Measuring Old Corals & Coral Reefs (Part 2)

Reposted from Jennifer Marohasy’s blog

January 20, 2021 By jennifer 

Late last year, I went on an expedition in search of a type of very old coral known as massive Porites. Stuart, Shaun and I dived five very different coral reefs between Cairns and Townsville.

The first was an inshore fringing coral reef to the leeward side of High Island. High Island is close to the Australian mainland, and not far from the Russell and Mulgrave rivers that drain a catchment with sugarcane farms. More than almost any other coral reef along the Queensland coast, this inshore reef would likely show impacts from agriculture – if there are any.

High Island with its fringing coral reef.

This coral reef has a very broad and long reef crest. On the afternoon of 28th September, when we visited, this habitat was covered in perhaps one metre of water. Along the seaward edge of this fringing coral reef, the crest gives way to the reef slope where we found so many massive Porites – so many of the old corals that we were searching for.

The water was quite turbid, which is common at these inshore reefs depending on the prevailing wind.

On the reef slope, many of the Porites (these massive bolder corals), were more than 2 metres in height and width, and a golden colour. There were lots of little fish. I found a peg that perhaps marked a Porites that been cored more than 17 years ago. The Australian Institute of Marine Sciences (AIMS) once cored corals at this reef.

Once upon a time, the scientists drilled into the corals and extracted a core from which they created a slither. Then, under x-ray, they counted the annual bands with the varying lengths and thicknesses of each band being a measure of annual growth rates. Yes, these massive bolder corals have annual growth rings – like tree rings.

Then we found another peg, perhaps marking another of the corals that used to be cored. But our job was not to count the pegs, rather to measure the height and width of the Porites – of the old corals.

The massive Porites at the beginning of the reef slope were of a uniform height. This is because their vertical growth is constrained by sea level. The growth rates of coral colonies slows as they come within 2- 3 metres of the surface. So, the annual growth bands of these Porites, at this reef, may not be a good indicator of climate change, because they are so constrained by sea level.

Our expedition was in searching for Porites, but not any Porites: Porites suitable for coring to determine the effect of climate change on coral growth rates.

The Porites are growing to a uniform height, just below the sea level.

At any given location, the sea level changes with the tides. Sea level, the tides, can vary by 3 metres in one day at this reef. And the very lowest tide in the 18.6-year lunar (moon) declination cycle may cause a tide that is a foot (30cm) lower than the lowest tide in an average year. (There is more about this in our new book ‘Climate Change: The Facts 2020’, see page 267, and there is also a Factsheet about tides falling on corresponding El Nino events at the book’s dedicated webpage, see figure 4 at the second link.)

The tides, and so much else that happens at coral reefs, has a lunar/moon influence – both the good and the bad. Coral spawning happens exactly 5 days after a full moon, and the worst coral bleaching events, which were in 1998 and then again in 2016, correspond exactly with the lunar (moon) declination cycle of 18.6 years. If the massive Porites at the coral reef fringing High Island were not constrained by sea level, they would be more dome shaped. But as they grow closer to the surface, their tops are bleached on the lowest tides and then die, so they become flat topped.

The decayed top of a massive Porites growing on the slope at this fringing coral reef.

As the reef crest grows seaward and the coral colonies now growing on the slopes are incorporated into it, these massive Porites may eventually grow into a donut-like form referred to as a microatolls. A microatoll has dead coral in the centre and is surrounded by a ring of live coral.

There are so many ‘donuts’ – Porites microatolls with diameters of perhaps two metres – in the aerial photographs from above the reef crest at High Island. These corals may have become incorporated into the reef crest as the coral reef prograded seaward and so may also be two metres in depth, or the coral colonies/the Porites microatolls may be quite flat bottomed, having started life on-top of the existing reef platform and only ever had the opportunity to grow laterally because they have always been constrained by sea-level.

The High Island reef crest from 10 metres altitude.
The High Island reef crest from 120 metres altitude.

From 120 altitude above the reef crest at High Island, and indeed above most reef crests, it mostly all looks rather drab and desolate – except for the donuts. It is from about this altitude that the chief scientist at the ARC Centre for Coral Reef Studies at James Cook University has decided that more than 50% of the Great Barrier Reef is bleached. His reports make newspaper headlands around the world, and so most people now believe that the Great Barrier Reef is half dead.

