ChatGPT & DALL-E generated panoramic image of a Caribbean underwater view with a coral reef being printed by a large 3d printer

Sheer Scale & Complexity Of Reefs Makes Adaptation & Preservation Challenging

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Recently I hosted Professor Amy Wagoner Johnson, a US materials scientist who is leading a global research project on coral reef restoration, on my podcast Redefining Energy – Tech. In the theme of providing transcripts of presentations I’m giving in various places for people who prefer the written word, this is the lightly edited transcript of the second half of our conversation. The first half, with embedded podcast, is here.


Michael Barnard (MB): Hi, welcome back to Redefining Energy Tech. I’m your host, Michael Barnard. My guest is returning for the second half of our discussion, and that’s Professor Amy Wagner Johnson, a material scientist. She has a day job or three with the landlocked University of Illinois Urbana Champaign, a couple of hours south of Chicago and 750 miles from the Atlantic. But she’s leading a global initiative to restore coral reefs based on her work 3D printing human bone scaffolding and tissues. And that story includes machine learning, wave flumes, and Curacao. Listen in for the second half of our conversation.

We have another factor for coral substrates. Let’s talk briefly, artificial reefs versus natural reefs, because I think the first time I became aware of artificial reefs was due to a competitor to IBM. When IBM brought up its original personal computer, it had a crappy hard drive, and the competitor, what they did is they had a trade in. They give you a better hard drive from them, and they take the crappy IBM hard drive, and then they intentionally dump them in the ocean off Boca Raton, Florida, to create an artificial reef. At the time, I thought that was quite remarkable, good marketing because Boca Raton had the IBM research center in Florida.

Prof. Amy Wagoner Johnson (AWJ): It’s quite symbolic.

MB: Now, of course, with my greater knowledge of chemistry and the discussions you and I are having, I’m wondering about the chemicals leaching off those hard drives and the implications there. I know that right now there’s a place in the Pacific where old tires were dumped to become an artificial reef. But the tires are leaching negative chemicals into the local biosphere and creating significant problems. They’ve created an underwater toxic waste dump as opposed to a vibrant reef. The more we can help nature help itself and live within the constraints of nature, the more likely we are to do less damage.

AWJ: It’s absolutely true. And again, that goes back to why, when my colleague and I were originally thinking about, oh, let’s 3D print stuff for coral reefs, and then just had to take a step back, because even putting concrete in the ocean, it leaches out things that are not good. It can result in growth of things that you don’t want, rather than growth of things that you do want. I’ll mention just, there was a DARPA call a couple of years ago to make giant reefs, basically to protect shorelines near military bases. The team I’m working with now did apply, but unfortunately we didn’t get it. The idea was to build a living structure, exactly what you’re talking about. In some sense an artificial reef, but the intent was for it to be a living structure.

How can we form this quickly and really get it to populate with healthy corals and animals that would help, you know, create this sustainable and healthy ecosystem to protect the shoreline. DARPA funds really risky things and they like really out there projects. It was fun to kind of think about those things. Unfortunately, we didn’t get it. But that’s okay. Somebody’s working on it.

MB: Right now I’m hearing multiple conditions for successful artificial reefs from what you’ve shared so far. There needs to be fractal granular structures on anything you put down to create micro eddies, which allow the cilia for the larvae to attach. It needs to be a suitable substance for the larva to attach to calcium carbonate. Typically it needs to have strontium, magnesium, and other trace elements in the right proportions, roughly inward, still stumbling our way to understanding what those are. Then it has to have chemical signals from the flat algae plates that you’re talking about, or something similar from them, some chemical trigger. Then it has to be in the right temperature zone of water for the stacked symbiote to work. Then it has to be close enough to this, the surface of the water for the. For that to persist, for the photosynthesis to persist. Oh, what a mix.

I’m going to make a hypothesis just because this is kind of fun, right? I can imagine 3D-printing 50 centimeter by 50 centimeter cubes in a lattice with perhaps centimeter wide pieces, kind of a simple cubic structure, centimeter wide pieces with the strontium, the magnesium, and the calcium carbonate as the structure. Something you can stack and drop offshore. I can see two ways to do this, because you need to enhance evolution along with the chemical release of the whatever chemical it is from a flat algae. But you want to do that closer to shore and further from shore from the reef to allow the ones that happen to be more heat resistant to populate the near-shore ones and the ones that are more sunlight deprived, capable to populate the ones further from shore to help them migrate a bit.

