Category Archives: Biology

Newt troublemakers settle in

An entirely new order of invasive amphibians has set up residence in Australia, with populations of newts thriving on the outskirts of Melbourne.

Two smooth newts (click to embiggen)
Smooth newts, Lissotriton vulgaris, look a bit like skinks, and the worry is that native predators may make the same mistake (Photo: Museum Victoria)

The smooth newt, Lissotriton vulgaris, is native to Europe, but the similar climate in south-eastern Australia appears to have helped it establish breeding populations at at least four sites around Melbourne (Tingley R, Weeks AR, Smart AS, van Rooyen AR, Woolnough AP & McCarthy MA 2014, “European newts establish in Australia, marking the arrival of a new amphibian order”, Biological Invasions, DOI: 10.1007/s10530-014-0716-z).

This is a big deal, because there are no newts native to Australia. In fact, the only indigenous amphibians are frogs, many of which—like the Baw Baw Frog—are endangered due to an infectious disease caused by chytrid fungus.

However, newts were imported as pets up until 1997, when the Victorian government declared it a “controlled pest animal.” It’s likely that the current populations originally came from escaped or released pets.

Being a relative newt-comer, it’s not yet known how bad an impact they will have. The newts eat invertebrates, crustaceans, and the eggs and hatchlings of frogs and fish, so it’s likely that they will compete with and even prey on native species.

It’s possible they could also transmit the frog-killing chytrid fungus. But the researchers are also concerned about a toxin they produce. So far it’s looking like the toxin is at too low levels to do any harm, but there is still a worry that they could poison other native species that may prey on them.

Fortunately, it still seems to be early days for the newt invasion, so there is some hope that quick intervention could get them under control.

Anyone who encounters a newt is encouraged to report them to the Department of Environment and Primary Industries (DEPI).

Beth spoke to researcher Dr Reid Tingley about the newts on our show on 10 July 2014. You can listen to the podcast.

Fish still radioactive near Fukushima, but mostly safe elsewhere

Recent catches of fish with record levels of radiation show there is still contamination in the waters around Fukushima following the nuclear disaster in March 2011, but fears of dangerous levels reaching the West Coast of the United States seem to be mostly exaggerated.

In January 2013, a bottom-dwelling Murasoi fish was caught with 2,540 times the legal limit for radioactivity of 100 becquerels per kilogram (about the same level as a banana). And then in February 2013, a greenling with 7,400 times the limit was caught in a cage next to the Fukushima Dai-ichi plant.

Fat greenling, Hexagrammos otakii, seen on some oyster shells
Fat greenling, Hexagrammos otakii, the fish (not the actual fish) found near Fukushima with radioactive caesium at a record level of 740,000 becquerels per kilogram (photo from OpenCage, via Wikimedia Commons)

Although most fish caught in the area are actually below the safe level, a paper published by Ken Buessler of the Woods Hole Oceanographic Institute in the United States found that the number above the limit is not decreasing with time as you’d expect. This indicates that radioactive caesium is still entering the food chain, either from sediments—these were bottom-feeding fish, remember—or from ongoing leaks (Buessler Ken O 2012, “Fishing for answers off Fukushima”, Science, vol. 338, pp. 480–482, DOI: 10.1126/science.1228250 [PDF 3.7 MB]).

This has since been admitted by the Japanese government, with radioactive water leaking from containment tanks into groundwater, which then flows into the Pacific Ocean at a rate of about 300 tons per day. This could mean that fish from Fukushima will be inedible for at least a decade, which could paradoxically mean that they benefit from the lack of fishing—although the long-term effects of radiation on the fish themselves is rarely discussed.

This may be because many of the fish don’t live long enough for it to have an impact, and conversely could be why radioactive isotopes have been detected in long-lived, migratory species like Pacific bluefin tuna (Thunnus orientalis), although even then at levels comparable to natural sources (Fisher NS, Beaugelin-Seiller K, Hinton TG, Baumann Z, Madigan DJ and Garnier-Laplace J 2013, “Evaluation of radiation doses and associated risk from the Fukushima nuclear accident to marine biota and human consumers of seafood”, Proceedings of the National Academy of Sciences, vol. 110, no. 26, pp. 10670–10675, doi: 10.1073/pnas.1221834110).

(Of course, there are other reasons to avoid tuna, such as overfishing or build-up of mercury and other toxic chemicals.)

As for fears of radiation directly reaching the United States, it was expected to take about 3 years to travel across the Pacific, so should be arriving right about now. The Woods Hole Oceanographic Institute is keeping an eye on that too, with a citizen science project asking people to send in samples of seawater for testing. As of yet though, their results are showing no detectible caesium from Fukushima.

