X-ray analysis hints at answers to fossil mystery

Host: Benjamin Thompson

Welcome back to the Nature Podcast. This week, solving the mystery of an unidentified fossil fish.

Host: Noah Baker

And uncovering ancient architecture buried in the Bolivian Amazon. I’m Noah Baker.

Host: Benjamin Thompson

And I’m Benjamin Thompson.

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Host: Benjamin Thompson

First up, there is a fossil fish that has puzzled researchers since it was discovered over 100 years ago. And the reason it's had scientists stumped is that no one could quite figure out what sort of a fish it was. But now, thanks to a new paper in Nature, that might be about to change. Reporter Anand Jagatia takes up the story.

Interviewer: Anand Jagatia

If you travel to the northern tip of Scotland, right up in the Highlands, you'll find Achanarras Quarry. It's famous for its fossils, and the quarry is full of them. A single square metre of rock might contain up to 200 specimens. Achanarras is also one of the only places in the world where you can find the preserved remains of an animal that lived around 385 million years ago called Palaeospondylus.

Interviewee: Jorge Mondéjar

Palaeospondylus is a very small fossil fish, just a few centimetres in length. And for all the world, it looks like a small tadpole. It was first described in 1890 and, since then, it has become one of the most debated and most mysterious fossils ever known to science.

Interviewer: Anand Jagatia

This is Jorge Mondéjar, a vertebrate palaeontologist at the Senckenberg Museum of Natural History in Germany. He says that ever since its discovery, scientists have argued about how exactly to classify this tiny animal.

Interviewee: Jorge Mondéjar

So, first, it was considered to be a jawless fish. These are fishes that still live today and have no jaws, like a lamprey or a hagfish. But then it was also considered to be a placoderm – a very bizarre, extinct armoured fish – a shark, and even it was considered to be a herring.

Interviewer: Anand Jagatia

So, why is this small, ancient tadpole-looking fish so mysterious?

Interviewee: Jorge Mondéjar

You find fragments of the skull and of course the vertebral column and some parts of the tail fin. But besides that, you have no traces of a dermal skeleton. You have no scales, you have no bones that cover the skull and there are also no paired fins. So, paired fins are structures that are used in swimming by fishes and because of that it's actually quite difficult to identify what kind of fish it is.

Interviewer: Anand Jagatia

Without paired fins or even teeth as clues to go on, palaeontologists have struggled to place Palaeospondylus on the tree of life. One problem has been trying to figure out if the fossils are adults that never had these features or lost them over the course of evolution, or whether they were actually juveniles in their larval stage that just hadn't developed them yet. But now, a paper in Nature offers some new evidence that might help to solve the Palaeospondylus riddle. A team has produced the first high-resolution imaging of its tissue structure from two incredibly well-preserved specimens.

Interviewee: Tatsuya Hirasawa

We scanned the specimens with a very bright X-ray from a synchrotron, which enables to increase the resolution and also contrast.

Interviewer: Anand Jagatia

This is lead author Tatsuya Hirasawa from the University of Tokyo in Japan, who used these high intensity X-rays to peer inside the rocks and uncover tiny anatomical details of Palaeospondylus which had never been seen before.

Interviewee: Tatsuya Hirasawa

We believe we finally solved the mystery because we succeeded in imaging 3D morphology of Palaeospondylus. For example, we identified the boundary between part of the skull called the intracranial joint. And also, I was so excited to find three semicircular canals of the inner ear at the first glance of the scan data.

Interviewer: Anand Jagatia

These are features that might finally help us work out what kind of animal Palaeospondylus was. Jorge, who you heard from earlier, has written a News and Views article about the work. He told me that the fact you can see three semicircular canals points towards Palaeospondylus being a jawed vertebrate, and the presence of an intracranial joint narrows things down even further.

Interviewee: Jorge Mondéjar

This feature is only present in one particular group of fishes. It’s called the lobe-finned fishes or the sarcopterygian fishes. So, finding an intracranial joint in Palaeospondylus is huge because that means that Palaeospondylus is not a shark. It’s not a jawless vertebrate. It's actually a sarcopterygian and it belongs in a group to which we also as humans and as mammals and as tetrapods belong.

