Livers, guts and gills: understanding how organisms become fossils

Livers, guts and gills: understanding how organisms become fossils

It’s 10am and Thomas Clements, a 3rd year palaeobiology PhD Student, is getting ready to check on his latest experiment. Full kited up in what can only be described as a space suit, Thomas carefully approaches the fume cupboard home to his latest specimen: a decaying seabass, balanced on a specially designed ‘hammock’ in a tank of salty water. Opening the lid to check on the rotting fish, Thomas is hit by the smell, so atrocious the fume hood and protective overalls only go some way toward shielding his sense of smell. It might be a bleak start to the day, but it is central to Thomas’ research.

While the fossil record is dominated by the hard mineralised parts of organisms such as shells, teeth and bones, in the past few years palaentologists have started to rely on different fossilised remains and techniques to discover more about extinct animals.

“In fact, soft-bodied fossils are much more informative about the anatomy, physiology, ecology and behaviour of ancient organisms. They also give scientists a much better idea as to the type of conditions, ecosystems and environments in which the organisms lived,” explains Thomas.

However, before the vital clues held in the remains of soft-bodied fossils can be accurately interpreted by researchers, the processes which cause them to be preserved in the first instance must be fully understood too. This is where Thomas’s smelly study of decaying fish carcases comes in. Using seabass, because its genealogy can be traced back in time (organisms related to the blue fish are known to exist in the ancient fossil record), Thomas aims to better understand how decay processes affect the fossilisation potential of soft-tissues – especially of internal anatomy.

Thomas injects the silica gel around the probes to make sure the incisions are sealed. You can see the fish in it’s hammock. (Credit: Thomas Clemens)

Thomas injects the silica gel around the probes to make sure the incisions are sealed. You can see the fish in it’s hammock. (Credit: Thomas Clemens)

Along with the Palaeobiology Lab Group at Leicester University, Thomas has devised a series of novel experiments to investigate the process. Because he is particularly interested in how internal organs decay, Thomas cuts millimetre sized incisions into the fish, sourced from a local fishmongers, to place probes into liver, guts, stomach and even kidneys. The chemical data measured by the probes allows him to unravel both the timing and sequence of anatomical decay of the different organs.

“One of the most important parts of the experiment is to accurately recreate the natural death of the animal,” describes Thomas.

That is why it is vitally important that the wounds caused by the incisions are fully sealed with inert silica gel so as not to speed up the decay process. This also means that before any experiment, he painstakingly practices cutting and sealing for hours. By the end of his practice runs he is intimately familiar with the exact location of each internal organ and able to perform only the smallest cuts required to insert his probes.

Recreating the conditions under which an ancient fish would decay is also important. Surgical incision complete, probes inserted ready to acquire data, the fish is gently placed on a hammock of inert plastic netting (again, so that no chemicals plastic may give off will interfere with the natural break down of the body parts) and lowered into an aquarium of salty water.

Thomas’ experiments are sustainable and environmentally friendly too! Rather than placing the hammock directly on the tank floor, it is suspended in the water, by way of plastic ropes attached to the corners of the aquarium. This means that as the fish is left to decompose over time, most fish parts sink towards the base of the tank an eventually dissolve in the water – making it extremely foul-smelling, as you might imagine! Once the experiment is complete, whatever fish parts may remain on the hammock can be simply discarded and the (washed) plastic used in a new experiment.

Thomas teaches visiting PhD student, Yujing Li, about the anatomy of a Seabass. (Credit: Thomas Clemens)

Thomas teaches visiting PhD student, Yujing Li, about the anatomy of a Seabass. (Credit: Thomas Clemens)

The experiments performed so far show that the decay process is actually very quick. After 60 days, the majority of the fish has fully decomposed, with only fins and very small tissue parts remaining. It takes no more than 20 days for muscle fibres to disappear and as little as five days for ultra-structures to break down. Through his work, Thomas now knows that the preservation of soft tissues during fossilisation has to happen very quickly or conditions have to be just right.

