The Race to Save the Greatest Library on Earth

Intrepid explorer and ichthyologist Richard Pyle, Ph.D., is best known for his pioneering work on the deep coral reefs of the twilight zone — the part of the ocean that is between 150 and 500 feet deep, also called the mesophotic coral ecosystems. With expertise lying at the intersection of three distinct yet overlapping worlds — fish, diving and databases — he’s considered to be in the vanguard in each. Now 50, Pyle has been studying deep reefs since he was a teenager.

Having suffered decompression sickness (DCS) at age 19 after running out of air on a 140-foot-deep collection dive in Palau — his third and shallowest dive of the day — Pyle was an early convert to mixed-gas diving in the 1980s. Soon afterward he purchased a rebreather developed by explorer Bill Stone, founder of Cis-Lunar Development Laboratories, who remains a collaborator. A self-described fish nerd, Pyle has been an important voice in the rebreather community ever since.

Richard Pyle, in a blue button-down shirt, wears a tank and sits on the side of a boat
Richard Pyle prepares for a rebreather dive to nearly 500 feet in the Philippines.

More recently, Pyle applied his considerable computing chops to help perfect the algorithms for Poseidon Diving Systems’ innovative oxygen-sensing systems and participated in field-testing the units to depths approaching 500 feet. As an associate zoologist, database coordinator and dive safety officer at the Bernice Pauahi Bishop Museum in Honolulu, Hawaii, he continues to lead scientific diving expeditions throughout the Pacific.

Born in Hawaii to a family of naturalists, Pyle reckons his improbable path can be traced back to the family saltwater aquarium. As a toddler, his mom would park him in front of the glass to keep him occupied. By age 8 he had aquariums of his own and was making collection trips to island tide pools.  

In March 2017 Pyle was featured in a cover story in Science magazine. The previous year he discovered and named a new fish, Tosanoides obama, in honor of President Obama, who designated the expansion of Hawaii’s Papahānaumokuākea Marine National Monument. This species is the latest of more than 100 fish Pyle has discovered. He has also published more than 200 papers, including a comprehensive 10-year investigation of mesophotic coral ecosystems of the Hawaiian archipelago in October 2016.

Richard Pyle wears a rebreather
Richard Pyle test-dives a Cis-Lunar MK-4P rebreather in 1994.

Despite his long list of discoveries and publications, he has yet to catch up to his mentor, 93-year-old ichthyologist Jack Randall, who has discovered 830 species and published more than 900 books and papers. Randall presciently hired Pyle to type labels for fish specimens at Bishop Museum following Pyle’s diving accident, which left him partially disabled for more than a year. It was there the boy wonder (he was later named one of Esquire magazine’s “Best and Brightest” and received the prestigious NOGI Award from the Academy of Underwater Arts and Sciences in 2004) discovered his love of taxonomy, nomenclature and databases, which might someday be judged as his most important contribution. “I don’t know if I’m obsessive-compulsive or just mildly neurotic, but I have a fetish for organizing and analyzing information,” he explained.

Today, Pyle is at a nexus of scientific organizations that are reshaping our understanding of biodiversity. He’s one of the leaders of the International Commission on Zoological Nomenclature (ICZN), the arbiter of scientific animal names since 1895, which is in the process of radically revising its animal naming conventions. He’s also the visionary and architect behind ZooBank, the ICZN’s online registry that aims to document all named animals. In addition, Pyle serves as the Convenor for the Taxonomic Names and Concepts Group at Biodiversity Information Standards (also known as the Taxonomic Databases Working Group, or TDWG), where he is developing new software tools, data models and standards for managing biodiversity information.

Pyle’s unique vision, experience and body of work make him one of the preeminent library scientists at what could reasonably be called the library of life. As such, his contributions may not only promote our understanding and application of our global genomic inheritance, but they also might ultimately help ensure humanity’s future.

In the early 1990s you inspired technical divers with tales of the twilight zone, and you discovered many new species of fish and coral. What led you to the broader questions of biodiversity?

I got involved in the All Species Foundation, which was founded by Kevin Kelly, Ryan Phelan and Stewart Brand to catalog all species on Earth. They invited me to be a part of the conversation with leading biodiversity people. It was through those conversations that I began formulating the metaphor of a genomic library.

Give me your elevator pitch.

All living things today are the endpoint of a 4-billion-year-old chain of information that has been passed down through successive generations via reproductive events. This information is what separates life from nonliving chemistry. You can think of it as a library; the 10 million to 30 million species that we estimate inhabit Earth represent 10 million to 30 million stories, which are embedded in our genomes and have been edited and fine-tuned over time by natural selection and other processes.

An orange-and-white striped peppermint angelfish floats through the water
Pyle discovered the beautiful peppermint angelfish (Centropyge boylei) on deep reefs in the Cook Islands.

We are creatures of story!

Yes, but these aren’t just any stories — they are nonfiction stories of survival. I would argue that the information embedded in the global genome, along with the ways these organisms interact with each other, is the most valuable information that exists anywhere in our solar system and probably in this vicinity of the galaxy. Biodiversity is our most valuable asset. It’s truly extraordinary.

Are you making that assertion just as a biologist or with a broad scientific perspective?

Bill Stone asked me the same thing when I first presented this idea to him. He argued that physics was much more valuable than biology. It took me an hour of explaining, but by the end his jaw was on the floor. He agreed with me.

Let me take a Rumsfeldian approach (from former U.S. Secretary of Defense Donald Rumsfeld). First there are the known knowns. We already know that biodiversity performs what some have calculated to be trillions of dollars of ecosystem services for us. Examples include bees pollinating our crops and plants absorbing our carbon dioxide and producing oxygen. These are just a few examples among millions that keep us healthy and alive.

