Measuring the world – the joys of analytical geochemistry

‘Measure what is measurable, and make measurable what is not so.’ – Galileo Galilee

Science is measuring.

Of course, it is about much more than measuring.  The scientific approach includes deduction, induction, lateral thinking and all of the other creative and logistical mechanisms by which we arrive at ideas. But what distinguishes the ideas of science from those of religion, philosophy or art is that they are expressed as testable hypotheses – and by testable hypotheses, scientists mean ideas that can be examined by observations or experiments that yield outcomes that can be measured.

Earth scientists use astonishingly diverse approaches to measure our world, from the submolecular to the planetary, from bacterial syntrophic interactions to the movement of continental plates. A particularly important aspect of observing the Earth system involves chemical reactions – the underlying processes that form rocks, fill the oceans and sustain life. The Goldschmidt Conference, held this year in Firenze*, is the annual highlight of innovations in geochemical methodologies and the new knowledge emerging from them.

Geochemists reported advances in measuring the movement of electrons across nanowires, laid down by bacteria in soil like electricians lay down cables; the transitory release of toxic metals by microorganisms, daily emissions of methane from bogs, and annual emissions of carbon dioxide from the whole of the Earth; the history of life on Earth as recorded by the isotopes of rare metals archived in marine sediments; the chemical signatures in meteorites and the wavelengths of light emitted from distant solar nebulae, both helping us infer the building blocks from which our own planet was formed.


The Goldschmidt Conference is often held in cities with profound cultural legacies, like that of Florence.  And although Florence’s legacy that is perhaps dominated by Michelangelo and Botticelli, Tuscany was also home to Galileo Galilee, and he and the Scientific Revolution are similarly linked to the Renaissance and Florence. Wandering through the Galileo Museum is a stunning reminder of how challenging it is to measure the world around us, how casually we take for granted many of these measurements and the ingenuity of those who first cracked the challenges of quantifying time or temperature or pressure.

And it is also exhilarating to imagine the thrill of those scientists as they developed new tools and turned them to the stars above us or the Earth beneath us.  Galileo’s own words tell  us how he felt when he pointed his telescope at Jupiter and discovered the satellites orbiting around it; and how those observations unlocked other insights and emboldened new hypotheses:

‘But what exceeds all wonders, I have discovered four new planets and observed their proper and particular motions, different among themselves and from the motions of all the other stars; and these new planets move about [Jupiter] like Venus and Mercury… move about the sun.’

The discoveries of the 21st century are no less exciting, if perhaps somewhat more nuanced.


I could give so many examples!  But allow me to just draw on some of the contributions from my University of Bristol colleagues from that conference in 2014.  Laura Robinson presented a new approach to estimating water discharge from rivers, based on the ratio of uranium isotopes in coral; the technique has great potential for studying flood and drought events over the past 100,000 years, helping us to better understand, for example, the behaviour of monsoon systems on which the lives of nearly one billion people depend.  Heather Buss presented research quantifying the nature and consequences of reactions occurring at the bedrock-soil interface – and by extension, the processes by which rock becomes soil and nutrients are liberated, utilised by plants or flushed to the oceans. Kate Hendry presented her latest work employing the distribution of zinc in sponges (trapped in their opal hard parts) to examine how organic matter is formed in surface oceans, then transported to the deep ocean and ultimately buried in sediments; this is a key aspect to understanding how carbon dioxide is ultimately removed from the atmosphere.  The Conference is not entirely about measuring these processes – it is also about how those measurements are interpreted; Andy Ridgwell evaluated the evidence for how and when oceans become more acidic or devoid of oxygen using an intermediate complexity Earth System Model.

What next?  Every few years, a major innovation opens up new insights.  Until about 20 years ago, organic carbon isotope measurements (carbon occurs as two stable isotopes – ~99% as the isotope with 12 nuclear particles and ~1% as the isotope with 13) were conducted almost exclusively on whole rock samples. These values were useful in studying ancient life and the global carbon cycle, but somewhat limited because the organic matter in a rock derives from numerous organisms including plants, algae and bacteria. But in the late 1980s, new methods allowed us to measure carbon isotope values on individual compounds within those rocks, including compounds derived from specific biological sources.  In the past decade, John Eiler and his team at Caltech developed new methods for measuring the values in specific parts or even at a single position in those individual compounds within those rocks (work that builds on ideas of John Hayes 20 years prior).  Now being explored by many colleagues, this isotope mapping of molecules could open up new avenues for determining the temperatures at which ancient animals grew or elide what microorganisms are doing deep in the Earth’s subsurface.

