Tag: biology

Horizon: What Makes Us Human?; Royal Institution Christmas Lectures: Meet Your Brain

What Makes Us Human? was a recent episode of Horizon, presented by Alice Roberts while she was pregnant with her second child. So the frame was lots of gooey shots of little babies or shots of Roberts looking pregnant, and the meat of the programme was about some of the things that do or don’t set us apart from our closest relatives in the animal kingdom (chimpanzees, of course!).

One obvious difference between people & chimps is that we’re more intelligent than them. But actually the differences appear to be more subtle than one might expect. Roberts visited some researchers who look at co-operation in chimps & humans. Chimps will co-operate to get a reward, but if the reward is uneven – one gets more or one gets the reward before the other – then the chimps don’t care. Well, the one that loses out does, but not in a way that gets them their “fair” share. But if you do similar experiments with young children (toddler age) then an unequal reward gets shared out. Importantly this only happens if they had to work together to get the reward – co-operating means sharing.

Another difference is the helplessness of a human baby when it arrives on the scene. This is something that has had an “answer” for decades, but recent research has suggested the “answer” isn’t the whole story. Babies are born at the point where they only just fit through their mother’s pelvis, and it has been assumed that there are two selection pressures on the width of the birth canal – one is that wider makes it easier to have bigger headed babies, and the other is that narrower makes walking more energy efficient. So the theory is that women’s pelvises are at the sweet spot between easier childbirth with more developed babies and walking efficiently. But new research is suggesting that women’s walking (and running) is no less energy efficient than men’s despite a difference in gait because of the different shape of pelvis. So that may not be the explanation, you’d think if walking efficiency was the important factor then women’s hips could be wider. The new theory is that women’s metabolisms can’t continue to improve to keep up with the demands of their unborn child – babies are born at the point where their mother can no longer supply all their energy needs. Something about this segment left me with questions about whether there was more data than was explained, because it felt a bit pat & a bit too much jumping to conclusions.

When you look at a human brain & human nerve cells they show more connections (and dendrites) than other animals. Humans have more duplicates of a particular gene to do with dendrites than chimps & if you duplicate this gene in mice then you get more dendrites & connections – in the right proportion to explain the difference between humans & chimps. In this segment Roberts also talked to a scientist who is starting to map, to visually image, actual brains – at the moment he’s just doing mouse brains (very slowly) as they’re small. But eventually the plan is to be able to investigate a human brain this way. They end up with a colour coded three dimensional diagram of all the nerve cells in a brain with connections mapped etc. This looked cool, but I’m not sure how much it actually tells us in the long run – as I understand it brains are all unique in detail, even if similar in general. And does “neuron A connected with neurons B, C, D & E” tell us much about what any of these do?

(And am I cynical about Horizon’s presentation of science because I go in thinking it’ll be shallow, or do I go in thinking it’ll be shallow coz it often leaves me with questions?)

The Royal Institution Christmas Lectures are a series of lectures aimed at children and broadcast on the BBC. I used to watch them every year when I was a kid. We recorded the series in 2011, and have only just got round to watching them – that year they were about brains and the lectures were given by Bruce Hood. The first lecture in the series was titled What’s In Your Head? and covered the basics of what a brain is, how nerves work and the sort of modelling brains do to make sense of the world.

As it’s aimed at children I don’t think it covered anything I didn’t already know, but it did it with style and involved a lot of demonstrations – some of which were rather neat. For instance Hood & another scientist showed that brains work on electricity by disrupting the ability of the other scientist to move his hands properly using in electromagnet against the head. So the chap was clapping and then they switched on the moving magnetic field & he could no longer co-ordinate bringing his hands together. There was also a little bit about MRI scanners to look at brain activity – with a striking visual demonstration of how powerful the magnets involved are: a nurse went into the room with a spanner on a string and then the machine was switched on and the spanner swung up and pulled towards the machine.

Another bit was about how the brain sets up patterns as it learns about the world and how that can lead to being disconcerted by new experiences – like if you eat grapes then your brain learns that round, green, sweet is a pattern associated with grapes. The first time you meet a green olive, you see round and green and then your brain fills in “sweet” because that’s the learnt pattern. So when you eat it you get a nasty surprise. This example particularly stuck in mine & J’s heads coz until recently neither of us ate olives (I’ve somehow acquired a taste for them over the last couple of years) – so the “yack!” reaction he was talking about amused us 🙂

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Ice Age Giants; Australia with Simon Reeve; TOWN with Nicholas Crane

The last episode of Ice Age Giants looked at why there are none of these large animals left. The first half of the programme concentrated on North America where there were the greatest proportion of extinctions. Roberts started by talking about the idea that it was people – we were treated to a proper true crime documentary moment where the voiceover was all “but beneath the peaceful streets of this Tennessee town lies a dark secret” etc etc. And saw how there is an excavation pretty much in someone’s back garden – of mastodon bones that look to have been hunted & butchered by humans. So was it people? Roberts pointed out the problems with that theory – not many people in North America at the time, lots of megafauna, and a few thousand years of overlap of people & megafauna.

So what else? How about the floods that created the coulees (also known as the Channeled Scablands) in Washington (the state). These features of the landscape are vast vast canyons that have been scoured out of the rock, but there’s no sign of a river. The theory to explain what caused them is that as the glaciers melted a great lake of meltwater was formed in Montana which is known as Glacial Lake Missoula, this was penned in by a dam formed by the melting glaciers. When it broke through it did so catastrophically and the water rushed to the west of the continent carving its way through the rock as it went. This happened several times as the glaciers advanced & retreated, I think she was saying a couple of hundred times over just a few thousand years. This would’ve killed anything in it’s path (and created what still looks like a blasted landscape today). But that can’t’ve killed all the animals, it would just’ve got the ones in its path.

