Apple wins privacy row, and microbes dictate chocolate taste

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0:47All engine running. Absolute genius. Get this. Welcome. Welcome. This is the show where we bring you science. What that essentially means is... Discovery is... Advances. Research. Technology. Unbelievable. Without further ado, this is The Naked Scientist. Hello, welcome to the Naked Scientist podcast, the programme where we bring you the biggest breakthroughs and talk to the major movers and shakers in the worlds of science, technology and medicine with me, Chris Smith. Coming up, Apple locked horns with the UK government who were demanding a security backdoor through the company's encryption.

1:21So what was the outcome? Also, scientists discovered the secret of the tastiest chocolate. It is all down to microbes, and we'll hear how, and archaeologists uncover the earliest evidence yet of our ancestors using stone tools.

1:45Up first this week, the UK government has backed down on its controversial demands to be allowed access to the most secure customer data on Apple's iCloud service, so says US spy chief Tulsi Gabbard. Apple offers users the option to protect their personal data, including photos and so on, with their Advanced Data Protection Service, which is an encryption tool which excludes even the tech giant itself from being able to read the content. The Home Office in London, though, had instructed Apple to build a so-called backdoor into the service back in February, citing security. This was met with staunch opposition from the corporation, as well as privacy advocates.

2:25It was widely reported this week, though, that Apple had won and the UK government had backed down. But the story's a bit more nuanced than that. And James Ticko caught up with the technology editor at Bloomberg News, Mark Gurman, to hear why. So for years, Apple has offered this iCloud service. But one thing it didn't have was top-tier encryption for things like backups, for things like text messages stored in the cloud, for things like your reminders, your calendars, your voice memos, your notes. your web bookmarks. And so a few years ago, they rolled out a feature called ADP, or Demand Data Protection.

3:02And they launched this pretty much globally. You turn on this feature, and everything in your iCloud account were able to be encrypted. You mentioned it's an opt-in service, and there must be a drawback to this extra security, or everyone would have it. If you, for some reason, maybe you forget your password, your data is harder to get back. That's exactly right. The drawback is that it's a little tricky to set up. There are some compatibility issues. You need newer OSs, newer devices. And of course, you have the risk of what if you forget your passcode, you are a bit in trouble because Apple won't be able to unlock the account.

3:40So what was it the UK government demanded back in February when this row all kicked off? So the UK government demanded that Apple build a backdoor, which would allow them to go into user accounts and get data as needed, do investigations as needed. Apple refused to build a backdoor, but instead they removed advanced data protection for users in the UK. So that turned off the highest levels of encryption. So they didn't build a backdoor, but they essentially left the door as it was before a little open. They left people in the UK less safe from intrusion, from hackers, and of course, from the government.

4:19I suppose Apple would probably say, even if they wanted to build this backdoor, which it sounds like they don't want to, any cyber criminal worth their salt would probably store their files elsewhere anyway. And if a government can get in, perhaps a nefarious hacker could exploit the infrastructure set up to be able to do that. That's exactly right. Apple didn't create the advanced data protection feature to prevent governments from going into user accounts. This was created for far less nefarious purposes. This was created to prevent hackers or vulnerabilities or leaks and whatnot from user accounts.

4:57And they don't want to build that backdoor. They claim they can't build that backdoor and they would never build that backdoor. But the next best thing to building that backdoor is disabling that extra level of encryption. That leaves the opportunity there for both hackers, but of course, the governments to do what they want to do. Apple sees privacy as kind of a key tenet of its products at the moment, doesn't it? Encryption as a concept now seems to have entered the public consciousness. And is that why they're so reticent to budge on issues like this? For Apple, privacy is very core to how they develop all their products.