Thomas thinks that “slowing down the decay process is what gives soft-bodied parts a better chance of preservation.”

This is why during the experiments he has been testing how changes in the conditions, from lowering the water temperature, reducing agitation of the tank, changing salinity or even reducing bioturbation (the disturbance of sediment caused by sea floor dwelling critters),  affect how likely it is for tissues to be preserved.

Despite the advances and better understanding gained through the experiments, enigmatic questions still remain: why are some organs, such as guts, often found preserved in the fossil record, but why are others, such as eyes, so much rarer? And so, Thomas’ work in the lab, complete with rotting fish, surgical gloves, spacesuit-like protective equipment and stomach turning smells continues.

By Laura Roberts Artal, EGU Communications Officer

Thomas Clements presented his work at the 2016 EGU General Assembly, at a press conference entitled: How ancient organisms moved and fed: finding out more from fossils. The full press conference can be streamed here. In addition, the work was presented in session SSP4.2: Experimental solutions to deep time problems in palaeontology. Thomas’ abstract can be found here.

Share the work you presented at EGU 2016: upload your presentations for online publication

Share the work you presented at EGU 2016: upload your presentations for online publication

This year it is, once again, possible to upload your oral presentations, PICO presentations and posters from EGU 2016 for online publication alongside your abstract, giving all participants a chance to revisit your contribution  hurrah for open science!

Files can be in either PowerPoint or PDF format. Note that presentations will be distributed under the Creative Commons Attribution 3.0 Licence. Uploading your presentation is free of charge and is not followed by a review process. The upload form for your presentation, together with further information on the licence it will be distributed under, is available here. You will need to log in using your Copernicus Office User ID (using the ID of the Corresponding Author) to upload your presentation.

Presentations and posters will be linked to from their corresponding abstracts. If your presentation didn’t have an abstract (this is the case for Short Courses and others), but you still want to share it with the wider community you can consider uploading your presentation to slideshare or figshare as a PDF to share it instead.

All legal and technical information, as well as the upload form, is available until 19 June 2016 at:

Geo Talk: One of the youngest EGU 2016 General Assembly delegates sends sensor to space

Geo Talk: One of the youngest EGU 2016 General Assembly delegates sends sensor to space

Presenting at an international conference is daunting, even for the most seasoned of scientists; not so for Thomas Maier (a second year university student) who took his research (co-authored by  Lukas Kamm, a high-school student) to the EGU 2016 General Assembly! Not only was their work on developing a moisture sensor impressive, so was Thomas’ enthusiasm and confidence when presenting his research. Hazel Gibson and Kai Boggild, EGU Press Assistants at the conference, caught up with the budding researcher to learn more about the pair’s work. Scroll down to the end of this post for a full video interview with Thomas. 

Thomas Maier might seem like your average bright and enthusiastic EGU delegate, but together with his co-author Lukas Kamm, he has invented a water sensor that very well might help change the way astronauts live in space. Not only is their invention helping to revolutionise aerospace, but they are also the youngest delegates at the conference, Thomas is a second year university student at Friedrich-Alexander Universität Erlangen-Nürnberg and Lukas is attending high school at Werner-von-Siemens Gymnasium. We caught up with Thomas to speak with him about his invention.

Could you explain to us what led you to develop this water sensor?

We started this project four years ago for a contest called Jugend Forscht, a German youth sciences competition in Germany and the project we came up with was about giving plants demand driven watering. After we built our first sensor, we continued our work until it was possible to send the sensor into space, for a project called EU:CROPIS.

Can you tell us how your sensor works?

The sensor is based on a capacitive measuring method. So, you have two electrodes close to each other, which have an electrical capacitance (or ability to store an electrical charge) between them. The change in water content close to the electrodes changes the capacity of the sensor. Then we measure the capacity of the electrodes by measuring the time constant of the capacitor over time.

The greenhouse which forms part of the EU:CROPIS project. The greenhouse is home to Thomas and Lukas' water sensor. (Credit: Kai Boggild/EGU)

The greenhouse which forms part of the EU:CROPIS project. The greenhouse is home to Thomas and Lukas’ water sensor. (Credit: Kai Boggild/EGU)

Can you tell us more about the EU:CROPIS project?