Interviewer: Anand Jagatia

Tetrapods are four-limbed vertebrates, which includes the mammals, the birds and the amphibians. So, rather than being some obscure, extinct animal, these new observations suggest that Palaeospondylus is a sarcopterygian – a member of the lineage that eventually led to us. So, is that it? Has the mystery of the tiny fossilised fish found 100 years ago in a Scottish quarry finally been solved? Well, not quite. There are still some big questions to answer, like whether the fossils are adults or larvae. But Tatsuya’s scans also provide some clues about the skeleton that might help to settle this issue too.

Interviewee: Jorge Mondéjar

For a long time, we thought that the skeleton was entirely made of cartilage, so like in a shark, for example. But recently, other colleagues have identified that this skeleton was mainly cartilaginous but it showed some traces of bone, perichondrium bone. It's a very thin layer of bone. And the article also showed that this perichondrium bone was quite common, was quite developed in Palaeospondylus, and thus it shows that it was actually caught in the act of mineralising its skeleton even further.

Interviewer: Anand Jagatia

In other words, rather than being an adult with a skeleton made of cartilage, Palaeospondylus could be a larva in the process of turning that cartilage into bone. But if it is a juvenile then that begs the question, what does the adult form look like? Well, according to Jorge, we can't really know yet. And really, there's only one way to find out.

Interviewee: Jorge Mondéjar

Firstly, I would say we need more specimens. But this is the silly answer because we have thousands of specimens of Palaeospondylus already known. But I think what we would need are more developed specimens, I mean older specimens, so that we can actually more properly see certain features developed in time, such as paired fins or scales or even teeth.

Interviewer: Anand Jagatia

Tatsuya agrees that finding fossils with more features, particularly with dermal bones from the skull, is the only way to confirm what this creature is and where it fits on the tree of life, once and for all.

Interviewee: Tatsuya Hirasawa

I believe the dermal bones covering the skull is the key because there are many features important for phylogenetic analysis in the dermal bones. We need new fossils.

Host: Benjamin Thompson

Tatsuya Hirasawa there. You also heard from Jorge Mondéjar. Look out for links to Tatsuya’s paper and Jorge’s News and Views article in the show notes.

Host: Noah Baker

Coming up, the archaeologists that have used lidar to uncover ancient settlements hidden in the Bolivian Amazon. Before that, though, it's time for this week's Research Highlights, brought to you by Dan Fox.

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Dan Fox

A new silk-based version of mother of pearl is stronger and tougher than hard plastics – but also biodegradable. Oyster shells are lined with a tough natural composite material called mother of pearl, which has an internal structure that resembles a brick-and-mortar wall. Researchers wanted to combine this structure with sustainable biological materials to create a new composite that was both versatile and biodegradable. To do this, they dissolved silk proteins in water and froze the resulting solution inside a mould. The shape of the mould caused the water to freeze in sheets, trapping the silk protein molecules between them. Vaporising the ice allowed the team to form silk bricks that, when exposed to a humid environment, could be compressed together to form a durable and shapeable material that can be completely biodegraded in 30 days using an enzyme. The researchers say this could be an alternative substitute to conventional composite materials. Read that research in full in Science Advances.

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Dan Fox

Some parrots are known to be very smart, but this isn't the only way these birds can use their heads, as researchers have observed one species of parrot using their head to propel themselves while climbing. Parrots use their legs and beaks while climbing, but it has been unclear whether the beak does more than stabilise the birds on their ascent. To find out, researchers studied rosy-faced lovebirds moving along a runway. As the researchers adjusted the runway steepness, they counted how often the birds used certain body parts. When the runway reached a 45-degree angle, the parrots began to use their tails and beaks to help them climb. At a 90-degree angle, the birds used their tails to brace themselves. They also propelled themselves upwards with their beaks, exerting forces comparable to those produced by the arms of humans and other primates while climbing. The researchers concluded that the parrot’s head has been repurposed to function as a third limb. Use your head to read that research in full in Proceedings of the Royal Society B.

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Host: Noah Baker

Next up on the show, we’re travelling to South America – specifically, western Amazonia, where archaeologists have been using lidar tech to uncover new evidence of an ancient civilisation. Their data suggests that the region wasn't as sparsely populated in pre-Hispanic times as previously thought. Reporter Shamini Bundell is here to tell us more.

Interviewer: Shamini Bundell

In the Amazon basin, in the lowland forests of Bolivia, archaeologists have been using lidar technology to virtually peel back generations of forest growth. And underneath the canopy, they've discovered unexpected new evidence of an ancient civilisation.

Interviewee: Heiko Prümers

It’s 20 metres high. Nobody expected that kind of society in that region.

