How climate change is affecting global timekeeping

Nick Petrić Howe

Welcome back to the Nature Podcast, this week: how DNA damage and inflammation may help you remember…

Lizzie Gibney

…and how melting ice caps could affect the world’s timekeeping. I’m Lizzie Gibney.

Nick Petrić Howe

And I’m Nick Petrić Howe.

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Nick Petrić Howe

Before we start the show proper, we’ve got a bit of exciting news to share. We had a message recently asking “where’s Shamini?” and I’m happy to say we haven’t kidnapped her, she’s actually away on family leave and will be back next year. So I’m delighted to say that filling in from time-to-time will be someone who’s voice will be very familiar to long-term listeners: Lizzie Gibney!

Lizzie Gibney

Yes thanks, Nick, great to be here. Shamini and I kind of high-fived as I came back from my parental leave, and she went off. And yeah, it’s exciting to be on this side of the booth.

Nick Petrić Howe

Well, you’re not just on this side of the booth, you’re also on the show later with a story about leap seconds. But before that, I’ve been finding about how memories are made, as this week in Nature, neuroscientists have found that inflammation may play a key role in longer-term memory formation.

Jelena Radulović

The process that we discovered, normally would not be associated with normal functions, such as a memory function. And yet, it triggers in motion processes and pathways, which help the neuron actually retain information better and easier.

Nick Petrić Howe

This is Jelena Radulović, one of the team behind the paper on the new discovery. Now typically, when we think of inflammation in the brain it’s associated with neurodegenerative diseases, like Alzheimer’s. But Jelena and her team have shown that TLR9, a protein that triggers an inflammatory response, has a key role in memory, as without it mice had trouble remembering.

Jelena Radulović

So we use three different ways of knocking out Tlr9. One is genetic, the other is using silencing of the gene expression. And the third is using the specific oligos which inactivate Tlr9. And we had slightly different effects of the different manipulations. The gene knockout, obviously, was very powerful and we couldn't see any memories formed when we knocked out Tlr9. With the other two manipulations, what we primarily see is disruption of the persistence of the memory. So memories, which usually are easily recalled, over a month would dissipate within a week.

Nick Petrić Howe

This kind of inflammation-based memory formation is quite unlike other known mechanisms, where populations of neurons, brain cells, within the hippocampus express certain genes. But those neurons seem to be largely involved in the very early stages of memory formation. What Jelena and the team were interested in is what happens on the longer timescales.

Jelena Radulović

So what we did was, we looked after four days, up to a week, and we saw a very surprising thing, which is that in some brain cells, in some hippocampal cells, we had detected a very interesting inflammatory response. This type of response is typical to the innate immune system, but usually occurs when we encounter foreign genetic material. And the pathway that we identified is the DNA sensing pathway, which is coordinated by the protein TLR9.

Nick Petrić Howe

TLR9 typically is stimulated by foreign DNA, from things like bacteria, so Jelena and the team double-checked that that wasn’t anything like that present. Satisfied that there were no infections, they figured that the DNA must be coming from within the neurons themselves. And indeed the population of neurons with this inflammatory response had DNA damage.

Now, that may sound bad, but it’s already known that DNA damage is seen in specific neurons involved in early memory formation. However, that DNA damage is repaired within 10 minutes. The damage Jelena and the team were seeing was in a different population of neurons and persisted for four days.

Which led them to believe that these neurons are involved in longer-term memory.

Jelena Radulović

When we disrupt this pathway, what we really see suffer the most is the persistence of memories. So, even if some memories are initially formed, they will not last.

Nick Petrić Howe

How this inflammatory pathway might lead to memory formation isn’t quite clear yet, but Jelena and the team believe that it’s something to do with how that DNA damage is repaired.

Jelena Radulović

What we also saw is that these cells are mounting a very unusual type of DNA damage response. Namely, what we see is that outside of the nucleus, at the site of organelles, which are called the centrosomes, there is a very strong accumulation of enzymes, which help repair the DNA damage. Now, the types of repair that we see, normally in divided cells, would result in separation of the nucleus and cell division. But in brain cells, which are not dividing, the DNA repair remains organised in these two centrosomes. However, without division, we see cycles of DNA damage and repair independently. So we believe that these cycles of DNA damage and repair are changing the state of the cell, which is making them become more dedicated to represent certain type of information.

