James Cook university crookedness in support of global warming continues

We see now why JCU resisted Peter Ridd's call for validation  of their alarming "dying reef" studies.  Ridd knew that they were fudging the facts but, in good scientific form, did not say exactly that.  He just called for their studies to be validated, where replication is a major form of validation.

JCU illegally fired him for saying that and are still challenging him in the courts.  After one verdict against them, you would think that they would cave in.  But they cannot afford to. Admitting that they had no legal grounds to fire him would open up a whole can of worms about why they DID fire him.

Replication studies are the death of crooked or negligent research and the need for them has come to the fore in recent years after lots of high profile studies in both medicine and psychology have failed careful replication. Much of what we thought we knew was wrong.

So a big replication of some JCU research is of great interest. And the replication was an abject failure.  The JCU results could not be repeated.  Peter Ridd implied that their findings about the reef were nebulous and we now hear that their findings about reef fish were nebulous.  It's a disturbing coincidence.

The chief JCU author on this occasion complains that the replication was not exact but the differences he points to should have been trivial in their effects.  If an effect is real it should emerge in a variety of contexts.  It did not

My best guess about how JCU got their alarming results is that they used much higher levels of acidification than is realistic. Less detectably, they may have manipulated every one of their parameters until they got the result they wanted


Over the past decade, marine scientists published a series of studies warning that humanity’s burgeoning carbon dioxide (CO2) emissions could cause yet another devastating problem. They reported that seawater acidified by rising CO2—already known to threaten organisms with carbonate shells and skeletons, such as corals—could also cause profound, alarming changes in the behavior of fish on tropical reefs. The studies, some of which made headlines, found that acidification can disorient fish, make them hyperactive or bolder, alter their vision, and lead them to become attracted to, rather than repelled by, the smell of predators. Such changes, researchers noted, could cause populations to plummet.

But in a Nature paper published today, researchers from Australia, Canada, Norway, and Sweden challenge a number of those findings. In a major, 3-year effort that studied six fish species, they could not replicate three widely reported behavioral effects of ocean acidification. The replication team notes that many of the original studies came from the same relatively small group of researchers and involved small sample sizes. That and other “methodological or analytical weaknesses” may have led the original studies astray, they argue.

“It’s an exceptionally thorough replication effort,” says Tim Parker, a biologist and an advocate for replication studies at Whitman College in Walla Walla, Washington. Marine scientist Andrew Esbaugh of the University of Texas, Austin, agrees that it’s “excellent, excellent work.”

But marine biologist Philip Munday of James Cook University, Townsville, in Australia, a co-author of most of the papers the Nature study tried to replicate, says there are “fundamental methodological differences” between the original and replication studies. “Replication of results in science is critically important, but this means doing things in the same way, not in vastly different ways,” he wrote in an email.

Munday helped launch research on the behavioral impacts of ocean acidification together with Danielle Dixson, now at the University of Delaware. In 2009, their paper in the Proceedings of the National Academy of Sciences showed that orange clownfish (Amphiprion percula) reared in seawater with elevated CO2 levels no longer recognized the chemical cues that could help them find a suitable habitat on the reef. (“Losing Nemo” was a popular headline for stories about the paper.) That study was followed by dozens of others showing similarly striking, and often large, behavioral effects in clownfish and other species, mostly from tropical waters.

Timothy Clark, the first author on the Nature paper and a marine scientist at Deakin University, Geelong, in Australia, says he initially set out to probe the physiological mechanisms behind those behavior changes. But after he failed to reproduce the changes—let alone explain them—he invited other scientists to set up a systematic replication attempt. It focused on three reported effects of acidified waters: making reef fish prone to swim toward their predators’ chemical cues rather than fleeing them, increasing their activity, and altering the fish’s tendency to favor either their left or right sides in some behaviors. The researchers didn’t seek to repeat each previous experiment one for one, but Clark estimates the entire effort covers the research reported in at least 20 studies.

Overall, the group reports, exposing fish to seawater with acidification levels predicted for the end of the century had “negligible” effects on all three behaviors. The Nature paper also reports the results of a statistical analysis called a bootstrapping simulation, designed to calculate the probability that Munday and co-authors could have found the striking data on chemical signal preference presented in seven papers. The authors say the odds are exceedingly low: “0 in 10,000,” as they put it.

Clark declined to elaborate on the implications of the bootstrap finding, but says he “would encourage any other avenues of investigation to find out what has caused the stark differences between our findings and theirs.” Esbaugh calls the bootstrap analysis “a little concerning,” but he objects to the “somewhat nefarious undercurrent” in the Nature paper. “I know both of these research groups,” he says, “and they’re both very, very good.”

Munday stands by his papers and plans to detail many “critically important” differences in the designs of the two sets of experiments in a response to the Nature paper. For instance, he notes the replication group didn’t study clownfish, used different water volumes and experiment durations, and used a different setup to study chemical cue avoidance. Dixson—who presented her findings at a 2015 White House meeting—also says methodological differences make a direct comparison between the studies “inappropriate.” But the Nature authors say some methods had to be adapted because they didn’t work as described in the original papers. They add that they could not catch enough clownfish, so used six other species also used in the previous studies.

Replication studies often cause quibbles about methods, Parker says. But, he argues, “If the original finding is reasonably robust,” then researchers using even somewhat different methods should be able to replicate it. And he notes that the replication team went to great lengths to be transparent. Unlike the original authors, the team released video of each experiment, for example, as well as the bootstrap analysis code. “That level of transparency certainly increases my confidence in this replication,” Parker says.