Interviewer: Shamini Bundell

That was Heiko Prümers from the German Archaeological Institute. Heiko has spent his career working in Amazonia, first heading to Bolivia nearly 30 years ago, to the surprise of some of his peers.

Interviewee: Heiko Prümers

Most people said, ‘What are you doing there,’ when I went to Amazonia because it is supposed that in the Amazon region there was almost nothing but small tribes.

Interviewer: Shamini Bundell

But for Heiko, the Amazon held bigger secrets. In 1999, he started to investigate large mounds in the lowlands of Bolivia.

Interviewee: Heiko Prümers

If you go to southeast of the Llanos de Mojos, which is a savannah region in the lowlands of Bolivia, people will tell you of the ‘lomas’. Those lomas are mounds that exist over there and that are normally covered by vegetations.

Interviewer: Shamini Bundell

When Heiko and colleagues started excavating some of these mounds, archaeologists theorised that they were rubbish heaps – the result of waste accumulated over centuries. But hidden beneath the earth, the teams found evidence of rectangular platforms, graves and artefacts – signs of a society with a social hierarchy.

Interviewee: Heiko Prümers

We found something like 120 graves in that site. And some did have offerings and they were special locations, so all those data combined showed that society itself was much more complex than anybody had supposed before.

Interviewer: Shamini Bundell

So, in 2019, a team set out by helicopter to try and uncover the true scale of this ancient civilisation, with the help of lidar technology.

Interviewee: Heiko Prümers

You use a laser adapted to the helicopter or small aircraft, and then you fly over an area and by the reflections of the laser, you get the distance from the objects. And the fascinating thing is that you can eliminate virtually, digitally, the vegetation afterwards.

Interviewer: Shamini Bundell

Beneath the thick canopy was structures, rectangular platforms, conical pyramids, defensive banks, canals, reservoirs, and long straight causeways, connecting hundreds more settlements large and small.

Interviewee: Heiko Prümers

If you are overflying those signs, you won't see anything but trees and vegetation. And when you see afterwards the lidar images, well, you know, you have been flying over sites, archaeological sites, you'll see everything.

Interviewer: Shamini Bundell

The discovery is part of a huge change in what archaeologists think about the history of the Amazon.

Interviewee: Heiko Prümers

If we talk about Amazonia, we’re generally talking about people without agriculture. And if you look at the anthropological literature on the tribes, as they were called, some years ago, the ethnic groups in that region, they normally make something like gardening, garden culture, but not what we call agriculture. And to recognise as a first step that they were sedentary and they that were agriculturalists, that is a big step.

Interviewer: Shamini Bundell

Even just from the air, the newly found settlements give hints of a complex and unexpected way of living.

Interviewee: Heiko Prümers

And near to every site, in one hour of walking, you will find at least one other site. Nobody expected that kind of society in that region. So, that's a new thing, to find a densely populated area with settlements much larger than before.

Interviewer: Shamini Bundell

So, what does that tell us about the Casarabe culture, who constructed these settlements and the two mounds that Heiko and colleagues have already excavated?

Interviewee: Heiko Prümers

When I'm giving conferences in Bolivia and people ask, ‘And who were those people that construct those moulds,’ I say, ‘Well, we just commenced our studies here. We don't know.’ if I were working in Switzerland or in Germany and after excavating two sites, I would dare to say, ‘It's like that, it's like that,’ they would get me out of the country. So, we need to be patient and wait for further excavations in those sites to be able to explain some of what we are seeing right now. The big thing is that we can say there is new civilisation, new culture waiting for us to study them. For me, with work over this last 20-25 years in that region, it's sort of really coming true.

Host: Noah Baker

That was Heiko Prümers from the German Archaeological Institute. You can read that paper over at nature.com or follow the link in the show notes.

Host: Benjamin Thompson

Finally on the show, it's time for the Briefing chat, where we discuss some of the articles that have been featured in the Nature Briefing. Noah, what have you got for us this week?

Host: Noah Baker

So, I have a story that was written by reporter Sara Reardon and it's in Nature, and it's all about kidney transplantation but specifically pig kidney transplantation, not into other pigs, into people.

Host: Benjamin Thompson

Well, that was my first question, is it animal to animal, but, no, animal to human, right, and there's been a lot of that in the press recently.

