It’s strange how imagination often becomes reality. In the 13th century, Leonardo da Vinci designed machines that were extremely similar to modern day machine guns, submersibles and helicopters. Jules Verne’s sci-fi novels, written in the 19th century, such as Around the World in Eighty Days, Twenty Thousand Leagues Under the Sea, and From the Earth to the Moon all had elements in them which were deemed quite marvelous, if not impossible, at the time when they were written. Fast-forward two centuries, and we find ourselves with the technology that allows us to travel around the world in much less than eighty days, explore the bottom of the Mariana trench, which is eleven kilometers deep, and we can adventure far beyond the Moon.
In the 21th century, in a world brimming with various forms of multimedia, it is not surprising that we can find our next scientific potential in the world of television. A curious Japanese children’s animated program called “Pokemon” (short for “Pocket Monsters” as it is known in Japan), features a parallel universe in which creatures called pokemon (similar to animals in our world) are collected, reared and trained by Pokemon “trainers” for their special abilities. These creatures vary widely in sizes and shapes; therefore these Pokemon trainers often have to resort to a small piece of gadgetry called the Pokedex in order to determine the types of Pokemon. The Pokedex is a small, portable encyclopedia that allows to identify Pokemon on the spot, and gives the statistics on that particular Pokemon. It’s an essential tool that trainers use to capture Pokemon. (In fact, the show’s catchphrase is “Gotta Catch ‘Em All!”)
What does this have to do with scientific advances? Well, wouldn’t it be wonderful if we had something similar to a Pokedex in our world, a portable reference that allows us to identify organisms on the spot? This technology would make it easier for researchers to identify the organisms that they want to work with, and would make plant field guides or bird handbooks obsolete. They could also be updated by automatically downloading the latest version from the Internet, so one would never be stuck with an old or incorrect edition either.
Sounds like fantasy? According to Dr. Paul Hebert of the University of Guelph, this may not be such a silly idea after all. He’s the father of the Barcoding of Life Data (BOLD) initiative, which endeavors to compile a public library of DNA barcodes for all known named species. The system works similarly to the barcodes found on packaging in supermarkets. Each species has a unique, naturally existing DNA “barcode” of its own, found in its genome. A library of such barcodes would make it much easier for researchers to identify what species they are working with. It would decrease duration of the identification process from several days to a few hours!
To produce these “barcodes,” short genetic markers found in the mitochondrial DNA are used to identify species. All eukaryotic cells have mitochondrial DNA, and as mitochondrial DNA mutates relatively fast between species, the markers procured from this source should have variance that reflects the differences between individual species.
Appropriate genetic markers must fall under the following criteria:
(a) It must reflect significant genetic variability and divergence on a species level.
(b) It must be a short sequence that allows for ease of DNA extraction and amplification.
(c) It must have conserved flanking sites that may be used to produce universal primers. (Primers are short DNA strands that attach to single stranded DNA and allow specific sizes and sequences of DNA to be replicated.)
A commonly used genetic marker for barcoding is the cytochrome c oxidase 1 (CO1) gene. It’s approximately 648 base pairs long, and 95% of all animals have this. Researchers picked CO1 because it fulfills all of the requirements as noted above, and it also is an essential gene. Cytochrome c oxidase is a transmembrane protein that is found in the mitochondria, and it is the last protein in the electron transport chain. The electron transport chain is responsible for creating the cell’s ATP or energy, and as such, it is an essential gene.
Using this CO1 gene, Hebert et al barcoded 260 of 667 breeding bird species in Canada, and found that every single bird had a different CO1 sequence. All of the North America birds, to date, have already been barcoded using the CO1 gene.
Even ancient life could be barcoded using the same methods and genes. Lambert et al published a paper in 2005 that discussed how extinct flightless birds called moas were sequenced from 26 moa fossil bones, and all 26 CO1 sequences obtained were found to be unique. Researchers could do the same to other extinct creatures – recently extinct ones such as the Tasmanian wolf and the quagga to the ancient creatures such as dinosaurs and mammoths.
Researchers estimate that it would take approximately 20 years to barcode most species. It sounds like a relatively straightforward process, doesn’t it? However, as anticipated, there are many problems that arise with this methodology of barcoding.
The initial hurdle is that most living things are expected to have a CO1 sequence, in reality, some do not. Many insects are known to not have this sequence. Even if the CO1 sequence exists, it may still be ineffective as a genetic barcode sequence. Plants are known to have CO1 sequences that evolve too slowly for barcoding purposes. To solve this problem, other sequences will have to be used for other Kingdoms or Phyla. Many different sequences are already being suggested and debated upon. Kress et al (2005) suggested using the nuclear transcribed spacer region and plastid trnH-psbA intergenic spacer as DNA barcode. An example of one that also works well for plant barcoding is the essential matK gene that codes for a protein (an intron splicer) required in DNA transcript processing.
