When you can see the sea in the dark

You may have seen bioluminescence, also known as phosphorescence, in the movie Life of Pi. Or possibly in the Gippsland Lakes (“Plankton put on a show at Lake Victoria”, The Age, 29 January 2013).

Bioluminescent plankton lighting up splashes of water in the Gippsland Lakes in January 2009 (Photo by Phil Hart)

The short explanation for what causes it is that it’s oxidisation of the chemical luciferin, in the company of the enzyme luciferase, releasing energy in the form of light. This reaction is found in all kinds of animals and fungi, from fireflies and glow worms, through to Anglerfish and Colossal Squid, and of course marine plankton.

The long answer is best found by listening to Beth in our podcast from 24 January 2013. Go do that, along with our other previous shows.

Smelling asparagus wee is a mutant superpower

Some people report that their urine smells funny after eating asparagus, and some don’t. But is it because their wee is different or their sense of smell is different? Cue: science!

Actually, you can test this at home fairly easily. If you’re able to smell asparagus wee but you know someone who can’t, simply go into the bathroom after they’ve visited it following an asparagus meal. I’ve tried it – in the name of science – and I can say that I could definitely smell their urine, even though they couldn’t (a condition called specific anosmia).

However, that’s not a terribly rigorous experiment, and the plural of anecdote is not data. But answering it properly turns out to be a rather tricky puzzle, and one that has mildly interested scientists for centuries.

If you’re an asparagus-wee-smeller, you know exactly what the result of eating these will be. If you’re not, then you’re probably wondering what all the fuss is about (Photo by Jeremy Keith from Brighton & Hove, United Kingdom, via Wikimedia Commons)

The phenomenon of asparagus wee was first documented in the 18th century, by French botanist Louis Lémery in 1702 and English physician John Arbuthnot in 1735. Arbuthnot particularly observed that it’s more common after eating tastier, young asparagus.

Not a scientist, but renowned for his appreciation of smell and taste, was Marcel Proust, who said that asparagus “as in a Shakespeare fairy story transforms my chamber-pot into a flask of perfume.”

But the cause of it has taken a while to pin down, partly because it doesn’t appear to have any medical significance, so there isn’t really a pressing need to solve it. This is unlike, say, the tendency of some people to have red urine after eating beetroot, which has been linked to things like absorbing too much iron (see Mitchell SC 2001, “Food idiosyncrasies: beetroot and asparagus”, Drug Metabolism & Disposition, vol. 29, no. 4, pp. 539-543).

The other problem is that it’s subjective. Most studies have involved simply asking people “does your urine smell weird after eating asparagus?” But how do you define “weird”?

And we still don’t even know what causes the smell. Chemical analysis of urine can alter some of the volatile compounds that might be responsible. And even if you do find something unusual, how do you know that that’s actually causing the smell?

What you really need to look at is the vapour above the urine. Fortunately, a few dedicated souls have done just that, revealing a number of possible candidates, all of them sulphur compounds (see for example Waring RH, Mitchell SC & Fenwick GR 1987, “The chemical nature of the urinary odour produced by man after asparagus ingestion”, Xenobiotica, vol. 17, no. 11 , pp. 1363-1371, doi:10.3109/00498258709047166).

The main one that people have identified – and for a long time was believed to be the primary source of the smell – is methanethiol (CH₃SH). It’s also found in faeces, bad breath, farts and other decaying organic matter, and it smells like rotten cabbage. It’s sometimes added to natural gas to give it a smell, for safety reasons.

So it’s famously smelly, which is one reason to doubt that it’s the culprit. After all, everyone can smell things like faeces and farts, but asparagus smell is a little more idiosyncratic. Which means it’s probably a combination of it and the other sulphur compounds; things like dimethyl sulphide, dimethyl disulphide, bis-(methylthio)methane, dimethyl sulphoxide and dimethyl sulphone.