5:35They have a privacy engineering team. They have a privacy policy team. And they're involved in product development from the very beginning to understand the implications of features and how that could create privacy issues, right? Not only in certain countries, but on a global level. And for Apple, as they fall behind on other areas, they've hiked up their interest in privacy because it truly is a differentiator and something they found in their marketing campaigns to actually be a reason they can get people onto Apple products versus the competition. What was the update we got this week over this row with the UK government?

6:12So it's actually pretty nuanced. When the news first came out, the way it was digested is that Apple had won this back and forth with the UK. They also said there was involvement from J.D. Vance, the vice president under Trump in the US, and it was positioned as a victory. But it was only really a victory for the U.S., which really isn't the center of attention here. This is a U.K. issue, and nothing has changed in the U.K. Apple never removed the advanced data protection feature for American users. It was always continued to be available for American customers, people with United States-based Apple accounts.

6:57This news development only impacts the idea of the UK having a backdoor into Americans. The advanced data protection feature is still unavailable for UK users. So the issue for British users continues. Might it remain this way in this sort of deadlock for a long time? I anticipate this deadlock will continue for the foreseeable future. Apple doesn't remove features lightly. And I don't anticipate that Apple would have removed that feature if they didn't expect this to be a multi-year, several months, maybe even indefinite debunk between their privacy stance and the UK government. This is all covered by different acts that don't allow these things to be public.

7:42But my assumption is Apple is fighting the UK government in court about this locally in the UK. So for now, this issue has been solved for American users. But that was really never the point. So we'll have to watch this space. Nevertheless, the news this week, some might interpret as a bit of a blow to the Home Office here in the UK. Is there a serious point here that they've been repelled quite effectively when trying to tell a tech company to do their bidding? The Home Office has indeed been repelled. But at the same time, the UK continues to do what they want for the UK from their perspective.

8:21That's a lot more important than being able to snoop on Americans' phones. It's amazing that the UK is not going to be able to snoop on American accounts anymore. Very happy about that. But for users in England, they're still going to be facing this issue of not being able to have that top tier encryption level. Bloomberg's Mark Gurman. He was speaking with our own James Titco. Now, chocophiles, listen up, because UK scientists say that they have unlocked the secret to the tastiest chocolate. We make chocolate from cacao beans, which are the seeds inside cacao pods, which are themselves oblong-shaped fruiting bodies about the same size as an aubergine that grow on the cacao trees that are cultivated chiefly in West Africa and South America.

9:06Now previously, the industry had argued that different calibres and qualities of chocolate stemmed from the different tree species or cultivars and also differing growing conditions. But Nottingham University's David Gapulchan argues this isn't true. Much more significant, he's shown, is actually the effect of microbes which colonise and ferment the beans when they're scraped out of their pods surrounded by a mushy material that's called mucilage. He can recreate a range of different chocolates indistinguishable to the refined palettes of a panel of professional tasters just by tweaking the microbes he adds to a batch of beans.

9:42Cocoa beans are the raw material for producing chocolate. Depending on where the beans are grown, you can get different flavor profiles. For instance, beans are from West Africa. It's usually very strong in chocolate flavors. While if you source beans from Latin America, it's usually filled with lots of fruity floral notes. It's pretty much like the wine industry. Depending on where it's produced, you can get different flavors. is the same with the chocolate industry. The question we had was, why? If you asked, and you use wine as an example, a wine grower, that question, they would talk about terroir.

10:23They talk about things coming up from the soil. They talk about the environment, the grapes are maturing and ripening in. So what do you think it is then with the cocoa? And how have you sought to try and explore that? We first went to Colombia. So depending on the locations, you can get different flavors. So we selected three farms in Colombia to study this phenomenon. We went to these farms to analyze the processing of cocoa. So at these locations, the farmers would grow the trees, produce the fruit and harvest the beans and let it ferment. And during this fermentation is where the magic happens.