To be clear, Professor Terry Hughes flies over hundreds of reef crests, looks out the plane window, and scores them. If more than 60% of the corals looks dead to him the reef is given a score of 4.

Except that at this altitude, at which the plane flies, it is actually impossible to see any individual corals – beyond the large donuts, which are Porites microatolls.

While it is impossible to see the littler corals and the colourful fish at this high altitude – from such a distance – there were so many delicate and pretty corals on this reef crest, and even pretty blue fish as you can see in the transect photographs. (There is a new webpage with the photographic transects and a bit more. It will become the data page for High Island reef eventually, hopefully, incorporating species lists and analysis of coral cover and coral health.)

The chief scientist claims to ground-truthed his scores from the aerial flyovers by laying belt transect that are ten metres in length over some of the reef crest. We laid such transects at the High Island reef crest on 28th November 2020. We also laid transects at 5 metres depth. We are planning to go back and lay transects at 10 metres depth.

Photograph of the first transect at 2 metres from the reef crest at High Island.

Just considering the first 10 metre transect from the reef crest at High Island: at 2 metres along, I can see such a pretty beige Lobophytum pauciforum coral. The tentacles are extended along several of the branches. So, I can conclude this is a healthy coral.

Photograph from the transect at 5 metres, at the High Island reef crest on 28th November 2020.

But what about the coral at 5 metres along this photographic transect? It looks bleached! But perhaps this is actually a soft coral, perhaps Sinularia polydactyla which is a type of coral that never has any zooxanthellae, so it can’t bleach.

Photograph from the transect at 10 metres, taken at the reef crest at High Island on 28th November 2020.

But the last photograph in this transect, at 10 metres: the corals are almost all dead and covered in algae. There are, though, two young nobly Porites emerging from the destruction that could become microatolls eventually. After a hundred years these two pink nobly things could grow to a metre in diameter and be donut shaped.

While taking the transect photographs at this reef crest Shaun found and also photographed a blue lionfish, Pterois sp..

A lionfish at the High Island reef crest.

While Shaun took the photographs, Stuart took video of the corals along the tape measure, along the transects. This video transect gives a more continuous and a wider-angle view of the corals along each of the ten metres sections of reef. Considering just the last three of the ten-metre sections of video transect which are from the reef crest, how would you score this reef crest?

Given the great variability in coral cover, and coral health, and the diversity of coral species and just along 10 metres of transect, I find it quite difficult to make such a judgement.

Science is not a truth. It is a way of getting to the truth.

If we use the method applied by the chief scientist then we have to choose from just one of five categories for this reef. According to his method, the result of which are regularly reported across the world, you need to choose one of the following categories:
<1% dead, 1-10% dead, 10-30% dead, 30-60% dead, >60%.

So, what is your decision! Is this reef crest 10-30% dead?

Perhaps it would be easier if you just looked at the reef crest from 120 metres altitude and made a decision based on your impression of the corals from this altitude, as the chief scientist does.

The High Island reef crest from 120 metres altitude.

So, what is your decision? From this altitude could it be concluded that this reef crest is more than >60% dead? Would this be a fair assessment, and would it then be fair to conclude that the entire ecosystem at this fringing coral reef is more than 60% dead?

I actually think that there are major problems with the methodology used by Professor Hughes to decide on the state of our coral reefs. I think it inappropriate to attempt to categorise the state of corals from such a high altitude, from more than 100 metres away. I think that the professor should be getting in, and under, the water.

If there is anything that a high altitude aerial photograph is useful for, beyond finding Porites microattols at reef crests, it is perhaps distinguishing the different habitat types at coral reefs. From high up in the air above High Island it is easy enough to see that the reef crest is quite different from the reef slope.

The reef crest ends at the reef slope which is along the seaward side of the High Island coral reef. This aerial was taken on 28th November, 2020. Our 40 foot boat provides some scale, you can see about half of it in this aerial.

The reef slope is the section that falls alway to the sea floor. The most prolific growth and highest biodiversity at a fringing coral reef is typically down the reef slope. I wonder how far down the Porites and other corals grow at this reef? I wonder how far from the reef crest, down the reef slope before the sea floor?

