Tuesday, September 01, 2015

Dark taxa, drones, and Dan Janzen: 6th International Barcode of Life Conference

6thBOL logo 300x237 A little over a week ago I was at the 6th International Barcode of Life Conference, held at Guelph, Canada. It was my first barcoding conference, and was quite an experience. Here are a few random thoughts.

Attendees

It was striking how diverse the conference crowd was. Apart from a few ageing systematists (including veterans of the cladistics wars), most people were young(ish), and from all over the world. There clearly something about the simplicity and low barrier to entry of barcoding that has enabled its widespread adoption. This also helps give barcoding a cohesion, no matter what the taxonomic group or the problem you are tackling, you are doing much the same thing as everybody else (but see below). While ageing systematists (like myself) may hold their noses regarding the use of a single, short DNA sequence and a tree-building method some would dismiss as "phenetic", in many ways the conference was a celebration of global-scale phylogeography.

Standards aren't enough

And yet, standards aren't enough. I think what contributes to DNA barcoding's success is that sequences are computable. If you have a barcode, there's already a bunch of barcodes sequences you can compare yours to. As others add barcodes, your sequences will be included in subsequent analyses, analyses which may help resolve the identity of what you sequenced.

To put this another way, we have standard image file formats, such as JPEG. This means you can send me a bunch of files, safe in the knowledge that because JPEG is a standard I will be able to open those files. But this doesn't mean that I can do anything useful with them. In fact, it's pretty hard to do anything with images part from look at them. But if you send me a bunch of DNA sequences for the same region, I can build a tree, BLAST GenBank for similar sequences, etc. Standards aren't enough by themselves, to get the explosive growth that we see in barcodes the thing you standardise on needs to be easy to work with, and have a computational infrastructure in place.

Next generation sequencing and the hacker culture

Classical DNA barcoding for animals uses a single, short mtDNA marker that people were sequencing a couple of decades ago. Technology has moved on, such that we're seeing papers such as An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. As I've argued earlier (Is DNA barcoding dead?) this misses the point about the power of standardisation on a simple, scalable method.

At the same time, it was striking to see the diversity of sequencing methods being used in conference presentations. Barcoding is a broad church, and it seemed like it was a natural home for people interested in environmental DNA. There was excitement about technologies such as the Oxford Nanopore MinION™, with people eager to share tips and techniques. There's something of a hacker culture around sequencing (see also Biohackers gear up for genome editing), just as there is for computer hardware and software.

Community

The final session of the conference started with some community bonding, complete with Paul Hebert versus Quentin Wheeler wielding light sables. If, like me, you weren't a barcode, things started getting a little cult-like. But there's no doubt that Paul's achievement in promoting a simple approach to identifying organisms, and then translating that into a multi-million dollar, international endeavour is quite extraordinary.

After the community bonding, came a wonderful talk by Dan Janzen. The room was transfixed as Dan made the case for conservation, based on his own life experiences, including Area de Conservación Guanacaste where he and Winnie Hallwachs have been involved since the 1970s. I sat next to Dan at a dinner after the conference, and showed him iNaturalist, a great tool for documenting biodiversity with your phone. He was intrigued, and once we found pictures taken near his house in Costa Rica, he was able to identify the individual animals in the photos, such as a bird that has since been eaten by a snake.

Dark taxa

My own contribution to the conference was a riff on the notion of dark taxa, and mostly consisted of me trying think through how to respond to DNA barcoding. The three responses to barcoding that I came up with are:
  1. By comparison to barcoding, classical taxonomy is digitally almost invisible, with great chunks of the literature still not scanned or accessible. So, one response is to try and get the core data of taxonomy digitised and linked as fast as possible. This is why I built BioStor and BioNames, and why I continually rant about the state of efforts to digitise taxonomy.
  2. This is essentially President Obama's "bucket" approach, maybe the sane thing to do is see barcoding as the future and envisage what we could do in a sequence only world. This is not to argue that we should ignore the taxonomic literature as such, but rather lets start with sequences first and see what we can do. This is the motivation for my Displaying a million DNA barcodes on Google Maps using CouchDB, and my experiments with Visualising Geophylogenies in Web Maps Using GeoJSON. These barely scratch the surface of what can be done.
  3. The third approach is to explore how we integrate taxonomy and barcoding at global scale, in which case linking at specimen level (rather, than, say using taxonomic names) seems promising, albeit requiring a massive effort to reconcile multiple specimen identifiers.

Summary

Yes, the barcoding conference was that rare thing, a well organised (including well-fed), interesting, indeed eye-opening, conference.

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