Host: Noah Baker

Yeah, so xenotransplantation – transplanting organs from one species into another species –is one of these kinds of like sci-fi ideas become reality. And you're right, over the last year or so in particular, there's been a lot of attention on xenotransplantation, largely inspired by the first xenotransplantation of a heart, a pig heart, into a human, which happened in January this year. Sadly, the patient there died after two months, but it was still a huge step. And in this case, there's a story that kind of rounds up a load of recent studies that have been done with pig kidneys. So, these are genetically modified kidneys that are being transplanted, in these cases, into people that have recently died, not living patients.

Host: Benjamin Thompson

And that seems like quite a significant difference.

Host: Noah Baker

Yeah, absolutely. So, this technique to use people that have recently died as a way to kind of test the xenotransplantation process is not new. It's been suggested before. It's been done before. And the kind of concept here is it's the closest we can get without potentially doing harm to a human study. So, lots of studies have been done with genetically modified kidneys and other organs in nonhuman primates with great success. For example, there was a baboon that lived for two years with genetically modified pig heart. But many scientists point out that baboons, for example, have very different metabolism. They have different immune systems. There are regimes of immunosuppressant drugs that are used in people that don't work in baboons. And so, it's really hard to get a clear sense of how this xenotransplantation might work in a human unless you use a human subject. But ethically, that can be complicated. And so, the first step you can do is use someone who has been declared legally dead because they are brain dead, however, there are other systems are still functioning or can be kept functioning. And so, there is a kind of a window there, where ethics boards can allow scientists, with permission of the subject and with their family’s permission of course, to see whether or not a kidney, for example, in these cases, can function in a human system.

Host: Benjamin Thompson

And you say this article is a bit of a roundup of what's been done then and so, what has been done and how have the experiments been progressing?

Host: Noah Baker

Yeah, so the latest study, which was published in the New England Journal of Medicine, which is kind of the lead for this story, I suppose, used a kidney from a genetically modified pig. Now, this pig has been modified to have a more human-like immune system. Specifically in this case, a gene, which has a very long complicated name, but I'm just going to call alpha gal, has been switched off, and that's in order to try to prevent the rejection by the human immune system of this organ. And this organ, along with a pig thymus, has been transplanted to a subject who has recently died in the previous day or two. It wasn't transplanted to where the kidneys would be. The subject still had two kidneys of their own. It was actually transplanted onto their leg and joined up to the artery and vein systems there as a kind of a third kidney, I suppose, and then monitored for just over two days to see whether or not it's functioning and to see whether or not it's going to be rejected.

Host: Benjamin Thompson

And what happened then? What did the researchers find?

Host: Noah Baker

Yeah, well, and that's very much the headline. I suppose the story is that this kidney was not rejected in the relatively short amount of time that it was grafted onto this leg. And what they were monitoring was the volume of urine produced and the concentration of something called creatinine, which is a toxin that the kidneys can filter out. And they did see an increase in the urine production and they saw a decrease in creatinine, which they say suggests that the kidney was working, was functioning and was not being rejected. Now, there are other researchers that are more sceptical about this finding, pointing to the fact that there were two other kidneys that could have been doing this, and it's very difficult to work out exactly which kidney is causing which outcome. But, still, it's a step in a direction, which is quite encouraging for people that are trying to get xenotransplantation off the ground.

Host: Benjamin Thompson

Yeah, and I guess one of the reasons that people have been looking at this for so long is there is a distinct lack of organs to transplant, so this is potentially a way to increase that pool. But I'm guessing there are still many, many questions to be asked and answered about this before it gets ready for use in a clinical setting.

Host: Noah Baker

Absolutely, the idea of being able to xenotransplant organs could be really huge. There are a lot of people that are waiting for organs, and part of the reason that this research has progressed so quickly in recent years is because of innovations like CRISPR-Cas9, which is allowing more specific editing of genomes to try to create these organs with more human-like immune systems. But there are, as you say, lots and lots of questions to answer. Some of the scientists that are quoted in this story are questioning how much more use we can get out of these studies using people that have recently died. It's known that many of the problems with rejection of organs happen a few weeks or months down the line, not immediately, and so it may well be that we can't learn very much about whether an organ is likely to be rejected by a study that can only last for two days. As it stands, ethically, it's difficult to keep people who have recently died in this study condition for much longer than that. In fact, as it stands, their bodies need to be given to their families. And there are scientists that are arguing that the kidney is the perfect organ to start doing more in-depth human trials because kidneys, if something were to go wrong, they can be removed, and the person can be put on dialysis. It's not quite the same as a heart, where you can't really live without a heart for any long period of time. And so, that is what many researchers are calling for. There's still just an awful lot of questions about when we'll get to that stage and exactly what that will look like from an ethical perspective and a scientific perspective.

