NATURE PODCAST

The quark of the matter: what’s really inside a proton?

The surprising structure of protons, and a method for growing small intestines for transplantation.

Listen to the latest from the world of science, with Nick Petrić Howe and Shamini Bundell.

In this episode:

00:45 Probing the proton’s interior

Although studied for decades, the internal structure of the proton is still throwing up surprises for physicists. This week, a team of researchers report an unexpected imbalance in the antimatter particles that make up the proton.

Research Article: Dove et al.

News and Views: Antimatter in the proton is more down than up

07:08 Research Highlights

How an inactive gene may help keep off the chill, and Cuba’s isolation may have prevented invasive species taking root on the island.

Research Highlight: Impervious to cold? A gene helps people to ward off the chills

Research Highlight: Marauding plants steer clear of a communist-ruled island

09:48 A new way to grow a small intestine

Short Bowel Syndrome is an often fatal condition that results from the removal of the small intestine. Treatment options are limited to transplantation, but donor intestines are hard to come by and can be rejected by the body. Now researchers may have developed a method to grow a replacement small intestine using stem cells and a small section of colon.

Research Article: Sugimoto et al.

15:50 Briefing Chat

We discuss some highlights from the Nature Briefing. This time, the landing of Perseverance on Mars, and the researchers speaking with lucid dreamers.

Nature News: Mars video reveals Perseverance rover’s daring touchdown

Nature News: Touch down! NASA’s Mars landing sparks new era of exploration

Nature News: The hunt for life on Mars: A visual guide to NASA’s latest mission

Science: Scientists entered people’s dreams and got them ‘talking’

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Transcript

Listen to the latest from the world of science, with Nick Petrić Howe and Shamini Bundell.

Host: Shamini Bundell

Welcome back to the Nature Podcast. This week, the surprising interior of a proton…

Host: Nick Petrić Howe

And how to grow a new small intestine. I’m Nick Petrić Howe.

Host: Shamini Bundell

And I’m Shamini Bundell.

[Jingle]

Host: Shamini Bundell

First up, reporter Adam Levy has been peering inside the proton and finding out that this particle is full of surprises.

Interviewer: Adam Levy

When you think of the fronters of physics, you might think of high-energy particle colliders probing the limits of our understanding and creating iconic particles like the Higgs boson. You probably don’t think of the trusty old proton and why should you? Most school kids already know all about this particle – that it’s positively charged and sits in the nucleus of atoms, making up much of their mass. Boring. Except protons are anything but boring. The closer you look, the more complex these particles appear. Here’s physicist Haiyan Gao.

Interviewee: Haiyan Gao

So, they’re not really a point-like particle, like an electron for example. It has a very, very rich internal structure.

Interviewer: Adam Levy

You may have heard that protons are made up of three smaller elementary particles called quarks, two ups and one down quark to be precise, but that’s only the tip of the particle iceberg, as proton researcher Paul Reimer explains.

Interviewee: Paul Reimer

And then something has to hold them altogether and being very original, physicists thought that something had to glue them together, so we call that the gluons.

Interviewer: Adam Levy

Aside from gluing the proton together, gluons can create ephemeral quark-antiquark pairs, for example an up quark and an anti-up quark. Okay, so let’s take stock. The proton is much more complicated than first meets the eye. We’ve got the main three quarks, but swimming within the protons we’ve also got gluons holding everything together and these quark-antiquark pairs springing in and out of existence. Now, a gluon is just as happy making an up quark and an anti-up quark as it is making a down and anti-down quark. They’re not fussy. Plus, up and down quarks, or u and d quarks for short, have very similar masses. This means…

Interviewee: Haiyan Gao

You should not really expect any difference between the amount of anti-u quarks I should expect to see compared with anti-d quarks, right?

Interviewer: Adam Levy

Well, physics has a way of confounding expectations, and there was already some evidence of a difference between the numbers of anti-quarks in the proton. So, Paul and his team set out to carefully investigate the numbers of anti-up quarks compared to the number of anti-down quarks. They do this using physicists’ favourite technique – smashing things together. More specifically, they smash protons into other protons. This can give off shrapnel with a clear signature when a quark and its anti-quark counterpart annihilate. The trick is then to repeat this experiment by smashing protons into neutrons, since a neutron is, in some sense, a mirror image of the proton.

Interviewee: Paul Reimer

So, if you do this measurement on neutrons and protons and compare the two, you then get a ratio of the number of anti-down quarks to the number of anti-up quarks in the proton.

