Thomas M. DeCarlo
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Research blog

Understanding coral calcification with Raman spectroscopy

13/5/2018

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Most days, I get up, go to work, and zap corals with lasers. No, I am not building some twisted underwater version of a fly swatter, nor would I ever want to harm a coral. Rather, I am studying the chemical composition of coral skeletons to better understand how they grow, and hopefully improve our understanding of their sensitivity to ocean acidification.
 
I am using a technique called Raman spectroscopy. It is fundamentally different to conventional approaches for analyzing the chemistry of coral skeletons. While many studies have investigated element and isotope ratios by putting dissolved skeletons into a mass spectrometer, Raman spectroscopy is based on the scattering of light from a laser directed onto the coral skeleton. This offers several advantages: (i) it is fast, taking only 1 second per measurement, (ii) it can be applied on small spatial scales, down to about 1/100 the width of a human hair, and (iii) it is non-destructive, as the skeleton is not damaged in any way.
 
Based on the way the laser light is reflected from the skeleton, I can infer the chemical composition of the fluid from which it precipitated. This provides us with key insights into the mechanisms by which corals build their skeletons, and whether the skeleton-building process is sensitive to the rapid changes in seawater chemistry driven by invasion of human CO2 emissions into the ocean.
 
This new avenue of research into coral growth has led to several recent publications. The first paper developing the technique was published in November 2017 in Biogeosciences. Two follow-up application papers were both published this month, in Proceedings of the Royal Society B and Frontiers in Marine Science special issue on coral calcification. Within just the past year, we have already gained key insights into coral calcification with Raman spectroscopy, and this is just the beginning! Stay tuned for several new publications coming in the near future.
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Transparent science

3/5/2017

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Have you ever tried to repeat the analysis described in a paper and found it difficult? Whether it's some missing raw data or you aren't sure which R package was used, this can be quite frustrating. Wouldn't it be nice if authors published all of the raw data and codes needed to run the analysis with a single click of a button? Now this is possible! Code Ocean is a new online tool that lets you upload data and run scripts written in a variety of languages (Matlab and R being most relevant for me). The great part is that one need not have these programs on their computer or even download the data; the scripts are run through the cloud with literally the click of a single button. (I realise this may sound like an advertisement, but I assure you that it is not. I am just genuinely excited about this.)

I think this could be a great leap forward in making science transparent and reproducible. Imagine if every published paper were accompanied with a post on Code Ocean allowing the full analysis of the raw data to be executed by anyone. This would (1) save people a lot of time trying to recreate published analyses, (2) encourage collaborations, (3) improve reproducibility, and (4) ultimately scientists would probably write better code. Why this last point? If you are writing code and know that you will make it publicly available at some later stage, you are a lot more likely to write a neat and well-commented code, in much the same way that you will carefully write the paper describing the code.

Of course, I can see reasons why people may hesitate to post their code. What if someone finds a mistake in the code? What if someone tries to reuse the code in an inappropriate way? Plus, it takes some effort to check and upload the working code.

But surely the benefits vastly outweigh these downsides (more like excuses, really). The problem I foresee is that, unfortunately, there is little direct incentive to post a code. It won't directly affect one's ResearchGate, Google Scholar, or CV, and as far as I know there are no journal requirements to upload executable codes. I suspect that for this to gain momentum it will have to be required by either funding agencies or journals; or perhaps if enough researchers voluntarily post their codes then there will be a peer-pressure incentive to follow suit.

I tried this out for one of my previous publications. I will admit I was skeptical that Code Ocean would work in this case. This is some of the more complex code I have written. There are multiple ordinary differential equations embedded in multiple optimisations embedded in a Monte Carlo simulation. I imagined that Code Ocean must have some simplified Matlab compiler that would get caught up somewhere in this. But I was wrong! I literally just dragged and dropped the several Matlab .m files and the text files with the raw data into Code Ocean, changed the paths in the code to point to the raw data, and clicked "Run". Ok ok, actually I did need to write a few new lines at the end so that the main results would export export as a simple text file (I used structures in a .mat file for my original analysis). But really, this took a whole 20 minutes of my time. I even got personalised feedback on the script from a Code Ocean staff member. And now the entire analysis is traceable, from the very raw data to the final results in the published tables. Check it out below.

