The Best Australian Science Writing 2014 (19 page)

Competing – and cheaper – systems could be built with software developed by Zeynep Gümüs¸, a computational biologist at Weill Cornell. Gümüs¸ had used her institution's CAVE to identify genes specifically involved in mouth cancer development and to find regions of noncoding DNA that help drive cancer more generally. After being approached at conferences by scientists who told her they would conduct similar network visualisations but for the lack of a CAVE, Gümüs¸ and her graduate student Vaja Liluashvili designed iCAVE – the interactome CAVE. According to Gümüs¸, this software works just as well in a CAVE as on a desktop system assembled from off-the-shelf components that generally cost less than US$2000.

But price and infrastructure hurdles aside, perhaps the biggest challenge for CAVE2s and other full-size visualisation facilities is awareness – ‘people not knowing what is possible,' as Andy Johnson, head of research at EVL, puts it. Johnson doesn't see this problem as insurmountable, though. ‘Once people see an example that's close enough to what they want to do, it starts to click and they start getting ideas,' he says.

Scientists like Ajilore are only too happy to be leading the charge. ‘I think there's a huge upside in having new ways of visualising large data sets,' he says. ‘If we have innovative ways of being able to visualise that data and understand that data, hopefully that will lead to better discoveries.'

Life, the universe and Boolardy

The quantum spinmeister

High-tech treasure hunt

Sarah Kellett

Geologist Steve Hill moves through the outback, collecting leaves and looking for a sign. ‘What you see of a tree on the surface of the land is only the tip of the iceberg,' says Hill, director of the Geological Survey in South Australia. ‘Tree roots extend down very deep to bring up water, particularly in arid parts of Australia. When they bring the water up, they're also sucking up a lot of the chemicals that are coming out of the rocks. We then sample the leaves and send them off to a chemical laboratory for analysis.'

Eucalypt roots can extend 30 metres down into the ground – the height of a 10-storey building. Through the process of transpiration, water is drawn up from the roots and transported in the xylem to small pores in the leaves, where it evaporates.

As well as gold, uranium, lead, zinc and copper, geologists are looking closely at leaves for elements that indicate mineral deposits might be nearby, such as buried granite, basalt and quartz vein host rocks. Mining companies are interested in this technique as a cheap alternative to drilling a hole for exploration, which costs thousands of dollars. Analysing a plant sample only costs around $40 – and it's much gentler on the ecosystem.

River red gums and mulga trees are popular species for sampling, as is grassy spinifex.

‘Spinifex has been incredible for us,' says Hill. ‘Although it's a little spiky grass at the land surface, [it lives] to be hundreds of years old and sends roots down very, very deep.'

The quantity of gold in a single leaf is tiny. So, at first, scientists couldn't be absolutely sure whether it was being drawn up from below or had just blown in on the wind. Mel Lintern at the CSIRO set out with a team to find conclusive evidence of the origin of leaf gold.

‘Of course we can't see the gold in the leaves with the naked eye,' says Lintern. ‘This is where we needed the analytical powers of the Maia mapper at the Australian Synchrotron. This remarkable machine – the size of a small cricket oval – was able to show us that the gold was actually within the plant rather than stuck on the outside as dust.'

The 3D images revealed tiny nuggets within the leaves. ‘We all know gold produces nuggets, but the nugget effect actually carries on into the vegetation,' says Lintern.

Gold isn't distributed evenly throughout the tree, but instead is dotted around; so, some leaves have more than others. To best detect gold, the research suggests geologists will need to sample all over the tree to get a nice average.

The team also found that gold seeps out onto to the surface of the leaf, and may be washed away by rain. Steve Hill has also noticed that they detect less gold in leaves after rainfall.

* * * * *

Animals can make handy prospectors too. The compass termite cleverly angles its nests to stay cool during summer and warm in winter. The cooling and ventilating tricks of termite mounds have inspired architects for years. Now they are helping geologists, because their masterpieces can be decorated with traces of gold.

‘The termites burrow down to the water table and also eat spinifex grass and cycle those chemical elements into the termite mound,' says Steve Hill. ‘We can take a little chip off the termite mound and analyse that, and that can tell us lots about what's happening underneath.'

The termites lose a bit of their house in the process, but can rebuild it within a few hours. And compared to a drilling operation, the impact is tiny.

Another eco-friendly alternative comes from kangaroos – or rather, their poo. As they roam around the few kilometres of their home range, they eat leaves and drink water, leaving little balls as they go.

‘The kangaroos are effectively sampling all of the plants in the area for us,' says Hill. ‘So we put on our latex gloves, pick up the poo – usually it's fairly dry – then we can grind it up just like if we were looking at plant material.'

If there's something promising inside, the geologists go back and look for exactly where the minerals might be by sampling the leaves.

‘The roo poo tell us the haystack, the plants might tell us where to find the needle,' he says.

* * * * *

Far above the treetops, a different kind of hunt is on. Carsten Laukamp from the CSIRO uses remote sensing by satellite to map the surface of Australia.

‘The maps we are creating look like Google maps, but Google maps are collecting only data from the visible part of the spectrum of light – everything we can see with our eyes,' says Laukamp. ‘In the infrared spectrum there are more colours that we can't see.'