Because all these chemicals contain sulphur, they have to originate from a sulphur compound that’s unique to asparagus. The only possible candidate is called, surprisingly, asparagusic acid (S₂(CH₂)₂CHCO₂H). It’s deadly to insects, and found more in young asparagus, presumably to protect them from pests. So Dr Arbuthnot back in 1735 was right.

However, it’s not the asparagusic acid itself that ends up in the urine, it’s what the body metabolises it into. Which is the methanethiol and all the dimethyl et ceteras.

So we have some possible culprits, but we still can’t isolate the recipe for the smell. Which means we can’t just hand people a flask of the odour, and instead we have to go back to smelling urine.

One of the most comprehensive urine-sniffing studies was published in 2010. It used a technique called ‘two factor forced choice’, where they presented people with asparagus and non-asparagus wee, both their own and from other subjects, and they had to say which was tainted. Pelchat ML, Bykowski C, Duke FF & Reed DR 2010, “Excretion and perception of a characteristic odor in urine after asparagus ingestion: a psychophysical and genetic study”, Chemical Senses, published online 27 September 2010, doi: 10.1093/chemse/bjq081

Unexpectedly, in this study they got a spread of results, rather than a simple yes-no, can-can’t smell it. Only 3 people out of 38 did not produce smelly urine, i.e. when other subjects were asked which of the samples came after eating asparagus, results were no better than chance. And only 2 were unable to smell it at all. But there was certainly a range of ability to smell, and a range of smelliness.

Alongside this they also did some genetic testing. This concentrated on a single nucleotide polymorphism – that’s a variation in just a single base-pair in the DNA molecule – near a gene call OR2M7 (the OR is for ‘olfactory receptor’). They showed that that variation was strongly associated with the ability to smell the asparagus in urine.

But there was no association with the ability to produce it. Although there was a range of smelliness, which would have to be related to how their bodies process asparagusic acid, the cause is as yet unknown.

So it seems that the main difference between people is due to this mutation in OR2M7. If you have it, you can smell asparagus wee, and if you don’t… Well, you can probably smell it at high concentrations, but not as well as the mutants.

Which all concurs with my not-so-scientific, DIY test. Which is reassuring, but I still wouldn’t expect my study to be published in a peer-reviewed journal.

(This story first aired on 24 January 2013 – you can listen to the podcast.)

Every cigarette is doing ectoparasites damage

¡Feliz Año Nuevo! If your new year’s resolution is to quit smoking, consider donating your used butts to Mexican birds, who appear to be using them to get rid of parasites.

After noticing that local birds were incorporating cigarette butts into their nests, researchers in Mexico City decided to test whether they might be doing because of the parasite-repellent properties of nicotine (Suárez-Rodríguez M, López-Rull I & Garcia CM 2013, “Incorporation of cigarette butts into nests reduces nest ectoparasite load in urban birds: new ingredients for an old recipe?”, Biology Letters, vol. 9, no. 1, 20120931, doi: 10.1098/rsbl.2012.0931).

Sure enough, nests with more butts were found to have fewer ectoparasites (creatures like mites that live on the outside of organisms) than those without. Although, they also found that smoked butts worked better, as they were more toxic to parasites.

Further research is needed to determine whether the birds are choosing the butts for their anti-parasite properties, or if it’s just because they make good insulation. Also, the researchers hope to find out whether using cigarettes does actually benefit the birds, or if the toxicity harms them as well.

But it’s good at least to see that birds can adapt and make use of urban environments, even if it is through poisonous litter. A kind-of good news story to start the year!

(This story first aired on 20 December 2012 – you can listen to the podcast.)

A pox on your detox

Last week on the show, Stu talked about something that catches the attention of many of us who over-indulge during this silliest of seasons: detox. In particular, the detox programs hawked by manufacturers of vitamin supplements and weight-loss plans, which claim to cleanse your body of toxic substances.

These pseudomedicines are a beloved bane of science communicators everywhere, so I don’t really have much to add. Instead, I recommend you listen to our podcast.

