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Jon Brodie was snorkelling at Agincourt when the closed-door decision was being made to approve the dumping of 3 million cubic metres of dredge spoil in the Great Barrier Reef’s waters, part of a massive expansion of the Abbot Point coal port.

Brodie, chief scientist at the Centre for Tropical Water and Aquatic Ecosystem Research at James Cook University, first dived on the reef 43 years ago, when he was 23 and on his honeymoon. “When you first see it, and for me it was in the 1970s, it’s just magical,” he told The Saturday Paper. “The fish, the coral – there’s just so much going on. And later when you see the smaller things – like the nudibranch, like a Spanish dancer in red and white with its skirts – you see the smaller things going on and it’s incredible.”

From 1990 to 2001, Brodie was a director of water quality and coastal development at the Great Barrier Reef Marine Park Authority, which is charged with the management and conservation of the reef. He has regularly authored reports for the Queensland and federal governments on issues affecting the reef.

He will likely be a key scientific witness in a federal court action brought this week by the Mackay Conservation Group against the federal government’s decision to allow the dredging, which will permit ships to collect coal from Abbot Point, halfway between Mackay and Townsville. The group’s Ellen Roberts says it will be a test case for Environment Minister Greg Hunt’s obligation to not act inconsistently with Australia’s obligations under UNESCO’s world heritage convention. Hunt is named in the court filing.

It is the second legal challenge to the Abbot Point development. In February, the North Queensland Conservation Council launched action against the Great Barrier Reef Marine Park Authority in the Administrative Appeals Tribunal, claiming its decision to issue a sea dumping permit was not made in accordance with the London Protocol, which controls marine dumping.

Environmentalists have been watching the Abbot Point plans closely for the past three years, when Indian miner Adani bought a 99-year lease to the port to ship coal from the rich untapped thermal coal reserves of the Galilee Basin, 500 kilometres inland.

The mood of the miners then was bullish. The port they intended to build on the edge of the reef would be the biggest in the world. There would be a new airport, too, and 300 kilometres of rail. But with coal prices falling, BHP Billiton, Rio Tinto and Anglo American, as well as infrastructure developer Lend Lease Group, have pulled out of plans for the Abbot Point expansion. Indian billionaires G.V. Krishna Reddy and Gautum Adani remain as the last major investors, caught in a bear market with projects totalling $17 billion.

Reddy’s company GVK bought the coal assets in 2011 for $1.26 billion from Gina Rinehart, who retained a 21 per cent stake in the company’s Alpha mine. Mining magnate turned politician Clive Palmer is also a more than interested bystander, with his company, Waratah Coal, planning a new $6.4 billion mine and associated infrastructure near Alpha in the Galilee Basin.

Darren Yeates, the CEO of GVK Hancock – Reddy’s joint venture with Rinehart – has described the go-ahead to expand the port, near Bowen, as a significant milestone in developing the company’s Galilee coal projects, “which represent the creation of over 20,000 direct and indirect jobs and over $40 billion in taxes and royalties”.

1 . "The strictest conditions"

When Hunt announced he had given the green light to the Abbot Point port expansion in December, he said he had imposed “some of the strictest conditions in Australian history”, including a requirement for North Queensland Bulk Ports to achieve a 150 per cent net benefit for water quality by reducing fine sediment runoff from elsewhere. He had, he said, also taken into account “the latest and best science and management practices”.

Hunt said the size of the dredge had been reduced from the 38 million cubic metres previously proposed to 3 million cubic metres. The government was “drawing a line in the sand” to protect the reef.

Brodie is far from reassured. Rather, he tells The Saturday Paper that the government and the marine park authority have opted for the “quickest, cheapest, dirtiest option” with a decision that was “a direct slap in the face for UNESCO and their concerns”. Like many scientists, he fears the reef may not be resilient enough to fend off another disturbance. “I’m not prepared to say that dumping spoil is going to kill the Great Barrier Reef tomorrow, but it’s cumulative and it’s a large amount – around 5 million tonnes dumped in an area that doesn’t have a lot of sediment from rivers, and it will cause damage. There’s no doubt about it.”

2 . Alternatives to the dredging project

Brodie says there were many options that would have better protected the reef but which were ignored. He said the present jetty could have been lengthened or a second medium-length jetty could have been built with a small amount of dredging. Alternatively, the spoil from dredging could have been dumped behind a bund wall or on land.