The EU:CROPIS is mainly about this here [indicates greenhouse model], and this is a greenhouse which will go into space, July next year. The greenhouse will rotate and will generate different gravitational forces that may impact the amount of water available to plants which will be grown in here. And now, after a lot of work, our sensor will be placed on the very right [hand side] of the greenhouse and will measure the soil moisture for the plants.

What are you plans for this project into the future?

Our plans for the future are in taking part in the EDEN-ISS project, this is a project on the International Space Station, that is looking into planting 20 square meters of plants in the ISS and our sensor would be used too. So that is the next aim of this project.

Thanks Thomas for showing us your invention, and good luck to Lukas, who couldn’t attend the conference this year as he is busy with his high-school exams!

Interview by Hazel Gibson, video interview by Kai Boggild, EGU Press Assistants


The final days of the mountain glaciers

The final days of the mountain glaciers

In 1896 British lawyer, mountaineer and author Douglas Freshfield climbed an obscure mountain in the Caucasus called Kasbek and in his book detailing his adventures he described the mountain:

“From this point the view of Kasbek is superb: its whole north-eastern face is a sheet of snow and ice, broken by the steepness of the slope into magnificent towers, and seamed by enormous blue chasms.”

D Freshfield (1986) The Exploration of the Caucasus, page 93

A photo of the mountain taken at the same time highlights the Gergeti glacier (called at the time the Ortsveri glacier) running down the centre of the image. In 2015 Levan Tielidze took another photo of the same view which highlighted a shocking change.

The photo above echoes photos taken of mountain glaciers from across the globe over the last 100 years. All these photos, when compared with their older counterparts, show the comprehensive retreat of mountain glaciers in every country. The retreat of mountain glaciers was called a ‘canary in the coal mine’ along with other indicators of global climate change. But new data presented this month at the European Geosciences Union General Assembly, shows us that that canary is now past saving.

Ben Marzeion, professor of Geography and Climate Science at the University of Bremen, has found that mountain glacier retreat (and eventual disappearance) is now inevitable. In a session relating to the Paris agreements (where 195 countries from around the globe agreed to work towards limiting global temperature change to two degrees) Marzeion presented evidence that indicates that even if that ambitious target were achieved, 60% of current mountain glaciers will still melt away. In fact the impacts of climate change are more severe than even this number suggests. Prof Marzeion explains:

‘Even if climate warming were to stop today – which is physically impossible – about one third of the glacial ice in the world would still melt in the long term.’

Is this a farewell to the mountain glacier? (meeting of the penitents credit Simon Gascoin)

Is this a farewell to the mountain glacier? Credit: Simon Gascoin (distributed via

This is because the ice in the mountain glaciers responds to climate change with a time delay. Mountain ice is not sustainable and more than half of the ice in a mountain glacier is responding to temperature change that has already happened. The ice of the mountain glaciers has been melting for decades and once that process begins, it is very difficult to stop. Smaller glaciers and those at lower altitudes are at greater risk of complete loss, but Professor Marzeion says that any glacier where the summer snowline rises above the mountain peak will not survive. This has wider implications for water use in mountainous areas.

‘Saving the glaciers is an illusion in many mountain ranges,’ says Marzeion. ‘We will have to adapt to the consequences of glacier melt. This will affect the coastal regions of the world, but also populations in the mountainous regions, who will have one fewer source of water at their disposal in summer.’

Although the question of global temperature change is still one that we have to solve, it seems that our desire to take responsibility for our actions comes too late for those ‘magnificent towers’ and ‘blue chasms’ that Douglas Freshfield described over 100 years ago.

By Hazel Gibson, EGU General Assembly Press Assistant and Plymouth University PhD student.

Hazel is a science communicator and PhD student researching the public understanding of the geological subsurface at Plymouth University using a blend of cognitive psychology and geology, and was one of our Press Assistants during the week of the 2016 General Assembly.


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