But if you really need to read something about it, try the following:

• consumer advocate Choice’s investigation of 10 diet detox products, CHOICE says you don’t need a pill to purify (media release), or Do diet detox products work? (full article).
• British doctor and author of Bad Science Ben Goldacre’s classic take-down of The detox myth (The Guardian)
• another British group, Sense About Science’s comprehensive, 18-page Detox dossier
• academic website The Conversation’s recent feature Monday’s medical myth: detox diets cleanse your body.

But if you really, really want something without having to click a link, take the following example: cigarette smoke.

Cigarette smoke and the damage it causes cannot be cleansed by taking a magic pill. The only way to get it out of your system is to stop smoking for good (Quit poster, Australian Government)

Cigarette smoke is one of the toxins most frequently listed by detox proponents. But as we all should know after decades of government advertising – like the Quit poster shown above – the only way to rid yourself of its toxic effects is to stop smoking.

There is no magic pill, lemon drink, ear candle, or – heaven forfend – colonic irrigation, that will protect you from harm and allow you to keep smoking. Similarly, quitting for a couple of weeks, or 10 days as many of the detox plans seem to run for, won’t undo the damage from years of tobacco.

As for other, less deadly toxins that you consume in moderate amounts – like say, chocolate – well your body is quite capable of handling them itself, thank you very much. You don’t need to swallow another substance to chase them out of your system.

When you think about it, detox programs are a bit like the old lady who swallowed a fly. And look at what happened to her…

Bottom of the food chain at the bottom of the world

Australian scientists recently completed a mission studying algae and krill that live under Antarctic sea ice, in an effort to understand the workings of their ecosystem and how it may be affected by climate change.

The 2 month investigation was part of the international Sea Ice Physics and Ecosystem eXperiment-II, or SIPEX-II, and it took place onboard the icebreaker Aurora Australis – currently back in Antarctica on its never-ending mission to transport supplies and personnel to and from Australia’s Antarctic stations.

One part of the mission used an underwater robot called ROV – short for ‘Remotely Operated Vehicle’ – equipped with a light sensor to measure reductions in blue and green light beneath the ice, and hence estimate the amount of algae.

The other part involved capturing larval and juvenile krill and examining their metabolism, growth rate and diet. These tiny crustaceans go through 12 larval stages, about which not much is known as previous research has mostly focused on adults, and even then usually in the Antarctic summer rather than winter as experienced by SIPEX-II.

Krill feed on the sea ice algae, and are themselves food for larger animals like penguins, seals and whales. So together the krill and algae form the foundations of the Southern Ocean ecosystem.

Other members of SIPEX-II looked at different physical and biological aspects, such as ice and snow cover measured with laser and radar-equipped helicopters, algae physiology, sea ice biogeochemistry, and water temperature, oxygen content and salinity.

With climate change predicted to reduce sea ice by 35% by the end of this century, we need to know how the Antarctic ecosystem works so that we can understand the impact of losing its cover.

Find out more about this project on the website of the Australian Antarctic Division.

(This story aired on 13 December 2012 – you can listen to the podcast.)

Lost in science fiction: The Fifth Element

Let’s get the obvious out of the way: there are way more than five elements, and – despite what Captain Planet would have you believe – ‘heart’ is not one of them.

However, one bit of Luc Besson’s 1997 movie The Fifth Element may be coming true. Somewhere near the beginning, a gloved hand retrieved from a crashed alien spaceship is cloned to create a masking tape-clad Milla Jovovich. Except she isn’t just cloned: her body is constructed bit by bit, some in layers and some woven from a biological spinning wheel (see from about 1:30 in the video clip embedded below).

This method is startlingly similar to one used by scientists from the Wake Forest Institute for Regenerative Medicine, North Carolina USA, to create artificial cartilage (Tao Xu, Binder KW, Albanna MZ, Dice D, Weixhin Zhao, Yoo JJ & Atala A 2013, “Hybrid printing of mechanically and biologically improved constructs for cartilage tissue engineering applications”, Biofabrication, vo. 5, 015001, doi:10.1088/1758-5082/5/1/015001).

