Podcast: Callused feet, and protein-based archaeology

Host: Shamini Bundell

Welcome back to the Nature Podcast. This week, we’ll be learning about ancient proteins…

Host: Benjamin Thompson

And hearing about the feelings in your feet. I’m Benjamin Thompson.

Host: Shamini Bundell

And I’m Shamini Bundell.

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Host: Benjamin Thompson

First up, reporter Nick Howe has been looking into how being shoeless may affect our soles.

Interviewer: Nick Howe

Many years ago, on a podcast – the name of which I’ve long forgotten – I heard that wearing shoes may be bad for you, which, at the time, made a kind of sense to me. After all, humans haven’t really been wearing shoes for that long.

Interviewee: Kris D’Août

Humans and their direct ancestors have been walking on two feet for about 6, maybe 7 million years. Anatomically modern humans, they have been around for maybe 100,000 to 200,000 years, so in the grand scheme of things, we have developed into who we are today without shoes at all. It’s only much later that we decided, for whatever reason, we wanted to wear shoes.

Interviewer: Nick Howe

That was as Kris D’Août, a researcher who studies the evolution of how humans move. In fact, according to the archaeological evidence, humans may have only been wearing shoes for about 40,000 years, and even then, these were simple foot wrappings, not the cushioned shoes we’re so used to today. So, if these ancient humans could go without shoes, why couldn’t I? Being the science-interested and suggestible person that I am, I decided to do an experiment with a sample size of one – myself – and shunned my shoes. After several months, I had discovered a couple of things: one is that no shoes, no service is definitely still a thing and two, that not wearing shoes gets easier with time. At first, I spent more time hopping in pain than walking, but eventually I could easily stride across all manner of materials without discomfort. From being a sensitive sole, I’d become quite thick-skinned. I developed heavy calluses which protected my feet from the prevalent pavement perils. This is also something that Dan Lieberman, who studies the evolution of human activity, noticed after his own adventures being shoeless after publishing a paper on barefoot running.

Interviewee: Dan Lieberman

As sort of part of studying that paper, I got interested in trying out being barefoot myself, and what happened is that every spring, I would take off my shoes and start running barefoot and my calluses would develop and I noticed that as I ran, the calluses protected my feet but I kind of felt that I wasn’t losing sensory perception, the way you would with a shoe.

Interviewer: Nick Howe

Dan went about trying to test his theory – do thick calluses stop feet feeling things beneath them? This week in Nature, he publishes his answer to this question. Firstly, Dan set about trying to determine if people’s calluses do indeed get thicker when they don’t wear shoes. To do this, he studied the feet of a population of people in Kenya, some of whom never wear shoes, some that wear them infrequently and some that wear them all the time. By using an ultrasound device, Dan could image the inside of a foot. These images allowed him to see the size of people’s calluses. Perhaps unsurprisingly, by doing this he was able to show that people who are usually barefoot tend to have thicker calluses.

Interviewee: Dan Lieberman

Nobody had actually tested that before, so that’s nice to know.

Interviewer: Nick Howe

Once he had shown that this was the case, the next question was, do these thicker calluses mean that people feel less through their soles? To test this, he and his colleagues used a vibrating probe, that could be placed on the soles of people’s feet. By changing how fast the probe vibrated and seeing when people could feel it, he could measure the sensitivity of nerves on their feet called mechanoreceptors.

Interviewee: Dan Lieberman

No matter how thick your calluses were, there was no loss of sensory perception, so that people with thick calluses more or less had the same sensory perceptions as people who had thin calluses.

Interviewer: Nick Howe

Calluses then can give feet protection without compromising on their perception. But how does this work? Logically it might seem that having a thick callus would block the nerve receptors in the sole of the foot. Kris D’Août, who you heard from earlier, has written a News and Views article on this new research. He explains that the reason this isn’t the case is likely down to the structure of the calluses themselves.

Interviewee: Kris D’Août

They are like a very hard layer, what would be like a very rigid, thin foot sole, if you will, and their assumption is that because the foot sole is so hard, it just transmits the stimuli through the calluses into the deeper layers of the skin where these mechanoreceptors are located.

Interviewer: Nick Howe

Such solid soles will transmit the forces from the ground directly – they won’t cushion the forces like a shoe. Whilst it may sound unintuitive, Kris wasn’t too surprised by these findings.