Scientists are going to continue to measure the world around us.  And while that might sound cold and calculating, it is not!  We do this out of our fascination and wonder for nature and our planet.  Just like Galileo’s discovery of Jovian satellites excited our imagination of the cosmos, these new tools are helping us unravel the astonishingly beautiful interactions between our world and the life upon it.

*I originally wrote this in 2014, after the Goldschmidt Conference in 2014 and a visit to Firenze’s Galileo Museum.








The Organic Geochemistry Unit’s ‘Mission to the Moon’

Y’all! A blog adapted from my 19 July 2019, 50th anniversary twitter thread about the Apoll0 11 #Apollo50th lunar samples and the search for life. Adapted from a presentation by @ogu_bristol founder Geoff Eglinton, who led the search for biomolecules. The team included him, James Maxwell, Colin Pillinger, John Hayes and others, titans of the organic geochemistry field. University of Bristol press release here:  (…)

Today, the @ogu_bristol studies archaeology, past climate, the Earth system, environmental pollution, astrobiology and the evolution of life. We are all proud to build on the legacy of Geoff and James, shared between @UoBEarthScience and @BristolChem (…)

Geoff’s involvement dated back to 1967 when @NASA first commissioned proposals for analyses of the rocks! (Geoff – like all of us – also smelled an opportunity for investment in fantastic new kit!)

Slide from one of Geoff’s iconic presentations

This was exciting news in Bristol – but the @bristollive (Bristol Post) headline rather captured the gender stereotypes of the day. As we know, there were many hidden figures at NASA. And although the OGU was mostly men in 1969, women were a critcal part of the group.

“We choose to go to the Moon in this decade and do these other things, not because they are easy but because they are hard, because that goal will serve to organize and measure the best of our energies and skills’ JFK, 1962. A thrilling statement of scientific intent.

Everyone had their own role to play in the post-mission effort do derive as much scientific value as possible from this great human endeavour. This is Geoff’s list of the ‘Big Questions’:

Images of the launch…

… and some of Geoff’s favourite images from the mission. All courtesy of @NASA

The Rocks Arriving at NASA! They had to be quarantined for three weeks in the Lunar Receiving Lab to ensure they were not contaminated with extraterrestrial life, radiation, toxins.

And then processed via different labs for different analyses, partitioning, etc. This flow chart looks SO simple, given what we have all personally experienced in distributing far less precious samples!

Love these photos.

This discussion over how to process some of the most valuable samples in the history of humanity just looks too damn chill.  I’ve seen scientists nearly come to blows over how to partition a marine sediment core!

Bristol newspapers took this seriously: “The Four Just Men of Bristol.” The rocks arrived in Bristol on 23 Oct 1969, an event that we celebrated with a talk by James Maxwell and a fantastic introduction by Colin Pillinger’s wife, Judy.

Sidebar: (John Hayes was Kate Freeman’s PhD supervisor; and she was mine. The legacy of this mission and the analytical techniques that spun out of it is vast. And now I co-lead this same group. This is humbling.)

This is James Maxwell and Colin Pillinger transferring the moon dust. I never had the privilege of working with Colin, but James, Geoff and John are titans in the field from whom I had the privilege to learn.

This is it. This is what we got.

The most precious samples in the history of humanity. Looking for trace quantities. That could change how we perceived our place in the cosmos. No pressure.

What. Did. They. Find?? The @ogu_bristol had two scientific goals. The first, as we are organic geochemists), was looking for molecular evidence for life.


They found none. Despite at least some pop culture suggestions to the contrary!

Including our own Bristol pop culture, right @aardman?

One of my fondest memories of Geoff was Richard Evershed asking him at the end of the seminar ‘Did you expect to find any evidence?’

Geoff: ‘Ha ha ha ha… No.”

Another newspaper article reporting the findings. The press back then was really keen on making sure we knew what gender these scientists were….

But they did make fascinating discoveries! They found traces of methane embedded in the lunar soil. This important organic compound could be formed in minerals by solar wind bombardment of the surface with carbon & hydrogen. But lunar surface is also bombarded by micrometeorites

So which was the correct mechanism? Geoff’s explanation in his own words/slides and drawings!

