August 8, 2022 | David F. Coppedge

Fossil Soft Tissue: An Apatite for Rotten Fish

Scientists put up with the smell of rotting sea bass for 2.5 months
to learn why some fossils preserve soft tissues. They didn’t learn much.


One can only imagine how disgusting an experiment became that was conducted by scientists at the University of Leicester. They stuck probes into organs of a dead sea bass to measure what happens after death. Even though their experimental setup was enclosed in a “fume hood,” it must have become intolerably rancid. A press release says from August 8, 2022 says,

Sarah Gabbott is a Professor of Palaeobiology and co-author of the paper. Professor Gabbott added: “Watching and recording (and smelling) how a fish rots may not be most people’s idea of science, but for palaeontologists understanding the process of decay is crucial to revealing which anatomical features of an animal are likely to become a fossil, and what they will look like.”

The experiment was prompted by numerous reports of exquisite soft tissue preservation of fossils going all the way back to Cambrian trilobites. Indeed, Figure 1 in their paper includes a trilobite with clear impressions of its gut, along with photos of soft tissue in a frog, fish, snake, worm and octopus.

Source: Clements, Purnell and Gabbott, “Experimental analysis of organ decay and pH gradients within a carcass and the implications for phosphatization of soft tissues.” Palaeontology (65:4), July-August 2022, e12617. Open access.

Soft-tissue bearing fossils yield information about the biology, ecology and evolution of ancient organisms that is not available from skeletal remains alone; they are thus of significant scientific and public interest. However, to correctly interpret the information captured by such fossils, we must understand the processes of decay, maturation and preservation which led to their formation and the timescales over which these processes operate (Purnell et al. 2018).

The reference at the end of the quote shows that Purnell and Gabbott were working on the problem four years ago, calling for better terminology of and methodology in the determination of soft tissue preservation. In that paper, “Experimental analysis of soft-tissue fossilization: opening the black box,” (also open access in Paleontology), the authors stressed, “Our focus must remain on the key issue of understanding what exceptionally preserved fossils reveal about the history of biodiversity and evolution, rather than on debating the scope and value of an experimental approach.”

Well, the new experimental approach seems to have done little to provide understanding about anything except the well-known observation by any fisherman’s wife: dead fish begin to smell awful after a few days. Lead author Dr Thomas Clements of the University of Binghamton tried to put a happy face on it:

“We designed an experiment observing rotting fish which was disgusting and smelly, but we made an interesting discovery.

“The organs don’t generate special microenvironments – they all rot in a kind of ‘soup’ together. This means that it is the specific tissue chemistry of the organs that governs their likelihood to turn into fossils.”

It’s hard to see how the experiment could have proved anything at all about fossilization. Their dead fish (6 of them) were not buried; they were suspended in fake seawater the whole time. What did they expect? Holding her nose, Sarah Gabbott smiled and told the press office,

We were really pleased with the results because we can now explain, for example, why fossils often preserve an animal’s gut but never preserve their liver.”

She bases that conclusion only on a possibility: that organs containing high levels of phosphate might “phosphatize” (mineralize into calcium phosphate) faster than other organs.

Micrographs of soft tissue from dinosaur bone from a 2018 study (click to read).

Apatizing Menu

The team knows that mineralization within a fossil can take various forms. This quote indicates that most of the finest details are preserved in apatite, a mineral made of calcium phosphate:

In most conditions, soft tissues are typically lost rapidly post mortem due to decay and cellular autolysis. However, one mode of preservation that can preserve soft-tissue anatomy is authigenic mineralization, the replacement of tissues by minerals that precipitate and grow in situ. Whilst the post-mortem soft-tissue preservation may occur through mineralization by silicates, clays, pyrite and carbonates, it is replacement by calcium phosphate (phosphatization) that is widely regarded as the form of mineralization that yields the highest fidelity of soft-tissue preservation (see Briggs (2003) for a review; Fig. 1). Generally, during the process of soft-tissue phosphatization, minute crystals of apatite (c. <30 nm) form on and within the decaying tissue substrates and can faithfully replicate morphology on a cellular and even subcellular level (Martill 1988; Wilby 1993).