Interviewee: Kris D’Août

So, as an evolutionary biologist, I would say that the evolutionary pressure from having a system that combines both functions – protection and sensation – the pressure will be so high that evolution would come up with a fairly good solution, which it has.

Interviewer: Nick Howe

Wearing shoes is a pretty new thing for humans, who have evolved with all the sensory information of bare feet. Shoes blocking some of this data could have costs.

Interviewee: Kris D’Août

So, if we don’t feel what happens during impact or we feel it less, then our body, our neural system, it doesn’t have the same amount of information to work with and it will find it harder to adjust gait, to adjust how we unroll our foot exactly to what’s required given the impact we have. I would compare it a little bit like wearing sunglasses when it’s already dark.

Interviewer: Nick Howe

So, if humans have evolved a system to protect their feet while providing the maximum amount of information on what they’re walking on, what is the impact of wearing shoes? To find out, Dan looked at how energy is transmitted through the feet when they collide with the ground during a step. He was able to show that these forces change when people wear shoes compared to when they’re barefoot. It’s not clear what the consequences of these differences are on other parts of the body, but Dan believes even subtle changes across many years could have effects.

Interviewee: Dan Lieberman

If you think about how many steps a person takes a day, multiply that by 365 days a year and then multiple that by how many years you’re walking around, that’s millions and millions and millions of these collisions, and those collisions today are fundamentally different in terms of the energy that our bodies are experiencing than the collisions that we evolved to cope with.

Interviewer: Nick Howe

For me, not wearing shoes was a bittersweet endeavour. There was something awfully freeing about being barefoot and walking became a whole new experience. On the other hand, many people were perturbed by my shoeless strolls, including my poor mother. In the end, the world wasn’t quite ready, and Kris thinks it’s not quite time to throw out our shoes just yet.

Interviewee: Kris D’Août

Calluses are quite amazing evolutionary solutions to a problem and we can be inspired by these calluses in footwear design because what’s not to like about it? We have good sensation. If we can keep that whilst protecting our feet, that would be ideal, and I think we can make shoes that do that, maybe as good as natural calluses, maybe even better.

Host: Benjamin Thompson

That was Kris D’Août from the University of Liverpool in the UK. You also heard from Dan Lieberman from Harvard University in the US. You can read Dan’s paper over at nature.com along with Kris’ News and Views article.

Host: Shamini Bundell

Later in the show, we’ll be hearing a special report about the ongoing Ebola outbreak in the Democratic Republic of the Congo – that’s coming up in the News Chat. Now though, it’s time for the Research Highlights, read this week by Anna Nagle.

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Anna Nagle

New measurements of magma’s movements may mean that methods of modelling eruptions need a bit of a rethink. The time it takes for magma to rise from deep within the Earth to erupt as lava on the surface isn’t well understood. To get a better idea, a team of researchers from the UK studied some lava flows that erupted from a now dormant Icelandic volcano around 10,000 years ago. By looking at the chemistry of crystals within the lava, the researchers estimated that the magma moved to the surface from 24 kilometres below in just 10 days, making it the most rapid rise for this type of magma yet recorded. As the magma rose so quickly, there wasn’t time for it to lose much of the carbon dioxide trapped within it. This suggests that measuring CO₂ emissions – a common strategy for monitoring active volcanoes – might only provide a day’s warning for certain types of eruption. Head over to Nature Geosciences to read more.

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Anna Nagle

You’ve likely heard of 3D printing, but what about 4D printing? This technology adds a whole new dimension to otherwise static objects, allowing them to transform in response to a stimulus. While many 4D materials are only able to perform a single transformation – perhaps folding up in response to an electrical current – researchers from China and the UK have developed a new printing method that can produces multi-transforming materials that can change both shape and colour simultaneously. The team achieved this by mixing a shape-changing polymer with heat-responsive pigments, which they used to print a blooming flower that changed from orange to yellow, and a miniature octopus with arms that shifted hue and stretched out at different rates when warmed up. The researchers say that these are just a proof-of-concept examples, but suggest that the technology could be used in camouflage and soft robotics. Shift over to Advanced Materials Technologies to read more.

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Host: Shamini Bundell

In recent decades, archaeology has been transformed by the study of ancient DNA, which has been recovered from skeletons that are hundreds of thousands of years old. Now, researchers are also turning to ancient proteins which could survive for even longer. Anand Jagatia takes up the story.