Nick Petrić Howe

But to figure out how these repair processes make the neurons more able to be involved in memory storage, there’s still a lot to uncover.

Jelena Radulović

So we're really interested in looking at the DNA repair response more carefully. We are trying to understand why do these cells develop this kind of repair response. We are also looking at understanding how the inflammatory response is controlled. We want it to be tightly regulated, and not exceeding its beneficial values and becoming pathophysiological. And we're trying to figure out the constraints. What are the limits that nerve cells can endure? And what are the breaking points when DNA damage shifts in becoming harmful relative to beneficial?

Nick Petrić Howe

Jelena hopes that this work will help identify different ways to preserve our memories, especially in different neurodegenerative disorders, like Alzheimer’s. For example, if this DNA repair could be boosted, could that help retain memories? And also, as I mentioned before, inflammation is often seen as a bad thing, but maybe we need to think a bit more about that.

Jelena Radulović

We can't have this unified front in talking about neuroinflammation as something bad and something damaging. We clearly have a neuroinflammatory mechanism which we found was essential for both learning and memory, but also for preserving genomic stability. So, very often when we think about treating various neuropsychiatric diseases, we think that we need to combat inflammation. And I think we need to be really careful there and look at different neuroinflammatory components, which can be harmful relative to protective.

Nick Petrić Howe

That was Jelena Radulović, from the Albert Einstein Medical College, in the US. As always, remember to head over to the show notes where you'll find a link to that paper.

Lizzie Gibney

Coming up, how melting ice caps are affecting global timekeeping. Right now, though, it’s time for the Research Highlights with Dan Fox.

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Dan Fox

A view of wind turbines can reduce the value of a home – but not by much, or for very long. Wind-generated electricity is one of the fastest growing sources of energy in the United States. But turbines have spawned resistance, with some communities arguing that they reduced the value of nearby properties. To get a broad overview of any potential impact, researchers analysed more than 300 million US homes sales that took place between 1997 and 2020. The team found that after turbines were built near a neighbourhood, property values dropped by an average of 1% if a turbine could be seen within 10 kilometres. But this impact peaked around three years after the turbines’ arrival, after which property values normalized. If you're blown away by that research, read it in full in Proceedings of the National Academy of Sciences of the United States of America.

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Dan Fox

Waste word can be broken down and used to 3D print new wooden objects. Typically turning natural wood into useful structures also creates waste, leading to depleted resources and high production costs. One alternative might be to use 3D printing to manufacture wooden objects, layer by layer. And now a team of researchers have formulated a new ink for this type of printing derived from waste wood. Wood is mainly composed of lignin and cellulose and so the team broke down leftover wood into those two building blocks, combined them with water and made a clay-like ink. By forcing this substance through a narrow nozzle, the researchers 3D printed centimetre scale wood objects, which ranged from miniature furniture to honeycomb structures. They found that the strength of their 3D printed wood could be improved by freeze drying, and then hot pressing it creating a result of material that closely resembled natural wood in terms of appearance, texture, and mechanical properties. Form your own opinion of that research over in Science Advances.

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Lizzy Gibney

For our next story this week, how climate change may affect how we keep time.

Now, you’ve no doubt heard about leap years, but we also have leap seconds too. Since the early 1970s, these seconds have been occasionally inserted into Earth’s official time, which is kept using ultra-accurate atomic clocks. These leap seconds are needed because the length of an Earth day, from sunset to sunset, changes depending on how fast the planet rotates, and is rarely exactly 24 hours long.

In fact, it’s often a fraction longer, and over time these tiny bits of extra time add up, meaning a leap second has to be added to atomic-clock time to make sure the two stay in sync.

At least, that’s what’s happened in the past few decades.