It forms our biological infrastructure.

Exactly. Other known knowns include chemicals we have found that can cure diseases.

Then there are the known unknowns. We know these things exist, but we don’t know how to harness them yet. For example, Craig Venter sampled plankton from all over the Sargasso Sea and ran them through a sequencer to find out what kind of genes were there. Prior to Venter’s work, there were a few dozen known biological photoreceptors used in photosynthesis. But Venter found genes that represented close to 800 photoreceptors. We know nothing about the vast majority of microbes in the sea because we can’t culture them; we can detect their existence only through what amounts to sequencing the water.

The diversity of life has had 4 billion years to figure out how to convert sunlight energy into chemical energy, and it can do so with something like 97 percent efficiency. Typical photovoltaics are somewhere in the 20 percent efficiency range. Imagine if we understood enough to convert sunlight into chemical energy with 97 percent efficiency — it would be monumental.

My point is that biology has already figured out solutions to our problems; we just need to discover them. That’s one of the known unknowns. Some thinkers believe that the cures to all human diseases are somewhere in the biodiversity genome; it’s just a matter of finding them.

I believe the combination of the known knowns and the known unknowns represent only a small percentage of the actual value, the remainder of which are the unknown unknowns — the stuff we don’t even realize we don’t know. As we start to peel back the layers of what biodiversity has created, I think we’re going to end up finding bioengineering solutions to almost every problem. Most of these discoveries will be at the molecular level in the form of specific proteins that do specific tasks.

Any time you explore a new domain, the real magic is in the things you weren’t expecting to find. The stuff you expected justifies the exploration, but the unexpected finds are what really makes it all worthwhile in the end.

A blue fish sparkles
The deep blue chromis (Chromis abyssus) is one of many stunning new species discovered on deep coral reefs in recent years.

We’re still in the very early stages of exploration.

Absolutely. The wealth of information contained in this genomic library goes far beyond our current ability to understand it. We are like kindergarteners running through the aisles of the Library of Congress, surrounded by an almost incomprehensible trove of information, yet our ability to read and understand it is not much beyond “see Spot run.”

Being able to sequence DNA is orders of magnitude from being able to harness the power of that knowledge. If we really understood genomics, we would have the power to do things we can barely imagine right now. It would be like Christopher Columbus having a GPS. But we’re learning fast. Within a few decades we will be able to read and understand much of what biodiversity has to offer. The question is: How much of it will be lost by then?

You’re speaking of what scientists are calling the sixth mass extinction event —the extinctions that are now occurring because of human activity: climate change, pollution, deforestation, etc.

There are plenty of lines of evidence that show this is happening, and it appears the rate of extinctions is accelerating faster than in some previous extinction events. In the past these events happened over a couple of centuries. The fact that we are observing so many extinctions is the scary part. It means we’ve accelerated the process to the point that it’s happening over of decades rather than centuries. As my friend Sylvia Earle put it, “What we do in the next 10 years will impact the next 10,000 years.”

The library of life is burning. What is science doing about it?

Well, the most correct and direct answer to that question is “not enough.” Of course all scientists say they need more money for research, so it’s kind of cliché to say we’re not doing enough. My point is we aren’t doing enough in this area relative to other areas of science.

You mean compared to things like funding the space station or the Large Hadron Collider?

Exactly. I’m a big fan of space exploration, and physics is my second calling in life. I get why it’s important to understand the Higgs boson and the finer scale of matter. What I’m saying is let’s not neglect this other thing, which is arguably much more pressing, lest its potential value be lost. Space and the laws of physics will be here 1,000 years from now, biodiversity will not.

So it’s a matter of balancing priorities?

We are more likely to find solutions sooner through understanding biodiversity than through understanding quarks. At the very least we ought to fund biodiversity research and documentation on a scale that’s within an order of magnitude of the funding of these other big science projects, not five orders of magnitude lower.

Team of rebreather divers conduct experiments
A team of rebreather divers conducts experiments with the Hawaii Undersea Research Lab (HURL) deep-sea submersible at 300 feet off Maui.

You’re saying that we spend 100,000 times more on physical science than we do on biodiversity?

Basically, yes. The closest thing that the National Science Foundation (NSF) has done to address biodiversity is something called the Planetary Biodiversity Inventory (PBI), which began as a partnership with the All Species Foundation. They gave out grants averaging $3 million over a 10-year period for a total of $30 million. Compare that to $9 billion for the Large Hadron Collider, $144 billion for the Apollo Project and $150 billion for the International Space Station. Heck, we spent $196 billion on the space shuttle.

So $196 billion down to millions is about five orders of magnitude. I’m not saying we need $196 billion to solve biodiversity, but how about $3 billion as opposed to $3 million?

Are decision makers listening?

Big ideas like climate change and the human genome project were around for decades before they captured widespread attention and received financial support. That’s where the “biodiversity matters” movement is today; the scientists are all on the same page. As one biodiversity expert put it, “If the physicists can get billions of dollars to fund their ‘super-conducting trash compactors,’ why can’t we?”

Our focus now is to spread the word as widely as possible. Think of the role the film An Inconvenient Truth played in catalyzing the climate-change movement. Once the public starts to care, politicians will too, and scientists can build a case for them to get behind. That’s how priorities get set for government-funded agencies such as the National Oceanic and Atmospheric Administration (NOAA), the NSF and others.

And what about you?

I think the biodiversity story is the most important issue confronting humanity, and so I try to convey this message at every opportunity that I get, whether it’s to a group of scientists or my wife’s high school students. It just makes sense to me, so I’m going to keep preaching it. I’m not going to stop.

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© Alert Diver — Q4 2017