Interviewer: Anand Jagatia

Around 9,000 years ago in modern-day Turkey, a population of early humans began to settle down from their hunter-gatherer lifestyle, laying down roots and taking up farming. They built one of the most well-preserved early urban settlements, known as Çatalhöyük.

Interviewee: Jessica Hendy

We have houses, mud-brick houses, which are all joined together, and the way that people enter their house is not through the front door but it’s actually from descending from above, from ladders that go into the houses from above and it seems like maybe people were walking on top of the houses, so it has this really unusual architectural feature.

Interviewer: Anand Jagatia

This is Jessica Hendy, an archaeological scientist from the University of York. But Jessica wasn’t at Çatalhöyük to study its architecture.

Interviewee: Jessica Hendy

My interest really is in the study of ancient proteins for understanding diet in the past and the kinds of foods that people have eaten through time.

Interviewer: Anand Jagatia

The study of ancient proteins, known as ancient proteomics, has many applications for understanding the past, including prehistoric cuisine. At Çatalhöyük, Jessica was looking for proteins on some 8,000-year-old fragments of pottery.

Interviewee: Jessica Hendy

And they basically had this white residue on the inside and we performed an experiment using protein analysis to try and understand what these residues might be and what they might contain, and what we found was incredible protein preservation. We found evidence of dairy products, we found evidence of plants, so we found peas, and also, we were able to see what kind of tissues were being used in terms of the food. So, we could see, for example, that when we were identifying wheat and barley, we could see that we were identifying proteins that were actually from the grain of the wheat and the barley. So, we can get kind of a much richer understanding of not only what species are being used but what kind of part of that plant or animal is being used.

Interviewer: Anand Jagatia

Just like the study of ancient DNA which came before it, ancient proteomics could revolutionise archaeology. In some ways, proteins are less informative than DNA because while a genetic sequence is unique down to the individual, protein sequences maybe almost identical across many different species. But the major advantage of proteins is that they can survive in the fossil record for much longer.

Interviewee: Matthew Collins

At the moment, our guess is that for anywhere that you can find ancient DNA, you can probably find ancient proteins about ten times further back in time.

Interviewer: Anand Jagatia

This is Matthew Collins, professor of proteomics at the University of Cambridge and at the University of Copenhagen. Matthew worked on the development of a technique called ZooMS, or zooarchaeology by mass spectrometry, which is now used by researchers around the world.

Interviewee: Matthew Collins

We call it ZooMS because it’s quick, and it’s a very simple fingerprinting approach, and if you have a pure protein, what you can then do is digest that protein and the constituent fragments which carry different masses will have a characteristic fingerprint.

Interviewer: Anand Jagatia

ZooMS can be used on unidentified bone fragments to work out which species they came from by fingerprinting a bone protein called collagen. Earlier this year, ZooMS was used by a team to study a piece of ancient human jawbone in a cave on the Tibetan Plateau, dating to 160,000 years ago. They weren’t able to recover any DNA but thanks to the proteins they were able to tell that the jaw belonged to a Denisovan. Denisovans are a mysterious group of ancient humans. Until now, all that we’ve found of them is a few bits of bone and teeth from a cave in Siberia. This work represents the first time a Denisovan specimen has been found anywhere else and the first time an ancient hominin has been identified solely using proteins. But bones aren’t the only place you can go hunting for proteomes. You can also find them in enamel where they tend to stick around for even longer, as researchers discovered recently at the Dmanisi site in Georgia.

Interviewee: Matthew Collins

And they were able, using enamel from a rhinoceros, to recover a sufficiently detailed proteome at 1.9 million years. So, in something like a bone where water might flow through the sample, we will not get such good preservation, but in enamel, it’s a very tight, closed system and they were able to recover a sufficiently detailed proteome to place that in a phylogenetic tree. And in addition, one of the nice things about enamel is in some instances, it can discriminate proteins expressed from the X and the Y chromosomes so they could discriminate male and female animals.

Interviewer: Anand Jagatia

That paper is currently uploaded as a preprint on bioRxiv, and so it hasn’t yet been peer reviewed. But the oldest bit of authenticated ancient protein discovered so far is even older, and it was found in an ostrich eggshell.

Interviewee: Beatrice Demarchi

So, ostrich shell is a really, really nice system, a really tight closed system. So, we have proteins that have the function of initiating, promoting and regulating the actual mineralisation of the shell. So, they become trapped in these huge crystals that compose the ostrich eggshell.