Interviewer: Adam Levy

So, that’s exactly what Paul and his collaborators did. Previous experiments had shown that for some conditions, the proton preferred anti-down quarks, but that perhaps this preference switched for other conditions. But this new experiment, which is published this week, paints a much more conclusive story.

Interviewee: Paul Reimer

Nature seems to always prefer within the proton to make more anti-down quarks than anti-up quarks, and this is a really weird observation because there’s nothing that we know of that should distinguish in nature between it making more anti-up quarks or more anti-down quarks.

Interviewer: Adam Levy

Haiyan, who didn’t work on this study, is intrigued to learn about this clear-cut proton preference for anti-down quarks.

Interviewee: Haiyan Gao

So, the result is actually very significant and also of course very interesting, and it will be extremely exciting or important to understand the origin for this particular behaviour this paper has reported.

Interviewer: Adam Levy

Because at the moment, the cause of this imbalance remains unclear. One avenue is through another property of the proton – the spin. And Haiyan also hopes that starting from the fundamental physical laws and comparing the results with experiments could reveal new insights.

Interviewee: Haiyan Gao

We would like to see theoretical predictions from computer simulations based on the first principles. People are working on that but at this moment have not been able to reach the kind of precision that can be compared with the experiment.

Interviewer: Adam Levy

So, it’ll take some time before physicists can lay this mystery to rest and clarify the complex inner life of the proton. Doing so could expand our understanding of the law of physics that governs quarks and gluons – the strong nuclear force. But in the meantime, one thing is for sure. For physicists like Haiyan and Paul, the proton is well worth a closer look.

Interviewee: Haiyan Gao

Protons and neutrons, they just continue to amaze physicists. I’m just speechless when I think about all the exciting things going on in the protons. I’m always kind of saying, ‘Can I actually somehow get a ride inside a proton just to see what’s going on?’ I mean it’s just fascinating.

Interviewee: Paul Reimer

So, this type of exploration is something I’ve wanted to do all my life, since I was a little kid. And it’s really exciting and sort of mind-boggling that it is my job to look inside the proton and say, ‘Hey, what’s going on.’ Yeah, I love it.

Host: Shamini Bundell

That was Paul Reimer from Argonne National Laboratory in the US. You also heard from Haiyan Gao from Duke University, also in the US. To read more about the bizarre internal makeup of protons, be sure to check out the show notes where there’ll be a link to Paul’s paper and a News and Views article written by Haiyan.

Host: Nick Petrić Howe

Coming up, we’ll be hearing about a potential new method to treat a debilitating condition known as short bowel syndrome. Now, though, Dan Fox is here with this week’s Research Highlights.

[Jingle]

Dan Fox

As the first shoots of spring start to appear here in the UK, it seems winter may not have been quite as chilly for some people as for others, especially if they have a genetic variation that appears to make them more tolerant to the cold. 1.5 billion people globally have two non-functional versions of the gene ACTN3. This non-functional gene is more common in colder climates like in central and northern Europe than in Africa. To find out why, researchers recruited a group of volunteers with and without the functional gene and then immersed these participants in cold water. The scientists found that more of the volunteers with the non-functioning gene could maintain a higher body temperature than those with the functional variant. They also noted that those lacking functional ACTN3 seemed to stay warm not by shivering but by tensing their muscles, an energy efficient way to preserve heat. This mechanism could explain why the non-functional gene became more abundant as human migrated to colder climates. Chill out with that paper in the American Journal of Human Genetics.

[Jingle]

Dan Fox

For more than 60 years, the rocky relationship between the United States and Cuba has helped to steer tourists and businesses away from the Caribbean island. Now, researchers have found that Cuba’s economic and political isolation might also have limited the spread of invasive plants. Researchers used lists of non-native plants to estimate the number of invasive species on 45 Caribbean islands and found that larger islands tend to have more exotic species than smaller ones. But Cuba, the biggest island in the Caribbean, is home to hundreds fewer such species than expected for its size. The team found that mass tourism seems to favour the introduction of invasive plants, probably because hotels plant exotic ornamental species and tourists carry seeds in their bags or on their shoes. Cuba, with one of the region’s lowest share of holidaymakers, has about the same number of invasive species as Puerto Rico, which is one tenth the size but has many more visitors for its land area. Read that research in full at Frontiers in Ecology and the Environment.

