Today, if I wanted, I could go on a
bushwalk and sequence a genome.
That might not sound very remarkable as my
joints freely bend, I can see, and I don’t mind getting wet, muddy, sweaty and molested by insects, or my skin breached by armed plants and burned by the sun. In
fact I sort of enjoy all of those things; well, not individually and in
isolation (no, I do not have a dungeon...), but as part of the rich
experiential symphony of life in the great outdoors. And being a taxonomist,
field work is actually part of my job. I describe life, not in epic poetry, or
stunning photography, but in scientific papers that are by some measures, a bit
dour. I describe new species – taking the raw, unvarnished thrill that the
discovery of an organism unknown to science elicits, and turning it into a scientific
manuscript reporting in methodical, formal terms the characteristics of that
new organism and giving it a scientific name such that that species becomes
available for science and society.
And the life that I describe is found in the bush, and not uncommonly
in a country like Australia where about 200 new plant species are described by
taxonomists like me every year. THat's an extraordinary figure - 200 new plants a year - and even more startling when you realise it is ten percent of the
world’s total. For a taxonomist, Australia really is the lucky country – so
many species, and so much bush in which to walk and discover. And with so many
new species of plants turning up, discovering a new one is often rather unremarkable.
It is also rather unremarkable that today,
I can sequence a genome. I mean unremarkable not in the sense that it is unworthy
of awe (because sequencing genomes is awesome), but unremarkable in the sense that
everybody, at least in biology and medicine, is doing it. But this socialisation of genomics is very recent.
The technology for reading genomes - the sequence of nucleotide bases (A, C, G,
T), or ‘letters’ that inscribe the language of life, DNA – has advanced in such
a mad headlong rush that by the time the sun set on 2015 it became possible to
do in a weekend for less than $2000 something that in the 1990’s
took more than a decade and at least half a billion dollars. This
extraordinary efficiency gain has outstripped even that most celebrated example
of technological advance, the decline in cost of computing power represented
by Moore’s Law. This law describes the observation that the number
of semiconductors that can be packed onto a silicon chip roughly doubles each year,
which roughly translates to a halving of the cost of computing power each 18
months because of the additional savings made through chip manufacturing
advances. Because of Moore’s Law my new mobile phone is more powerful in
computing terms than my ten year old desktop machine, now unloved and gathering
dust under the desk and accidentally assaulted by the toe of my leather
winklepickers whenever I yawn and stretch. But the rate of advance in DNA
sequencing technology blows Moore’s Law away. It wasn’t always the case. Prior
to 2007 the cost of sequencing genomes was falling in line with that of
computing power, meaning it could be roughly described by Moore’s Law.
Thereafter however, things got really interesting. The cost fell
catastrophically because new, more efficient sequencing technologies came
online and in the years following drove cost reductions so spectacular that in
the time it took computing power to become about 15 times cheaper, sequencing genomes
became
about 10,000 times cheaper. It’s
hard to underestimate the impact this has had on biology and medicine, which
are being revolutionised by access to genome data. Even
taxonomists like me, working in small labs on small budgets, can now sequence
genomes. It is fast becoming a routine, unremarkable, part of the work that we do.
But what is truly remarkable – transformative, disruptive, revolutionary ...
whatever – is that it is now technically possible to go for a bushwalk and
sequence a genome at the same time and in
the same place. I’ll let that sink in.... as a scientist, I am now able to
carry all the equipment necessary to sequence a genome into the field with me
and sequence the genome of an organism I collect on the spot. Recently, Oxford Nanopore, a biotechnology company
based in Oxford, UK, started selling a new DNA sequencing device, the minION. This device is smaller
than a mobile phone, plugs into the USB port of a laptop computer, costs about
$1000, and can sequence a bacterial genome between lunch and tea. The company
is not the only one producing genome sequencing machines, but it is pretty much the only
one whose signature device does not require a large, sturdy benchtop to hold it
up, a specialist technician to run it, and hundreds of thousands of dollars of
cold hard cash to purchase it. This is truly disruptive technology, which is
really saying something in the context of a field that has been in constant
disruption for nearly ten years. Its a game changer. While some technical
details of the device need improvement (its accuracy is still unacceptable for
many applications) this early generation product brings us within sight of the
day when genome sequencers will be as much part of the field biologist’s
toolkit as a GPS unit is now.
Will this day come? I think so. In fact it
will come pretty soon for me. I am hoping to take one with me in March 2017
when I participate in a species discovery expedition on Cape York Peninsula in
the remote northeast of Australia. As part of the multiyear BushBlitz species discovery partnership, I
will be helping survey Quinkan
country, a sandstone landscape renowned for its extensive Aboriginal rock art
near the small town of Laura. I’m astounded that I will witness scientists
bring samples in from the field that they think may represent species new to
science, extract the DNA and offer a small drop to the sequencer who in a few
hours will deliver its verdict, confirming or denying their hunches. Imagine
the field efficiency gains this will drive: “Jenny, the DNA of that one doesn’t
match anything known so very probably a new species. See if you can get more
specimens tomorrow.”, or “Boring, just a malnourished and malformed individual
of a well known species, don’t bother with any more of that one”. The
efficiency gains are important, but rather prosaic. What is deeply inspiring is
the utter collapse of the barriers to genome knowledge. A species discovered in
the time of the so-called father of taxonomy, Carl von Linne (a.k.a Linnaeus,
1707-1778) would have to wait around 250 years to have its genome revealed. A
species discovered today need only wait a few hours...
And what kind of world will this technology
usher in for taxonomists and other biologists? What will we do when we are as
blase about sequencing whole genomes in the field as we are about cooking our
camp dinner? Its hard to fully imagine, but here are a couple of possibilities
beyond the obvious “What species is it, what is its population genetic
structure and who is it related to phylogenetically?”:
·
Real time species tracking: by discovering
DNA discharged downstream by defoliation, defecation or death, field biologists
could determine the presence of species of interest upstream and adjust survey plans
accordingly.
·
Real time population diversity
assessment: by comparing sequences of samples from across the local range of a
species one day, researchers may be able to pinpoint the best areas for the
following day’s sampling or survey.
This new world is one of great promise and
to maximise its opportunities, I want some bright spark to build me a mobile
genome lab. I’m thinking a capable 4WD with a raised roof and internally fitted
out with a bench, a portable electricity generator and fridge, and the small lab items
needed for extracting and purifying DNA to load into the sequencer. And if I
pitch this vehicle as the ‘Genome-o-Rover’ then I might just attract the attention
and sponsorship dollars of a certain vehicle manufacturer that shall remain
nameless. I would volunteer my time to travel the nation, sequencing genomes in situ in the most remote and
inhospitable locations, and dropping in to schools and communities along the
way to talk about what I am doing. And if I do my job well, I just might find
myself a couple of decades from now passing the baton (or sequencer) to some bright
eyed graduate who asked me a probing question about plant DNA in the outback 20
years prior.
Who will join me?