Interviewer: Anand Jagatia

This is Beatrice Demarchi from the University of Turin. Her group was trying to see just how far back in time ancient proteins might survive in warm environments where they usually break down much more quickly. They studied ostrich shell at several important archaeological sites, including in South Africa and Tanzania.

Interviewee: Beatrice Demarchi

So, we found something that we couldn’t quite believe. We found that there were bits of proteins surviving up to 3.8 million years ago in a climate that is really, really hot. And so, in the future if people want to find ancient protein sequences, then they’re better off looking at things that contain, for example, calcites, which is a very stable mineral because these things will have a better potential for preserving proteins.

Interviewer: Anand Jagatia

Results like this suggest we might be able to peer much further back in time using proteins than ever before. But that being said, there are some teething problems in the field. For example, contamination of ancient samples with modern proteins is a big concern, and another challenge is trying to reduce the amount of actual precious sample you need in order to do your analysis. But Matthew Collins is confident we can overcome these hurdles, and he has big hopes for the future.

Interviewee: Matthew Collins

Really, for me, the sky is the limit. I mean we know these proteins are surviving. They’re surviving over long periods of time. But more than that, so much of what humans have done is to work with proteins. They could be meat or blood or milk, but also, many of those materials are used to make gums and paints, as well as all of the remains such as bones and teeth and parchment and leather, all of which are made of protein. So, the range of materials that we have used as humans which contain proteins and the technological ability to recover ever smaller samples with greater precision, and to be able to interpret these data in a more sophisticated manner, leads me to be extraordinarily optimistic as to the future of this field.

Host: Shamini Bundell

That was Matthew Collins from the University of Cambridge in the UK and the University of Copenhagen in Denmark. You also heard from Jessica Hendy who’s at the University of York in the UK and Beatrice Demarchi from the University of Turin in Italy. If you want to learn more about ancient proteomics then you can head over to nature.com/news where you can read a Feature all about the field.

Interviewer: Benjamin Thompson

Listeners, we’ve got something a bit different for the News Chat this week. Amy Maxmen, a senior reporter here at Nature, has been in the Democratic Republic of the Congo. She’s reporting on the ongoing Ebola outbreak in the country, with support from the Pulitzer Center on Crisis Reporting. It’s a complex situation as there have been multiple conflicts in the country unrelated to the outbreak. I spoke to Amy at the backend of last week on a slightly wobbly phone line when she’d just returned from Beni, a city in the east of DRC – the region where the outbreak is centred. I started our chat by asking her about the current situation there.

Interviewee: Amy Maxmen

So, as of June 19^th, now we’re entering the tenth month of this outbreak. It’s in North Kivu and Ituri, two provinces in eastern DRC, and there have been just over 2,200 cases of Ebola so far and almost 1,500 deaths.

Interviewer: Benjamin Thompson

So, this is now the second biggest outbreak of Ebola on record, and the WHO Director-General has been in the country to assess the situation.

Interviewee: Amy Maxmen

Yes, right when I arrived, I met the Director-General of the WHO, Tedros Ghebreyesus – he likes to be called Dr Tedros – and when I first met up with him, he was in Kinshasa and he spent the day meeting with big leaders like the Prime Minister of the DRC. He actually met with opposition leaders because it’s important to sort of make this a bipartisan effort. He met with the Minister of Health. He was also warning them that later that day he was going to meet with an emergency committee of experts on a conference call, so he wanted to warn all of these different leaders that they might be declaring what’s called a Public Health Emergency of International Concern. So, after that morning of meetings, he then went into a conference room for a couple of hours to speak with this emergency committee. Now, I didn’t get to sit inside that – that was confidential – but I thought maybe they would declare this an outbreak because there had been a couple of confirmed cases in Uganda. It’s important to know that as far as anyone had seen, there was no spreading of the virus to Uganda. What had happened, was a mother from Uganda had gone to a funeral for someone who had died of Ebola in DRC and then returned with her baby to Uganda and that’s where they noticed the case.

Interviewer: Benjamin Thompson

And what did the committee decide?

Interviewee: Amy Maxmen

They decided to not declare it – this Public Health Emergency of International Concern. That made some people, I would say, upset because the World Health Organisation, right now, is lacking funds in order to fight Ebola, and so the thought is that if they made this declaration, finally funders would start pumping money into the response that’s required.