11:03So we went about studying this using a range of methods, It's mainly the DNA sequencing of microbial communities that drive the fermentation process. And just to be clear, because in a younger life, I used to trade coffee and cocoa on the London Commodity Exchange. So I'm one of the few people who's actually seen the raw material, the beans that you're referring to, because they're actually effectively the seeds that come out of the big pods that come off the cocoa growing trees, aren't they? And those are the bits that we grind the bean up to get the raw material that becomes the cocoa solids.

11:37in the chocolate bar but around those is all this mushy stuff and that is the the material that you're saying then ferments you've got various microorganisms that get on that and ferment it when the beans are drying yeah essentially these beans are covered with a white sweet mucilage and the farmers believe the beans for maybe five to seven days is where we have microorganisms would now infect the beans and drive the fermentation. And the fermentation, essentially, with these microbes, they transform the beans from just being tasting like cardboard or just plant into something closer to what we would know as chocolate.

12:19So the microbes drive this chemical process. How did you identify what microbes were doing what in this study then? To do the study, we sequenced the total DNA from the fermentations. So we use Oxford Nanopore DNA sequencing, and we analyze samples from day zero all the way to the end of the fermentation, about five to seven days afterwards. We were then able to identify which microbes were present and how much of it was present. And we did this across the three locations. And then we were able to compare the microbes and see which ones differed and by how much and link this to actual chemical changes in the beans.

13:02And this allowed us to link microbes to chemical profiles. Obviously, the proof is in the eating. The way to test that would be to take what you think is the profile of microbes that goes with a profile of flavor and apply those microbes to a different starting material and see if you can turn it into the other one. Did you do that? Yeah, so to go about actually testing this hypothesis, we actually collected microbes, so we isolated them, and then we inoculated beans, and then we monitored the changes in these beans. So we let these beans ferment in our lab. And what we saw was quite remarkable.

13:41We saw similar chemical changes to the beans happening. So a lot of flavor-precursive compounds. We were able to measure these volatiles, and then ultimately we had trained taste panels evaluate our lab fermented beans and compare them to naturally fermented beans and essentially what they found was when it is we fermented in the lab it was very similar to what we saw in nature and we were able to replicate this process. This argues then that you could take beans from pretty much anywhere even cheaper ones and with the right magic from the right microbes, get something that tastes like really high-end chocolate.

14:26I can see that having both pros and cons, though, because the industry purists are going to say that's removing some of the magic. On the other hand, the mass manufacturers are going to say, well, that's brilliant. We'll have a much higher quality product and we can keep our cost base low. I think, for the very least, what we've shown in this study is that there is a lot of potential and also it can be very disruptive to the industry. it's true you can potentially take any variety but having the right combination of microbes create flavor profiles that for instance if it is you want to produce a very high quality all these auxiliary notes in your beans you just need the right combination of microbes to do this david gapulchan and he just published that tasty piece of research in nature microbiology while every other channel is fighting for your customers attention podcasts are where they've already given it.

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15:51The Naked Scientist podcast is produced in association with Spitfire, cost-effective voice, internet and IP engineering services for UK businesses. Find out how Spitfire can empower your company at spitfire.co.uk. Music in the programme is sponsored by Epidemic Sound, perfect music for audio and video productions. This is the Naked Scientist podcast with me, Chris Smith. still to come, the earliest evidence of when our ancestors first began making and using stone tools. But first, an international mission to save what many regard as the world's most beautiful snails is underway in the UK and the animal's native Cuba.

16:34The tree-dwelling mollusks known as polymeter snails are prized for their incredibly colourful shells. Despite being protected though, people collect them and turn them into jewellery and other ornaments which are then internationally traded, illegally, for very high prices. And this is driving the animals towards extinction. To try to better conserve them, evolutionary geneticist Angus Davison at the University of Nottingham has teamed up with researchers in Cuba to catalogue and study the snails and sequence their genomes. For him, it's a story of love at first sight several decades ago. They're beautiful and they have an extraordinary variety of different colours.