They used a ‘hybrid 3D printing’ technique, where fibres of polycaprolactone, a biodegradable polyester, were spun to form a framework onto which rabbit cartilage cells, or elastic chondrocytes, were deposited by an ink-jet printer. The printed cartilage was then implanted into mice, and after 8 weeks appeared to be taking on the properties of natural cartilage.

Although these are really early days, the technique has promise for creating custom cartilage replacements for human patients. The current alternatives are either joint replacement or an elaborate process of causing the cartilage to bleed and hoping that scar tissue covers any gaps.

Of course, building a complete ‘perfect human’, or alien or whatever she was, is even further off.

(This story aired on 6 December 2012 – you can listen to the podcast.)

Quality, not quantity, important in whale food

During the FV Margiris Abel Tasman supertrawler fiasco, one issue that worried people was the impact of overfishing on marine ecosystems. But recent research suggests that, at least for some whales and dolphins, getting the right food is more important than getting enough food.

This study looked at the diets of 11 species of cetaceans (whales and dolphins) in the North Atlantic and found a close correlation with their ‘cost of living’, i.e. those species whose muscles burn more energy tended to seek out higher calorie food (Spitz J, Trites AW, Becquet V, Brind’Amour A, Cherel Y, Galois R & Ridoux V 2012, “Cost of living dictates what whales, dolphins and porpoises eat: the importance of prey quality on predator foraging strategies”, PLoS ONE, vol. 7, no. 11, e50096, doi:10.1371/journal.pone.0050096).

A sperm whale, Physeter macrocephalus, eating a fish on the ocean surface near Kaikoura, New Zealand. Sperm whales normally feed in the ocean depths rather than the surface, but this one was clearly being opportunistic – and in fact they were one of the species found to get by on low quality, don’t-care-what-they-eat-as-long-as-there’s-enough food. The classic ‘see food’ diet, if you will. (Photo by Richard Giddins, via Wikimedia Commons)

This was independent of body size, as some similar species – such as the Common and Striped Dolphins – had very different feeding patterns.

The researchers put this down to evolution, in that high-energy prey moves faster, so their predators need to burn more energy to catch them – which means that in turn the prey needs to move even faster to escape, and so on.

The implications for conservation are that some whales and dolphins need the right kinds of high quality food to survive, so we can’t just assume that large amounts of low quality ‘junk food’ will be good enough.

(This story aired on 6 December 2012 – you can listen to the podcast.)

How to make a self-filling water bottle

Generating water out of the air is tricky, but it can be done thanks to the Namib Desert Beetle, which figured out the trick long ago, and a bit of biomimicry.

Biomimicry is the use of inspiration from nature to create new technologies. A good example is Velcro, which is based on burrs from plants and their habit of sticking to socks. In this case though, the kudos for cleverness really does belong to the beetle in question.

Namib Desert Beetle, Stenocara dentata, with its black wing casings covered with water-attracting bumps. Click to see the bumps up close (Photo by Hans Hillewaert, via Wikimedia Commons)

This beetle belongs to the genus Stenocara and it lives in the Namib Desert, on the coast of Namibia in south west Africa. The desert is very dry, receiving less than 10 millimetres of rain per year, but about six times per month there are morning fogs that sweep across the sand. And it’s from the fog that Stenocara gets its water (Parker AR & Lawrence CR 2001, “Water capture by a desert beetle”, Nature, vol. 414, no. 6859, pp. 33-34, doi:10.1038/35102108).

It’s a member of the family Tenebrionidae, or the darkling beetles, so-called because they have black wing casings. In the Stenocara these wing casings (which are actually the forewings, or elytra) are fused together, and the whole thing is covered with little bumps about half a millimetre in diameter.

The trick is that these bumps are hydrophilic, meaning that water sticks to them, much like it clings to and spreads out on smooth glass. But the areas in between the bumps are waxy and hydrophobic, i.e., they repel water.

