GeoLog

Stratigraphy, Sedimentology and Palaeontology

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.

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

 

Imaggeo on Mondays: Earth Wave

Imaggeo on Mondays: Earth Wave

Take a stroll along the norther beaches of the French Channel Coast, some kilometers east from the entrance of the Channel Tunnel, and you’ll encounter an imposing cliff of soft, sandy composition which dominates the landscape.

On close inspection, the sediments which make up the Quaternary aged deposits of the Sangatte Cliff, are beautiful, revealing intricate patterns which hold the key to the geological processes that formed them. Even at present, the landscape is being continuously shaped by marine processes which continuously erode the Quaternary soft deposits – especially during storms coupled with high tide events.

The Sangatte sedimentary sequence outcrops along a stretch of about 1.5 km along the French coast. Today’s featured image was taken by Pierre Antoine, at the base of the Quaternary sequence of the Sangatt Cliff. It corresponds to an observation window of about 80 cm large.

“At this location, explains Pierre, the Quaternary record is composed of raised beach deposits (flint pebble bar and sandy beach deposits, ± 3m thick) dating from a Middle Pleistocene interglacial (± 300 ka) and to a high sea level (± 5 m above the present day level), covered by a thick succession of chalky periglacial slope deposits, formed during periods of repeated freezing and thawing, associated with loesses and fossil soils know as palaeosols (8 to 12m).”

The greenish sandy deposits exposed at the base of the photo represent the top of the ancient marine beach deposits. These were overlain by a thin, dark bown, peat layer indicative of a phase of sea level drop. It is likely that during this time a peat bog, which was isolated from the sea by wind-driven sand dunes, developed .

This peat layer has, more recently, been strongly compressed and reworked during the deposition of the overlying thick bed of dense chalk mud. The greyish muds are the result of the weathering of the massive chalky slopes of the Sangatte Cliff,  which occurred following a cold period after the sea-level decrease. The delicate rusty bands seen in the otherwise creamy chalky muds, are the result of infiltration of iron oxide minerals throughout the cliff.

Reference:

Antoine, P. 1989. Stratigraphie des formations pléistocènes de Sangatte (Pas-de-Calais), d’après les premiers travaux du Tunnel sous la Manche. Bulletin de l’Association Française pour l’Etude du Quaternaire, 37, 5-17.

Imaggeo is the EGU’s online open access geosciences image repository. All geoscientists (and others) can submit their photographs and videos to this repository and, since it is open access, these images can be used for free by scientists for their presentations or publications, by educators and the general public, and some images can even be used freely for commercial purposes. Photographers also retain full rights of use, as Imaggeo images are licensed and distributed by the EGU under a Creative Commons licence. Submit your photos at http://imaggeo.egu.eu/upload/.

Imaggeo on Mondays: Through the hole

Imaggeo on Mondays: Through the hole

The Gunung Mulu National Park is an area so geologically remarkable and home to such incredibly diverse fauna and flora it has been declared a World Heritage Area.  Located on the island of Borneo, the park is famous for its over 100 different palm species and 3500 other plant types. Geologically speaking, a trip though the varied landscapes will be rewarded with views of deep gorges and hidden valleys, as well as towering limestone and sandstone pinnacles. The predominantly calcareous landscape means most make the journey to remote area to catch a glimpse of the world’s second largest cave chamber. With dimensions of 600 m by 415 m and 80 m high, Sarawak Chamber is a natural wonder worthy of making the journey to Borneo for!

“The picture was taken in February 2014 while I was on a two month trip to Indonesia and Malaysia after graduating from my Master studies. Eventually I found one of the most beautiful places on the island of Borneo: the Gunung Mulu National Park,” explains Juliane Krenz, a PhD candidate at the Department of Environmental Science of the University of Basel.

Aside from the staggering Sarawak Chamber, the national park is crisscrossed by at least 295 km of explored caves.  Made up of the Mulu Sandstone Formation, overlain by the Melinau Formation – which formed in coral rich lagoons some 20 million years ago – the caves are home to a host of species, from bats to swiftlets.

“After spending a few days exploring one of the largest cave systems in the world, I wanted to get deeper into the rainforest and climb Mount Api to see the so-called “pinnacles” – an incredible limestone karst formation everybody was talking about,” Juliane says.

The journey to reach the “pinnacles” involved an hour’s boat ride and three hours walk through the rainforest, eventually reaching a small base camp impressive for its setting: three houses next to a crystal clear stream surrounded by mountains covered in dense forest.

The hike to the sandstone spires began in earnest the next morning. To reach the impressive formations Juliane had to climb an endless number of natural steps made of slippery roots and stones of varying heights from a comfortable 20cm up to 1m, with a total elevation increase of 1200 m in little over 2km – turning the hike into an adventurous climbing trip.

“After 3 hours hiking mostly vertically we reached the top and looked down on an innumerable amount of silver-greyish rock pinnacles spiking out between the dense bright green forest, some of them being up to 40m tall. None of us would have guessed that there were so many,” describes Juliane.

Capturing the beauty of the setting was no easy task.

“I had seen many impressive photographs of the spikes but I was looking for the special focus. Eventually I chose the hole as a frame making the largest pinnacles look like they are part of a miniature world – like me wandering through the rain forest.”

By Laura Roberts Artal , EGU Communications Officer and Juliane Krenz, a PhD candidate at the Department of Environmental Science of the University of Basel.

For more information on the Gunung National Park:

In 1977-78 there was a large expedition (followed by many others known as the Mulu Cave project) founded by the Royal Geograpical Society to explore the dimensions of the cave system. The “pinnacles” at Mount Api are part of the limestone ridge between North Thailand and New Guinea.  The area is full of limestone spikes of various sizes (from few centimeters up to several meters) that are formed through weathering and dissolution over centuries. Nowadays, most research is focused on the ecology and biodiversity in the caves and the surrounding areas.

An earlier version of this post stated Sarawak Chamber was the largest cave chamber in the world. That accolade goes to Hang Sơn Đoòng in Vietnam. With thanks to @TerjeSolbakk for helping us improve this post. 

 

Imaggeo is the EGU’s online open access geosciences image repository. All geoscientists (and others) can submit their photographs and videos to this repository and, since it is open access, these images can be used for free by scientists for their presentations or publications, by educators and the general public, and some images can even be used freely for commercial purposes. Photographers also retain full rights of use, as Imaggeo images are licensed and distributed by the EGU under a Creative Commons licence. Submit your photos at http://imaggeo.egu.eu/upload/.

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