Visions from nature

Paul Hebert: The Inventory of Life

By Sam Perrin

Humans have always tried to categorise the world around us. From our early interpretation of the four elements to Linnaeus’ revolutionary system in the 1700s, we’ve always sought to understand better the life that we share the planet with. On my visit to the University of Guelph this year, I was able to sit down with a scientist who is attempting to classify all multi-cellular life.

Professor Paul Hebert is Scientific Director of the International Barcode of Life project, a consortium whose goal it is to document all life on our planet. I spoke with the man nicknamed the “father of DNA barcoding” about the magic that has revolutionised biodiversity science in the last 50 years, and how it’s being used today.

Professor Paul Hebert, the "father of DNA barcoding", is attempting to classify all muticellular life
Professor Paul Hebert, the “father of DNA barcoding”, is attempting to classify all muticellular life (Image Credit: Guelph University)

Sam Perrin: You completed your PhD in the Genetics Department at Cambridge in the 1970s. How has the landscape for molecular ecologists changed over the last 50 years?

Paul Hebert: In a revolutionary way. In the late 60s and 70s, we knew DNA was the hereditary material, but didn’t contemplate that it would soon be easy to read genomes on a nucleotide by nucleotide basis. This advance is magical. I mean that’s what science does, right? It makes the impossible possible.

I was among the first generation of researchers who were probing biodiversity through molecules, but we were studying protein variation in populations rather than DNA. And that was really the first opportunity for people to move away from morphology and start using molecules to ask questions about organisms. My PhD work was only possible because of this new molecular approach, but we were still one level away from DNA. We couldn’t imagine being where we are today, being able to read DNA sequences with ease.

SP: How has what you do changed in the last 50 years?

PH: Well, we’re involved in the longstanding effort to inventory life on our planet, with a view towards better knowing and protecting it. 50 years ago, it would be fair to say that the tradition of taxonomy wasn’t riveted with technological transformation. It was a science based upon the careful study of morphology – the variation in size, shape, and colour of organisms; that’s how taxonomists discriminated species. And so the massive transformation now, the edge of the wave we’re riding, is discriminating organisms through strings of digital information, DNA sequences. This is the revolution that has occurred during my career, and with this shift to digital strings comes the capacity to scale biodiversity science in ways we couldn’t have imagined 50 years ago.

The taxonomic community has been registering biodiversity for 260 years, and over that time we’ve described about 1.9 million species. That translates into about 7,300 species per year. Today, a single DNA sequencer provisioned with access to an adequate supply of specimens could register half a million species in a year. This acceleration is nothing short of magic.

“I would have to say that what we’re doing right now was science fiction 50 years ago.”

SP: So what is DNA barcoding?

PH: DNA barcoding is founded on answering a simple question – How little DNA do you need to sequence to tell species apart? Can you, for example, find one gene region, a barcode, that discriminates all species in the animal, plant, and fungal kingdoms. Sadly, it’s not quite that simple; there is no single gene region that discriminates species in all lineages of life, but a handful of gene regions perform extremely well in telling species apart. For example, a short section of a single mitochondrial genome, less than a millionth of the total genome, can discriminate nearly all animal species, including humans and their primate allies.

SP: What is the International Barcode of Life (iBOL) project?

PH: The iBOL project was initiated in 2010; it involves an international consortium of researchers and institutions that joined forces to advance the development of a DNA-based identification system for life. For our first five years, we set the goal of assembling reference sequences for half a million species, and by August 2015 we met this target.

The International Barcode of Life project is based in Guelph, Canada, and involves 28 countries worldwide
The International Barcode of Life project is based in Guelph, Canada, and involves 28 countries worldwide (Image Credit: Centre for Biodiversity Genomics, University of Guelph)

SP: Was there anything back in the 70s, that seemed like science fiction to you at the time that has since come to pass?

PH: I would have to say that what we’re doing right now was science fiction 50 years ago. I certainly didn’t think the scientific community would complete the inventory of species within my lifetime, but now believe it’s within easy reach. We suspect there may be 20 million species of multicellular organisms on the planet, and within 20 years we can complete their registration because of a couple of advances. The development of DNA sequencers that can process large numbers of specimens, and the realization that tiny segments of DNA can discriminate species. In short, you couple technological progress with a conceptual advance, and, all of a sudden, the impossible becomes easy.

SP: Speaking of science fiction, if I say Star Trek, what comes to mind?

PH: The Tricorder, of course, a handheld device that Spock employed to read life. Developing that touchless capability here on earth is going to require some new technological magic. However, I am sure that it will soon be possible to touch any organism on the planet and gain its identity and find out everything that humanity knows about it. In fact, such devices will likely be available within a decade or so.

SP: What do you think the biggest challenge that the program has faced is?

PH: Biodiversity science doesn’t have the tradition of some other research domains, such as physics and astronomy, of leading mega-science projects. As a result, it’s a real challenge to acquire the resources needed for large-scale biodiversity project. However, I do find it strange that a project focused on something so important to everyday life – planetary biodiversity – encounters this difficulty, especially since it’s inexpensive as mega-science projects go. You would think that it would be easy to raise the required funds, but that task remains our great challenge.

There are other complexities related to the Convention on Biological Diversity and the constraints in moving biological materials around the planet. No-one minds if you look at stars, no-one minds if you fracture atoms, but if you want to inventory of life, there are certain nations where regulations prevent access, and that slows scientific progress.

“I’m convinced by the middle of this century we will be monitoring biodiversity just as we monitor the weather today.”

SP: So what’s the point of all this?

PH: If our mission were only to create an encyclopedia of life with a page for each species, it wouldn’t change our world. What use is an encyclopedia, what use is a dictionary, unless you’re actually using the words in the dictionary to communicate ideas? That’s the central goal of the second phase of iBOL. To make it possible for humanity to read nature, so that we can, for the first time, understand what our actions and other environmental changes are doing to the species that share our the planet.

We have a very good sense of how many humans live in every country, but how many other species do we have that knowledge for? We don’t have a clue, especially for smaller life forms. We don’t know what’s happening to their numbers, their diversity, their distributions. The technology that we’re adopting and advancing is going to make it possible for humanity to read life, just the way that we read temperatures. I’m convinced by the middle of this century we will be monitoring biodiversity just as we monitor the weather today.

SP: What’s the main barrier in terms of technology, the next hurdle that needs to be leaped for this to happen?

PH: The project began at a time when the characterization of DNA relied on Sanger sequencing. A decade later, we have access to third generation sequencers which make it possible to characterize single DNA molecules. Their capabilities are critical to make the inventory of life affordable. When I estimated the cost to complete the inventory of life with Sanger sequencing in 2015, the price tag was about $2.5 billion dollars. With third generation sequencing, this has dropped by 80%. While raising $2.5 billion for biodiversity science would likely fail, I think raising $500 million is achievable.

There are a couple of big challenges ahead as we move to complete the inventory of life and to activate a global bio-surveillance system. Firstly, massive sampling programs will be needed to monitor life around the planet. Secondly, the interpretation of the sequence data resulting from the analysis of these samples will be a serious challenge. We need to develop informatics platforms that can synthesize these data into reports that track what’s happening to life on a planetary scale. That will require serious effort.

Aside from gaining the capacity to analyze and interpret the massive volumes of data arising from global bio-surveillance, we need the technology to make it much simpler to access biodiversity information in any situation in a flash. This analytical path will require simplicity to provide a field-friendly capability to simply touch a leaf, a caterpillar, anything you see, and have the device generate a species readout. As simple as the checkout counter in the store. And that’s going to require more scientific magic.

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