What happens is that in the morning the beetle stands on its long, spindly legs facing into the breeze, with its body angled at about 45 degrees. As the fog flows past, tiny droplets accumulate on the hydrophilic bumps. When they get to about 5 millimetres in diameter, they become too big to stick to the bumps and they detach and roll down the hydrophobic grooves to the beetle’s mouth.

In a single day, the beetle can collect 12% of its weight in water. So it’s not surprising that people have been trying to make similar materials artificially, usually by depositing drops of hydrophilic substance on a hydrophobic substrate.

One company, called NBD Nano, is trying to commercialise it and create efficient, artificial fog harvesters. Of course, this isn’t the first technology that’s been tried for this purpose.

Dehumidifiers are a familiar example, taking water out of the air by cooling it and causing condensation. But of course that requires quite a bit of energy to run – although in 2011 an Australian inventor won the James Dyson Award for a device that cools the air using underground coils, so you only need enough energy to pump the air down a pipe.

Another low energy technique is that used in the Atacama Desert in Chile, and is basically just a piece of mesh strung between two poles, with a trough under it. They get a fog too, and as it flows through the mesh, drops of water condense and run down into the trough.

But NBD Nano claim that the beetle’s skin is several times more efficient than the Chilean method. So far they claim a square metre of beetle-inspired material, at 21 °C and 75% relative humidity, can produce 3 litres of water per hour.

Energy is still used to blow air across the collector, but so far they’ve gotten away with using solar panels and a rechargeable battery. So using this as a covering for a greenhouse would be a very simple way to generate enough water for the plants at fairly low cost.

Of course, you don’t need a fan to blow the air if there’s a foggy breeze, like in Chile or Namibia. But it’s also unnecessary if the collector itself is moving, like on a car or a boat, or even a marathon runner.

This is where the idea for a ‘self-filling water bottle’ comes in: imagine running along, carrying a bottle with a panel of this material, and your motion is what allows it to generate water.

That’s a long way off, but it’s a good reminder that the air carries a lot of water that’s just waiting to be harvested. All we need to do is copy the Namib Desert Beetle, and we can do it too.

(This story aired on 6 December 2012 – you can listen to the podcast.)

Great Barrier Reef coral loss is probably our fault

The Great Barrier Reef is the largest coral reef system in the world, stretching over 2,600 kilometres along the coast of Queensland and covering an area of 344,400 square kilometres. But over the past 27 years it’s lost half its coral, apparently thanks to human activity.

Researchers from the Australian Institute of Marine Science in Townsville have been monitoring the amount of coral since 1985. Back then, the reefs they studied had 28% coral cover, but in 2012 they only had 13.8%. That’s a reduction of 50.7% (De’ath G, Fabricius KE, Sweatman H & Puotinen M 2012, “The 27–year decline of coral cover on the Great Barrier Reef and its causes”, Proceedings of the National Academy of Sciences, vol. 109, no. 44, pp. 17995-17999, doi:10.1073/pnas.1208909109).

This reduction wasn’t uniform across the whole system, as the far northern reefs have remained fairly stable at about 24% coral cover. But there’s been a decline in the central region – which they classify as between Cooktown and Mackay – and in the southern region below Mackay, where there’s been a steep drop of over 75% in the past decade alone.

The researchers also looked at what caused these reductions, by modelling possible causes against the observed fluctuations in coral cover. What they found was that 48% of the coral reduction could be attributed to tropical cyclones, 42% to outbreaks of crown-of-thorns starfish, and 10% to mass coral bleaching (primarily two events, in 1998 and 2003).

Climate change would seem to be a factor here, as it’s been linked to the increasing intensity of tropical cyclones (see Knutson TR, et al. 2010, “Tropical cyclones and climate change”, Nature Geoscience, no. 3, pp.  157–163, doi: 10.1038/ngeo779 [PDF 641 KB]).