The colour, or frequency, of the light seen by satellites depends on the surface reflecting the sunlight. ‘Every rock type,
house and road has a certain spectral signature. It's like a fingerprint of the material,' Laukamp explains.

The satellite data were collected by ASTER (the Advanced Spaceborne Thermal Emission Reflection radiometer), which is one of the instruments on NASA's Terra-platform satellite orbiting the Earth.

Gold can't be detected directly, so geologists must look for host rock types or other minerals, like quartz or micas, which suggest there's gold nearby.

Laukamp says these maps can help geologists target their fieldwork – but there are challenges. ‘With this remote sensing technology, we are not only mapping the rocks but everything between the sensor and the Earth: its vegetation, its clouds, its roads … we can't see through material.' The CSIRO is finding ways to minimise this problem so their highly detailed, colour-coded maps cover as much of the country as possible, including places that are tough to visit on foot.

And gold isn't the only treasure waiting beneath the surface. In north-west Queensland, Riversleigh is a world heritage area containing fossils of prehistoric bats, tree-dwelling crocodiles and ancient koalas. Paleontologist Mike Archer from UNSW Australia wondered whether remote sensing could ‘retropredict', or rediscover, Riversleigh's known fossil deposits. Archer asked his PhD student, Ned Stevenson, to see if satellite data could identify areas that had fossils in the same way the ASTER project finds minerals.

‘It took a few months and he came back and he'd done it,' says Archer. ‘But the exciting thing was he said “wait, there's more” – and then he backed off the scale of the map and showed us that way beyond the world heritage area was another, bigger area giving the same signal. It was somewhere we had never been before.'

When Archer had the opportunity and permission from the
Waanyi community, the traditional custodians of the land, he took a helicopter to the area, and, ‘Bang – there were fossils'.

The area is even bigger than the Riversleigh area. ‘This new find from Wholly Dooley site, as it was called, looks like it's got very strange animals in it for two reasons,' he says. ‘One, it includes some species we haven't seen before, and that suggests it's from a different age. We're guessing maybe the age called the Late Miocene, and perhaps it's around 10 million years old.

‘The second reason this deposit is strange is that all the fossils we've been finding – and this is going to sound weird – they have got worn teeth.' Worn teeth are normal in modern wombats and kangaroos, but rare in the Riversleigh fossils that are from a time when the environment was lush. This new find might fill a gap in the fossil record when the vegetation became tougher stuff – and exploration on the Wholly Dooley site has only just begun.

A short walk in the Australian bush

The carnivorous platypus

The carnivorous platypus

John Pickrell

Was this animal for real? It sounded more like something from a poorly scripted, low-budget horror film. Could an ancient relative of everyone's favourite venomous, duck-billed, egg-laying mammal really have grown to epic proportions and had a taste for flesh? I could picture the scene through the Hollywood lens: maniacal monotremes marauding through the sewers of Sydney, ready to burst out of drains and clamp their bills around the ankles of unsuspecting pedestrians, dragging them to untimely deaths.

Implausible as it sounded, this prehistoric Platyzilla really did exist – even if descriptions of it were a little overblown in the press. Researchers led by Professors Mike Archer and Sue Hand, at UNSW Australia, announced in late 2013 that they'd discovered the remains of a metre-long species which had powerful teeth for preying upon turtles, frogs and fish.
Obdurodon tharalkooschild
inhabited pools and rivers in the rainforests that covered Queensland's Riversleigh region 5–15 million years ago.

The description of this animal as ‘giant' in news reports conjured images of an animal the size of a small car, so I was disappointed to find it had been much smaller. Nevertheless, by monotreme standards, it was huge. Today's platypus is about half
a metre in length and, as an adult, doesn't have teeth, instead relying on horny pads in its bill to crunch up invertebrates. Although
O. tharalkooschild
was only twice as long as a modern platypus, it is likely to have been about four times the weight.

Former UNSW student Rebecca Pian, now at Columbia University, discovered a fossil tooth at the Riversleigh World Heritage Area in 2012. The size and eating habits of the new species were later determined from a detailed study of the size, shape and function of the tooth, which is yet to be dated definitively.

Fossil discoveries over the past 40 years have given us snippets of information about platypus evolution, and have shown that similar animals have been a part of the Australian story for at least 110 million years. The most ancient platypuses have also been found in Antarctica, South America and possibly Madagascar. By around 25 million years ago, however, they were left only in Australia, where up to three species shared the streams of the lush north and centre of the continent.

In 1975, the first known ancient platypus was described from fossilised teeth found in central Australia – by Mike Archer and US palaeontologists Michael Woodbourne and Richard Tedford. They named the 26-million-year-old species
Obdurodon insignis. Obdurodon
means ‘persisting tooth' and distinguished this genus of prehistoric toothed platypuses from their modern descendants.

A second toothed platypus,
Obdurodon dicksoni
, was discovered by Mike Archer's group at Riversleigh in 1984 and dated to about 15 million years ago. Even more exciting was the discovery of the teeth of a 61-million-year-old South American relative in 1992. Hailing from Patagonia,
Monotrematum sudamericanum
demonstrated how widespread these early platypuses had been.