Researchers say the Nature paper allays one fear about the impact of ocean acidification. But Josefin Sundin of Uppsala University in Sweden, the Nature paper’s last author, stresses that climate change still poses a serious threat to sea life. “If the oceans were as acidic as we have been testing, it would also be much warmer, and that’s a huge issue,” she says.

Although replication efforts have blossomed in psychology, biomedicine, and other fields, they’re still rare in ecology, says biologist Shinichi Nakagawa of the University of New South Wales in Sydney. The new paper “sets a great example,” says Nakagawa, who hopes it “will instigate and inspire more replication studies—not to prove previous results wrong but to make our science more robust and trustworthy.”

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The journal abstract

Ocean acidification does not impair the behaviour of coral reef fishes

Timothy D. Clark et al.

Abstract

The partial pressure of CO2 in the oceans has increased rapidly over the past century, driving ocean acidification and raising concern for the stability of marine ecosystems1,2,3. Coral reef fishes are predicted to be especially susceptible to end-of-century ocean acidification on the basis of several high-profile papers4,5 that have reported profound behavioural and sensory impairments—for example, complete attraction to the chemical cues of predators under conditions of ocean acidification.

Here, we comprehensively and transparently show that—in contrast to previous studies—end-of-century ocean acidification levels have negligible effects on important behaviours of coral reef fishes, such as the avoidance of chemical cues from predators, fish activity levels and behavioural lateralization (left–right turning preference).

Using data simulations, we additionally show that the large effect sizes and small within-group variances that have been reported in several previous studies are highly improbable. Together, our findings indicate that the reported effects of ocean acidification on the behaviour of coral reef fishes are not reproducible, suggesting that behavioural perturbations will not be a major consequence for coral reef fishes in high CO2 oceans.

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Note: At roughly the same time as I first put up the above (on Facebook) Peter Ridd himself put up a critique very similar to mine above. Peter also mentions the dodgy work on Lionfish done by Oona Lonnstedt, a PhD student at JCU. Making stuff up would appear to be a major feature of the culture at JCU

Great Barrier Reef truth may be inconvenient but it is out there


PETER RIDD points out where the Australian Institute of Marine Science has got it wrong.  They cannot admit it or it would completely destroy their most trumpeted claims.  Their allies at JCU even fired Ridd to protect their claim of reef damage.  It's now political.  A lot of careers are at risk if Ridd is right

We have no data of Great Barrier Reef coral growth rates for the past 15 years. Has growth collapsed as the Australian Institute of Marine Science claims?

Is the Great Barrier Reef being affected by climate change, the acidification of the ocean, and the pesticides, sediment and fertiliser from farms?

One way to tell is to measure the coral growth rates. Our science institutions claim that coral growth rates collapsed between 1990 and 2005 due to stress from human pollution.

Remarkably, despite having data of coral growth rates for the last few centuries, there is no data for the last 15 years. We don’t know how the GBR has fared since 2005.

Corals have yearly growth rings similar to tree rings. By drilling cores from large corals, scientists can measure the growth rates over the life of the coral.

The yearly rings are roughly 10 millimetres thick so a coral many metres across can be hundreds of years old. In a landmark study, AIMS took cores from more than 300 corals on the GBR and concluded that for the past 300 years coral growth was stable, but in 1990 there was an unprecedented and dramatic collapse of 15 per cent.

With Thomas Stieglitz and Eduardo da Silva, I reanalysed the AIMS data and, in our opinion, AIMS made two significant mistakes.

The first was incorrect measurement of the near-surface coral growth rings on most of the corals that were giving data from 1990 to 2005. After years of argument AIMS has begrudgingly agreed that it made this mistake. The other problem is that it used much smaller and younger corals for the 1990-2005 data compared with the mostly very large and old corals of the pre-1990 data — it changed its methodology and this is what caused the apparent drop at 1990. When we corrected this problem, the fall in growth rate disappeared.

AIMS continues to dispute this second error and still claims there was a worrying reduction in growth rate from 1990 to 2005. This disputed work is quoted in influential government documents such as last year’s reef outlook report. I am not cherrypicking a minor problem. It is a fundamental problem with a keystone piece of GBR science.

We thus have a situation that arguably the most important data that tells us about the health of the GBR is highly questionable from 1990 to 2005.

What is far worse is that we have no data since 2005.

The science institutions have not only failed to investigate probable major errors in their work, they have also failed to update measurement of this fundamental parameter while claiming, in increasingly shrill tones, that the GBR is in peril.

But ironically, this failure provides a fantastic opportunity

The coral challenge.

For the past 15 years we don’t know what growth rates have been. It is easy to fill in the missing data, and check the previous data, by taking more cores from the reef. AIMS has effectively stated that coral growth is falling at 1 per cent a year.

According to the AIMS curve, growth should now be 30 per cent lower than it was in 1990 — which would be a disastrous fall. I predict it has stayed the same. Either way, it would be nice to know what has happened — is the reef really in danger or not?

But a second and almost equally valuable outcome of measuring the missing data is that it will be an acid test of the trustworthiness of our major science institutions. AIMS has dug in its heels and denied it made a major methodological mistake. Let’s do the experiment and see if it is right, or untrustworthy.

Same for me. If this measurement is done, and done properly, and it shows there has been a major reduction in coral growth rates, I will accept I was wrong and that there is a disaster happening on the reef.

The coral challenge is a measurement that will have to be done sooner or later. The longer it is neglected the worse it will look to the public. Farmers accused of killing the reef are especially interested.

We need to make sure these new measurements are done properly and without any questions about reliability. They must be supervised by a group of scientists that are acceptable to both sides of the agricultural debate on the reef to ensure the methodology and its execution are impeccable.

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