So will you post the data and codes for your publications? Or what is your excuse?

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Lunar rhythms in coral growth

17/4/2017

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Last week, corals all over the world "leaped" higher up on their skeletons. What was the special occasion? Just another full moon. My latest publication in the journal Coral Reefs shows that Porites corals build new sheets of skeleton, called “dissepiments”, each lunar month. Dissepiments are essentially the ladder rungs in the skeleton that the living coral polyps uses to climb. The living polyp rests on the upper-most dissepiment for one lunar month while building the rest of its skeleton, and then builds a new dissepiment during the full moon. Why the full moon? Many corals, including Porites, are perforate, meaning that the skeleton does not completely enclose each polyp. Rather, the polyps across the colony are connected, and thus their growth needs to be synchronized. It seems that the full moon provides a cue to synchronize the dissepiment-building process. One key outcome of this finding is that we can use dissepiments as monthly time markers in the skeleton. In the paper, we demonstrate using dissepiments that seasonal changes in skeletal extension rates are responsible for producing the annual density bands in Porites corals. Further, we can detect stressful events in the history of a colony based on anomalies in the spacing between consecutive dissepiments.

I am especially proud of this research because it required a lot of patience of foresight. Due to the nature of this study, it took my entire PhD to complete. That lunar rhythms exist in coral skeletal growth was not an entirely new idea and it had been hypothesized for decades that dissepiments form on a lunar basis. But this had not been tested in a formal way. Previous attempts to test the lunar rhythm hypothesis were somewhat ambiguous because they tracked dissepiments over just a couple months. We knew we needed a longer study. We designed a study in which we first stained living Porites colonies in Palau with a stain that is incorporated into the skeleton. And then we waited for the corals to build their dissepiments. We waited 6 months before we returned to collected the first skeletal samples. Then we waited another 15 months before we collected another set of samples. This allowed us to track the formation of dissepiments over multiple periods of time. All told, by the time I analyzed all the samples, 4 years had passed since I first started designing the study.

​
Here is an example of the skeleton samples we collected and our dissepiment analysis. On the left (a) is the skeleton sample collected in the first return visit. The red line marks the stain line. We can see 4 dissepiments (black lines) above the stain. Then, in the sample on the right (b) collected 15 lunar months later, we counted a total of 19 dissepiments. Thus, over 15 lunar months, this coral built exactly 15 dissepiments!
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Local warming elevates the risks that corals face in a warmer world

17/4/2017

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Read the press release here
and the journal article here

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Nice commentary on our coral reef metabolism paper!

17/4/2017

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A nice commentary piece was recently published in JGR-Oceans that highlights not only the key findings​ of our recent study on Dongsha Atoll, but also the important questions that emerged from our analyses. Yuichiro Takeshita did a great job in explaining that while we have a good understanding how community metabolism affects seawater chemistry, we have much less understanding of how seawater chemistry feeds back to influence community metabolism. This is a key question that we need to address if we are to accurately predict the sensitivity of coral reef communities to ocean acidification.

Our study had several surprising results. Net community calcification (NCC) rates on Dongsha Atoll were significantly higher than any other reef studied to date, despite its relatively high latitude, the relatively low pH of the surrounding open-ocean, and the high cover of algae on the reef. What factor is responsible for the exceptionally high NCC on Dongsha Atoll? There are several possibilities: (1) the largest internal waves in the world collide directly with the reef and may stimulate calcification by nourishing the reef with high-nutrient waters from below the thermocline, (2) the wide and shallow dimensions of the reef flat are conducive for large changes in carbonate chemistry and especially high daytime pH, (3) the coral community was recovering from a bleaching event and may have been exerting rapid calcification as a response, (4) low nighttime oxygen levels may limit the action of dissolving bioeroders. While the growing number of coral reef community metabolism studies is providing a testbed for the drivers of NCC, there are clearly many questions remaining and much work to be done!

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