Interviewer: Benjamin Thompson

So, the experts didn’t announce a Public Health Emergency of International Concern – what does this mean then for the current outbreak and the response to it?

Interviewee: Amy Maxmen

No one knows if actually declaring it would in fact amplify funds and on the reverse, what could have happened is people – by that I mean lawmakers – could go against the advice of the World Health Organisation and shut down borders completely. Now, so many supplies coming into the region I was in – North Kivu and Ituri – are near the border of Uganda and all of the supplies going out would be cut off. Plus, right now, there’s a lot of conflict in Ituri especially. I think since June there’s been more than 300,000 people have fled murder, rape, violence, so that could put those people in danger as well, and they might just try and sneak through the forest at night and then we really have no idea how the virus moves. So, that was sort of the fears that I’ve heard from various people about declaring the outbreak. So, what the WHO did do and what also the governments of Uganda and DRC and Rwanda and surrounding places are doing is trying to make sure that they’re checking people’s temperatures, vaccinating people along the border, like health workers, to be as prepared as possible for the spread of the disease, without declaring this an emergency.

Interviewer: Benjamin Thompson

Amy, you’ve been out and about in DRC with healthcare workers and officials. Where have you been and what sort of things have you seen?

Interviewee: Amy Maxmen

I’ve managed to see quite a lot. I went with Dr Tedros from Butembo to Katwa, an area where there has been lots of attacks against the Ebola responders. There’s an Ebola treatment centre that had been shot out by assailants and it was later burnt, so he went to go visit that. Since these attacks, they now have snipers behind a barricade outside, there’s sort of sandbags within it for people to hide behind. These are things I’ve never seen before, and I should emphasise nobody likes that. These are really researchers, health workers – these are not military people. They don’t enjoy travelling with kind of rifles around them, but at the same time they want to guarantee the protection of patients and their own staff, so you can kind of see both sides of it.

Interviewer: Benjamin Thompson

And have your travels given you a sense of why it’s been so difficult to contain this Ebola outbreak?

Interviewee: Amy Maxmen

Well, the shortest answer is it’s the conflict that has been going on there for 25 years. There’s dozens, let’s say, of armed groups and whenever an attack happens, people run and they don’t exactly want to be followed. They’re not going to put their lives at risk to stay sitting in an Ebola treatment centre at the time of a conflict. And when people run, they might carry the virus with them somewhere else. The conflict also makes it really hard for Ebola responders to go and do their job. Already, the Ebola responders I’ve met, they’re far braver than I would ever be just to be there. So, you might train as an epidemiologist, but you really weren’t prepared to be on the other side of people throwing rocks.

Interviewer: Benjamin Thompson

So, you’ve been writing up some dispatches for Nature News about the things that you’ve seen in what is clearly a very serious outbreak that is affecting a lot of people, but in your reporting, have you seen any bright spots at all?

Interviewee: Amy Maxmen

Yeah, so, one thing that I found remarkable was the role of Ebola survivors right now. So, once they get the virus, they’re sort of immune to Ebola – at least based on data from the last outbreak and everything we’ve seen so far. So, I was really moved to see survivors going to see Ebola treatment centres and sitting by the bedside of patients, and this includes children who are isolated who only see their nurses or doctors wearing the whole protective gear, kind of like this astronaut suit. So, they have no one to comfort them and yet survivors are sitting by their bedside, telling them listen, like I lived, you can live, and that means a lot. The other thing survivors are doing, there’s not a lot of ambulances for one – there were never ambulances there before. Second, there’s also not roads ambulances can drive on and people are used to travelling by motorcycle taxis. So, survivors are in some cases going out on their motorbikes and offering to take people who have symptoms of Ebola to the treatment centres. Whereas a normal motorcycle taxi driver would be at risk, they’re sort of like these powerful agents right now.

Interviewer: Benjamin Thompson

That was reporter Amy Maxmen. You can read her dispatches from DRC over at nature.com/news.

Host: Shamini Bundell

That’s it for this week’s show. If you’d like to get in touch with us, you can do so on Twitter where we’re @NaturePodcast, or you can reach us on email at podcast@nature.com and say hello. I’m Shamini Bundell.

Interviewer: Benjamin Thompson

And I’m Benjamin Thompson. See you next time.