The Best Australian Science Writing 2014 (34 page)

When she looks at her own children, now aged five, seven and ten, she appreciates all the things they are capable of. ‘When my healthy five-year-old acts like a pill, I simply enjoy the fact that she can.'

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What to do with potential findings that are unrelated to the focus of the search, caught up in the driftnet as you trawl through masses of information? The ethical considerations raised by genome sequencing are enormous. One of the pitfalls of sequencing and analysing a child's entire DNA is that researchers may find aberrations leading to conditions that only become evident later in life. For example, would a parent want to know that their sick child carries a gene that increases the risk of Alzheimer's as they age?

‘As scientists in the lab, we don't look at these incidental findings, but it becomes a thornier issue when rolled out in the clinic. For example, how do we deal with insurance companies who may look at the genetic readout of a potential client and refuse to insure them? There is a revolution on our doorstep and most people don't know it,' Taft says.

The Beijing Genomics Institute Shenzhen (BGI), the biggest genetic research centre in the world, is aiming to become a major player in this space. They have initiated a Cognitive Genetics Program, sequencing and collecting entire genomes of 2000 of the world's smartest people in an attempt to identify the genes
that determine human intelligence. They are explicit that they are looking for IQ markers that are unique. This rings alarm bells for me, not only as a physician, but also as the daughter of a survivor of Auschwitz. It doesn't seem like too far a leap away from genetic engineering. In fact, China passed a so-called ‘Eugenics Law' in 1994 – the Maternal and Infant Health Care Law. This law regulates support for maternal and child health and also requires physicians to recommend a postponement of marriage if either member of a couple has an infectious, contagious disease or an active mental disorder. If one member of a couple has a serious hereditary disease, the couple may only marry if they agree to use long-term contraception or to undergo sterilisation. If prenatal tests reveal that a foetus has a serious hereditary disease or serious deformity, the physician must advise the pregnant woman to have an abortion, and the law states that the pregnant woman ‘should' follow this recommendation.

Mining human genetic material can potentially uncover a huge bioethical earthquake. China is not widely known for its ethics when it comes to clinical research. Tests on a mother's blood or urine in early pregnancy can detect foetal DNA, which shows the sex as early as seven weeks. These foetal sex determination tests have a dark side that goes way beyond what one company advertises on its website – a marketing pitch that describes the kit as ‘a curiosity application for the parents who would like to know the gender of the baby'. This ‘curiosity' to know the gender of a baby has purportedly led to a rise in the number of abortions of female foetuses in China, where traditional preferences are for sons. China now has a sex ratio bias towards boys, creating a gender gulf of more than 30 million more men than women who will enter the mating game by 2020. This gender shopping is commonplace in India as well. In fact, with the identification of IQ markers, a couple will most likely soon be able to screen their frozen fertilised eggs for intelligence and select the
one to implant that will be the smartest of the lot. The project isn't such a big step away from becoming blatant eugenics.

There are more nuanced ventures than this though – several companies are currently offering non-invasive prenatal testing. They take a blood sample from the mother containing circulating foetal cells to identify the most common genetic syndromes such as Down syndrome and Trisomy 18. It does away with the need for amniocentesis, a more invasive test used currently. Yet where do we draw the line as to what is okay to know? What happens when technology improves to the point where we can get a full foetal genome simply by sampling maternal blood and parents can elect to abort if, say, the child's eyes aren't blue, or he won't be tall enough to play basketball?

Another area of deep concern is in the area of gene patents. In a recent article published in the journal
Genome Medicine
, the alarm was raised about companies laying claim to the human genome for profit. It showed that approximately 40 000 patents already exist on human DNA molecules, which in effect limit clinicians and researchers from studying particular genes in order to develop new drugs or diagnostic tests.

‘If these patents are enforced, our genomic liberty is lost,' says the study's lead author, Dr Christopher Mason.

‘The future of genomics is full of promise, but there are still issues to be resolved,' says Taft. ‘There has been an explosion in personalised medicine. Current genetic testing is faster and cheaper and will soon replace old diagnostic protocols. We are looking at the genetic structure of the genome and testing drugs using this technology that will work for the individual. In principle, a private hospital can already sequence every newborn born in their labour ward, with view to prevention and tailored treatment from the beginning of a person's life. What concerns me most is that the public doesn't understand this is happening.'

How do you start to lock this down, protect the rights of
individuals to the privacy of their own, or their child's, genome?

‘The horse left the barn a long time ago,' Taft says. ‘We need more public discussion about genomics and its impacts. It's going to affect everyone. The technology is out there and both public institutions and private companies are already using it. We need to ensure data security – how do you maintain your genome in a safe place? Do you carry it around with you on a chip, attached to your keyring? The cost has come down from around US$3 billion in 2001 – in theory today your genome can be sequenced in 72 hours for US$3000. Currently most clinicians use an MRI for diagnosis, which costs around US$1500. Within eighteen months to two years they will almost certainly be looking at a patient's genome as well.'

Where does Australia stand in this international genomics revolution? When I was a young child, watching Neil Armstrong take that Giant Leap for Mankind, I remember feeling so proud when the TV commentator spoke of the support role of Australia's Radio Telescope at the Parkes Observatory in relaying communications from the Apollo Mission to NASA. Sadly, we seem to be lagging behind in this new frontier of exploration and research.