How about climate change? This isn’t a case of it just getting a bit warmer all over – the melting of the ice sheets released more water into the rainfall systems, so the world got wetter as well as warmer. Still not quite that simple, the swamps that the glyptodonts lived in dried up & became desert because the rainfall moved north as the ice sheets retreated and the more southern regions warmed up. Roberts now skipped across to Europe and the woolly mammoths & woolly rhinoceroses of the Mammoth Steppe. These enormous herbivores relied on the dry grasslands to provide them with sufficient food all year round. As the world warmed up, and got wetter, forests grew where there had just been grassy plains. And it started to snow in the winters on the Mammoth Steppe. Woolly rhinos couldn’t cope with that – snow covers the grass and makes it harder to find, it’s also hard to walk through so you need more energy to move around and so more food. So that’s what killed off the woolly rhinos – an Ice Age Giant killed by it snowing too much, not at all what you’d expect.

And now we circled back to the mastodons of North America. There is research being done on fungal spores in soil that can indicate how many herbivores have left their dung on the land – if you look at soil from the past you can estimate herd sizes (or at least changes in herd sizes) over time. And these show that the large herds of mastodons & other herbivores died out before the climate change changed the vegetation (which you can tell by looking at seeds & pollen in the same soil samples). So probably not climate change as the whole story here. Roberts then talked to a palaeontologist who thinks he has an answer for the mastodon extinction. He has looked at the types of injuries on female mastodon specimens, and also looked at the types of mastodon that show signs of butchering. In modern elephants (which are close cousins of the mastodons) preferential hunting of mature adult males destabilises the herd structure. Normally a dominant male swoops in to a female plus offspring herd when the females go into heat and mates with the females. He also suppresses the behaviour of the adolescent males. When there is no dominant male, the younger males that still live in the female herd will go on a rampage when the females come into heat – and can injure females & calves (and each other) in the process. This palaeontologist thinks he sees evidence of this happening to the mastodons, so it was people that caused their extinction but in a very slow process caused by preferentially hunting solitary adult males which they wouldn’t’ve been able to see happening.

Last up for extinction were the woolly mammoths – which survived on a remote island north of Sibera until around 2000BC (when people arrived on the island). Apparently from the evidence on this island the mammoths were becoming dwarf mammoths … by mammoth standards anyway. Roberts talked a little bit here about the potential cloning of mammoths that is now becoming possible due to the extraction of DNA from very well preserved frozen specimens.

And Roberts ended the programme with a romantic notion of how we’ve also saved some of these Ice Age Giants – like horses. They became extinct in America, their ancestral home, but survived across Europe & Asia and were then domesticated. She was talking about it as a beautiful partnership, but I’m afraid I was amused by it rather than moved by it 😉

Anyway, I greatly enjoyed the series. The CGI wasn’t perfect (something always looked a little off about the way the animals moved, and there was a lot of repetition of sequences that made it a bit too obvious it was generated) but it was good. And the science was presented in an un-sensationalised way – lots of “we think” or “this is a possible explanation” rather than grand solutions to mysteries.

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Having finished watching Brazil with Michael Palin (post) we started to watch another travelogue we had been recording – Australia with Simon Reeve. We’re both pretty sure we’ve seen Simon Reeve present another programme in the past, but neither of us can quite remember what it was.

In the first episode of this series he started in central Australia then headed south to the coast followed by west to Perth. In central Australia he focused on an animal you don’t expect to be the subject of a programme on Australia – the camel. Camels were brought to the country as a means of transport, being well suited to the desert conditions in the centre. With the advent of cars they weren’t needed any more & were released to the wild where they now roam freely. Unsurprisingly they cause a lot of damage to the ecosystem and to the farms in the region & so they are regarded as pests. Some farmers just shoot them when seen, but Reeve talked to one farmer who was rounding them up and selling them back to the Middle East for food & for racing.

Next Reeve went to visit a winery – a vast commercial winery with gallons & gallons & gallons of wine in big tanks, supplying relatively cheap wine to supermarkets across the world (this was owned by Hardys). This segued neatly in to a segment about how water is a limited resource & it’s being over used in Australia as a whole. Reeve then visited another limited resource – tuna, which is being overfished in the seas near the Australian south coast. He visited a facility where they’re trying to breed tuna in captivity, which involves conning the tuna into thinking they’ve migrated by changing the lighting and so on as it would change if they really were migrating.

From there to resources that are booming – he visited an area which has a modern day gold rush & talked to some weekend hobbiest prospectors, and also visited a huge commercial mine. Next, Reeve visited a village where an aboriginal community lives having been moved off their land when the mining companies discovered resources underneath it. They haven’t been compensated for the loss of the land, nor have they earnt anything from the metals being dug up from under what they still regard as their land. Reeve said that the situation is complicated & the government is trying to help, but the aborigines are still living in third world conditions.

From there he went to the other end of the spectrum – he took a train to Perth where he visited some British ex-pats who are living the dream. The man he spoke to had been a bin man in Sheffield, he’s now teaching people to drive trucks so they can work for the mining companies. His pupils earn more than he does, but he earns about £60k and has a big house with a pool etc, just what he came out to Australia for. And the episode finished up with Reeve visiting an airport where “fifo” commuters fly from – that’s “fly in fly out”, the commuters work in the mines (doing things like driving trucks for lots of money) and live in Perth getting back & forth by plane.

The second episode covered the north of Australia, which is particularly sparsely occupied. He started out in a national park (Kakadu) helping to trap & cull cane toads. These are a non-native species that was introduced to eat beetles that were pests … they didn’t eat the beetles, and being poisonous & non-native they have no predators amongst the native animals. So they’ve spread & are killing off the wildlife in the park which dies trying to eat the toads. The cull seemed a bit like it would just make the people doing it feel like they were trying – if there’s millions of toads then catching & killing a couple of bin bags full won’t do much good.

Moving towards the east Reeve visited the Australian army, first one of their tank regiments then he spent a bit of time on patrol with a unit doing observation in the outback. This segment reminded us that Australia is actually right next to Asia, rather than being a stray bit of Europe stuck in a southern ocean. In the bit with the patrol they talked about how the unit was mixed race & that this didn’t cause problems in a way that made it sound like that was an unusual situation. They also talked about how the aboriginal members of the team were vital in teaching everyone how to live off the land – they made green ant tea for Reeve, which apparently was quite nice … not sure I’d’ve been keen to drink it. The follow up to this section was a visit to an asylum centre, Australian law is that asylum seekers must live in these detention centres while their application is processed which can take months or years. Reeve spoke to activists on the behalf of these immigrants who say that conditions in the centres aren’t good – lots of the inhabitants self-harm or commit suicide. Reeve spoke through the fence to some of the inhabitants, who’d come from the sorts of places you’d expect – Iraq, Afghanistan etc.