[Jingle]

Interviewer: Nick Petrić Howe

Next up on the show, I’ve been finding out about how regenerative medicine may be able to help treat a debilitating and often fatal bowel condition. Short bowel syndrome is a condition that occurs when most of the small intestine has been removed from a person. Typically, this is to treat diseases such as Crohn’s disease, where the intestine has become damaged or blocked. Without a large part of the small intestine, people are unable to absorb enough nutrients and must be fed intravenously. The only real treatment for this condition is a transplant, but this has its own problems.

Interviewee: Toshiro Sato

There remains several issues, such as donor shortage and immune rejection. Immune rejection frequently occurs after small intestine transplantation.

Interviewer: Nick Petrić Howe

This is Toshiro Sato. This week in Nature, he’s publishing a paper about an alternative method to treat short bowel syndrome that could get around problems like donor shortage and transplant rejection. The new alternative uses stem cells to create small, lab-grown intestinal organoids.

Interviewee: Toshiro Sato

Organoids are three-dimensional structures derived from stem cells. There are a variety of organoids that derived from embryonic stem cells and tissue stem cells and mimic the brain, kidney, liver and etc. In our case, we are isolating epithelium tissue from mice, rats and even humans and grow them in a culture dish as organoids.

Interviewer: Nick Petrić Howe

These organoids have been used in a lot of research but, so far, never as a treatment in humans. One of the challenges is that you can use the organoid to grow tissue resembling the small intestine, but it doesn’t have all the complicated structures and systems of a fully-fledged organ. So, how can you go from an organoid to a whole organ, from a lump of cells to absorbing nutrients in the gut. Well, Toshiro looked to the colon. Now, the colon is part of the large intestine, and it has some differences from the small intestine. For example, it lacks villi, small, finger-like structures that can help absorb nutrients in the small intestine. But crucially for Toshiro, the colon does have some key similarities to the small intestine. They’re both tube structures in the gut. So, Toshiro wondered if he could use the colon almost like a scaffold to put the small intestine organoids on so they would grow more like a fully-fledged organ. He tried this out in mice by first removing the outer surface of the colon and replacing it with the organoid tissue and then observing whether this colon-small intestine hybrid grew structures specific to the small intestine like the villi.

Interviewee: Toshiro Sato

Interestingly, after the transplantation of human ileum organoids, the mouse colon started to build up intestinal villi. This is gave us the idea that we can transform a colon into small intestine using organoid transplantation. We called the transformed colon a small ‘intestinalized’ colon.

Interviewer: Nick Petrić Howe

Creating these small intestinalized colons does actually replace part of the colon, but it’s possible to live a long and healthy life with only some of it. Compare that to short bowel syndrome and it seems like an easy trade off. The next step was for Toshiro to see if these transformed colons could actually treat short bowel syndrome. Could they replace the small intestine itself? So, he developed a rat model for short bowel syndrome and transplanted the small intestinalized colons into some of the rats but not into others.

Interviewee: Toshiro Sato

Without transplantation, all rats lost weight and died within 10 days. Whereas rats with transplantation survived longer.

Interviewer: Nick Petrić Howe

To confirm that this greater survival was down to the small intestinalized colons, Toshiro repeated this experiment with two different types of colon. One with the small intestinalized colons that we’ve been talking about, and the other were colons that had undergone a similar process but this time using colon organoids. Again, it seemed like the small intestinalized colons treated the short bowel syndrome and the rats survived longer. There’s still a fair amount to be done to perfect this technique, however Toshiro was encouraged by how similar these small intestinalized colons were to the real small intestine.

Interviewee: Toshiro Sato

In fact, one of the most surprising findings was that the colon developed not only intestinal villi but also small lymph ducts inside the villi – a hallmark of the small intestine.

Interviewer: Nick Petrić Howe

Other than lymph ducts and villi, the small intestinalized colons also seemed to actually work like a regular small intestine. They even contracted to digest food, and that is something that could only happen if the nervous system was operating similarly to a real small intestine. Whilst there’s still a lot of work to be done, this is a great proof of principle that organoids could be used as treatments for disease, and that’s where Toshiro is headed next. He’s trying to work out how to make such a treatment a reality in humans to regenerate organs as therapy for short bowel syndrome.

Interviewee: Toshiro Sato

The surgical procedure itself, it’s feasible in humans. To take a step further, we need to prove that feasibility of the entire system using a larger animal model such as pigs. When the safety is proven, it will also open up the possibility of organ regeneration therapy for patients with short bowel syndrome.