Now whether or not a leap second needs to be added - or maybe one even needs to be taken away comes down to several factors, and this week, geophysicist Duncan Agnew has analysed how the melting of the polar ice caps is slowing down how quickly Earth spins on its axis, which could have big implications for timekeeping around the world. I gave him a call to find out more, and he explained why the rate of the Earth’s rotation changes…

Duncan Agnew

So, earth rotation varies because of a lot of things. One is the effect of the tides interacting with the moon, which of course causes the tides. And over time, that slows the earth down, that's been slowing the earth down since a billion years ago, and will continue to do so into the future, that is a very steady thing. Second thing is harder to describe because it's about the earth's core, which is this giant ball of molten iron inside the earth. Because it's molten, there are currents in it, it flows around, which changes with time. So, we know that if it spins faster, the earth above it, which is what we're on, slows down. If it starts to slow down, the earth above, it spins faster. The final piece comes about from the melting of ice, and the poles. And the water from the belt, of course redistributes itself all over the oceans if some of its now near the equator. And that changes the shape of the Earth basically makes it in some sense, flatter, and that causes it to slow down.

Lizzy Gibney

So, the effect is something like an ice skater. So, if they want to go faster, they bring their arms in and if they're spinning, and if they want to go slower, they put them out. This flatter Earth is like an ice skater with their arms out. Is that right?

Duncan Agnew

That's the perfect analogy. Yes, that's exactly right.

Lizzy Gibney

And so, we've got three different major forces, we've got this long-term, slowing down, that's thanks to the tidal friction, then there's the core slowing which speeds up actually adds rotation. And then finally, climate change is kind of counteracting that, is hampering that, is that right?

Duncan Agnew

Yes, since 1972, the core has been basically steadily slowing down and speeding the rest of the earth up. Climate change, starting in about the 1990s, ice started melting it more and more rapid rates, sea level has gone up more and more rapidly and that has been slowing the earth down more and more rapidly. Although the effect of that is somewhat smaller than how much the core is speeding it up. So, on net, the Earth has been speeding up.

Lizzy Gibney

And now this actually looks like it's going to affect timekeeping. So, we now use atomic clocks and we have these things called leap seconds which we use to reconcile Earth’s time from its rotation with atomic time that doesn't have any of these fluctuations. Positive leap seconds are the ones that we might be familiar with they are when we kind of like stop time, and then we wait for Earth to catch up because atomic time aim has been going effectively, faster. But now Earth, it's finally catching up, but seems like it might be going faster. So, we actually have to take a second out of atomic time to catch up. Has that been done before?

Duncan Agnew

No, it has not. Every leap second between 1972 when these were instituted and now has been, let's have a minute that 61 seconds long. That's how it's done. And a negative leap second would be, let's have a minute, that's 59 seconds long, so there'd be an actual second, that just drops out and a negative leap second is something we have never had. And it's a question as to what effect that will have.

Lizzy Gibney

So, we know that a negative leap second is likely coming, what is the impact then of global warming on time, and with leap seconds?

Duncan Agnew

So, it's being delayed by global warming, I want to emphasise in case anyone thinks this is a positive aspect of global warming, it's completely outweighed by all the negative aspects. But yes, in the absence of this global warming effect, we would be very close to a negative leap second, as it is, we're not so close. It's being delayed by the effect of global warming. But I think the main takeaway here is the fact that we can actually see the rate of the Earth's rotation has been affected by the amount of melting of polar ice.

Lizzy Gibney

And leap seconds anyway, as I understand it, are a complete pain for anyone who runs a computing system, anyone who's trying to match time across the world. But a negative leap second, that's never been tried before, would that be even more of a pain?

Duncan Agnew

That would be much more of a pain, leap seconds are a pain because you want to synchronise computers very well. And I would emphasise that while a second doesn't sound like much, just for reference, the official standard for timing financial markets is a 1,000th of a second. And so if you had two computers that were a second apart, then that would not be good at all. The problem is that some human being has to effectively tell the computer okay, there's going to be a leap second at this time. And most computers have a programme in them that allows for this, but usually the programme just tells it the time of leap second doesn't necessarily tell it which way the leap second is going to go. Because everyone assumed when leap seconds were instituted that because of tidal friction, which is slowing the earth, that that would be the dominant effects. And the Earth would just get slower and slower, and we'd always have positive leap seconds, no one really anticipated that there would be a negative leap second. And so, we don't really know what will happen to the computer timing infrastructure of the world if there is one. This is a little bit like the year 2k problem.