And the inevitable @nature paper!  (It turns out that it is more complicated than that.  It is partially contamination and partially carbon chemistry on the lunar surface)

The adventure did not end there. They continued analysing samples from not only the Apollo missions but also the Soviet Luna missions.

Colin Pillinger went on to pioneer UK space science for the next three decades. And the scientists and methods thrived as the foundation for a multitude of disciplines here on Earth, from chemical archaeology to climate reconstruction to tracing pollution in the environment. And the legacy thrives through over 1000 scientists – undergraduates, PhD students, post-docs, visitors, and users of the Bristol node of @isotopesUK.

Many debate the cost and priority of space science and exploration, compared to tackling real world problems. That might seem especially true now as we grapple with the immediate challenge of Covid-19 and the long-term challenge of climate change. And I agree with that, especially when exploration becomes a vanity project rather than a shared and collective intellectual endeavour. But when done right, it brings out our very best, with inevitable and profound benefits for all of society. It ensures we retain our ambitions. It ensures we remember what we can achieve together. And it creates a legacy of knowledge, innovation and scholars #Apollo50th

The Weirdness of Biomolecules in the Geological Record

In the 1930s, Alfred E. Treibs characterised the structure of metalloporphyrins in rocks and oil, revealing their similarities to and ultimately proving their origin from chlorophyll molecules in plants.  From that the field of biomarker geochemistry was born, a discipline based on reconstructing Earth’s history using the molecular fossils of the organisms that once lived in those ancient lakes, soils and oceans.

Most biomarkers are lipids – or fats – although there are exceptions such as the porphyrins. Lipids are ideal biomarkers because they have marvelous structural variability, recording in their own way the tree of life and the adaptation of that life to the environments in which they live(d). And they are also ideal, because they are preserved, in sediments for thousands of years and in rocks for millions, often hundreds of millions and in some cases billions of years.

The classical way in which we use these biomarkers is to exploit those subtle structural changes as a record of environmental conditions – using the number of rings or branches or double bonds as a microbiological record of ancient temperatures or pH. We also use them to identify the sources of organic matter to ancient settings, helping us to characterise an ancient lake or sea or documenting the biotic response to a mass extinction.

They can even record the evolution of life. The rise and diversification of eukaryotes, the Palaeozoic colonisation of land by plants, the Cretaceous emergence of the angiosperms, the Mesozoic rise of red algae and the Cenozoic rise of certain coccolithophorids are all documented in the molecular record.

But that record also documents moments of profound weirdness in ancient oceans, transient events in which some ancient organism appeared, dominated the seas and thus the sedimentary record, and then disappeared, taking with them a suite of biosynthetic machinery.

The Jurassic Ocean

Take for example, the ancient Kimmeridge Sea, which covered much of the UK during the Jurassic about 155 million years ago and within which many North Sea oils were deposited as well as the magnificent sedimentary sequences of Kimmeridge Bay.

A core cutting from Jurassic Kimmeridge Clay Formation, collected from the @NERCscience-funded Kimmeridge Drilling Project. The slight colour changes reflect changes in lithology, with darker colours reflecting more organic-rich horizons.


The Blackstone, oil shale, east of Clavell's Hard, Kimmeridge, Dorset
Ian West has some great photos and descriptions of Kimmeridge Bay black shales at

Within the archived sediments of this ancient basin, we observe many of the biomarkers for common life that we’d find in any sediment from the past 600 million years: eukaryotic-derived steranes (from sterols, such as cholesterol, which occur in every plant and animal) and bacterially-derived hopanes (from compounds similar to sterols but present only in Bacteria).  But we also find very odd compounds, unusually-branched linear isoprenoids.  The isoprenoids, compounds constructed of the five-carbon atom unit isoprene, are not odd; in fact, steranes and hopanes are just linear isoprenoids folded into rings, and the membrane lipids of the third domain of life, the Archaea, predominantly comprise linear isoprenoids. More on them below.

But the isoprenoids from some sedimentary horizons deposited in the ancient Kimmeridge Sea have extra branches or missing branches, revealing an assembly from smaller molecules in a manner unlike any organism on Earth today.

A gas chromatogram from the KCF (you can view this like a bar chart – each peak is a compound and its area reflects its concentration). It shows the distribution of the unusual isoprenoids (letters and letter combinations), which in some parts of the KCF such as this particular sample dominate the entire assemblage.