From there we moved on to the slightly more cheerful subject of another aboriginal village which owns resource rich land. Whilst it looked as depressing as the place in the first episode the ray of hope here is a young woman who has set up her own company with the long term plan of the village itself doing the mining on the land closest to them. At the moment she rents 4 bulldozers out to the company who’re doing the mining, which I got the impression was proof of concept.

And the programme finished with another couple of segments looking at the natural world – first Reeve joined some scientists who were taking samples of the stinging tentacles from box jellyfish. These jellyfish are extremely poisonous, and live in shark & crocodile infested waters. From the way the scientists were acting (and not letting Reeve do much but observe) they weren’t exaggerating the dangers. The venom from the stings is useful for drug research – there’s a lot of complex biochemistry involved that does things like target the actual poison to particular areas of the body and other stuff like that. So understanding it might help make better more effective drugs.

Last up was the Great Barrier Reef. Changes in the water (due to increased use of fertilisers etc on land) have lead to destabilisation of the ecosystem there, and Reeve was shown how people are culling the starfish that are killing off the coral. He also joined a ship pilot who guides coal ships through the reef – there’s not much room to spare & it’s a dangerous task, but the wealth generated by the coal industry means that they are still permitted to run their ships through the area.

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In our quest to free up some space on the PVR we’re watching all the programmes we have recorded in HD first – and only recording new stuff in SD. Just before that decision we started to record TOWN with Nicholas Crane in HD so it’s come up to be watched a little quicker after airing than I think we might’ve got round to it otherwise. It wasn’t quite what we expected, guess I didn’t read the description that closely when I set it recording. Instead of being about towns as a general thing each episode is about a particular town.

The first episode is about Oban, a town on the west coast of Scotland that’s where you go if you want to get a ferry to the Western Isles. And the main theme of the programme was that that isn’t all there is to Oban, that the town is itself a worthwhile place to visit.

Oban wasn’t a town until comparatively recently so his talk about the history of the place started off with nearby Castle Dunollie which was the seat of the Chief of Clan MacDougall until 1746 when the Clan Chief moved to a new house nearby. Surprisingly “Battle of Culloden” and “Jacobite Uprising” weren’t mentioned during Crane’s discussion of this. I had a little poke around on wikipedia and it seems like the 1746 move was a coincidence as the MacDougall Clan Chief wasn’t involved in that Jacobite Uprising, but I’d’ve thought that was worth mentioning on the programme just to say it wasn’t involved. Oban became a town after this – the first industry in the town was tobacco but this collapsed once the ship that brought the tobacco over from Virginia sank. After that the primary industry in the town was whisky, Crane visited the distillery which is still making whisky today. In the 19th Century Oban was finally linked by road & rail to the rest of the country. It was a tourist destination, partly due to the links with the Western Isles but people did visit the town itself. Queen Victoria was one of those tourists. After that it fell into decline & most people who visit aren’t stopping, just moving on to the ferry. One more recent bit of history is that Oban was where the first transatlantic telephone line ran to, and this was an important link between Washington D.C. & Moscow during the Cold War.

In terms of the modern town Crane spent a bit of time looking at the major employers in the area. Oban is the hub of the postal service for the Western Isles, and everything there has to be run like clockwork to match up with the ferry services. Another major employer is the granite quarrying operation a bit north of Oban – all the people who work there commute by ferry because there are no road links to the quarry. Crane also visited a few of the cultural offerings of Oban. He met a local painter who paints a lot of the landscapes around the area. He also visited a cèilidh bar where there is a traditional band & traditional dancing. And he also ate at a gourmet restaurant which is on the harbour so that the fish & shellfish are very very fresh.

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Ice Age Giants; Brazil with Michael Palin; Guts: The Strange and Mysterious World of the Human Stomach

The second episode of Ice Age Giants was about the large mammals in Europe during the Ice Age. Roberts started by visiting Transylvania where there is a cave that contains fossil cave bears. The caves also have patches of the walls that have been worn smooth by the bears passing through the caves. These bears were larger than grizzly bears, and were vegetarians. As with modern bears they hibernated, and the animals found in the caves are mostly those that didn’t make it through the winter. But the cave bear specialist showing Roberts these also showed her two that seem to’ve slipped down a steep slope in the cave & failed to make their way out – there are scratch marks in the mud on the cave walls that look like the two bears, an adult & a cub, failing to scramble back up.

Also found in this cave is a cave lion skull. These were one of the top predators of the European continent and mostly ate medium size herbivores like deer. But it seems this one, through desperation or foolishness, had tried to sneak up on a hibernating bear and found it still awake. They had done a CGI fight between the bear & the lion which looked very impressive but not quite real enough. The lion’s skull showed signs of damage from teeth which is why it was thought to have died in a fight.

Cave bears were common early in the ice age, but became rarer as the temperature got colder and eventually became extinct at the beginning of the last glacial maximum. But some animals thrived in the colder weather and the first of these that Roberts talked about was the Woolly Rhinoceros. These animals looked exactly as you’d expect – a rhino with wool, with a bigger horn than a modern rhino. A well preserved one has been found near a remote town in Siberia so they know what the wool looked like as well as the skeleton. Preserved woolly mammoths have also been found in this area, including a baby one that I’m pretty sure we’ve seen before in another Alice Roberts programme.

Both the rhinos and the mammoths were herbivores, and ranged over a wide area from England to Canada – due to how much water was locked up in ice at the time Britain was linked to the continent via a land bridge, and Alaska & Russia were also linked. You’d think that during the ice age herbivores would have problems in the winter due to snow, but actually there was little snow across this area again due to the amount of water locked up in ice sheets. The Mammoth Steppe, as it is called, was an open grassland with lots of flowering plants. This is known from work done in Canada examining the contents of fossilised ground squirrel nests. The squirrels hibernated and stocked their nests with food for the spring before they slept. The nests of ones that failed to make it through the winter obviously still have their spring food store in them when they are excavated and this lets scientists see what seeds and fruits were around at this time.

