Marine physicist Peter Ridd has been victorious in his case for unfair dismissal against James Cook University, but his views as a climate sceptic were not on trial.

The controversial scientist was sacked by JCU in 2018 after being censured for allegedly breaching the University's code of conduct.

Among JCU's grievances were that Dr Ridd had publicly criticised the work of colleagues, including telling Sky News in 2017 that "scientific organisations like the Australian Institute of Marine Science and the ARC Centre for Coral Reef Studies can no longer be trusted".

Dr Ridd's controversial views also include that poor water quality and climate change aren't significant threats to the future of the reef.

But Judge Salvatore Vasta ruled in the Federal Circuit Court of Australia last week that the University's sacking of Dr Ridd was unlawful, and that JCU had "not understood the whole concept of intellectual freedom" in respect to their enterprise bargaining agreement.

Dr Ridd's supporters were quick to claim the win for academic freedom and freedom of speech. And before long some were equating the court victory to a win for climate-change scepticism.

However, Dr Ridd's views on the impact of climate change on the Great Barrier Reef were not on trial in this case.

The decision was confined to his industrial rights and the judge made no comment on the validity of his climate views.

What makes a 'reef expert'?

After over two decades spent researching marine physics in the Great Barrier Reef region, Dr Ridd's scientific expertise cannot be disregarded.

He pioneered research techniques for studying marine sedimentology, and has published widely on coastal oceanography and the effects of sediments on coral reefs.

Dr Ridd is respected in this field despite some differences in opinion about his results — which is standard in all fields of science, according to marine scientist Jon Brodie from the Centre of Excellence for Coral Reef Studies.

However, Dr Ridd's comments on the overall health of the reef, and his harsh criticism of coral-bleaching science, have caused many scientists to question the limits of his expertise.

Dr Ridd has previously claimed that the Great Barrier Reef is healthy and that studies published by the Centre of Excellence for Coral Reef Studies in Townsville about coral bleaching are inaccurate.

Dr Ridd does accept that cyclones and ocean acidification may pose a threat to the reef. ( Supplied: Peter Mumby )

In response to questions about his authority as a Great Barrier Reef expert, Dr Ridd told the ABC that his experience living and working as a scientist on the reef for over 30 years qualifies him to make these comments.

"All the so-called threats to the reef are based on physical processes," Dr Ridd said.

"I can draw conclusions from [biology-based] papers in the same way as a biologist can do that to my papers which are physics-based.

"To say I'm not qualified to comment because I'm a physicist... what sort of argument is that?"

It is true that any scientist working on the reef has to have a basic understanding of reef processes outside of their direct field of research.

However, to argue publicly that the Great Barrier Reef is "one of the best preserved ecosystems in the whole world" needs to be backed by very solid evidence, especially when it flies in the face of strong scientific consensus.

The vast majority of reef scientists would disagree with Dr Ridd's views, Ove Hoegh-Guldberg, director of the Global Change Institute at the University of Queensland, told AM.

"It would be over 99 per cent of [research] papers that show we are facing very challenging times as average global surface temperatures increase," he said.

But Dr Ridd continues to argue that research published about the recent coral bleaching events is flawed because there is not a "system of checking".

Contrary to the scientific consensus, Dr Ridd believes coral bleaching is part of a "natural cycle" on the reef. ( Supplied: ARC Centre of Excellence for Coral Reef Studies )

He takes issue with what's called the "replication crisis" in science — the ability to reproduce the results of a study using the same methods — which he also cites as the catalyst for him speaking out in the first place.

His evidence for a quality problem in reef science is based largely on the fact the problem exists in other fields of science.

"Why are [reef scientists] so clever that they have been immune to the problems affecting every other area of science?" Dr Ridd said.

It's not an invalid question — but the question of whether Great Barrier Reef science is actually flawed has to be addressed before Dr Ridd can single out pieces of research to criticise.

Currently, Dr Ridd claims that "the exaggeration of the bleaching events is disgusting" while also saying the science needs to be double-checked.

Dr Ridd is seeking reinstatement at James Cook University. ( Source: Facebook )

He has published an article in the journal Marine Pollution Bulletin calling for greater quality control processes in reef science — using examples from nine key reef studies.

The article has been rebutted, also in Marine Pollution Bulletin, by a group of reef scientists arguing the piece "demonstrated biases, misinterpretation and selective use of data" as well as failing to acknowledge many of the claims had already been addressed within the scientific literature.

Dr Brodie was an author on one of the studies criticised, and said Dr Ridd cherry-picked papers.

"He picked quite old studies, and I've alone published 50 to 60 papers since then on the same areas, none of which he cited," Dr Brodie said.

Dr Ridd said the nine studies were chosen because they "were some of the most important papers that there are" about the reef.

Despite being the target of some of Dr Ridd's criticism, Dr Brodie has previously said that JCU's handling of the situation, including searching Dr Ridd's emails, sent a "terrible signal" to the rest of the university staff.

Concern that sceptics will seize on court win

Dr Ridd's court win this week has emboldened his climate sceptic supporters to continue disputing the state of the Great Barrier Reef.

While the substance of his climate views was not a factor in the unlawful dismissal ruling, supporters are describing him as a brave climate sceptic censored by his employer.

The Institute of Public Affairs (IPA) and other conservative commentators are painting Dr Ridd as the proof that dissenting voices about the Great Barrier Reef aren't tolerated.

"Fearmongering about the health of the Great Barrier Reef must now desist," Director of Policy at the IPA Gideon Rozner said in a statement.

And journalist at The Australian, Graham Lloyd, wrote in an opinion piece that Dr Ridd had "struck a powerful blow against the notion that science can be conducted by consensus".

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Professor Hoegh-Guldberg is very concerned that climate sceptics have seized on the courts' decision in this fashion.

"Climate change is a major threat to places like the Great Barrier Reef and Australia in general," he said.

Dr Brodie is not surprised that Dr Ridd's supporters are using his case as evidence climate change is not a serious threat, but thinks most people — but particularly young people — now understand that isn't true.

"They see it happening around them right now, it's so obvious," Dr Brodie said.

"The changes we're seeing on the reef have happened much quicker than we predicted 15 years ago," he said.

Dr Brodie says if anything, the predictions made by reef scientists underestimated how fast the reef would feel the brunt of climate change.