In those horizons, they eclipse all other biomarkers in abundance, indicating that these ancient organisms did not just persist at the fringes of life, an idiosyncrasy in a complex ecosystem, but were one of the dominant organisms.

And then they disappeared, taking these peculiar lipids with them.

An Archaeal Event in the Cretaceous

Deep in the Cretaceous, near the boundary between the Aptian and Albian Ages, about 110 million years ago, organic-rich sediments were deposited across the North Atlantic Ocean.  The event is called Oceanic Anoxic Event (OAE) 1b. Such events are not uncommon, especially in the Cretaceous when combinations of algal blooms, restriction of ocean circulation and depletion of deep ocean oxygen facilitated the burial of the organic matter (that in many cases became the oil and gas that fuels the Anthropocene). But unlike earlier and later organic burial events, this event was not an algal event; it was not a plant event.

This was an Archaea event.

Archaea are ubiquitous on the planet, but rarely do they dominate, instead ceding the modern Earth to the plants and Bacteria. Their hardy physiology allows them to dominate in very high temperature geothermal settings and they are uniquely adapted to a handful of ecosystems. Some Archaea, those involved with the oxidation of ammonia, also appear to dominate in parts of the ocean, but only in scarce abundances, representing a significant proportion of the biomass only because other organisms find it even more challenging to eke out an existence in that sunlight-starved realm.

But 110 million years ago not only did they dominate, they dominated in a way that led to the deposition of thick layers of archaea-derived organic matter on the seafloor.  We know this because nearly all of the organic matter – analysed through the lens of multiple analytical techniques probing the various pools of sedimentary organic matter, with names like bitumen and kerogen, maltenes an asphaltenes, saturates, aromatics and polars – are all dominated by compounds diagnostic for the Archaea.

Amorphous organic matter from OAE1b – structureless with no evidence of plant or algal cell walls. In many ways, this is a mundane image, similar to much organic matter in sediments, and keeping the secrets of its origin to itself. But its chemical composition is less opaque, revealing its unique archaeal origin.

But OAE1b was evidently not merely a brief explosion of the same Archaea that thrived at much lower abundances prior to and after it, and thrive at low abundances even today. No, this event included Archaea that biosynthesised subtle variations of classical Archaeal lipids, variations restricted -as far as we know – to this single event in all of Earth history.

A library of compounds found in OAE1b sediments. The archaeal isoprenoids I-V and XI to XIV dominate. And in the kerogen, similar fragments (XVII and beyond) dominate, indicating that the archaea dominate the production of all OM. But of all of these compound I is particularly unique, similar to the others but apparently confined to this one event in all of Earth history.

Compound I from the figure above might not look that special; it takes a keen eye to distinguish it from Compound II below it.  But like the unusual lipids of the Kimmeridge Clay Formation, it is apparently restricted to (and abundant during) only this one event.


These are weird biomarkers and that is why we love them. They prompt us to ponder the organisms that made them – and how and why?  And this prompts further questions that are perhaps more fascinating and profound, and not just the interest of organic geochemists.

Why have no other organisms chosen to make them?  Are these lipid simply an accident of phylogeny? Or are these a specific adaptation to the environmental and ecological needs of a particular moment in time, in a particular ocean basin? And that is both enigmatic and beautiful.  It speaks to the rapid emergence and then the casual discarding of a biosynthetic pathway and the associated enzymatic machinery.

And surely that must say something of the organisms that have produced them. Because these weird and unique biomarkers also reveal the expansion and disappearance of the microorganisms that made them, organisms comprising not just a truncated branch on the tree of life but a branch that what was, for a brief while, thick and thriving.  And now gone.


But as fascinating as these microbiological events are I am even more curious about those that we have we missed? Most life does not make such weird and singular lipids, relying on similar biomolecular solutions to similar ecological needs. Consequently, I suspect that there are many cryptic microbiological evolutionary events, invisible to the molecular fossil record. And by extension, are these simple organisms – the single-celled bacteria, archaea and microalgae – as primitive and eternal as we assume?  Or is Earth history replete with exotic microbiological events – a multitude of failed experiments or singular innovations appropriate only for a moment in time – and then rendered invisible even to organic geochemists because they have not been signposted by a peculiar lipid?