Massive Porites towards the top of the reef slope at High Island, photographed on 28th November 2020.


Stuart Ireland took all the aerial photographs, and filmed the transect video. Shaun Frichette took all the transect photographs. These provide some record of the health of this coral reef fringing High Island for that moment in time, for Saturday 28th November 2020.

There is a High Island data page, with the transect photographs and I’m hoping to add species lists and more to this page:

Part 1 of this series concerns Pixie Reef, just to the north of Cairns, and can be found here: . Like High Island, Pixie is so close to Cairns but such a different reef perhaps in part because it is not fringing a continental island.

This website is archived each year by the Australian National Library:

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January 21, 2021 6:11 pm

Signals, images, and inference. Science is, with cause, a philosophy and practice in a limited frame of reference.

January 21, 2021 6:14 pm

“…if you just looked at the reef crest from 120 metres altitude…”

I don’t think that’s all they do.

And if you just dived on five reefs?

Joel O'Bryan
Reply to  Loydo
January 21, 2021 6:24 pm

5, 1, or 100? Einstein said something about that 100 years ago. You should check it out Loydo.

Science is about disproving a hypothesis (rejecting the hypothesis in favor of the null hypothesis), not about “proving” anything. Successful scientists will have many more failed hypothesis than maybe just the one in their career they can continue to find support for as they investigate alternatives. Much of coral science became rent seekers, and in doing so chased the tenure security of grants arising from climate alarmism. The incentives to do so were built into a system to return results to support a desired political narrative.

Last edited 2 months ago by joelobryan
Reply to  Joel O'Bryan
January 21, 2021 11:20 pm

For the climate scientologists to disprove the hypothesis, they would first need a null hypothesis.

Joel O'Bryan
Reply to  Redge
January 22, 2021 12:07 am

Yes, the scientific method is an anti-science to today’s post-modern climate science practitioners. Post-modern science only deals with consensus and Group-think. And consensus science is the realm of politics and religion.
Science: RIP.

Reply to  Loydo
January 21, 2021 6:30 pm

You should have stopped at “I don’t think”.
“Aerial survey find reef bleach worse than previously thought” “TERRY HUGHES: We flew over about 520 reefs and unfortunately more than 95 per cent of those reefs we categorised into the two most severe bleaching categories. Only 1 per cent of the reefs, four reefs, had no signs of bleaching.”

Last edited 2 months ago by lee
Reply to  lee
January 21, 2021 7:10 pm

You should have just stopped.

(a) Survey locations
We assessed coral communities and their colony size structure on the reef crest and reef slope using a nested sampling design, on replicate sites and reefs in five sectors along the length of the GBR (figure 1a). Crest assemblages were surveyed at 1–2 m depths on 15 mid-shelf reefs, three per sector, in 1995 and again in 2017. Reef slope communities were assessed at 6–7 m depths on 15 different mid-shelf reefs in 1996 and in 2016. At each of the 30 reefs, we ran eight to ten 10 m line-intercept transects at each of four sites. We measured the length of the intercept of each physically discrete colony (i.e. contiguous colony tissue) with the transect tape to the nearest cm. Separate intercepts of the same colony were summed. We identified all intercepting colonies using the following 12 morpho-functional benthic groups of hard corals, predominantly composed of the species listed in parentheses: Isopora (I. paliferaI. cuneata), Montipora etc, etc etc.

Oh plus Manta tow estimates were compared with intensive scuba surveys undertaken by the Great Barrier Reef Marine Park Authority and with live coral estimates obtained from video footage

But you stick with Jennifer- I wonder how far down the Porites and other corals grow at this reef? – Marohasey’s assessment.

Reply to  Loydo
January 21, 2021 9:05 pm

“At each of the 30 reefs”

or “We flew over about 520 reefs” also at the reference -“It was a massive aerial survey.

Over four days the scientific team covered more than 1000 kilometres from Cairns to the Torres Strait and what they discovered was much worse than expected.”

Do you understand the difference between 30 and about 520? it is not insignificant. And no mention of dives on those 4 days. Excluding the bars of course.

Last edited 2 months ago by lee
Reply to  lee
January 21, 2021 10:28 pm

You think Marohasy’s blog post is more comprehensive and accurate than the surveys described above?