This insight led to their hypothesis. They thought that different organs might create their own microenvironments after death with pH levels suitable for phosphatization. If so, then some organs might preserve better than others. But like the previous quote above says, all the organs mixed together into a disgusting rotten soup. How does that simulate taphonomy, the study of fossilization?

Phosphates exist at higher levels in guts and muscles, where they might be liberated from phospholipids, nucleotides and adenosine triphosphate (ATP). But the probes they inserted into the fish’s organs (stomach, liver, intestines and muscle) showed that the organs barely reached a pH level where phosphatization was expected to occur. And if the organs turned into a soup, it seems that any hope of explaining selective preservation was lost in the experimental setup.

We were unable to reject our second null hypothesis; within the coelom [body cavity], each individual organ did not generate a unique pH profile. Rather, the decay of internal organs contributes to the formation of a pervasive pH environment throughout the body cavity. This pervasive pH environment persists until the dermis ruptures. When this happens the organs in the coelom are no longer in a ‘compartment’ (i.e. a microenvironment) within the fish, and consequently the pH within the fish rapidly equilibrates with the pH recorded in ambient external conditions, probably owing to both the escape of fluids from within the body, and the ingress of saltwater into the body. This raises the question: if, during decay, all internal organs within the coelom are inside a pH environment below the carbonic acid dissociation constant (pH 6.38), why are some internal organs consistently preserved in calcium phosphate in exceptionally preserved fossils, whilst others are lost?

Our data indicate that we can discount differences in tissue decay rate: most of the internal organs (i.e. stomach, liver, heart, gonads, kidney) became unrecognizable within just five days post mortem, and the gills and muscles lost their structure 24 h later (the flexing of the fish within 24 h of the experiment starting suggests that muscular decay begins rapidly). The intestine persisted for a slightly longer period, being lost at around 10–14 days. Within this highly condensed timeframe between death and complete decay, there is no correlation between the timing of loss of organs and their likelihood of occurrence in the phosphatic fossil record; commonly phosphatized internal organs are not the most persistent organs.

The smell must have been unbearable. How could Tom, Mark and Sarah be pleased with so little to show for it?

Exquisitely preserved Jurassic fish. It must have been buried extremely rapidly. Credit: Dean Lomax. Click to read about it in our 5 Aug 2022 entry.

The Missing Blink

British author Paul Dickson quipped, “No experiment is ever a complete failure. It can always be used as a bad example.” Any lab experiment on the decay process prior to fossilization can be useful to know about. Now we can learn from this paper without having to put up with the stench ourselves.

But really, if the three wanted to inform paleontologists about how soft tissue could be preserved in fossils, their efforts overlooked many important details about fossilization and Lagerstätte (exceptional preservation):

  • They didn’t bury the fish in rock.
  • They didn’t compress the fish and elevate the temperature.
  • They did not witness any exceptional preservation.
  • They did not answer how tissues could remain stretchy.
  • They didn’t discuss the most spectacular tissues found in dinosaur bones.
  • They did not observe what happened after 65 million years.
  • They only experimented on a fish, not on other types of creatures.

They admit that last point:

Currently, our data is limited to a fish taxon. Undertaking experiments to log internal chemical changes during decay is difficult, expensive and time consuming, but as technological advances continue and probes become smaller, cheaper and more robust, we recommend further experimentation using other taxa (arthropods, amphibians etc.) to expand our understanding of phosphatic mineral replacement. A complementary avenue of investigation would be to record Eh (oxidation potential) as well as pH, allowing an in-depth investigation into the stability of calcium phosphate during the decay of a carcass. Our data also indicate that experimental designs that only use external conditions as a pH proxy for internal conditions within a carcass should be interpreted cautiously.

According to the recommendations of the authors, the conclusions of this paper “should be interpreted cautiously” by readers.

We wish to thank the authors for making the paper open access even though it did little to further “understanding what exceptionally preserved fossils reveal about the history of biodiversity and evolution.” No experiment is a complete failure. Knowing what happens to a dead sea bass, we can all breathe easier.

The question remains: How can dinosaur soft tissue survive for 80 million years? or trilobite soft tissue for 500 million years?


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