I think that’s kind of where my brain is going now. This is my hypothesis based upon discussing this with you and some of the reading I did before prepping for this. Where are you guys actually going? Am I even in the ballpark?

AWJ: Sort of.One of my colleagues is Forest Rohr, and he has an interesting idea that we’re also working on with him that is called arcs, and these are floating structures. They’re kind of geodesic looking, where you might put panels of this material on this structure, and that material would allow larvae to settle. You might put some fragmented coral on there. That’s when you cut a little piece of coral off of the colony and glue it to a substrate and then put it somewhere else. And the idea behind these is sort of like the arc, right? They’re floating, and so you can move them to different locations depending on the conditions.

Let’s say the temperature is going to heat up. Well, you can move your arc to deeper water, where the water’s cooler and protect them, or there’s a pollutant that has come out where the arc is, and you can move it to cleaner water. You can kind of try to populate these arks with different species of coral, which might bring in urchins and fish and other things. That isn’t necessarily going to protect the shoreline in the same way because they’re floating, right? They can be, and they would be anchored, but they would move around and not necessarily serve that role of protecting the shoreline, but still be a little mobile ecosystem that could be used to try to maintain some healthy reef, but to allow it to be moved to safer places when there’s threat.

That’s one direction that the team I’m working with is going that’s different from, you know, printing blocks of this material and putting it around the shoreline. But I think that, honestly, I think that there’s so much that has to be considered in this. I think we really have to come at it from all directions because it’s such a complicated problem, and it’s really an important problem. Very complicated, very important. We need all scientific disciplines contributing to this.

MB: Back to the geodesic dome. What I hear you say is that it’s positively buoyant not floating on the surface, so floating below the surface, because then you’ve got in the right, you can get into the right temperature zone a little lower, the right sunshine zone a little higher, and you can then do that. The geodesic dome, of course — yay, Buckminster Fuller — is the strongest structure you can create with minimal materials. Much better than the cube that I suggest for stacking. Geodesic domes are terrible for stacking, but they’re great physical structures. That’s a really interesting kind of conceptual aquaculture reef.

AWJ: Yes.

MB: It’s still creating the habitat for the biodiversity. It’s still preserving a tremendous amount of that aspect of the reef. But it’s not creating the shoreline protection aspect. One of the things I spent a lot of time looking at a couple of years ago working with Natural Resources Canada, was the implications for shorelines with increases in storm surge, with increases in cyclonic activity globally, with increases in sea level. We can’t harden the shores. We have to re-soften them, which runs into political problems, because, of course, rich people with shoreline stuff don’t want to hear that they have to move away from the shoreline. They just want to know, how are you going to protect my beach?

AWJ: Yes, yes.

MB: Funny story. A set of rich homeowners in California got together and spent millions of dollars on putting new sand on their beach. Five days later, it had all washed away in a storm. People who just weren’t paying attention to the reality of the situation. The politics around coastal hardening and affluent communities and your infrastructure versus coastal softening and retreat are fascinating to watch play out globally. And coral reefs are part of that. It’s really interesting.

AWJ: If I can just go back to the geodesic dome. These are made with struts, so they’re not plates on there, so the water can flow through. Although you could cover some of the holes, but these could be put together in kind of Lego style, similar to the blocks, and connected in order to start to build that shoreline. I think that there have been some studies that show that having something that is not fully blocking the water is better than just having like, a concrete wall that the wave slams into. A structure like this would provide some of that kind of openness that some of the water could flow through, but it wouldn’t be like slamming into a brick wall.

At the moment, we don’t have plans to kind of do those connecting structures and putting them on the bottom of the ocean, but that is a possibility in the future. just wanted to mention that before we moved on.

MB: I will say if the oil and gas industry was actually a good player on the planet, all their subsea engineering skills would be great for building artificial structures that elevated the seafloor to the right level of temperature in the ocean and stuff, and put an artificial reef on top of that. Just saying, but not going to happen. The oil and gas industry is retrenching to their core. They’re going to extract the last barrel and cubic meter of natural gas they can and sell it for the highest price they can, and that’s what they’ve become.

AWJ: Agreed.

MB: We’ve talked about micro scale. We’re talking about millimeter scale here, and this is very small. We’ve been talking about some meso scale things like the half meter or meter square cube concept that I just came up with, which is much better articulated as a geodesic dome of struts. These are smaller scale structures. But let’s talk about the scale. Do you happen to have the size of the great barrier reefs or one of the other great barrier reefs? The mass, the volume, just the sheer area?

AWJ: I do not have a number, but I know it can be seen from satellite. That says as big as many countries.