Lizzy Gibney

And so, will your work help in at least being able to predict when this problem might occur when we might need to have the first ever negative leap second?

Duncan Agnew

I would like to think so because it breaks down the rotation changes into the different causes. And so, if you extrapolate what the core has been doing since 1972, and add global warming and tidal friction, you discovered that there should be a negative leap second in 2029. And if global warming hadn't occurred, and you take that effect out, it would have been about three years earlier in 2026. Now, the problem is the core is fundamentally unpredictable. We don't know much about it. It's changed abruptly in the past — this is rather like trying to predict the stock market. And so, we're not determined that we're going to have a negative leap second, we can only say that this is what the data indicate at the moment.

Lizzy Gibney

You’ve worked in geophysics and climate change for years. Did you imagine that you'd see a point where humans we're having this scale of an effect that actually our actions are impacting how fast the very planet spins. And as a result, time itself.

Duncan Agnew

I mean, I've been around climate change for a long time, the place where I work is where the famous carbon dioxide curve comes from. I had not thought until recently about the effect on rotation and I was surprised to see that it's as large as it is.

Lizzy Gibney

That was Duncan Agnew from the Scripps Institution of Oceanography, University of California San Diego in the US. For more on that story, you can find the paper in full in the show notes.

Nick Petrić Howe

Finally on the show, it’s time for the Briefing Chat where we discuss a couple of articles that have been featured in the Nature Briefing. Or actually some of the other briefings that Nature’s now producing, as I know Lizzie you’ve been working on the AI briefing, so have you got a story from that for us?

Lizzy Gibney

Yes, I do. So, this is a story from one of my colleagues here at Nature, Ewen Callaway, and it's based on a paper on the bioRxiv, so it's not peer reviewed. What it's looking at, is trying to design antibodies using AI. So, you may have heard of antibodies in your body. They’re used to fight disease, well, they're also using treatments. So, these are able to go and recognise fine target specific proteins like cancer cells or viruses and obviously used to tackle that disease. So how do we find them for use and treatment. Well in the past, you either have to screen through a lot of possible molecules or use kind of trial and error and a lot of immunisation in animals. This paper is looking at how to do that design but using AI. So, it's a proof of principle, it's very preliminary. And what they did was it was a team at the University of Washington in Seattle. And they used a tool called RF diffusion it’s based on things you'll have heard of a lot in AI neural networks, are the kind of things that behind image generating AIs, like DALL·E. And they use that they trained it on lots of experimentally determined structures of antibodies, and how they attached to their targets. And they use that to design 1000s of new possible antibodies against a whole range of virus and bacterias, such as SARS-CoV-2, and then they tested a subset of those in the lab.

Nick Petrić Howe

I mean, it almost sounds to me like an AlphaFold but specifically for antibodies. So could this really speed up like trying to find these different antibodies and how successful was this AI in doing that.

Lizzy Gibney

I think, eventually, maybe it could. So, at the moment, it was something like 1 in 100 worked as they hoped. So, you know, that's not great hit rate. But you know, this is a long way from the clinic at the moment. There is a hope that maybe it could be used for targets that have proved really challenging in the past to find antibodies for. And yeah, this is early stage, these were very simple antibodies they made, they didn't bind all that strongly to the target proteins, and they would need a lot more work to work in humans. But it shows that designing antibodies with AI is possible. And this kind of co-design, you know, you can use the AI to design and then you can test it and hone the results. And there was a quote that really stood out to me in the story, somebody said that this is how we'll be doing it in 10 years time. So, at the moment, this is very early stage, but it clearly is very promising. And there's a lot of excitement about the very fact that this proof of principle works.

Nick Petrić Howe

Yeah, I guess so because normally, people have to test a whole range of antibodies, and they just have to literally try and see how they bind. But this could I guess, streamline that process.

Lizzy Gibney

Absolutely. And particularly be useful in cases where they've tried to do that and failed in the past.