The last animal discussed were human species. Starting with Neanderthals who are known to’ve killed & butchered mammoths. The expert Roberts talked to thought that they probably did this by herding one down a dead-end gorge and then flinging rocks down from above to kill it. The CGI for this bit was a little less than convincing, which was a shame. The other human species at this time was our own one, and Roberts looked at evidence that they used the mammoths for more than just food. It’s though that they built houses from mammoth tusks (as the tent poles) with hides stretched over them for a roof. Roberts also looked at a piece of carved ivory, in the shape of a bison, from this time.

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In the third episode of Brazil with Michael Palin he travelled through the south east of Brazil to Rio de Janeiro. First up was an old gold mine and a current iron mine – this region is a source of a lot of Brazil’s mineral wealth. The gold was mostly mined on behalf of the British (I almost said “by the British” but that’s very much not true). There was a brief stop off at a couple of places, one of which was a farm where a man had a cow with 5 legs and two digestive systems, which was actually mostly to show us how the rural poor lived I think.

Then on to Rio de Janeiro where the rest of the programme was set. Palin didn’t just visit the rich bits of the city but also the poorer areas. The Brazilian government is making a huge effort to clear up these areas and drive the drug lords out and drag the communities into the 21st Century before the World Cup and the Olympics. First armed troops go in for the “Pacification” and then there is investment in the infrastructure and projects like schools and boxing clubs for the youth.

And in last episode he visited places in the far south and the south-west of Brazil. He started by visiting a current heir to the no longer existent Brazilian throne … I hadn’t even been aware that Brazil had been an independent monarchy, apparently they’re descended from the Portuguese royal family. And from that leftover from the past he went on to visit an aeroplane making company, very much an example of Brazil’s future.

Palin then spent some time in Sao Paolo, concentrating mostly on the poorer side of the city, and also pointing out how many Japanese immigrants there are in this part of Brazil. He then went to a town that was like a theme park Germany transplanted to Brazil – Blumenau. Obviously they’d dressed up to do their traditional dances for the benefit of the cameras, but when he then talked to some of the residents of the area they were saying they felt German first & Brazilian second, even though they weren’t necessarily first generation immigrants.

And the series finished up with a trip through some of the more unspoiled areas of wilderness in the south. J commented while we were watching that one of the places was the sort of place an Ancient Egyptian might want to end up. Pantanal is an area of wetlands, that floods annually. The residents farm cattle and the wildlife includes species of ibis.

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Guts: The Strange and Mysterious World of the Human Stomach was a programme we’d recorded a while ago, but I wasn’t sure if I was going to be too squeamish to watch. In the end it turned out to be mostly OK – just one sequence where I kept my eyes shut most of the time, and only a couple of contenders for “worst job ever” 😉

The thread tying the whole programme together was a demonstration Michael Mosley had done at the Science Museum. He swallowed a small camera which transmitted pictures from his digestive system over the course of the day. First it travelled down his oesophagus into his stomach, and spent a while there. They supplemented this batch of pictures with a set from a more high resolution camera on a tube that went down his nose, and he ate a selection of brightly coloured veg so that we could see them arrive in the stomach and start to mix with the gastric juices. Then after that second camera was removed he ate a large meal, and there were pictures of that being digested – most of what you could see was the veg, the steak had pretty much disintegrated by the time it got to the stomach. After that the camera moved through the small intestine, where we could see the intestinal villi which are little frondy projections from the surface of the small intestine to increase the surface area available for absorbing food. The stat they quoted was that the surface area of the inside of the human small intestine is about the size of a tennis court. Then the camera proceeded into the large intestine where it mingled with the faeces.

In between the various pictures of Mosley’s insides there were a series of short segments about related things. In the first of these he visited a historian who told him about the discovery of the composition of gastric juices. This was fairly astonishing – a doctor (William Beaumont) in Canada had a patient who had been shot in the stomach, and when the wound healed it left behind a small (inch or two diameter) hole in his flesh straight into the stomach. So afterwards the doctor did various experiments both putting things through the hole into the gastric juices to see what happened, and also drawing out some of the gastric juices to do other tests. Before that digestion was thought to be purely a mechanical process, but this doctor showed that the chemical action of the acidic gastric juices was a critical part of it. There was also a very brief segment just after this where Mosley dipped a coin in a beaker of artificially made up gastric juices and saw that it cleaned the coin.

Still on the subject of the stomach there was a segment about gastric bypass surgery. Which is the one I shut my eyes for most of – I can cope with pictures of someone’s insides, but not so much with surgical stuff stuck into someone. The operation we watched (or in my case listened to) was on a severely overweight man who’d had a heart attack in his late 20s, after a couple of years of unsuccessfully trying to shift the weight his doctors decided that gastric bypass surgery was the best option. I didn’t know before that what actually makes most of the difference after these operations is that there are behavioural changes. Partly because a hormone secreting part of the stomach is segregated from food so doesn’t do its normal job with increasing appetite, and partly because the bit of the small intestine that sends signals to say “full now” is closer to the stomach so the signal is sent sooner after eating starts. 6 weeks after the surgery the patient was saying he’d lost 3 stone, and had gone from never feeling full to being satisfied after eating quite small meals.

When talking about the small intestine there was a segment on perception of gastric pain, and the correlation with differences in personality. For this Mosley filled in a personality test then went through some pain tests (tube down the nose, balloon inflated in oesophagus till it hurt) while hooked up to blood pressure & heart rate monitors. The doctor doing the research was classifying people into either neurotic or extrovert categories, and he had found that the two groups had different responses to pain. Neurotics (like Mosley) showed reduced blood pressure and reduced heart rate. That’s not at all the expectation Mosley went into the test with – the textbook reaction to pain is increased heart rate & blood pressure, which is what extroverts show. The doctor was saying this has implications for treatment of gastric pain – different treatments will work better with different types of patients.