MB: I’m going to cheat. So the Great Barrier Reef, Google is our friend for this. Almost 350,000 km². That is bigger than many countries. Volume. Do I have a volume statement? Okay, I’ve got hectares. Yes, great barrier, 400 types of coral, 1500 species of fish, 4000 types of mollusk.

AWJ: It’s unbelievable.

MB: I’m surprised that I can’t find the mass in kilograms. Huge, huge area. It’s one of the great wonders of the world, natural wonders of the world, and going through significant bleaching. When we say 350,000 km², now, the corals I’ve tended to see have been fairly, in fairly shallow water, amenable for scuba diving or snorkeling, because, you know, I could snorkel in the Caribbean. I’m not a scuba diver. So do you have any sense of how thick a coral is top to bottom, like the height of a coral?

AWJ: When we dive in Curacao, and just full disclosure, I would not call myself a diver by any means. I have a postdoc who works on this project in my lab, and he goes and does all the diving. It’s like, don’t let the professor in the lab kind of thing. Professors break stuff in the lab. But I did do it a couple of times. And some of the core corals that we were looking at were kind of, you know, those exercise balls that you sit on, they’re kind of like that. Some of them were like that, some a little smaller, some a little bigger. Some of the corals that we were looking at were about that size. They were mostly not encrusting corals and not branching corals, but rather these kind of stony coral types. Some of them were isolated and some of them were near other colonies.

MB: My experience with corals was some snorkeling in a cove in Hawaii and some snorkeling in the Caribbean. The corals I saw were half a meter to 2 meters, kind of the range of height. We have 350,000 km² with perhaps a meter thick. You know, that’s 350 billion cubic meters [bad math on the top of my head in discussion replaced with actual math] of material that stretches 1000 or 1500 kilometers. It is a non trivial engineering task to even consider it at the scale it exists.

AWJ: Absolutely.

MB: We’ve been talking about this millimeter scale, and this gets back to 3D printing. You’re a mechanical engineer, you’re in a mechanical engineering department. You probably had experience with the very first deposition 3D printers. You’ve probably worked with CNC machines at some point in your career. Before they became popular, you were probably playing with them and certainly had them around. You’re familiar with how long it takes for deposition printing to do stuff. And because you’re a nerd, you’ve probably spent time thinking about nanotechnologies and nano building structures and how long that would take at the atomic and molecular level for anything to turn into anything even visible. And this is kind of the stuff we’re talking about.

We’re talking about machines, biological machines the size of rice that build 350,000 km², massive offshore structures over thousands of years.

AWJ: It’s crazy. It’s unbelievable.

MB: Every time I start exploring aspects of it, it’s really apparent most people never bother to look at the math in terms of the scale. It’s really challenging. Your team has spent time looking at the scale. How long will it take for an artificial reef to accrete sufficient polyps to become effectively a natural reef, even with the geodesic dome concept you have?

AWJ: That’s a great question. The Great Barrier Reef, I think there’s a number that’s like several hundred thousand years that took to make. I don’t think we have to make great Barrier reefs. I think we can make pockets of reefs that will have maybe smaller ecosystems, but that can benefit the local area.

How long does it take? I think it’s a tough question because you’re constantly battling disease and pollutants. I would say like a decade for a fully healthy reef, but I’m just throwing a number out there because you can’t just have one type of coral growing. We work on a couple of different species, and some work better than others.

If you just grow one species, that’s not going to be sufficient for the ecosystem. I don’t know. I hate to even say, but it’s not in one season and it’s not in five seasons.

MB: I go back to the voyage of the Beagle, Darwin and Galapagos islands, and his differentiation of finches on different islands, depending upon the size of the nuts that were there. I can see, you know, obviously the microclimates within a reef will favor different species of corals.

AWJ: Yes.

MB: The open water basketball corals are very differently branching, massive structure corals. Let me ask this question in a different way. I’m thinking about black fly lifecycles. Fruit flies are used in genetic testing because they entire lifecycles in 24 hours. How long does a polyp last? How long does a larvae take to build a polyp? What’s the lifespan of a polyp?

AWJ: I can tell you that when we collect the gametes and they turn into the larvae and either die or settle within a couple of weeks. When they settle, they turn into a polyp, a single polyp. We don’t know whether they sort of start, I’ll say, like, collecting the materials when they’re larvae that are used to build the skeleton. There’s evidence of having a little bit of skeleton very early. Those polyps don’t just grow radially. A little polyp doesn’t just become like a huge polyp. It divides, then there are multiple polyps. You might start with one polyp on your substrate, and a year later, maybe there’s four or five polyps on the substrate, and it sort of starts to grow laterally.