“There were really perfectly good options at Abbot Point that would have allowed the port to go ahead and not involved dumping at sea,” he says. “It was never looked at properly in terms of cost versus damage to the Great Barrier Reef. In the end we got the … option that would do the most damage. We have to trust in compliance and monitoring, and the only other example we have to look at is Gladstone. Lots of conditions were set there, too.”

In January, even as he gave the green light to Abbot Point, Hunt ordered an independent inquiry with sweeping investigative powers into Australia’s biggest dredging project, at Gladstone, which coincided with mass deaths of fish, turtles, dolphins and dugongs inside the Great Barrier Reef World Heritage area. The inquiry was likely to examine links between the Labor Party and the state-owned Gladstone Ports Corporation. In a separate inquiry, two marine park authority board members, Tony Mooney and Jon Grayson, were cleared of conflict of interest claims linking them to mining interests.

Asked whether he was aware of tension within the marine park authority over the decision to issue dumping permits, Brodie would only say “of course there has” been.

“A difficulty for them was they were only given the one option to decide upon – dumping in the marine park. The process is terribly broken, run by developers and consultants with no real government oversight, especially when the state government is part of the proponents. They come to their preferred option and put it up.”

3 . Environmental opposition

Confidence in the Abbot Point dredging project was further eroded earlier this month, when Greenpeace discovered through freedom of information requests that the environmental assessment and management unit of the marine park authority had recommended against the project.

In a series of draft documents dated from 2012 to August last year the authority repeatedly warned that the reef could be irreversibly damaged by the plan and argued for an alternative that would see trestles extended one kilometre beyond the original plan, to avoid dredging new coal shipping berths.

“The proposal to dredge and dispose of up to 1.6 million cubic metres of sediment per year for three separate campaigns between 2014 and 2020 has the potential to cause long-term, irreversible harm to areas of the Great Barrier Reef Marine Park, in particular seagrass meadows and nearby coral reefs,” the executive summary of the draft report said.

The chairman and chief executive of the marine park authority, Russell Reichelt, said the documents were only preliminary and the assessment was conducted before stringent conditions were imposed by Hunt. He added that “absolutely no political pressure was brought to bear” on the authority.

Reichelt has acknowledged that the dredging and dumping plans had attracted “passionate commentary around the world”, but has been at pains to dispel concerns.

In a long piece for The Conversation on March 3, a week after the North Queensland Conservation Council announced its action in the Administrative Appeals Tribunal, he described the dredging as a “highly regulated activity”.

He said the dredged material would not be toxic, although that is disputed by some scientists. Dredge material would not be “dumped on the reef”, but in a defined four-square-kilometre site 40 kilometres from the nearest offshore reef. Dredge disposal would only occur between March and June, Reichelt said, outside coral spawning and seagrass growth periods, and when oceanographic conditions were favourable. Disposal would be stopped if prevailing conditions could sweep sediment towards sensitive habitats, including the Catalina World War II plane wreck.

The authority was confident that with 47 stringent conditions in place, there would be “no significant impact on the reef’s world heritage values”. Reichelt said the authority understood the need to “learn the lessons” from past port developments, including Gladstone.

Three months on from Hunt’s announcement, environment campaigners, a large number of scientists and commercial operators are in agitated agreement, showing no sign of being persuaded by the assurances offered by the federal and Queensland governments, the authority and the companies at the centre of the dispute, which complain about “hysteria” and “misinformation”. The Queensland government pointed out the dredge disposal site is 0.0005 per cent of the total area of the Great Barrier Reef Marine Park.

In Mackay, Ellen Roberts says considerable adverse scientific opinion about the dredging was available to Hunt at the time he gave the project the go-ahead, and that the conditions he placed on it, far from being the strictest ever imposed, were “uncertain and unverifiable”.

North Queensland Conservation Council’s Wendy Tubman said it is hard to reconcile the dredging decision against scientific findings that the reef is under threat from climate change and other factors, and should not be subjected to additional pressures.

“We have to relieve the World Heritage area of as many pressures as we can, so that it has the resilience to cope with and survive climate change,” she says. “Everyone knows that the condition of the reef is poor and declining. To add this is just crazy.”

At the University of Queensland, coral specialist Selina Ward rallied her peers in January to try to stop the marine park authority from issuing dumping permits, gathering the signatures of 240 marine scientists in just 48 hours.