But what about Australia, you may ask? Well, because we’re in the southern hemisphere, it will take even longer to reach here—about 5 years, according to a report from the Australian Radiation Protection and Nuclear Safety Agency [PDF 1.7 MB] (although a small amount of atmospheric fallout was detected here in April 2011).  By then though, it will be diluted even more than it is in the United States, so is unlikely to be of concern.

Brain boxes build bottle brains

The brain in a vat is a classic philosophical thought experiment, but now an actual vat has been used to grow actual brains. Well, tiny, tiny brainlets, grown out of stem cells.

Glass contraption used to grow the brains, which can be seen as tiny specks in a closeup (click to embiggen)
The spinning bioreactor system used to grow the brains, which you can see as little specks on the right (photo by Madeline A Lancaster)

Dr Madeline Lancaster and her colleagues from the Institute of Molecular Biotechnology at the Austrian Academy of Sciences grew embryonic stem cells into what they called “cerebral organoids”, in a gel-like substance under conditions similar to the human womb (Lancaster MA, Renner M, Martin C-A, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP & Knoblich JA 2013, “Cerebral organoids model human brain development and microcephaly”, Nature, doi:10.1038/nature12517).

The miniature brains, each about 3-4 mm in diameter, developed simple cerebral cortices, retinas and other kinds of brain tissue.

Of course, it’s not really an attempt to create disembodied consciousness, but rather models to help understand brain functions and disorders.  The team has previously made models of other organs, like eyes, pituitary glands and livers, but these were the first brains.

To demonstrate how this can help understand disorders, some of the organoids were made from cells from a patient with microcephaly. As you’d expect, those brains turned out smaller, but in the process they revealed why: the stem cells seemed to differentiate earlier, before they could grow in volume.

So this miniscule grey matter, although not able to think, has already taught us something.

And next time someone tells you to grow a brain, you’ll know how to do it.

(This story first aired on 12 September 2013 – you can listen to the podcast.)

10 crazy frogs

I’m guessing that many Lost in Science readers and listeners could do with some cheering up at the moment, and there’s nothing that does the job like outrageous amphibians.

The following are ten facts about frogs – and toads – that will at the very least give you something else to shake your head about.

1. Frogs that hear with their mouths

This is actually the science news that inspired this post: the Gardiner’s Seychelle frog, Sechellophryne gardineri, a frog so small that it doesn’t have ears (I know, I never thought about frogs having ears either).

Diagram showing how the Gardiner's Seychelle frog's mouth amplifies the sound of its call and delivers it to the inner ear (click to embiggen)
Diagram showing how the Gardiner’s Seychelle frog hears with its mouth. 99.9% of all sound is reflected off its skin, but the frog’s own call resonates in its mouth (Image by R. Boistel/CNRS)

Only about one centimetre long, the Gardiner’s Seychelle frog doesn’t have room in its tiny head for all the intricate machinery of middle ear bones. Instead, its mouth acts as a resonant cavity tuned to the frequency of its call, which then transmits the sound to the inner ear.

(Boistel R, Aubin T, Cloetens P, Peyrin F, Scotti T, Herzog P, Gerlach J, Pollet N & Aubry J-F 2013, “How minute sooglossid frogs hear without a middle ear”, Proceedings of the National Academy of Sciences, published online 3 September 2013, doi: 10.1073/pnas.1302218110.)

2. Wolverine frog, with hair and retractable claws

Actually known as the hairy or horror frog, Trichobatrachus robustus comes from Cameroon in central Africa. The males have long, thin growths on their skin that look like hairs but are probably more like gills for breathing.

Hairy frog, Trichobatrachus robustus (click to embiggen)
Trichobatrachus robustus, showing its horrid hair, but not its terrifying claws (Photo by Gustavocarra, via Wikimedia Commons
But most startling is that when threatened – or picked up by a human handler – the hairy frog intentionally breaks the bones in its toes and forces them through its skin like claws. And because frogs are good at regenerating, it’s believed to slowly heal over when it relaxes.

3. Frog that keeps its babies in its stomach and comes back from the dead

Well, it hasn’t quite come back from the dead yet – Australia’s gastric-brooding frog, Rheobatrachus silus, became extinct in 1983. But while they were alive, female gastric-brooding frogs swallowed their fertilised eggs and stopped eating while they incubated. After about a week they gave birth to baby frogs – not tadpoles – through their mouths.

The extinct gastric-brooding frog, giving birth through its mouth (click to embiggen)
The extinct gastric-brooding frog, giving birth through its mouth (Photo by Mike Tyler)

If you think that sounds complicated, it’s even trickier now they’re extinct. But Professor Mike Archer and his team from the University of NSW have succeeded in cloning frozen tissue, producing living embryos. Yes, just like in Jurassic Park.

