Dan Janzen Vision: DNA Barcode Readers. . ..
Now Is The Time
Phil. Trans. R. Soc. Lond. B (2004) 359, 731–732 DOI10.1098/rstb.2003.1444
The spaceship lands. He steps out. He points it around. Itsays
‘friendly–unfriendly—edible–poisonous—safe–dangerous—living–inanimate’.
On the next sweep it says‘Quercus oleoides—Homosapiens—Spondias mombin—
Solanum nigrum—Crotalus durissus—Morphopeleides—serpentine’. This has
been in my head since reading science fiction in ninth grade halfa
century ago. I am sure it was in the heads of Linneaus, Alexanderthe
Great, and Timid the Mastodont Stomper. And it has been on thewish list
of every other human confronted with the bewildering blizzard ofwild
biodiversity at the edge, middle and focus of society.
Imagine a world where every child’s backpack, every farmer’spocket,
every doctor’s office and every biologist’s belt has a gadgetthe size
of a cell-phone. A free gadget.
Pop off a leg, pluck a tuft of hair, pinch a piece of leaf, swata
mosquito, and stick it in on a tuft of toilet tissue. One minutelater
the screen says Periplaneta americana, Canis familiaris,Quercus
virginiana, or West Nile virus in Culex pipiens. A chip the sizeof your
thumbnail could carry 30 million species-specific gene sequencesand
brief collaterals. Push the collateral information button onceand the
screen offers basic natural history and images for that species,or
species complex, for your point on the globe. Push it twice andyou are
in dialogue with central for more complex queries. Or, thegadget,
through your cell-phone uplink, says ‘this DNA sequence notpreviously
recorded for your zone, do you wish to provide collateralinformation in
return for 100 identification credits?’.
Imagine what maps of biodiversity would look like if they couldbe
generated from the sequence identification requests of millionsof
users. Such a gadget would allow access to true bioliteracyfor
all humanity. Such a gadget would be to biodiversity what theprinting
press was to literacy (and reading glasses, chairs, newspapers,the
Library of Congress and the computer). The blessing ofinformation
access through such a gadget is what the taxasphere—thecollective
intellectual might of taxonomists, museums, collections and
their centuries of literature—has within its power to offersociety,
global society, everyone. But will it? If it does not, wildbiodiversity
will continue its inexorable decline into the pit under the humanheel,
and the taxasphere will continue its accelerating slide into therealm
of quaint esoterica shared by a very few enthusiasts who lovetheir
bugs, ferns and birds.
The gadget requires two things and a third. Thing one is theeconomic
and social selective pressure to miniaturize what today occupiestwo
tabletops of machinery and a technician down to the size ofa
cell-phone; reusable and cheap. This miniaturization istechnically
feasible in any one of many industrial centres of the world. Itwould
take US$1 million and five bright people. This has not happenedin the
past decade because no one saw any particular reason to do it.However,
there is a reason. Real bioliteracy requires on-site real-timehand-held
cheap identification of hundreds of thousands of species, eventhough
any one person at any one time may care about only one organismin one
place.
Thing two is the global library of partial DNA sequences of afew
cleverly selected target genes that among them carryspecies-specific
combinations of nucleotides. Such a library can be constructed intwo
phases running concurrently. The world’s greatbiodiversity
collections—museums, herbaria and microbe depositories—haveon the
shelf, in some sort of order, easily half (if not more) of thespecies
of wild biodiversity encountered daily and consciously by 99% ofthe
world’s people.
One phase is to quite straightforwardly organize and fund SWATteams to
simultaneously polish the taxonomic organization and extract theDNA
samples for target gene species-level sequencing for theseshelves of
items. The other phase is to simultaneously reinforce theongoing
biodiversity inventory of the world and its taxonomic processing,so as
to sequence and characterize the as-yet uncollected wildbiodiversity.
Both the in-house taxonomic processing and outdoor inventory mustbe
congruent with the agendas of the taxon- and site-focused primaryusers,
so that as the sequence libraries emerge from the greatcollections,
these same collections are also receiving and taxonomicallyprocessing
the stream of new material (much of which may be sequencedas
collected). The cross-phase potential for mutual anditerative
reinforcement between the taxasphere and building thesequence
library—and populating its collaterals—is enormous. Icannot
over-emphasize the necessity for collaterals. A phone number isno good
if there is no one at the other end.
Thing three is the commercial–entrepreneurial process such thateach
time the gadget processes a sequence, a penny drops into a bucketthat
fuels the taxasphere to do what it does best and with such joy,and
fuels the conservation community to actually conserve that whichis
being sequenced in its wild home. Such a feedback system is
imperative to saving the present and future biodiversity Libraryof
Congress, so to speak. The goal is not to support yet anotherguild of
biodiversity administration and consultancies, but rather todeliver
bioliteracy to the world. And once people can read, ensure thatthere
still be books to be read.