How long does a single polyp live? These reefs are living thousands and thousands of years, and I’m sure some of those polyps are long-lived.

MB: Does the larvae, the living part of the polyp, have a short lifespan, and then the structure gets reinhabited by another larvae? Is that something that occurs?

AWJ: No, I don’t think so. Let’s say you had a colony, and some diver came in and kicked it and knocked off some of the polyps or injured the polyps. Some region of that colony, meter-sized colony, breaks off or gets an injury, and then that portion of it dies and falls off. What would happen there is the polyps in the surrounding area would divide and start to cover that new area. It’s not likely that, you know, larvae would come and land exactly there unless there was some assistance.

You could assist that by, for example, when you capture your gametes, you could bring them over to that colony, and you could tent that colony and release your larvae in there, and that would sort of trap them and sort of force them to land there. But if it’s a different species, then those two species might fight and kill each other. It has to be larvae from the same species and maybe even the same colony. I think it’s more likely that the living polyps would spread over that area that was damaged by something else.

MB: This does suggest that coral, which has been bleached and died, one of the methods for restoring it would be to get the gametes and larvae tent the bleached stuff and release the larvae in there, and they could repopulate the reef. You’re nodding your head. This is my hypothesis. Is this actually something that is being explored, to your knowledge?

AWJ: There’s a group that does this similar research at Carmabi lab. What they have done is they’ve created bins in one of the bays there in Curacao, and they put a bunch of their substrates in them. They’re looking at different types of substrates, and they put a bunch of those substrates in the bin, and then they put larvae in there and kind of tent it to try to get the larvae to settle in those bins. I’m not sure how successful that’s been.

We have tried and are going to repeat where we tent the arc, the geodesic dome, have substrates in there, collect the larvae, and put them in the geodesic dome and tent it to try to get all those larvae to settle. So it’s not totally clear, like, how successful that will be. You still have to have the right conditions.

If the larvae are sniffing around and they don’t like the smell, then you can’t force them to settle there. You still have to understand, what are the conditions that are conducive to the larvae settling? These juvenile polyps are really vulnerable to other things that might come and settle adjacent and grow over them, or maybe a parrot fish will come and munch on them. If it’s a single polyp, then it’s done. If it’s a colony it can afford to lose a couple polyps from a parrot fish or somebody kicking the colony, or whatever the insult might be.

MB: I’m just thinking about, you know, back to that exercise ball scale globular thing. That’s probably millions or hundreds of thousands of individual polyps.

AWJ: I never thought about estimating the number of them, but, I mean, it’s a lot, right?

They’re different sizes as well. So we’re trying to look at the growth rate of polyps that settled on our substrates, and we’re still going through that data from about a year ago. We settled the larvae on substrates, and we put them in some tanks at Carmabi, this lab in Curacao, where we do some of our fieldwork. Then we had an intern who came and would keep them clean. He’d go in and he’d brush off any bad stuff to kind of protect this single polyp on this substrate. Then we measured them, like, every month, and it’s pretty slow. We’ll let you know when we’re done compiling the data. But I can tell you that it’s pretty slow.

You want them to become mature enough so that when you put them out in the water, that they’ll be able to take some of the insults that they would be exposed to.

MB: Back to the lifecycle. There’s a couple of weeks for the larvae, then there’s an extended period of time as a polyp. Consider that the baby, teenage, and middle-aged years? When do they become a teenager? How long before they’re able to reproduce? When do they have a home that’s actually stable? It sounds like it’s more than a year, to be sure.

AWJ: It probably, again, varies by species and conditions, but I’m not sure when they become sexually mature. But yes, it’s not like rodents or rabbits. It’s lots longer than that.

MB: They’re building their skeleton around them on the outside from stuff. They’re straining ions from the sea.

AWJ: It’s kind of underneath. It’s like a little dumpling. When they first settle, you have this larva that’s kind of like a soft grain of rice, kind of elongated. Some are a little bit more spherical, but then it kind of sets one end down and then shrinks down and forms. It looks like a little dumpling. Then they start developing little tentacles. And the tentacles are at first, little short and stubby tentacles, like, you know, like toddlers. Their proportions are kind of short and stubby. These short and stubby tentacles grow longer, depending on the species. When they sit their bottom down and make this dumpling and then start forming tentacles, they’re building a skeleton, and they’re building it underneath them, and then through the walls of the dumpling.