Even with successful barcoding sequences found for various species, another issue rises up with questions how reliable this method of barcoding may be. Some suggest that DNA does not provide reliable data above the species level, while others argue that it’s the flip side of things in that the obtained data is inapplicable at the species area and should be used at the higher levels of the taxonomic hierarchy!
As such, some researchers are worried that this barcoding method, rather than in collaboration with traditional cladistic methods (which refers to evolutionary trees), may end up being the method used to determine species, not describe them. Two terms are at play: delimiting and describing. Delimiting means to highlight genetically distinct levels of divergence, including morphological and behavioral differences, to suggest species status. Describing is exactly as it sounds: it does not endeavor to judge whether or not the specimen tested is a worthy to be given a species status based on the barcoding sequence.
To make things even more complicated, there are some species that may share the same sequence for that gene (just by sheer luck), and there may be more than one sequence of mitochondrial DNA for individual species. For example, plants are known to hybridize, which means that they will cross-breed between species and the resulting offspring will contain both parent’s DNA. Such species hybrids will undoubtedly make the barcoding endeavor much more difficult as then one would have to identify which plant species are the parents. Animals will cross-breed as well.
If barcoding is so problematic and taxing (even if everything worked out smoothly, there are still a plethora of species to deal with and barcoding all of them would require a lot of time and elbow grease), why should we even try to do it in the first place?
Aside from facilitating researchers in identification of species, there are also other (unexpected) perks from making such a barcode library. 350 DNA barcoding scientists met recently in Taipei (Sept. 2007) in the Barcoding of Life Conference held by the Consortium of Barcoding of Life (CBOL) to discuss the methodologies of barcoding process and also uses for the barcoding project.
Many individual geographic-bound or group-specific barcoding endeavors have already been established for conservation of biodiversity and environmental monitoring. Several to note are the Polar Barcoding of Life Initiative (PolarBol) that focuses on species living in the arctic/tundra region, and the Mosquito Barcoding Initiative (MBI), which works with mosquito populations to find out which species are the infection-carrying strains, especially of those carrying malaria and West Nile viruses.
Barcoding is beneficial for the general masses as well! Consumer protection was a big issue that popped up in the Barcode of Life Conference. Many stores sell plant-based medicines and herbal remedies, but how would one tell that it’s actually made from the actual (expensive) plant or from one that merely looks like that plant? To put this in perspective, some Asian herbal stores may sell average grade American ginseng that should cost about $60 USD/lb, but it is just as easy to sell fakes (cost: $40/lb) that look and smell almost the same! Better quality of American ginsengs are priced at over $335/lb, which is why consumers need to know if they are actually buying the right species and not just a look-alike.
Along the same line, DNA barcoding can protect consumers from buying products made with endangered plants or animals. Some illegal products can easily be masqueraded as those that are legitimately transportable. Living species such as star tortoises, ornamental fish and plants, even rare birds are sometimes smuggled out of their native countries. Dried medicinal herbs and plants, as well as animal parts treasured for their medicinal properties, such as leopard and tiger penises, are often hidden with other legitimate animal products as well. One of the Barcoding of Life Conference discussions highlighted the use of DNA barcoding as part of the procedures used when checking parcels or luggage crossing Sri Lankan borders. Similarly, it can also be used to provide quick and reliable identification of fish that are caught on commercial vessels and at the docks.
As we can see, DNA barcoding affects not just the scientific community; it has a huge impact on the economic world. Being able to identify pests and invasive species in all their life stages makes it much easier (and less costly) to prevent damages in crops worldwide. In Canada alone, the presence of invasive species causes damages in the ranges of $13.3 to $34.5 billion CDN annually! Canadians are sorely lacking the manpower and financial resources to deal with this problem, but if more is known about these pests, it would facilitate in ways to mitigate the problem. For example, specific life stages that are more susceptible to pesticides could be selectively targeted.
One use of DNA barcoding that had been proposed was one that would decrease the number of bird and airplane collisions that happen each year. Carla Dove of the Smithsonian Institute notes, “”Knowing which birds are most often struck, and the timing, altitude and routes of their migrations, could avert some of the thousands of annual collisions between birds and aircraft, military and civilian.” These collisions could result in injury for the plane and the passengers as well, especially if the birds become mangled up in the plane’s machinery or turbines. Aside from being dangerous, it’s also costly: the U.S. Aviation Industry loses approximately $400 million per year. Ironically enough, the culprit is often the Canadian goose.
Of course, a great use of the DNA barcoding would be to produce a Pokedex-like instrument. Insert a small sample of DNA into the machine, and away we go! (Of course, the machine would have to be a compilation of today’s PCR machine, sequence programs, and nucleotide sequence alignment programs.) Of course, it would then be called something like “LiveCyclopedia” or something similar to that. Think of all the business propositions in research and education! The person who could produce such a gadget would be the Bill Gates of the next millennium!