Nick Petrić Howe

I mean, that sounds like exciting news for people want to use antibodies to treat disease. For my story this week, I'm looking a bit more heavenwards. And I've been reading a story in Nature, about a new observatory that's going to try and map the cosmic microwave background radiation.

Lizzy Gibney

Okay, so that's the kind of leftover buzz from the Big Bang, right? In the universe?

Nick Petrić Howe

Yeah, that's right. It’s the sort of like leftover bits from the Big Bang. And so, this is the Simons Observatory, which is going to be opening in a couple of weeks in the Atacama Desert in Chile. And it's basically trying to map out this cosmic microwave background radiation. And it's going to look for traces of gravitational waves in it as this may be a key indicator of the cosmic inflation expansion that happened just after the Big Bang.

Lizzy Gibney

This is ringing bells. Is this the same thing they're looking for that they claimed to find out maybe almost 10 years ago now? There's a BICEP2 experiment that thought they've seen gravitational waves in these remnants of Big Bang radiation. And I think in the end, that was disproven.

Nick Petrić Howe

Yes, that is exactly right. So, the BICEP2 what they actually saw was a bit of dust from the Milky Way. So, the idea of this–

Lizzy Gibney

–not the same thing–

Nick Petrić Howe

–not the same thing, as it turns out, so the idea with this observatory, is it's far far more sensitive, it's got 10 times greater sensitivity than the previous best thing for looking at this. And the hope is because it's so sensitive, you'll be able to ignore things like dust from the Milky Way and find some of these tiny traces. Because one of the really difficult things about this is, we don't know a lot about this cosmic inflation. And so, there are different theories as to how strong these gravitational waves might be. So, they could be really tiny ripples that we're looking for. So, the hope is this will be sensitive enough to actually find them. And then if we do, we can figure out where the sort of tiny quantum fluctuations were that ended up becoming like the big clusters of galaxies we now see throughout the universe.

Lizzy Gibney

So, this is like the connection between, that's why it's all about inflation from when these tiny quantum fluctuations existed. And then they got turned into much, much bigger signals because the universe underwent this massive expansion in a short amount of time.

Nick Petrić Howe

Yes, exactly. Exactly. So, some cosmologists are very excited about this new observatory. It's, as I said, it will be finished in a couple of weeks, we won't get results from it straightaway. There'll be a few months of testing and fine-tuning and all that sort of fun stuff before we start up and we actually get some of the cool data from there. But it's not just going to do that as well. It's also going to try and map out some of the temperature fluctuations from the cosmic microwave background radiation, and also the polarisation of the radiation from the Big Bang. And that can tell us bits about like this sort of age and composition of the universe. And also, it should allow researchers to visualise the universe at an early age because they can exploit gravitational lensing, which is where something big is in the way of what you're trying to look at. And so, gravity sort of like bends around it–

Lizzy Gibney

–like a cosmic magnifying glass–

Nick Petrić Howe

–yeah, cosmic magnifying glass. And that could help them measure things like the mass of neutrinos, which as you know, has been quite tricky to pin down.

Lizzy Gibney

Wow, it does still blow my mind that you can, you know, just have these really fine, precise telescopes that are able to see these tiny little wispy traces, of polarisation of light coming from really, really far away really, really ages ago. And that could tell us about how the whole universe started.

Nick Petrić Howe

It is kind of mind boggling to imagine that these tiny little specks and things that we didn't even know that we could look for years ago, are out there that could tell us so much about the universe we now all live in. And yeah, we'll be keeping an eye on this particular observatory as it opens up, and maybe there'll be a couple of Nature papers we'll talk about in the near future. But for now, I think that's all we've got time for on the Briefing Chat. Listeners, for more on those stories check out the show notes are some links, and there's a link there where you can sign up to the Nature Briefing or even the AI Briefing and get more stories like them delivered straight to your inbox.

Lizzy Gibney

That’s all for this week. But before we go, just time to say that you can reach out to us on X, we’re @NaturePodcast, or via email, on podcast @nature.com. I’m Lizzy Gibney.

Nick Petrić Howe

And I'm Nick Petrić Howe. Thanks for listening.