Moving on to the large intestine we had the two candidates for “worst job ever”. First up was the woman who cultures samples of faeces in the lab to look at the types of bacteria they contain. The ecosystem of the large intestine is very complex, with a large number of different types of bacteria. These can aid us in our digestion by breaking down the things we can’t, or they can be the cause of problems. She also talked about flatulence (which is a by-product of a healthy digestive system) and how the differing smells of farts is down to differing compositions of bacteria in the large intestine. Smelly ones are down to having more hydrogen sulphide producing species. Flammable ones down to having more methane producing species. Second candidates were the two people who were doing faecal transplants – in these faeces from a healthy person are mixed with salt water and put into an unwell person’s stomach via a tube down the nose. This can introduce a better mix of bacteria to the gut.

So this turned out to be quite an interesting programme, although I was somewhat glad that we ate our pudding during the other programme we watched on Wednesday rather than during this one!

Ice Age Giants; Wonders of Life

Ice Age Giants is a new series presented by Alice Roberts about the large animals that lived during the last ice age. It’s a nice blend of Roberts talking to various experts & looking at fossils, and cgi of what they think the landscape & animals look like. Of course I always wonder what we’re wrong about looking at stuff like that, but it’s cool to see.

The first episode was all about animals in North America. She started with Smilodon fatalis, the sabre-tooth cat – this segment mostly concentrated on how it killed its prey. The sabre teeth are actually pretty fragile (relatively speaking) and one might think that they would be easily broken by getting stuck in struggling prey. They also can’t kill the way modern big cats do – like lions – because they actually suffocate their prey by crushing the windpipe between their jaws or pinching the nose shut. But if you look at the width that a sabre-tooth cat’s mouth can open (to an angle of 120°, twice as wide as lion’s) and the big boned & heavily muscled front legs then another hypothesis becomes apparent. The cats killed by pinning down their prey (to keep them still) then slicing through the throat & ripping out the windpipe or cutting the various arteries there.

Roberts then moved on to talking about the Shasta ground sloth – a large (grizzly bear sized) relative of modern sloths. She visited a cave that had been a ground sloth lair with a palaeontologist who studies these animals – the cave contained a very large amount of sloth excrement. Apparently it hadn’t rotted because the conditions in the Grand Canyon (where this was) are so dry. They looked at bits of this & could see that sloths clearly didn’t digest their food all that well (bits of twig & so on still recognisable). And there was even a large pile near the back of the cave that had distinct layers and so on running from ~40,000 years ago through to ~20,000 years ago – a bit like the geological record in rocks.

Next up were glyptodonts, an animal I’d never heard of before. In the cgi sequences they looked a bit like massive armadillos or turtles on steroids. According to the palaeontologist Roberts talked to these creatures are often found belly up – if they die in water then the weight of their shells makes their body flip over & they sink to the bottom upside own. They had a reconstruction of two of these fighting – they don’t just have massive armoured shells and armoured tails, they also have little armoured hats that look about right for protecting the brain as two of them clash together in a dominance fight (a bit like stags).

Roberts then went to look at large standing rocks with a scientist who is looking at the weathering/wear patterns on the rock. He thinks that the smooth patches must’ve been polished by animals rubbing up against the rocks to scratch their backs as the wear patterns don’t look like any of the other possible causes he’s investigated. The lower bits & bobs could’ve been many things (including modern domestic livestock), but the 14 foot high patches were almost certainly mammoths! The Columbian Mammoth was bigger than the Wooly Mammoth of Europe, and was even taller than modern elephants. And they weren’t hairy, I had no idea you got bald mammoths.

And the last segment of the programme was about the La Brea Tar Pits. Which as soon as she said the name I remembered I knew of them, but I’d forgotten till I was reminded. These are in California, and are a source of natural asphalt. It’s sticky (obviously) and sometimes creatures get trapped in it and die – and to date 3,000,000 specimens of 600 different species of fossils from the era of the ice age have been found in these pits. I don’t think they’ve actually dug through much of them – there was one batch found when an oil company was digging up the tar, and another batch was dug up when some where wanted to build a car park. They’re still processing this batch – it was moved in blocks so they can now excavate it properly. So they aren’t just finding the big animals (which include sabre-tooth cat kittens!) but also the little ones like snails & beetles and such. And this is generating a lot of useful information about the general environment and climate in the area during the ice age period.

Once upon a time I wanted to be a palaeontologist, but I’m not really an outdoorsy enough person to do the work. But you can picture me watching this programme filled with glee and bouncing up & down a bit going “oooh, look at that, isn’t that cool?”. And there’s another episode next week! 🙂

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We’ve now finished watching Brian Cox’s Wonders of Life, the final episode was mostly looking at the physical & chemical properties that make life possible on our planet. The ingredients that make it home, as he put it.

So he started out with water, and explained hydrogen bonds. These form because water molecules are polar – the electrons in the molecule are more around the oxygen atom than the two hydrogen atoms. So the oxygen atom has a slight negative charge & the hydrogen ones are slightly positive. These means that bonds called hydrogen bonds form between the oxygen of one molecule and the hydrogens of another. Which makes a body of water not just a bunch of separate molecules but instead it’s a more cohesive thing. This makes water a good solvent (I’m not sure I followed this, but I’ll take his word for it), and so it carries many of the other nutrients we and other life forms need. Its solvent properties also make it a good place for our own internal chemistry to happen – and all living things have a large percentage of water. The cohesiveness of water also gives it surface tension. Cox demonstrated this by looking at pond skaters, which live on the top of water supported by surface tension. Surface tension is also how water moves through plants, all the way from the roots to the leaves.

Next up was light, and he started by looking at all the ways that the light from the sun is harmful concentrating mostly on talking about UV. UV light damages DNA and can burn skin, so most animals and plants have some sort of adaptation to prevent this. Humans (and other animals) use melanin, which is a brown pigment that is particularly good at dissipating the energy of the UV radiation. Cynaobacteria evolved a different way of dealing with light – they absorbed & used the energy. The coupling up of two energy using systems to take the energy of light plus CO2 and turn it into sugars (ie food) and O2 appears to’ve evolved only once – plants do it too using organelles which are descendants of cyanobacteria that now live inside plant cells. And this provides the third of the ingredients we need for our sort of life – oxygen. He went into a cave with a sulphurous lake to look at the sorts of organisms that life in oxygen-free environments – slimy ones, it seemed.