Reply to  Loydo
January 21, 2021 10:41 pm

What aerial surveys? 🙂
BTW – Just how many of those 30 reefs were still dead. How many had the miraculous Lazarus treatment.
From your RS reference -“All modelling analyses were carried out in a Bayesian framework with brms [25].”

That sounds really cool. A model to tell them stuff.:)

Last edited 2 months ago by lee
Reply to  Loydo
January 22, 2021 12:07 am

You think its NOT !?

… at 120m

Seeing only the surface coral affected by LOW WATER LEVELS.

Marohasy’s blog post is ALMOST CERTAINLY MUCH MORE HONEST. !

Not the pack of LIES and DISTORTIONS that Hughes is renowned for.

Ron Long
Reply to  Loydo
January 22, 2021 2:49 am

I think Jennifer’s observations are a direct view of reality, which offers much more potential to arrive at a correct interpretation than the apparently inappropriate aerial surveys. In the airplane Hughes sat on his ass and did science? When I am driving and doing road-cut geology I stop and verify anything interesting looking. Don’t criticize Jennifer for going face-to-face with reality.

Reply to  Loydo
January 21, 2021 9:57 pm

Realistically Loydo, you know that what Hughes does with his GBR ‘studies’ is just ‘drive-by’ (‘fly-by’?) impressions, which every one us who have ever flown over parts of the GBR has done.

I’ve got packets, boxes and discs of aerial pics of the GBR dating back to 1970, many from low altitudes, but I wouldn’t for one moment purport that they are any kind of scientific study.

Jennifer Marohasy
Reply to  Loydo
January 22, 2021 12:36 am

The Royal Society study is a different study, Terry Hughes has not concluded 50% of the Great Barrier Reef is dead based on this study. There are different methodological issues with the Royal Society study that I have detailed here:

Reply to  Jennifer Marohasy
January 22, 2021 1:41 am

“…that I have detailed here”

Well you mention the “new proxy method” in passing but make no attempt to explain why you don’t like it. The only other mention of their methodological issues is that you think they surveyed too soon after a bleaching event and that there was a cyclone. Their surveys were spread along each section of the reef so cyclone damage can only have occured on a small number of the reefs surveyed.

Reply to  Loydo
January 22, 2021 5:04 am

Loydo you did a Griff again did you read your own link … here start with the abstract and tell us again how reliable the manta tows are according to science … LOYDO shoots and scores an own goal

There is limited information on the validity and reproducibility of estimates of benthic cover from manta tow surveys. To address this, benthic cover estimates from the same reef area were compared (i) among observers and (ii) with an independent assessment using-under-water video. Benthic cover was classified into 11 categories. There was generally unbiased agreement within one cover category, both among observers (89%) and for comparisons between manta tow and video (86%), While estimates of dead coral cover were reproducible, they were not valid because the concordance between observer estimates and video estimates was not greater than would be expected by chance. Manta tow estimates of the cover of sand and rubble were biased in that they consistently overestimated sand and rubble cover in comparison with estimates from video. The results indicate that manta towing, is generally effective for the broadscale estimation of live coral cover, providing observers receive adequate training.

Last edited 2 months ago by LdB
Reply to  Loydo
January 21, 2021 10:08 pm

“And if you just dived on five reefs?”


If you actually dive on the reefs, you find they are in great shape.

But poor GULLIBLE little worms like you can’t seem to grasp that FACT.

You do know that bleaching is from exposure due to lower sea levels events, don’t you. Or were you UNAWARE…. as always.

Last edited 2 months ago by fred250
Reply to  fred250
January 21, 2021 11:16 pm

So you don’t get bleached coral in deeper water?

Reply to  Loydo
January 22, 2021 12:10 am

Displaying your ignorance , yet again, hey loy-dumb.

That is why diving and direct observation as Jen does…

is FAR MORE accurate and HONEST.

Now do you have ANY SCIENTIFIC EVIDENCE AT ALL that the periodic bleaching has ANY human CO2 causation whatsoever. ???

Or is EVIDENCE something you are TOTALLY EMPTY of as always..

Reply to  fred250
January 22, 2021 12:31 pm

It is noted that YET AGAIN, loy-coward posts moronic comments elsewhere, but RUNS AWAY from actually producing ANY scientific evidence at all !!