Ward’s letter to Reichelt said the best available science made it clear expansion of the port at Abbot Point would have detrimental effects on the Great Barrier Reef. “Sediment from dredging can smother corals and sea grasses and expose them to poisons and elevated nutrients. Claiming to ‘offset’ the 5 million tonnes of dredged sediment by catchment work is the wrong approach and very unlikely to be possible with the limitations of budget and workforce … Exporting the vast quantities of coal from the Galilee Basin through Abbot Point and other port developments will result in a rapid rise in future greenhouse emissions, which will further exacerbate the effects of climate change on the Great Barrier Reef. Increasing ship movements through the GBR will increase the probability of ship groundings, oil spills, animal strikes and the introduction of marine pests.”

In its environmental impact statement, Adani noted that coal combustion was recognised as “a significant contributor to greenhouse gases and the global effects of climate change” and pledged to use renewable energy technologies in its port operation. Greenpeace estimates that if the Galilee Basin mines reach their maximum potential, 705 million tonnes of carbon dioxide will be released each year, compared to Australia’s current annual emission of 400 million tonnes.

Ward says there is a major flaw in how environmental impact assessments are done, with developers selecting and paying consultants, binding them to confidentiality agreements and including no provision for independent scientific peer review.

A spokeswoman for North Queensland Bulk Ports, Mary Steele, said environmentalists and scientists had produced no evidence to support their claims that the reef could be damaged, and that her authority had undertaken 22 dredge campaigns since 2002 without impacting the Great Barrier Reef.

4 . UNESCO report

In May, the UNESCO World Heritage Committee is set to respond to an Australian government assessment of conservation in the Great Barrier Reef.

Last year, the World Heritage Committee welcomed developments in a number of reef conservation areas but expressed concerns about limited progress in meeting key concerns. It urged the Australian government to “ensure rigorously that development is not permitted if it would impact individually or cumulatively on the outstanding universal value of the property”.

The committee will meet on June 15 to decide whether or not to list the reef as a World Heritage Site in Danger, and is likely to consider issues it has identified as emerging, including “port expansions and increases in shipping activity”.

A second Outlook Report prepared by the marine park authority, and independently peer reviewed, is due to be presented to Hunt by the end of June. The report was established to provide information about the condition of the ecosystem, social and economic factors influencing that system, the effectiveness of managing the reef, and a risk-based assessment of the future of the region.

The first report in 2009 identified long-term challenges for the marine park authority in the protection of the reef, including climate change and a continuing decline in water quality. In 2012, Australian Institute of Marine Studies research showed that the reef had lost half of its coral cover in the previous 27 years, due to storm damage, the crown of thorns starfish and bleaching.

The environmental threat to the reef from new coal terminals at Abbot Point and Clive Palmer’s Yabulu nickel refinery could also face a Greens-led parliamentary inquiry.

5 . Tourism doubts

Tony Brown is among a group of tourism operators who fear the reef will come under increasing pressure and worry the Whitsundays is being sandwiched by proposed coal port expansions at Abbot Point in the north and Dudgeon Point, close to Hays Point, in the south.

Brown, the president of the Whitsunday Charter Boat Industry Association, spent this week tramping the halls of parliament house, lobbying Queensland senators and Labor’s environment spokesman, Mark Butler.

Brown says marine operators are looking for “an adult conversation” about development in the park and reassurance that “the science is being done properly”. He says their views were jaundiced by the 2006 dredge at Hays Point, south of Mackay, which resulted in sediment finding its way into the Great Barrier Reef over a 12-month period. There is little faith in the Abbot Point modelling done by North Queensland Bulk Ports and its prediction of how the plume will travel.

Brown has spoken to Hunt twice and is sympathetic. “It’s a political machine – that’s what we’ve been learning these last few days – and mining is a very strong economic driver and we need to find that balance. Dredging is by no means the only concern, but it’s something we can manage. We can’t manage cyclones or the crown of thorns, but we can manage this.”

GVK said this week it remained committed to development of the Galilee Basin, which was “one the most significant pieces of regional and economic development that Queensland has seen for decades”, and was continuing to develop the project to a point where construction can commence.

The company said it was “extremely confident” that North Queensland Bulk Ports Corporation would successfully deliver its 23rd incident-free dredging campaign and there would be no impact on “the outstanding universal value of the Great Barrier Reef.”

But two court challenges and at least 240 marine scientists do not share GVK’s confidence. It is on this confidence that Hunt’s credibility and the Great Barrier Reef’s health is staked.