And the last of his ingredients was time. Both the sort of time that gives us our circadian rhythms and gives the monarch butterflies their navigational systems, and also the sort of time that gave us a chance to evolve. If you look at the history of life on this planet there’s a loooong couple of billion years before you get beyond single celled organisms. Even a billion years to get from simple cells (prokaryotes) to complex cells (eukaryotes). Cox was asking “is it necessary to have all that time?”, and saying that we don’t know because we only have one sample so not enough data. I’m not sure I agree – there’s clearly random chance involved in whether or not the right mutations came up, so it could’ve happened immediately or it could never’ve happened. So I don’t think the length of time it did take is significant or necessary. It’s just indicative of how rare a chance it is – because each of the big jumps (non-life -> life, simple -> complex cells, single celled -> multicellular, development of photosynthesis etc etc) has only happened once despite the four billion years available (a third of the age of the universe, don’t forget).

Overall I’ve enjoyed watching this series. It really wasn’t what I was expecting (though I’d find it hard to tell you what I was expecting) but in retrospect it’s obvious that a physcist would tell us about the physics & chemistry behind the biology. And it was more interesting for me because it wasn’t what I was expecting. I did feel he was stronger on the physics & chemistry than the biology which sometimes felt a bit like he was saying things he didn’t quite understand. A bit like me talking about physics to be honest 😉

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Wonders of Life; Brazil with Michael Palin

The third episode of Wonders of Life had the theory of natural selection as its theme, but once again didn’t approach it from the direction I expected. Instead Cox started by talking about how the most important element for life is carbon, because of its versatile chemical properties that allow it to form large & complex molecules with a variety of other elements. These molecules include proteins (which are the building blocks of organisms) and DNA (the instruction set). So he started by telling us about carbon being formed in stars, and then talked about how carbon in the atmosphere gets into organisms. The first stage is photosynthesis – where plants take CO2 and energy from the sun and turn them into sugar (a molecule with a carbon backbone) and O2. From here Cox moved on to talk about how the carbon that the plants are made up of move through the food chain – a lot of animals eat plants, but they are hard to digest because a lot of the carbon is bound up in molecules like cellulose & lignin which are important structural parts of plants. Termites solve this problem by farming fungus in their colonies, which digests the wood they bring it and then the termites eat the fungus. Giraffes in common with other ruminants have a complicated digestive system with multiple stomachs, one of which contains bacteria which help break down cellulose. Other animals take the shortcut of eating animals instead of plants – there was some great footage here of a leopard coming to pay a visit to the (very open!) car that Cox & camera crew were sitting in. I don’t think I’d want to go on safari, that’d freak me out!

Having established how animals get their basic components (to some extent) and talked about foodchains, Cox now moved back to DNA and how come there are so many different sorts of organisms. First he gave a brief description of how DNA codes for proteins (with not much detail) and then we talked about what drives mutations. He name checked the sorts of causes, and showed us one – cosmic rays. That was a pretty neat experiment, I don’t know that I’d seen a cloud chamber before and it was cool to see the cosmic rays passing through the vapour in the tank! He then talked about the incredibly high number of combinations of possible DNA molecules that there are if everything was down to random chance – most of which would be instructions for organisms that couldn’t live. So there must be something that constrains the set of combinations, and that something is natural selection.

I found his explanations here to be rather muddy to be honest, perhaps because I would’ve approached the subject differently if I was doing the explanation, perhaps because it was a high level overview of something biological told by a physicist so something got lost in the translation. But we got neat footage of lemurs in Madagascar, so that made up for it for me (and I hope that other people watching it who didn’t know what he was talking about in advance found it comprehensible). The gist of it was right, anyway – that variation between organisms affects their chances of survival (like having a slightly longer thinner finger for an aye-aye makes it easier for it to dig out insects from trees so that makes it easier for it to get food and to stay alive). If something survives more, it has more offspring so there are more like it in the population. And over time these changes can build up (the middle finger of an aye-aye looks really very different to that of other lemurs), and if the population is isolated in some way from the rest of its species then they will become a different species and no longer able to interbreed with the originals. Isolation can be geographical (he showed us how the break up of the supercontinent Gondwana had left Madagascar isolated for tens of millions of years), but it can also be within a geographical area by lifestyle or habitat. (After complaining about his muddy explanations, I think mine probably are too, ah well.)

The fourth episode was all about size, and how the laws of physics affect the size of organisms and the size of organisms affects which laws of physics are important to the organism’s everyday life. He started by swimming with great white sharks (he was in a cage so quite safe, but frankly I would really rather not have that experience personally), and using them to illustrate how the effort required to move through water constrains the shape an animal is – sharks, as with fish and aquatic mammals, are streamlined. He also talked about how living in water allows animals to grow larger, because the water counteracts some of the effects of gravity.

This moved nicely onto a discussion of how on land as animals get bigger they need bigger skeletons to support themselves, and this constrains the sorts of shapes they can be (big animals are proportionally bulkier) and the ways they can move. He illustrated this with Australian marsupials, and worked in an explanation of how kangaroos’ locomotion is so efficient because their elastic tendons store the kinetic energy that they have when they land, and then use that to spring back up again. But the main point of this sequence was to show us the relative femur (thigh bone) sizes of various marsupials both living & extinct. As the length of the bone increases (so the animal is bigger) then the cross-section increases significantly more (i.e. a five-fold increase in length but a forty-fold increase in cross-sectional area) – this is because the mass of the animal has increased in proportion with its volume, and volume increases as the cube of length.

Cox then turned from animals our sort of size (i.e. mice to elephants …) where gravity is the dominant force, and moved to the much smaller scale of insects. Particularly amusing in this bit was him dropping a grape then a watermelon off a balcony to demonstrate that small things bounce and bigger things … don’t. He talked about how this is due both to smaller things falling a bit more slowly (due to friction with the air) and also because big things have more kinetic energy that must be released when they hit the ground (because it’s proportional to mass, I think). And this is done via exploding in the case of the watermelon. So gravity isn’t the big thing for an insect, instead it’s the electromagnetic force, which controls the interactions between molecules – like the way you can pick up a small piece of paper by wetting your finger so the paper sticks to it. This principle is what lets insects walk up walls or across ceilings.