(We spoke to Professor Archer on 4 April 2013 – you can listen to the podcast.)

Click through to the next page for the remaining 7 frogs on our list. Continue reading 10 crazy frogs

Dinosaurs are terrible lizards

The idea that dinosaurs were warm-blooded is rather at odds with the popular image of them as large, lumbering reptiles. But that’s what’s suggested by recent evidence of their anatomy, behaviour and metabolism.

Despite the fact that the name dinosaur actually means ‘terrible lizard’ (from the Greek deinos and sauros), their closest modern descendants are birds, which are definitely warm-blooded, or endothermic.

And indeed, many fossils show dinosaurs with feathers, which they possibly used for insulation rather than flight. There’s also evidence they lived in polar areas, which would have been rather challenging if they couldn’t maintain a suitable body heat.

Artists' impression of a bird-like feathered Velociraptor
Artists’ impression of a feathered Velociraptor, looking much more like a bird than they did in Jurassic Park. They were also only around 50 cm high, so larger than a chicken – maybe more like a goose (Image by Matt Martyniuk , via Wikimedia Commons)
But there is a complication: dinosaurs’ other surviving relatives are crocodiles, and they’re cold-blooded, or ectothermic. So what gives?

Professor Roger Seymour from the University of Adelaide recently took a closer look at crocodile metabolism and found further support for the idea that dinosaurs are warm-blooded (Seymour RS 2013, “Maximal aerobic and anaerobic power generation in large crocodiles versus mammals: implications for dinosaur gigantothermy”, PLoS ONE 8(7): e69361. doi:10.1371/journal.pone.0069361).

The key was to look at muscle performance, which is related to the number of mitochondria in the cells. Mitochondria are the cellular power sources, and they not only work better at certain temperatures, but they also produce heat when they burn energy.

Warm-blooded animals – like mammals – tend to have more mitochondria and hence better muscle performance than cold-blooded reptiles.

Of course, to quantify this Professor Seymour had to actually go out and measure the physical fitness of big salt-water crocodiles in northern Australia. He and his colleagues captured them with loops, then let them thrash around till they were exhausted – that way he could determine how much energy their muscles produced.

He found that the larger a crocodile was, the weaker were its muscles – particularly compared to mammals. A 200 kg crocodile produced only 14% of the energy that an equivalent-sized mammal would have.

Crocodile feeding on a chicken carcass (click to embiggen)
A puny crocodile, which somehow manages to hunt and survive despite its feeble strength (Photo by Mickey Samuni-Blank, via Wikimedia Commons)
This isn’t normally a problem for crocodiles, because they hunt by just lying in wait, which doesn’t require much energy. But dinosaurs appear to have had many different styles of feeding and probably led much more active lives. Plus, they would have had to compete with early mammals, which were evolving at the same time.

As Professor Seymour put it, “If you imagine a fight between a crocodile-like dinosaur and a mammal-like dinosaur, it’s clear that the mammal-like dinosaur would win.”

Of course, there are still some unanswered questions. For one, aren’t humans mammals? Despite the calculations, I’d be reluctant to fight a crocodile my size.

But there’s another question: why are crocodiles cold-blooded if they’re related to warm-blooded dinosaurs?

Interestingly, this may be a recently evolved trait. Crocodiles actually have many physiological features that are similar to warm-blooded creatures, like a four-chambered heart (most reptiles have three-chambered hearts). Professor Seymour suggests that maybe the crocodile’s ancestors were warm-blooded, but as they evolved into their current, lie-in-wait niche, they needed less energy and went back to being cold-blooded.

Then there’s the question about whether all dinosaurs were the same. According to some calculations, the really big dinosaurs – which were mostly herbivores like Brontosaurus Apatosaurus – would have had to be cold-blooded. Huge bodies like theirs would take a long time to cool down, so if they weren’t cold-blooded they probably would have overheated.

But if crocodiles were able to adapt their metabolism to their lifestyle, it’s possible that the big sauropods did too, and so there may be more than one way that dinosaurs operated.

Then again, there may have been some big dinosaurs had other ways of using the excess heat…

Gojira 1954 Japanese movie poster (click to embiggen)
Image by Toho Company Ltd (東宝株式会社, Tōhō Kabushiki-kaisha) 1954, via Wikimedia Commons
(This story first aired on 22 August 2013 – you can listen to the podcast.)

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).

Glowing splashes of water illuminated by bioluminescent plankton in the Gippsland Lakes (click to find out more)
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.

A pile of green asparagus spears (click to embiggen)
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!

If smokers get ashtray breath, what must a cigarette butt nest do to birds?

(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:

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

Anti-smoking poster produced by the Australian Government's Quit program, explaining the benefits of stopping smoking and allowing your body and your wallet to start repairing (PDF, 777 KB)
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.)