Thing three is obviously the most difficult, given that Homosapiens is
notorious for not reinvesting its gains, ill-gotten or otherwise,in the
raw material source of those gains. Yes, start-up capital willbe
required, but rather than get this from classical venturecapitalism,
this is a time for the world’s philanthropic capitalists tofocus their
energy. Will the gadget user pay a penny per identification oncethe
system is in place? Yes, if it can deliver ‘one minute onesequence one
name’—and serious amounts of collaterals are available. Willthe users
feed new collaterals back into the information source toaccompany their
old or new sequence submitted? Yes, if they getidentification
credits, and as they see the value of retrieving their ownsubmissions
years down the road, to say nothing of the value of examiningeach
other’s submissions in real time and across geography.
The blending of these three things within their software glue andmatrix
is easily attainable in less than a decade with the technologicaland
sociological understanding already available, for a total budgetin the
range of US$1–5 billion. The process can be put in motion as aproof-of-
concept for a tiny fraction of this.
The viewpoint in this commentary was inspired by reading PaulHebert’s
enthusiasm and foresight in targeting just a part of the DNAsequence of
a single gene as a species’ ‘barcode’ (Hebert et al.2003a,b), by recent
planning efforts (Stoeckle 2003), and by witnessing the claritywith
which a portion of the CO1 gene sequence can discriminate amongmany
species of butterflies and moths, bees, birds and mammals.
Simultaneously, it has its roots in decades of attempting toprocess
millions of neotropical insects and plants through abiodiversity
inventory for a multiplicity of agendas. I am also frustrated byworking
for a half century in the field, nurtured and guided at longdistance by
the world’s best taxonomists, among hundreds of thousands ofspecies
of organisms, most of which are actually known to science yet canbe
identified in the field, at best, by only a select few. NeitherI, nor
the other millions of wild biodiversity users, can carry in theirpocket
the tens of thousands of pages of taxonomic descriptions, keysand
images, and their authors. Even if all were to be collapsed downinto
a single chip, I still could not connect the beast in hand toits
information as I stumble through the mud, rain and green of a 200000
species-rich patch of Costa Rican rain-forest. No one can learnthe
scientific language to read and hear the taxasphere’scollective wisdom
and facts for identification at the moment the bug is in the handor the
leaf in the mouth—even if we have the best access uplink toGoogle. If
each of us makes the long trek, which we will not, to the doorsof any
one of the great collections, in a matter of seconds thetotal
taxasphere will be over-whelmed. The gadget has huge potentialfor
relieving the taxasphere of the drudgery of routineidentifications at
those places where even today’s bioilliterate populace alreadyknows
that it needs to know what it is—the farmer’s field, ports ofentry,
doctor’s office, environmental monitoring, the kitchen, schoolscience
class, etc. Imagine what would happen if the environmentalmonitor could
know in a few minutes on-site the hundreds of species of insects,mites,
fungi and Protista in an environmental sample.
The answer does not lie in better keys, more keys, more images onthe
Web, more Web sites, species pages, more descriptions, morephylogenies,
more specimens, more anything. Those are necessary collaterals,but not
sufficient. The answer lies in a process that will, for the firsttime,
connect the collective species-level biodiversity knowledge ofthe world
to any and all users, on the spot, in real time, now. Fast, cheapand
on-site single (or very few) gene sequencing has the potentialto
deliver the species-specific linkage between the species and itshuman-
known collaterals. There is a huge opportunity for the taxasphereto
thrust itself into a position of friendly socialprominence—just as have
education, agriculture, medicine and communication.
We must move wild biodiversity from the category of something tobe
removed to make room for the extended human genome to a book tobe read,
and read, and read again. To illiterate people, a library is justneatly
stacked firewood. We must move the taxasphere from a ‘woe isus’ mode to
‘here is what we can offer at society’s negotiating table’.It is within
the technological power of the taxa-sphere to choose to move intoa
mutualism with directed molecular biology, miniaturizedengineering,
science writers and entrepreneurialism. Praise and supporttaxonomists
to be taxonomists, promote the emergence of those who enjoypackaging
species-level information for users, and enable us all to readwild
biodiversity. The time is ripe for a barcorder. Godfray (2002)noted ‘in
10 to 20 years’ time it will be simpler to take anindividual
organism and get enough sequence data to assign it to a“sequence
cluster” (equivalent to species) than to key it down usingtraditional
methods’. We do not have to wait one to two decades. Please doit now.
Daniel H. Janzen
Department of Biology, University of Pennsylvania,
Philadelphia, PA 19104, USA
REFERENCES
Godfray, H. C. J. 2002 Challenges for taxonomy. Nature 417,17–19.
Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R.2003a Biological identifications through DNA barcodes. Proc. R.Soc. Lond. B 270, 313–321. (DOI 10.1098/rspb. 2002.2218.)
Hebert, P. D. N., Ratsingham, S. & deWaard, J. R. 2003bBarcoding animal life: cytochrome c oxidase subunit 1 divergencesamong closely related species. Proc. R. Soc. Lond. B270(Suppl.), S96–S99. (DOI 10.1098/rsbl.2003.0025.)
Stoeckle, M. 2003 Taxonomy, DNA, and the bar code of life.BioScience 53, 796–797.
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