He then went on to talk about what the smallest possible size for an organism is. First for animals – of which the smallest known is a wasp that’s about 0.5mm long, and is a parasite that lays its eggs in the eggs of a moth that feeds on & lays eggs on macademia nuts. And then for bacteria (skipping viruses because they’re not really alive) – where the smallest possible size is 2nm (I think) which is constrained by the size of atoms. You can’t be smaller than the volume necessary to fit all your cellular machinery, and those molecules are the size they are because their atoms are the size they are.

And then Cox talked a bit about how size affects metabolism, and how that in turn affects longevity. Smaller things have a higher surface area to volume ratio (because as something gets longer its surface area goes up by the square of the length change but its volume goes up by the cube). And this means they lose more heat than a larger version. And if you’re an endotherm (like people are) and generate your heat inside you, then the more you lose the more energy you must use to replace it. So smaller animals tend to have a higher metabolism and generate more energy from more food more quickly. Bigger animals both don’t need so much energy (if they’re endotherms) but also there are other constraints that mean that they need to slow down their metabolism. I think one of those was that it takes longer for things like nutrients to get through the circulatory system and so cells at the periphery can’t run too fast otherwise they’d burn up all their resources before they could be replenished (I’m not sure I’ve remembered that right though). Then Cox finished up by using crabs to illustrate that things with a slower metabolism tend to live longer (and this segment made J shudder because he hates crabs!).

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The second episode of Brazil with Michael Palin was called “Into Amazonia” and covered (roughly speaking) the north west of the country, including the capital (Brasilia) and some of the indigenous people. The programme was bookended by the two tribes he visited – starting with the Yanomami who are very isolated and trying to remain so and ending with the Wauja who are assimilating some bits of modern Western culture while still preserving their own culture. The leaders of both peoples are worried about the impact that government projects (such as dams and mines) will have on their way of life, and frustrated about the lack of consultation.

Palin also visited one of the last remaining rubber tappers – rubber was a major export from Brazil before the British got hold of some seeds and grew rubber trees in Malaysia. A bit of a sad segment, because the industry has just dried up & gone away. As a counterpoint I think this was where he got to swim with the pink river dolphins, which right up till they showed up I had assumed were going to be some sort of euphemism (particularly with the solemn young man explaining how sometimes girls turn up pregnant & they say the dolphins did it)!

I’m not going to run through everywhere he went or everything he saw, but the other bit that stuck in my mind was Fordlandia. This was a planned town, with a Ford factory, and it was supposed to be a perfect America (this is back in the 1920s). But what it was was a perfect failure, and all the remains today are some abandoned ruined buildings in the jungle.

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Wonders of Life; Brazil with Michael Palin

Well, Brian Cox’s Wonders of Life series really didn’t start how I expected it to do. I suppose in retrospect it should’ve been obvious that a physicist would talk about the physics & chemistry of life rather than the biology! This first episode was asking the question “What is life?”. He made a brief detour to mention that this question is typically answered by reference to a soul or other supernatural cause, but then started to talk about the laws of physics and how life exists as a result of the ways these laws work (in the same way that a star exists because of how the laws of physics work).

Life probably got started in hydrothermic vents in the ocean – which are alkaline environments. The ocean of the time (3.5 or 4 billion years ago, or so) was slightly acidic, so there was a proton gradient set up between the alkaline waters of the vent & the acidic waters around about it. The protons moving along this gradient releases energy. This is the same mechanism by which batteries work – in this case the heat of the earth’s core drives the setting up of the gradient, and because of the first law of thermodynamics (conservation of energy) all of this energy must be released when the protons move down the gradient. The hydrothermic vents are also rich in organic molecules, and the energy drives the chemical reactions between these molecules. And the first life arises from that chemistry. All life uses proton gradients to get its energy – he showed us pictures of mitochondria from a variety of animals, but the same is also true of prokaryotes (which have no mitochondria).

At first glance life violates the second law of thermodynamics – that the universe tends towards disorder. Living things are obviously complex and over the last few billion years they’ve got more rather than less complex. I never quite follow this argument (physics really isn’t my thing) but I think what it boils down to is that whilst an organism is more complex it’s achieved that in a way that disorders its surroundings more than they would otherwise be. So yes living organisms are localised pockets of complexity but the universe as a whole is still more disordered than before.

He then moved on to talk about how come life isn’t still just chemical soup in rocks. And what keeps organisms the same as their parent organisms. The answer is DNA – the instruction set for making an organism. I was much amused by his DNA precipitation experiment – take cheek cells, add detergent, salt and alcohol, and hey presto! you have white strands of precipitated DNA in the alcohol layer in your test tube. That’s pretty much the basis of a lot of molecular biology labwork – only you don’t use fairy liquid or vodka. He then ran through the basic high level structure of DNA and talked about how it codes for proteins. And then proteins are both the building blocks & machinery of cells and organisms. The great thing about DNA as a molecule to store the instructions is how stable it is – he quoted 1 error per billion bases (I think) when duplicating DNA which is a pretty low error rate. And relatively small differences in the instruction set are enough to generate very different organisms – he pointed out we’re only 1% different from chimpanzees, 1.6% different from gorillas etc.

The second episode was all about senses. After a bit of scene setting he talked about paramecium, which are single celled organisms that swim about using wee hairs (cilia) in their cell membrane. When it bumps into something in the water the little hairs reverse direction and it moves away again. It does this using proton gradients – normally there’s a difference between inside & outside the cell, and when the paramecium touches something the membrane deforms & this opens channels in the membrane and the proton gradient equalises. The energy generated by this is used to switch the direction of the cilia and to open more channels (I think) which means the change in direction propagates right round the cell. This is the basis of how all our senses transmit the information back to the brain – this is how nerve cells work.

Cox then spent a bit of time talking about how different animals have different senses (and different dominant senses). Different species therefore sense the world differently to us – our dependence on sight & hearing, and our ranges of sight & hearing, aren’t some objective way of detecting the world. Like all other animals we have the senses that we need for our evolutionary niche. In this bit I was particularly amused by the footage from some experiments on frogs – if a small rectangle is move past a frog in a horizontal orientation it goes nuts trying reach it & eat it. If the same thing is moved past in a vertical orientation, the frog doesn’t even seem to see it. When it looks like a worm, then it’s detected, when it doesn’t look like lunch it’s not worth wasting energy paying attention to.