17:12Red, orange, pink, yellow, green, brown, black. And then on top of that, they have all different kinds of patterns which are overlaid on that. An individual is extraordinary in the way it looks. But then when you go to a place in Cuba and find some of them, and they're all different, it's just mind-blowing. It's amazing. How large are they? They are quite large. So some of the larger species would be approaching the size of a garden snail that you might see in those countries. And is that their downfall? They're pretty, so they're disappearing because people want them? Yeah, that's the irony, isn't it?

17:49The reason I'm interested in them as an evolutionary geneticist is to understand the colour and the genetics and the beauty that that brings to them. But that is also partly their downfall. So that means people are interested in them. People will collect them illegally, export them out of Cuba, where they'll sell them for quite high sums of money. So that's one of the reasons they're endangered. How did you get involved in them? So I've been working on snails for a ridiculous number of years now, 30, I think, or nearly 30 years. And if you open up any book of snails and you might see some quite pretty pictures of snails, and then eventually you're going to see a book with these amazing Cuban polymeter snails in them.

18:29And that's when your jaw just drops. You think, wow. So I was lucky enough to go to Cuba in, I think, 2001. For the first time, we collected samples of all of the species We're the only to try to initiate these studies, but the political situation then was too difficult. And so I had to leave the specimens in the country. And so it's taken another 20 years since then, really, to get this project going. More recently, we worked with my Cuban collaborators. The Cuban Polymeter won Mollusk of the Year in 2022, of which part of the prize for that was to have its DNA sequenced and assembled. That's kind of the starting point for a lot of the genetics that we might wish to do with the snails.

19:10Is it just one species then, or is it a whole group of related species that all have this characteristic, this trait, and are all similarly endangered? We believe there are six species, and I think that's probably correct. The genetic studies that we're undertaking will ultimately show whether there actually are six species or not. All the historical taxonomic studies have suggested there are six species. And knowing how many species is interesting from an evolutionary standpoint you can try and understand how they came about what species they evolved from but it's actually also important for conservation so if there are six species then of course you want to preserve six species but if it turns out that you have a cryptic or hidden species then you need to know that so you can preserve all of those species and so you can't always recognize the species just by looking at the outward shell can you also use the genetics in the same way that in say africa we can look at where ivory has come from by using genetics and that can help to bear down on illegal ivory trades could it form part and parcel of that for the snails that would be lovely yeah so i know that ivory study and it's just amazing work that they have done there that's exactly right so we're not doing that but that would be a wonderful thing to do so you could have a shell which has been illegally traded there is probably what we would call ancient DNA within that shell somewhere.

20:31And you could then extract that DNA and work out where it came from. I think in the same way they do for the elephants, you could work out whether it came from a population that is there now, so still present and still alive, or actually the person selling it might claim that it was, say, harvested more than 50 years ago, and therefore it might be legal to trade it in some way or something like that. There's further benefits of doing that, of course because we're studying the populations that remain today there are populations that have gone extinct but we don't know really how much of the underlying genetic diversity has been lost so you could for example use museum specimens to then get a picture of everything that was there in the past as well and what about initiatives like captive breeding programs and so on to try to boost numbers and therefore conserve what we do have before we lose any more yes that's a good idea so what my cuban collaborator is doing is trialing that at the moment so we're not quite at the stage where we think that's necessary but if it ever does become necessary then of course you need the methods in place already so that you can take the few remaining into captivity i have to say though it is difficult so one of the reasons the shells are colorful is probably because they live in trees tree snails themselves are quite difficult to keep in captivity in my view at the same time there are other reasons to bring them captivity so we don't really know what they eat so of course he can trial to see what they eat so it kind of adds to the picture of their biology as well at the same time nottingham university's angus davidson on the cuban polymeter snails the question of when our ancestors first began to use tools is a really important one it steers our view of how our brains were developing and the relationships that our ancestors had with their environment and various potential food sources.