Interviewer: Nick Petrić Howe

That was Toshiro Sato of Keio University School of Medicine in Tokyo, Japan. To find out more about organoid transplantation, be sure to check out the show notes where there’ll be a link to his paper.

Host: Shamini Bundell

Finally on the show, it’s time for the weekly Briefing chat, where we discuss a couple of articles that have been highlighted in the Nature Briefing. Nick, what have you found in the Briefing this week?

Host: Nick Petrić Howe

Well, Shamini, I’ve been looking at a story that’s been 3.9 billion years in the making, and that is the landing of Perseverance on Mars.

Host: Shamini Bundell

Okay, I knew that it had taken a while and quite a lot of planning. Is the planet Mars 3.9 billion years old? I’m not sure about this claim.

Host: Nick Petrić Howe

So, I’m being a little bit flippant here but basically, the crater that the lander landed in was created 3.9 billion years ago when a meteor collided with Mars and made this gigantic crater known as the Jezero Crater, and that’s where Perseverance has landed and is going to carry out its operations now it’s reached Mars.

Host: Shamini Bundell

Well, yeah, very exciting. Is this the first of the Mars trips to have arrived because I remember when they all set off last year in the launch window. Three missions were heading there so is this the first?

Host: Nick Petrić Howe

This is the first one to land on Mars. So, China are sending a lander sometime later this year, but the UAE, the United Arab Emirates, and China have orbiters now orbiting the planet. But this is NASA’s mission which is a rover that’s going to be going around Mars and looking for signs of life.

Host: Shamini Bundell

And did they, you mentioned this crater, did they specifically land in this ancient crater because it is flat, because it is fascinating, or is that just happened to be where it ended up?

Host: Nick Petrić Howe

No, surprisingly, they do tend to plan these things quite carefully, so they picked this crater out specifically because it looks like it used to be a river bed on Mars, so if there’s going to be signs of life anywhere, it’s likely to be where there was once water. And so, what Perseverance, or Percy as some of the engineers have been calling it, is going to be doing is it’s going to be going around here and collecting rocks that may have signs of life, maybe microbial life, that existed on Mars, if it did, billions of years ago. But this mission is particularly interesting because what Perseverance is going to do is it’s going to basically make little rock piles that will be collected by later missions and actually brought back to Earth, so this will be the first time that we’ll send some rocks back to Earth for further analysis.

Host: Shamini Bundell

I’m imagining it’s like making these little cairns and sticking these little flags on top as it goes everywhere. That’s wonderful. So, I saw there was some video going around on social media of the surface of Mars, which is actually from a previous mission when using some sort of audio seismological data, so do we have much from Percy yet? Can we see what Percy has seen?

Host: Nick Petrić Howe

So, there have been some videos and some photos that have been floating around, so one that just went up the other day was actually video of the descent, and if you’ve followed any missions from Mars you know that the descent is one of the most tricky and dangerous parts, but you can actually see the whole process go off. You can see the parachute come out and you can see this thing called a sky crane come out as well, which is the thing to sort of stabilise the rover as it landed on the planet. And we’ve got a few images of the surface as well. So far, it looks sort of rocky and barren – to be expected – but I’m sure there will be many more images to come. It’s able to take pictures of the sky. It’s actually got microphones on it as well, so we’ll be able to get some actual sounds from the planet too.

Host: Shamini Bundell

And you said that the little pile of stones, that’s for a later sort of mission, so we’re not going to have data from that yet. What kind of data can it get, can it send back straight away, and do we have any of that?

Host: Nick Petrić Howe

Well, it’s only just landed there, so at the moment, it’s just checking itself out and making sure everything is working properly. Some of the things that it will do, as I said, it’s got microphones so it will gather some sounds from the planet. It will be able to analyse rocks on the planet and that will be how it decides is this maybe a rock where there’s some evidence of life and things like that. But it also has a helicopter onboard, so it’s going to be able to send out the first flying vehicle on another planet to fly around and study the planet’s surface.

Host: Shamini Bundell

That is so cool. It’s pretty hard to beat a story like this, yeah, seeing what the surface of another planet is like. I think I have an also pretty exciting story from the Briefing however. Certainly, the headline jumped out at me when I read it, which is about talking to people who are dreaming.

Host: Nick Petrić Howe

Talking to people who are dreaming? How do you even do that? Surely they’re asleep.

Host: Shamini Bundell

They are very much asleep. That’s key. Right, so how much do you know about lucid dreaming?