Such a pathetic little trollette/weevil.

Reply to  Loydo
January 21, 2021 10:27 pm

Loydo it is such a shame that you can’t actually add any value to any of these conversations. You just keep showing your ignorance. Your comment is just ludicrous.

Joel O'Bryan
January 21, 2021 6:19 pm

The continued use of inexpensive, high resolution drone imagery across the GBR will continue to drive stakes through the heart of bad coral science.

Joel O'Bryan
Reply to  Joel O'Bryan
January 21, 2021 7:12 pm

Note to Jennifer (assuming you read WUWT posts).

A tech you should work on with a drone innovator on is dipping camera from a drone. Concept: Use an underwater camera on a 5-10 meter tether from the drone to record underwater images of reefs, quickly and easily, that are cued from the 20 meter aerial surveys. Diving, while fun, is time consuming and slow. A camera-dipping drone could make quick work of an entire reef section in one battery charge cycle.

Joel O'Bryan
Reply to  Joel O'Bryan
January 21, 2021 11:12 pm

First attempts should be not much more than a weighted GoPro 4K vidcam at the end of a weighted 5 or 10-meter, monofilament fishing line from a drone capable of carrying that 1-kg weight. Of course you’ll need a hexa- or octadrone to do that lifting with any battery life. An experienced drone operator will need to be confident to hover down to 1-2 meters over the water surface with that rig.
If that works (in daytime), then proceed on to night flights with an LED light at 1-2 meters on the tether line, above the GoPro, so to show the reef at 1am-3am when real life comes out there at night.

Just imagine nighttime dipping-camera videos and photos of supposedly “dead” reefs taken with a drone over an entire reef section, undisturbed by human divers.

Jennifer Marohasy
Reply to  Joel O'Bryan
January 22, 2021 12:38 am

Thanks for this information. Do you have a link with more information about this specific drone?

Reply to  Joel O'Bryan
January 22, 2021 8:02 am

How do you point and control the direction of a camera at the end of a 30 meter fishing line? Once it is in the water it will point in whatever direction the water is moving. And how to you maneuver it? Seems it might be difficult enough just raising it back up almost 30 meters against water pressure and weight. I could see an underwater tidal flow pulling the camera wherever, and drone along with it.

Paul Johnson
Reply to  BobM
January 22, 2021 9:04 am

You don’t need to control the camera. Use a slowly rotating saucer with a compass and multiple cell-phone cameras recording overlapping views. From this data, construct an immersive display or a 3D model along the reef transit. Note that reef transits are NOT the goal. They are only needed to calibrate/validate aerial observations to establish an optimum drone survey altitude.

Bob Thomas
Reply to  Joel O'Bryan
January 23, 2021 2:01 pm

Joel, interesting idea but having dived on the reef for 30 years it is not that linear. How do you allow for coral being at different distances away and the loss of light and clarity over any distance greater than a few metres? I am imagining your dipping drone hanging off a bommie and someone having to dive to retrieve it.
Hope you can overcome the many issues you will face as the idea has merit.

January 21, 2021 8:55 pm

Perhaps, if these bolder porites were a little less bold, they would strive less to breach the surface so they could looke more like their boulder porite brethren whom I have enjoyed diving with at other locales.

Add as many 😆😊 as you feel appropriate. I do wish I was already independently wealthy so I could fund and join you on many more of these dives!

Jennifer Marohasy
Reply to  QQBoss
January 22, 2021 12:39 am

I wish you were independently wealthy to fund us both doing many more dives. :-).

Bob Thomas
Reply to  Jennifer Marohasy
January 23, 2021 2:14 pm

Jennifer, how much do you need to fund this research? If you could put a figure on it and the amount of research that could be done then I am pretty sure a gofundme page would supply a fair amount of what you need.
My view is that this is important as there seems to be little actual science being done on the reef apart from James Cook University’s efforts and Peter Ridd has fallen foul due to his questioning of their processes.

January 21, 2021 10:22 pm

Thank you Jennifer for trying to keep things honest.