22:22And what Emma Feinstone, whose associate curator at the Cleveland Museum of Natural History has found in Kenya, suggests that tool use was very much embedded in our behaviour by as early as three million years, much earlier than we had evidence for previously. She's shown that early hominins weren't just picking up and using handy bits of stone that were lying around, they were venturing for sometimes tens of kilometres to find just the right sorts of stones to bring home and turn into tools, arguing that they very much knew what they were doing. One big question is how did tool use begin and how important was it to the earliest tool users and tool makers?

23:02When we think about humans today, we're really dependent on our tool technology to solve adaptive problems and to access different food items. It's part of our life that we are really tied to. Everyone on earth uses tools. And the question when we think of 3 million years ago, 2.6 million years ago, is how important was tool use to those early tool makers and how were they making and using tools and integrating it into their daily lives and their movements across the landscape? And what have we got to go on so far when you look at the fossil we have and the remains we have and the things we found, what sort of picture emerges before you come along with this current piece of research?

23:45The earliest period of tool use we know relatively little about because there are only a handful of archaeological sites that are older than two million years ago. What we do know is that hominins, which is a word that includes anyone in our family tree were making and using tools and accessing food items, but what we don't know is how big this investment was and how far they were ranging for food resources and for tool resources. Non-human primates are known to use stone tools and can accidentally produce flakes that look like the same ones we find in the archaeological assemblage unintentionally, but they do it through a very opportunistic process where they have a food item and then they have stones that are available locally and they're just breaking apart a food item to access that food.

24:39The big question is in the earliest archaeological record, when we're talking about older than two million years ago, were hominins accessing food items in a similar way to non-human primates where they're just cracking open a nut or maybe cutting something with an available stone nearby? or were they doing something more? Were they foraging for stones across the landscape and bringing them to places to process food? Is that the key then? Is that what you've built your story around? The fact that if you've got evidence that someone is going and getting particular bits of stone because they make good tools, that's evidence that this must have been common practice at the time at which those individuals were active.

25:19It's evidence that they were investing in tool behaviour because traveling a distance of several kilometers or 10 kilometers or more to get a specific type of rock, that takes a long time out of your day. And that shows that that's really integrated into your foraging strategy. If you're traveling to get stones, which in and of themselves have no caloric value to toolmakers or to humans and their ancestors. So traveling to get stones shows that this is a behavior that they're investing in. and it's part of their foraging strategy from the onset of tool technology. And it also shows that they've already incorporated stone tools into their landscape patterns in their mental maps, which is a step beyond what we see in non-human primates.

26:05So it's an indicator of having mental maps and cognition to incorporate stone resources into their foraging routine, and also an indicator that these hominins are foraging for stones as part of their foraging strategy, not just as an opportunistic one-off way to access a food item that they couldn't otherwise access. And you've got evidence that this was happening? Yeah. So at the site Nyong 'a, it's in Western Kenya, and we've been working there since 2014. We have a stone tool assemblage between 2.6 and 3 million years old that has been made using both local but also non-local stone materials.

26:48We did a landscape scale study where we were looking at which different materials are available throughout the landscape and which sources the hominins were accessing. And what we found is that the hominins were accessing not just local sources of stone, but they were accessing sources of stone that were 10 to 13 kilometers away from the Nyong 'a site, bringing them to the site and then processing food there using the stones that they obtained from further distances. And you're comfortable that those stones didn't arrive where the hominins were by accident and that you're saying they brought them there and in fact the environment somehow did.

27:25You're comfortable that this is active recovery of those stone pieces? Yes and how we know that we first do analysis of where stones are available on the landscape from ancient riverbeds and from transport through rivers from primary sources to outcrops and riverbeds, which is where hominins are accessing the stones. So we surveyed ancient riverbeds to check what stones are available in which places. And then we also did a type of analysis that looks at the geochemistry, which is the trace elements of things in the rock that can link them to the sources on the landscape to check which sources are most similar to the artifacts that we have in the assemblage.