Host: Benjamin Thompson

Well, Noah, it's a story that I'm sure we're going to cover again on the Nature Podcast. As you say, there's lots of developments in this field. But let's move on to my story this week, and it's a story based on a paper in Communications Biology and I read about it on the BBC News website. And it's all about a team of scientists who have been growing plants in some very, very rare soil.

Host: Noah Baker

Rare soil. Is this soil made of diamonds?

Host: Benjamin Thompson

No, it's a great guess. But actually, this soil comes from the Moon, and it was collected during the Apollo 11, 12 and 17 missions in the late 60s and early 70s. And one of the questions that maybe hasn't been answered about this soil is whether plants could grow in it, right? So, this is what this team have been doing.

Host: Noah Baker

Naturally, I was joking when I said soil made of diamonds, but actually, I think you have found even more rare soil than that. There must be a very small amount of that exists on Earth. My first thought is, it's maybe not that surprising that that question hasn't been answered. This super rare sample of soil, are they really going to use it to grow a carrot?

Host: Benjamin Thompson

Yeah, I mean, you're right in terms of its rarity, Noah, and these scientists spent 11 years trying to get a sample of this soil from NASA because not much has come back from the Moon. Only America, the Soviet Union and recently China have brought back samples of lunar soil. And so, the team spent a lot of time prepping for how they would do these experiments if and when they got hold of some. And in the end, they were loaned 12 grams of it, which is only a couple of teaspoons full, and what they tried to do then was use this soil to grow arabidopsis, which is a little plant that's a model organism and used in all sorts of genetics and molecular biology research. And so, they grew some single arabidopsis seeds, each in one gram of this soil, and compared them to seeds grown in volcanic ash, which has kind of got a similar particle size and sort of similar mineral content.

Host: Noah Baker

Okay, so a pretty simple experiment, albeit with incredibly unsimple components. What is it that they were trying to achieve here? I mean, I'm guessing this has something to do with can we grow plants on the Moon/other planets/other moons?

Host: Benjamin Thompson

Yeah, I mean, I think, as you say, there's of course a lot of interest in the Moon at the moment. Different countries are launching missions there, and I guess long-term I think NASA are looking to set up a base on the Moon, so answering questions about could we grow crops there, I guess, is a fairly important one. Now, I will say that plants have been grown on the Moon. In 2019, China's Chang'e 4 mission grew some plants, but in soil from Earth. This is kind of the flip round of that.

Host: Noah Baker

Okay, so put me out of my misery. Did it grow?

Host: Benjamin Thompson

Well, the scientists are quoted as being astonished to see that the seeds in the lunar soil sprouted within two days, right. And the plants in the Moon soil and the plants in the ash looked the same until about day six, after which they did not. I'm afraid to say the lunar soil plants started to show signs of stress, they developed more slowly, and they ended up, in many cases, quite a lot more stunted.

Host: Noah Baker

I have to say that, somehow, I'm not surprised that the plants didn't grow on the lunar soil. But I do wonder whether or not there is any hope for growing plants on lunar soil. I mean, what did they learn about the soil itself? Is there any part of the soil that's better than the others? Anything like that?

Host: Benjamin Thompson

Well, what's kind of neat is that the Apollo 11 samples were taken from the surface, where they got battered by solar winds and what have you, whereas the Apollo 12 and 17 samples were taken from deeper layers, and those plants appeared to be less stressed, so they had less stress genes activated within these plants. So, it shows that not all lunar soil is created equal and that, I guess, feeds into our discussion about how plants might be grown in the future, should we end up on the Moon for a long period of time.

Host: Noah Baker

Okay, well, I will hold out hope then that in the future we might get lunate asparagus, but for now, let's call it for another Briefing chat. If you'd like to read more about these stories, we'll put links to them in the show notes and a link to where you can sign up for the Briefing to have even more stories from the wide world of science delivered directly to your inbox.

Host: Benjamin Thompson

And that's all we've got time for this week. But don't forget, you can always reach out to us on Twitter – we're @NaturePodcast. Or you can send us an email to podcast@nature.com. I'm Benjamin Thompson.

Host: Noah Baker

And I’m Noah Baker. See you next time.