Jennifer Marohasy
January 22, 2021 12:33 am

With reference to earlier comments suggesting Terry Hughes has a methodology that is more sophisticated than flying over reef crest at more than 100 metres altitude and running a few underwater belt transects also across the reef crests … that is the extent of the methodology underpinning media reports that 50% of the Great Barrier Reef is dead from bleaching.

The methodology is detailed in Ecology 99(2), 2018

Data set identity: A spatial database of bleaching scores for 931 coral reefs on the Great Barrier Reef in the Austral Summer of 2016. 

B. Data set identification code: 

Coral bleaching scores of 931 reefs on the Great Barrier Reef (range: 142oE to 152oE, 9oS to 23oS). Bleaching scores are recorded in a .csv attribute table. The attribute table identifies each reef by a unique reef code (following Great Barrier Reef Marine Park nomenclature), reef name (where available), reef centroid (as longitude and latitude), coral bleaching score as a categorical variable: (0) less than 1% of corals bleached, (1) 1-10%, (2) 10-30%, (3) 30-60%, and (4) more than 60% of corals bleached, and date of aerial surveillance. 

Methods: We compiled an attribute table of coral bleaching scores for 1156 whole reefs on the Great Barrier in 2016. The attribute table identifies each reef by a unique identifier number and (where available) reef name, the longitude and latitude of the centroid of each reef, a categorical bleaching score of the bleaching status of each reef, and the date the reef was surveyed from the air. 
These data were generated from comprehensive aerial surveys of the Great Barrier Reef Marine Park and Torres Strait (Fig. 1) conducted on ten days between 22nd March 2016 and 17th April 2016 when bleaching was at its zenith, but before significant mortality had set in (confirmed by extensive underwater surveys at 260 sites (104 reefs) 

The aerial surveys utilised light aircraft and helicopters, flying at an elevation of approximately 150 m (500 ft). We assessed 1156 individual reefs from the coast to the edge of the continental shelf along 14o of latitude. Using the same protocols as earlier aerial surveys conducted in 1998 and 2002 (Berkelmans et al. 2004), each reef was assigned by visual assessment to one of five categories of bleaching severity: (0) less than 1% of corals bleached, (1) 1-10%, (2) 10-30%, (3) 30-60%, and (4) more than 60% of corals bleached. 

Underwater surveys of the coral bleaching were conducted at the same time on 104 reefs, to assess the accuracy of aerial surveys, using five 10 x 1 m belt transects placed on the reef crest at a depth of 2m at each site. Observers identified and counted each coral colonies and recorded a 6-scale categorical bleaching score for each one: (1) no bleaching, (2) pale, (3) 1-50% bleached, (4) 51- 99% bleached, (5) 100% bleached, (6) bleached and recently dead. The amount of bleaching for each location is the sum of categories 2-6, i.e. excluding unbleached colonies. 

Terry Hughes has authored other studies, some of which I have commented on in other blog posts including:

Bob Thomas
January 23, 2021 2:29 pm

Have a listen to Professor Terry Hughes taking a 1.5min each-way bet on the barrier reef.

Lewis Buckingham
January 23, 2021 2:36 pm

Here is the opportunity for some of those who are still working on the Reef and those who felt there was no future and folded their tents, to slip quietly away.
We need your input.
It may start here.
The science is not about one person or any ego.
The growing numbers of tertiary students working on the Reef need replication and exacting tasks that may yield reproducible results over years of hard work.
This fight for limited funds, control of data and news worthy coverage has happened before in
However the dead hand of University Administration was kept at bay.
The enlightenment still burned.
It didn’t sack people for transgression against ‘collegiality’.
So we now know a lot about our forebears.
Fossil Men The quest for the oldest skeleton and the origins of humankind.
Some quotes

‘And beside he would say, very often ,even if they did see the fossils they wouldn’t even know what they were looking at.’

‘Some peers vehemently disagreed with the conclusions, others dreaded engaging in arguments likely to end unpleasantly; and some thought to consign the fossil to irrelevance by ignoring it’

‘If we don’t tell him its wrong, it is like disseminating false information.’

‘He wants to be sure’.

‘verify everything’

“The question is’ how far does that adaptation go?'”

“As an empirical scientist ,Clark had been perturbed by the ‘mass of rather airy fairy model building’ that had permeated his corner of academia in recent years..'”

The prescript carries an


A man has come; a quarrel will come.

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