He then talked about human hearing while sat on a boat near some alligators. The point of the segment was that despite the little bones in our ears looking like they’re designed for the purpose, actually they’re re-purposed gill arches. And part way through this long process of re-purposing the bones are the reptiles, whose jaw bones are also re-purposed gill arches. So the alligators were illustration …I still wouldn’t’ve got that close to them myself!

And obviously he talked about sight. Rhodopsin, a pigment that reacts to light, has been around in organisms for a long time – way back to cyanobacteria which have existed for a couple of billion years. And Cox demonstrated how simple a basic eye actually is – even a “camera eye” like ours (retina which does basic light detection, some sort of case with a hole in in front, then a lens in the hole. Obviously the devil is in the details, but one thing Cox didn’t mention explicitly is that eyes are believed to have independently evolved several times (the figure I remember is at least 40 times, but I don’t know if that’s right). He then went diving to see an octopus in its natural environment – which is another animal with a camera eye like ours (and it evolved independently). Octopuses are pretty intelligent, and Cox speculates that perhaps intelligence is driven by the need to process the complex images that our sophisticated eyes produce. I’m not sure what I think of that, in the same programme Cox also showed us a mantis shrimp that sees more colours and detects distance more precisely than people – but there was no talk about them being particularly intelligent.

As I said, not quite what I expected from the name of this series, but that makes it more interesting I think 🙂

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We also started watching a series about Brazil with Michael Palin. I tend to be a bit wary of travelogues like this – sometimes the bits where the presenter joins in can cross the line between funny & cringe-making for me. Palin normally stays about on the right side of the line, but only just. But it’s still interesting to see the places & people.

The first episode was about the north-east of the country & was titled “Out of Africa”. A lot of people in this region have African ancestry – a lot of the slaves brought from Africa to the Americas ended up in Brazil. Palin quoted a statistic of 40%, and said this was more than ended up in the USA, which I was startled by. This has noticeable influences on the art & culture of the region – one notable example is the religion of Candomble which mixes African and Christian elements.

Palin visited a few different places in the region & a variety of different sorts of groups & events. The ones that particularly stick in my mind were the cowboys who were participating a race to catch bulls. And the national park that consists of a region of sand dunes that are blown miles inland to an area with heavy enough rainfall that there are lakes in the middle of the dunes – which looks pretty surreal.

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In Our Time: The Cell

This week we listened to the In Our Time programme on the cell while we had our Sunday morning breakfast. This is a subject about which I know rather more than the average educated layperson*, so I was curious to see if it’d hold up as still being interesting. It did 🙂

In the 45 minutes they managed to cover an impressively large amount of ground. Starting with a brief intro on what a cell is (building block of biological organisms, but just like the atom once you look more closely there’s a lot more going on inside than you thought), then moving on to how big (not very) and how many in a person (a lot, but even all those human cells still only add up to 10% of the cells in your body, the rest are bacterial). They then covered in chronological order the three main stages in life on earth (if you’re thinking from a cellular perspective). First there were prokaryotes – bacteria are this sort of cell. These are the simplest sort of cell – a membrane bag that makes the important chemicals be more concentrated inside than they are in the sea. They have DNA (the metaphor they used was of a library), RNA (copies of blueprints from the library) and proteins (built from the blueprints), and they make the needed energy to do their internal chemistry by transporting protons across the outside membrane. But they don’t have any divisions on the inside of the cell, everything’s in the bag together.

Then about a billion years later the eukaryotes appear (an amoeba is a single-celled eukaryote) … and Melvyn Bragg managed to mispronounce eukaryote more ways than I could count in 45 minutes – the best was when he turned it into something resembling “erotic” 😉 Eukaryotic cells have subdivisions inside them – they’re named for having a nucleus which is a compartment that holds the DNA, they also have mitochondria which were originally free living prokaryotic bacteria. These are the true determinant of eukaryotic cells – they evolved by one cell type engulfing another type, and then living in a symbiotic relationship where the internal bacteria provide energy for the outer cell. It’s thought this arose once and only once. So having more energy and having separate compartments (many of them, not just the two I mentioned) lets them maintain a bigger genome (the fragile DNA is kept away from the rest of the machinery, they have enough energy to do more reactions) and do more complex chemistry.

Next stage (after about another billion years) is the arise of multicellular organisms (like people! tho that took a while) – which are lots of eukaryotic cells stuck together. In this last section they managed to touch on the two sorts of cell division, cell specialisation by controlling which genes are switched on or off, and even some relatively recent research that shows that the control switches for the genes might be quite a long way away on the DNA strand so the way the DNA folds up in the nucleus is important (now that’s a hard problem to solve)**. Oh, and also to mention the true distinction between male & female (female gametes provide the mitochondria).

The experts on the programme were Steve Jones from UCL, Nick Lane (also UCL) and Cathie Martin (JIC and UEA). Unfortunately Prof. Martin wasn’t quite up to the normal standard – she was both nervous & used too much jargon. Either one alone would’ve been OK, but the two together made her contributions somewhat confusing to follow. Which is a shame, because she came across as someone who knew her stuff (as did the other two) but wasn’t comfortable with explaining it to non-scientists (in contrast to the other two).

But that quibble aside, it was interesting to listen to, and I thought it provided a very good high-level run through a complicated subject. It’s always nice when things like this hold up even if you already know what they’re talking about, gives you confidence that the ones you don’t know are equally accurate 🙂

*Amusingly one of the further reading suggestions on the Radio 4 website for the programme is for a textbook I had to buy for my first year undergrad – Alberts et. al. “Molecular Biology of the Cell” … it’s the 2nd edition I have on the bookshelf upstairs, seems they’re up to a 5th edition now.

**One of the things I was doing during my last post-doc was looking for the β-catenin promoter, so this was particularly interesting. Mapping the 3D structure of the DNA to make sure all the various bits line up with the right genes has got to be complicated. And I bet it changes based on what cell type, which other genes are switched on or off etc.