Host: Nick Petrić Howe

I think it’s a thing where you can basically just take control of your dream or something like that, but is that a thing that people can actually do?

Host: Shamini Bundell

I’ve never tried either. It is a real thing, and there’s actually quite a lot of people who are quite into lucid dreaming, and there are ways that you can either get better at it or try and allow yourself to lucid dream, so to be conscious while you’re dreaming that you are in a dream and thus potentially able to affect the dream. Obviously, the key thing about being asleep and being dreaming is that everything is in your head. All of the images are created by your brain and you’re sort of shut away from the outside world. But what this experiment does is try and say, okay, if people are lucid dreaming, they are able, to a limited extent, to control elements of their body such as facial muscle movements or eye movements. Can we use that to see if they can actually hear what’s going on in the outside world and potentially respond to it?

Host: Nick Petrić Howe

Well, I guess the obvious question is were they able to respond to sort of stimuli from the outside world?

Host: Shamini Bundell

So, yeah, well they tried it, a few different teams in a few different countries tried different methods. So, they got a whole bunch of people to come and have naps in the lab, daytime naps or just when people were going to sleep or when people sort of woke up in the morning, someone with narcolepsy, people who were already kind of quite good at lucid dreaming, people who they trained in lucid dreaming, and they taught them a few different ways of communicating, so like the eye movements, for example, was one, and then they tried different ways of communicating with them. So, for example, either just sort of whispering at someone or in one case beeping at someone in morse code.

Host: Nick Petrić Howe

Okay, so they’re whispering, beeping, what are they saying to them? How are they trying to communicate with these guys?

Host: Shamini Bundell

My favourite one of what they were doing was giving them maths problems while they were sleeping, and getting them to like facially twitch the answers. So, for example, one of them was like ‘What’s eight minus six,’ and the guy was just like moving his eyeballs from left to right twice to indicate ‘two’.

Host: Nick Petrić Howe

Wow.

Host: Shamini Bundell

And I think the trickiest thing here was that they wanted to show that they weren’t like reading too much into some twitches and that the people were genuinely responding. So, they did sort of a whole bunch of different tests, and for some people It didn’t work at all but for some people it worked on multiple occasions. But out of 158 questions that they asked sort of lucid dreaming people, of which they were also sort of monitoring the REM to prove that they were dreaming at the same time, 18.6% gave the right answer to the question. Most times there was no response. But the wrong answer was only 3% of the time, and then there were a few that weren’t very clear. So, I think it’s relatively convincing that even though it’s quite tricky to communicate with them, it wasn’t just by chance. They were able to integrate this experience from the outside world and actually some of them then when they woke up, some of them couldn’t remember at all and some of them sort of misremembered it, and some of them remembered like the voice coming out of the car radio in the dream or like they were in like a scene and there was this voiceover asking them questions that they recalled.

Host: Nick Petrić Howe

I mean, to me, getting in maths problems while I sleep sounds like a nightmare, but I’m sure this is quite a useful technique. What might researchers be able to do with this ability to communicate with lucid dreamers?

Host: Shamini Bundell

I think the main sort of advantage that showing that this is possible is that for people who study sleep and dreaming and obviously dreaming is a sort of quite weird thing that our brains do, so quite a lot of interest, but trying to study that from me telling you what I dreamt about after I’ve woken up is somewhat limited. Now, to be honest, me twitching my eyes at you to tell you while I’m in it is also limited, but it’s another avenue, it’s another insight into actually being able to study how dreaming works, what are our brain is going on. One of the researchers likened it to like talking to someone on another planet. They’re in a completely different world and we’ve finally been able to send a telephone wire between it.

Host: Nick Petrić Howe

Well, that’s a lovely link to my story as well – communicating with another world – and I think that’s probably all we’ve got time for for the Briefing this week, but thank you so much for talking to me, Shamini. And listeners, if you’d like to know more about Perseverance then there are several articles in Nature. And for more about lucid dreaming, check out the article in Science. There’ll be links to all of that in the show notes.

Host: Shamini Bundell

And if you’re interested in more stories like this but instead as an email then make sure you check out the Nature Briefing. Again, we’ll put links in the show notes where you can sign up.

Host: Nick Petrić Howe

That’s all for this week. As always, if you want to get in touch with us then you can reach us on Twitter. We’re @NaturePodcast. Or if email is more your thing then we’re podcast@nature.com. I’m Nick Petrić Howe.

Host: Shamini Bundell

And I’m Shamini Bundell. Thanks for listening.

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