‘It is a huge opportunity for Australia,' says Taft. ‘We have the potential to do it right. We have a socialised medical system, a well-educated, mainly middle-class population and some of the world's leading experts in the application and use of this technology. If we don't step up now, we may not be able to compete internationally.'

In the United States it is possible to have a sick child's exome sequenced within 72 hours nowadays. In Europe, this procedure has become a standard of care for suspected paediatric genetic disorders. In Australia, funding is scarce and the pull for top scientists to enter private industry is financially far more attractive. As the Damianis' GP, I have witnessed the family's ongoing
struggle from the outset as they have negotiated with various high-level players, trying to enlist their assistance and backing in finding a diagnosis for Massimo. They ended up paying for a lot of the testing themselves, although Illumina gave
pro bono
help with the reagents used in sequencing the family's genomes. I have been surprised at times to see the turning-up of some of my genetics peers' noses, the unwillingness to take risks into the unknown, or to simply keep up with state-of-the-art research and development happening in the field of genomics. Like many other visionaries, Stephen has met with a fair amount of resistance along the way. Thankfully, he is a stubborn and determined man and has followed those who were able to see beyond the tremendous obstacles, to have faith in his ability to facilitate the process.

The journey towards a cure has just started for little Massimo Damiani. What has been the hardest thing all along, according to his parents Stephen and Sally, is living with the uncertainty of their son's future. From here on in they take solace in knowing they are not alone. The Damianis are realistic in their expectations, but determined to take another leap into the unknown towards developing a therapy and maybe a cure for their son, and for others around the world with this condition.

‘We have something tangible to fight now that the disease has a name.'

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Postscript:
Ryan Taft has since moved back to the US to become a director of scientific research at Illumina. In June 2013, the US Supreme Court stated that ‘a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated'. The ruling invalidates all such claims on natural human genes.

From Alzheimer's to zebrafish

Uniquely human

Life, the universe and Boolardy

Richard Guilliatt

You can learn a lot travelling around the outback with an astrophysicist.

You learn that there are billions of galaxies out there, separated by mysterious dark matter that's technically known as ‘Dark Matter'. You learn that most galaxies spin like pizzadough, except for the ones that are fluffy. You find out that the universe was once a swirling blob of smooth hydrogen paste with not much going for it, until it started to change and become …

‘Lumpy – the universe is lumpy,' says Dr Lisa Harvey-Smith, as she steps down from a rented 4WD onto the rust-red earth of central Western Australia. ‘Early on the universe was pretty featureless, just a swirling eddy of gas – a pretty crap place to be, really. But then gravity took over and things started clumping together to form stars and galaxies and superclusters. So if you were God … well, I don't believe in God, but if you were the Big Fella looking down on the universe now, you'd see it's lumpy.'

Around us the semi-desert of the Murchison plains stretches out to a distant horizon, a vast expanse of scrubby saltbush, spindly skeletal mulga trees and waist-high termite mounds 300 kilometres inland from the mid-WA coast. In the neardistance, a cluster of what look like towering white satellite
dishes rises above the terrain, each of them roughly six storeys tall and pointed skywards. They're the reason we're here, and the reason Harvey-Smith is offering an idiot's guide to the cosmos while stepping artfully around sun-baked piles of cattle-dung. Those dishes are in fact radio telescopes, aimed at the further reaches of the universe, a few billion years back down the space– time continuum. Out here on Boolardy Station – population: two people and 1500 cattle – the world's most futuristic astronomy project is taking shape.

If all goes to plan, the ochre rangeways here will eventually be planted with 100 dishes and several million pole-antennae, all of them wired to computers that will piece together panoramic images of deep space. The first stage of the project, the prototype, is already built – 36 dishes now dot the landscape, like giant abandoned merry-go-rounds bleached white by the sun, while several hundred smaller telescopes resembling oversized robotic spiders squat on the earth in four-by-four formations. They're connected by fibre-optic cables that snake underground for several kilometres to a supercomputing centre, housed inside a hermetically sealed steel shed that's fenced off from the roaming emus and cows.

‘This is going to push the boundaries of astronomy,' says Harvey-Smith, a diminutive 33-year-old Brit who is so alarmingly youthful she could almost pass for a teenager. ‘When the first radio telescopes were built in the 1940s, they were revolutionary. This will be another revolution – it'll be like switching from a camera that can only see one small piece of the universe to using this very wide-angle lens to capture panoramic views.' The epic sky overhead seems to mirror those words – at night it's a light show of stars, planets and distant galaxies arrayed by the thousands. Yet that dazzling spectacle is not really why this 330 000-hectare cattle station has become an astronomy mecca. Technically, the telescopes here are blind. Rather than capturing visible light from deep space, they capture radio waves –
radiation from the low-frequency end of the electromagnetic spectrum. Boolardy was chosen primarily because it's
quiet
: across the surrounding 50 000 square kilometres of Murchison Shire there are only 113 people scattered around 29 properties, making electronic interference from mobile phones and other equipment negligible.

The WA government and Harvey-Smith's employer, the CSIRO, plunked down $5.42 million to buy Boolardy four years ago, a mere fraction of what has so far been a $435 million investment of state and federal money to make Australia an international leader in astronomy. This is a project so big it can make your head throb. The dishes and antennae will have a combined surface area of one square kilometre, hence their name – the Square Kilometre Array (SKA). Half of them will be here, the other half in southern Africa. The computers processing the data are so powerful they have to be watercooled to stop them exploding. The total cost of the project is more than $2 billion.