Temperature also seems to be a major cause of coral bleaching, which is when the coral loses its symbiotic zooxanthellae. These single-celled organisms photosynthesise and provide energy for the coral polyps - as well as the vibrant colours of the coral. In turn, they get nutrients and a home. However, the zooxanthellae seem to be sensitive to temperature, as a rise of only 1°C  can cause mass deaths of them and subsequently their host coral.

But even though climate change is the biggest culprit, the researchers admit it’s unlikely that in the near future we’re going to make a big impact or reduce temperatures. So instead, they suggest concentrating on the crown-of-thorns starfish. If we could cut out just the starfish, but cyclones and bleaching continued, the coral cover would still increase by 0.89% per year.

And we have a chance of doing this, because the crown-of-thorns starfish itself is influenced by human activity.

Crown-of-thorns starfish, Acanthaster planci, competing to eat the last remaining piece of Acropora coral (Photo by JSLUCAS75, via Wikimedia Commons)

As the name suggests, the crown-of-thorns, or Acanthaster planci, is a spiny starfish, or sea star. It’s the second-largest species of sea star in the world, with adults reaching 25-35 cm in diameter and having up to 21 arms. It feeds by latching onto coral with its multiple tube feet and then extruding its stomach out through its mouth to digest coral polyps.

It sounds like a nasty, introduced species, but actually it’s been in the Great Barrier Reef for at least 8000 years. In fact, it’s found in coral reefs across the Indian and Pacific Oceans, from the coast of Africa to the coast of America.

And at normal population numbers, it seems to be a natural part of the reef ecosystem. It prefers to eat the faster-growing coral species, giving the slower-growing species a chance to compete. But occasionally the numbers increase to plague proportions, and the starfish have to eat everything.

Now it’s not 100% certain what causes these outbreaks, but the leading theory is that it’s due to water quality. The starfish larvae feed on phytoplankton, and phytoplankton numbers increase with inorganic nutrients in the water. And these inorganic nutrients increase greatly when fertiliser is washed off farmland, particularly after floods.

So the researchers recommend more effort to improve water quality in order to reduce the numbers of crown-of-thorns starfish. This is in preference to hunting them down one-by-one – which is favoured by MP Bob Katter – because in the past that’s proven to be rather expensive and labour-intensive, but overall ineffective across the whole reef (although hunting does work for protecting a small area, so it’s good for tourist operators).

In the end, it all comes down to pollution, whether greenhouse gases or fertiliser run-off. And until we can cut the former, we need to concentrate on the latter. The crown-of-thorns starfish may in fact be a natural feature of the Great Barrier Reef, but it’s our activities that turn it into a threat.

(This story aired on 22 November 2012 – you can listen to the podcast.)

Synaesthesia mixing the senses at MONA

On 3 and 4 November 2012, I was lucky enough to visit Hobart’s Museum of Old and New Art (MONA) and enjoy a two-day event that mixed art and science to explore the psychological phenomenon of synaesthesia.

Synaesthesia is a ‘joining of senses’, where you perceive something with one sense and at the same time you experience it with another sense. For instance, you may see colours and shapes when listening to music, or colours associated with particular letters or numbers.

MONA’s Synaesthesia event represented this concept with the Tasmanian Symphony Orchestra playing music from composers such as György Ligeti, Henryk Górecki and Modest Mussorgsky, as well as performances from Brian Ritchie, Kate Miller-Heidke and Meow Meow. It blended this with visual art from the museum’s exhibitions, a film program, including Jonathan Fowler’s Red Mondays & Gemstone Jalapenos, embedded above, and fantastic catering.

It also included a panel discussion on the topic, with synaesthetes Andrew Legg and Margaret Hollis, pianist and music scholar Peter Hill (representing the synaesthetic composer Olivier Messiaen), and University of New South Wales psychologist Dr Karen Whittingham.

After the discussion, I had the pleasure of speaking to Dr Whittingham about her research on synaesthesia, as well as artist and synaesthete Steve Glass. You can listen to this interview on our podcast from 15.11.2012.

A transcript follows after the break…