widely used by researchers in our fields. These tools have made it easier to analyze and interpret data..

Spotlight on our Papers:

The magnesium isotope (δ26Mg) signature of dolomites
The magnesium isotope (δ26Mg) signature of dolomites

Dolomite precipitation models and kinetics are debated and complicated due to the complex and temporally fluctuating fluid chemistry and different diagenetic environments. Using well-established isotope systems (δ18O, δ13C, 87Sr/86Sr), fluid inclusions and elemental data, as well as a detailed sedimentological…

Diagenetic geobodies: Fracture-controlled burial dolomite in outcrops from northern Oman
Diagenetic geobodies: Fracture-controlled burial dolomite in outcrops from northern Oman

Diagenetic heterogeneities are difficult to predict in the subsurface. Nevertheless, such heterogeneities can be crucial in hydrocarbon exploration. Diagenetic processes can significantly alter petrophysical properties of reservoir rocks, especially in carbonate rocks because of the reactive nature of the carbonate…

Mineral texture classification using deep convolutional neural networks: An application to zircons from porphyry copper deposits
Mineral texture classification using deep convolutional neural networks: An application to zircons from porphyry copper deposits

The texture and morphology of igneous zircon indicates magmatic conditions during zircon crystallization and can be used to constrain provenance. Zircons from porphyry copper deposits are typically prismatic, euhedral, and strongly oscillatory zoned which may differentiate them from zircons associated…

Effects of oxygen plasma ashing treatment on carbonate clumped isotopes
Effects of oxygen plasma ashing treatment on carbonate clumped isotopes

For clumped isotope analysis (Δ47), hydrocarbon and organic molecules present an important contaminant that cannot always be removed by CO2 purification through a Porapak‐Q trap. Low‐temperature oxygen plasma ashing (OPA) is a quick and easy approach for treatment; however, the…

Laboratory calibration of the calcium carbonate clumped isotope thermometer in the 25–250 C temperature range
Laboratory calibration of the calcium carbonate clumped isotope thermometer in the 25–250 C temperature range

Many fields of Earth sciences benefit from the knowledge of mineral formation temperatures. For example, carbonates are extensively used for reconstruction of the Earth’s past climatic variations by determining ocean, lake, and soil paleotemperatures. Furthermore, diagenetic minerals and their formation…

Relative control of paleoceanography, climate, and eustasy over heterozoan carbonates: a perspective from slope sediments of the Marion Plateau (ODP Leg 194)
Relative control of paleoceanography, climate, and eustasy over heterozoan carbonates: a perspective from slope sediments of the Marion Plateau (ODP Leg 194)

In this paper we explore the relative control of paleoceanography, eustasy, and water temperature over the evolution of a carbonate slope system deposited on the Marion Plateau (Northeastern Australia). Growth of several carbonate platforms started in the early Miocene on…

Evaluating climatic response to external radiative forcing during the late Miocene to early Pliocene: New perspectives from eastern equatorial Pacific (IODP U1338) and North …
Evaluating climatic response to external radiative forcing during the late Miocene to early Pliocene: New perspectives from eastern equatorial Pacific (IODP U1338) and North …

Orbital‐scale climate variability during the latest Miocene‐early Pliocene is poorly understood due to a lack of high‐resolution records spanning 8.0–3.5 Ma, which resolve all orbital cycles. Assessing this variability improves understanding of how Earth’s system sensitivity to insolation evolves and provides…

A simple method for vaterite precipitation for isotopic studies: implications for bulk and clumped isotope analysis
A simple method for vaterite precipitation for isotopic studies: implications for bulk and clumped isotope analysis

Calcium carbonate (CaCO3) plays an important role in the natural environment as a major constituent of the skeleton and supporting structure of marine life and has high economic importance as an additive in food, chemicals and medical products. Anhydrous CaCO3…

Physicochemical Conditions of the Devonian-Jurassic Continental Deep Biosphere Tracked by Carbonate Clumped Isotope Temperatures of Granite-Hosted Carbonate Veins
Physicochemical Conditions of the Devonian-Jurassic Continental Deep Biosphere Tracked by Carbonate Clumped Isotope Temperatures of Granite-Hosted Carbonate Veins

Previous studies have shown that microorganisms thrive in oligotrophic fracture systems, and metabolisms include consumption and production of methane. In the Laxemar, Götemar, and Forsmark areas of Sweden, ancient microbial activity has previously been demonstrated by large δ13CVPDB variability of carbonate vein…

Significance of fracture-filling rose-like calcite crystal clusters in the SE pyrenees
Significance of fracture-filling rose-like calcite crystal clusters in the SE pyrenees

Fracture-filling rose-like clusters of bladed calcite crystals are found in the northern sector of the Cadí thrust sheet (SE Pyrenees). This unusual calcite crystal morphology has been characterized by using optical and electron microscope, X-ray diffraction, Raman spectroscopy, δ18O, δ13C,…

Rock-buffered recrystallization of Marion Plateau dolomites at low temperature evidenced by clumped isotope thermometry and X-ray diffraction analysis
Rock-buffered recrystallization of Marion Plateau dolomites at low temperature evidenced by clumped isotope thermometry and X-ray diffraction analysis

Much debate exists on the extent to which early dolomites recrystallize and preserve the signature of their primary diagenetic setting. Here, we combine clumped isotopes thermometry with X-ray diffraction and thin section petrography to study dolomite recrystallization under shallow burial…

Community software for challenging isotope analysis: First applications of ‘Easotope’to clumped isotopes
Community software for challenging isotope analysis: First applications of ‘Easotope’to clumped isotopes

The measurement of complex isotope systems, notably the multiply substituted isotopologues of CO2 derived from carbonates, is challenging from a mass spectrometric point of view, but it is also time consuming and difficult from a data reduction and normalization perspective.…