They have these septae that kind of divide it. If you slice an orange transversely and you see these septae that separate the boats of the orange. It’s kind of like that. They have these skeletal walls, but they also have kind of a skeletal pedestal that they are on, and then the soft tissue surrounds that.

MB: Okay. I think I was mistaking them for one of the species, which actually retreats inside its shell, but they surround the carbonaceous material much more. They built the pedestal. They build a skeleton, and it’s a structure, and then they presumably die at some point. Then something else, another larvae, comes in and builds another skeleton on top of the old skeleton. It grows and grows. And it’s not very quick.

AWJ: No, not at all.

MB: To summarize, for tens of thousands of years reefs grow in tropical waters avoiding glaciation. The Great Barrier Reef persisted during the period of glaciation. They’ve evolved for a specific set of temperatures, salinity, alkalinity, set of chemical components in the water, a set of symbiotic species stacked in the case of the polyps, with the algae inside the stomach of the polyp. They’re one of those integrated symbiotic systems as opposed to side by side symbiotic systems. Presumably they have a symbiotic relationship of some level with the mat algae.

They have to have the right trace elements of strontium, magnesium, they have to have the right temperature, they have to have the right degree of sunlight in order to build these structures that take a very long time to build. Now we’re changing everything around them in a very short period of time and they can’t adapt because they aren’t free floating.

Let’s briefly take an example. Birds are significantly at risk due to climate change, but they’re one of the most mobile species in the world. In many of their cases, they can just move a little bit north, a little bit south, a little bit east, a little bit west, quite organically. It’s just not the same for reefs.

AWJ: No, not at all. Not at all.

MB: We only have a couple minutes left. I want to be respectful of your time. Fascinating conversation. I would happily delve into all sorts of nerdy stuff with you, but there is one additional question and then the open ended thing.

What’s the biggest aha moment you’ve had in this intellectual journey over the past six or seven years?

AWJ: Well, I can tell you the first one was at the conference that I went to with my colleague Andrew Lean, who we work with on 3D printing. I was all excited. We’re just going to 3D-print these materials and they’re going to go in the reef and it’s going to be awesome and we’re going to make a huge difference.

Then I learned about what fragging is and how they cut something off and they glue it to the substrate. Then there’s this interface of glue between the coral and the substrate. And so I was like, I don’t even think, like, what are we even going to do? There’s glue there and they’re stuck on there. They’re not even interacting with the material. How do we think about what the material means in that case?

Then I learned about the larvae and I was like, that’s where we can attack this by thinking more about the larvae. But I think there are other things you can do. You can design materials to sit next to the reef to release chemicals or change the ph or collect pollutants or things like that. It doesn’t only have to be that you have a substrate for a larva to sit on. I think there are lots of other exciting possibilities to use materials in ways that will improve the health of the reef.

MB: This has been amazing. You have a global, nerdy audience. I get people from every continent listening in, and they are focused on climate solutions. They’re focused on nerdy technology and the money and scale of the problem. You have whatever length of time you want to say, whatever you want to them. What would you like to share?

AWJ: I would say that I think this is a scientific problem, that we really need people from all disciplines to lean in and try to contribute to this because, you know, we’ve talked about materials, we’ve talked about all different parts of biology. We didn’t even talk about microbiology, and we didn’t talk about genetics and we didn’t talk about cryopreservation. These are all areas where people can contribute. For cryopreservation we could use engineers who understand heat transfer. I think engineers can play a big role, but we have to work with the biologists, we have to work with each other. Pretty much many parts of engineering, many parts of biology can contribute to this.

The more teams we have coming up with creative ideas in what we can do, I think we have a better chance of addressing the problem so that we can save the reefs.

MB: Amy, it’s been a pleasure. Thank you so much.

AWJ: Thank you so much. This has been really fun. Thanks so much.

MB: I’m Michael Bernard, host of Redefining Energy Tech. My guest today has been doctor Amy Johnson Wagner, materials scientist, who’s for the past six or seven years been figuring out what it’s going to take to save the reefs from us. That’s it for today. Until next time.

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Michael Barnard

is a climate futurist, strategist and author. He spends his time projecting scenarios for decarbonization 40-80 years into the future. He assists multi-billion dollar investment funds and firms, executives, Boards and startups to pick wisely today. He is founder and Chief Strategist of TFIE Strategy Inc and a member of the Advisory Board of electric aviation startup FLIMAX. He hosts the Redefining Energy - Tech podcast ( , a part of the award-winning Redefining Energy team.

Michael Barnard has 747 posts and counting. See all posts by Michael Barnard