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Identifying World's Species With Genetic Bar Codes
Fokker writes "Reuters reports that scientists from around the world launched a project on thursday to genetically identify species using bar codes. By taking a snippet of DNA from all the known species on Earth and linking them to photographs, descriptions and scientific information, the researchers plan to build the largest database of its kind."
Wont this hurt the self esteem of the animals that already have barcodes?
sorry 'bout the mess...
"Could I get a price check on a large brown marsupial?"
that we will find more unique animals that we didn't know were unique. We are still identifying more unknown species every day, now with DNA species we thought are related will now be determined not to be.
When there are perfectly fine 2-dimensional barcodes called QR codes available, I hate to see scientists trying to get by with simple one-dimensional barcodes. Even the post office has started using QR codes, and all Japanese phones are equipped with readers.
Seems a little bit simple, but I guess it might be harder to put 2 dimensional barcodes on thin creatures like worms and snakes.
Wow. You're pretty "plugged in", or whatever you kids say nowadays.
I work in this lab. Specifically, I'm working on objective analysis of RNA sequence alignment heuristics.
..based on something from Star Trek. This is the very kind of thing I think of when they pull up their tricorder to some alien race, and poof, a strand of their DNA is up on one of those pretty LCD monitors behind them.
That being said, I think this is a brilliant use of computer technology. Catalogs and databases of this kind are what we need, especially while going through the jungles of various continents in search of miraculous wonder cures. Besides, if we had done this before with the Dodo and other animals that went extinct, we could rebuild the strands of DNA, and make the animal again for study. I tend to think more and more as we corrupt the planet with roads and sidewalks that research and food will be the only reason to have living stuff around, and knowing that we have a computer database of all that is alive and the ability through cloning to reproduce any of it is at least a comforting thought.
end rant.
"Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
I've got a better record stuck to the bottom of my fishing boots...how do people get paid for this stuf?
Step 1: Take chromosone.
Step 2: Unroll and lay flat on table.
Step 3: Push bar code stamp against inkpad, and stamp DNA strand.
Step 4: Request additional funding.
...actually finding and agreeing on the locus (piece of DNA) to use for this. It has to be present in all species, i.e. in gnat and cow and jellyfish, but also has to be variable enough to be able to differenciate between, for example, the Tennesse gnat and Alabama gnat.
The main problem is that the locus must contain two regions to the right and to the left of the sequence of interest that must be highly invariable. This is necessary so that the same PCR primers can be used to amplify the sequence in most species. The amplification step is necessary for sequencing.
sombody thinks about determining human species based on their DNA ?
Trolling using another account since 2005.
Bar Code Tattoos
Is it the African, or European?
Does this mean the pet stores of the future will allow a cashier to swipe an animal across an electric eye, greatly increasing the efficiency and speed with which people can buy large quantities of animals? Such a system could greatly help out my habit of buying as many mice as I can! Although, it becomes a problem when geneticists demand that barcodes be placed on individual fruit flies so that they, too, can be bought quickly and efficiently.
Yeah, I know the barcodes won't be put on the animals... but maybe after a trial run, customers will demand it!
You failed to answer his question.
Will they call it Project Titan?
What picture will they use for humans?
The sad part is that by the time they get around to barcoding all of them, we'll have a few less species around to bar code.
"And then I visited Wikipedia
Pig and elephant DNA just won't splice!
Someone hates these cans.
...barcode 666!
The initiative will begin with three projects. One will provide barcodes for the 10,000 known species of birds by 2010, another will tackle the 23,000 types of marine and fresh water fish and a third will genetically label the 8,000 kinds of plants in Costa Rica, Central America.
When they will be able to classify the 2,000,000(estimate number of known species) species??And who will be the poor soul that have to carry the weight of the task(An intern maybe??)
Wikipeople have free online directory of species WikiSpecies
who wonders when, upon reading "database", what variety the database is -- e.g., MySQL?
Assume I was drunk when I posted this.
... the find ever species and make a bar code for it. Then what ? Call me dumb - but the point of a barcode is to easily scan it .. last time i checked, frogs dont have barcodes on them.
.. 'oh - i'll just check the barcode database! oh wait, it doesnt have one .. damn'
.. just build the database (perhaps spending more time (and cash) on it you could have the full DNA sequence .. not just a scrap)
;)
You find a weird insect
scrap the barcode thing
So next time we wipe out some endangered swamp monster we have a backup
> As a creationist, the only question which concerns me is Which DB Would Jesus Use?
0 9.html)
I am quite sure Jesus would have endorsed Oracle 10g.
(Big Kahuna: http://www.christianitytoday.com/ct/2000/013/37.1
...they could also add 'women' to the index so we know how to identify one. Some list of suggestions for handling procedures might be welcome too as an appendix.
Beep beep.
Actually, most biological journals require submission to either GenBank (U.S.), EMBL-Bank (European), or the DNA Data Bank of Japan. The members of the International Nucleotide Sequence Database Collaboration exchange data every night, but that doesn't mean they are the same thing, or that it is run by NIH.
There's actually a real lack of genetic data on marsupials and monotremes. Interesting for evolutionary reasons, but also because understanding how koalas break down toxins (such as various eucalyptus oils) gives general insights into drug metabolism (there are people studying this in my lab, in fact). If you'd like to donate funds for sequencing the kangaroo, go here.
Identifying and naming (or bar-coding) all the species would require a very big name space. And we seem to be running out of them. Here's a very nice article about it.s etDet ail/assetid/39138
http://www.americanscientist.org/template/As
I agree with above posts suggesting that this datbase can easily be created using exisiting info from NCBI. Just add photos.
However, does anyone know what DNA sequence would be used as a "bar code"? Whole genomes arent avaliable for most of organisms. I am not sure that we have all the 16S DNA sequences for most of organisms. 16S (mitochondrial)DNA is the most common marker used to establish evolutionary relationships between organisms.
Hence, there still might be some work left especially establishing relationships for more obscure organisms.
Could this help find unknown species or help determine what *could've* happened in the evoultion of animals had things gone differently? i.e. presumably there is a finite number of genetic "bar code" combinations, so there would be a finite number of species that could exist... no? yes?
The american way is RFID and XML, none of this barcode and DNA stuff. I guess they haven't been following the latest trends
Best thing is they will scan the animal using a :cue:cat.
The fragment of DNA that they are sequencing is located on the mitochondria and is part of the cytochrome c oxidase gene (COI). http://en.wikipedia.org/wiki/DNA_barcode
I am a taxonomist and can tell you this is of limited usefulness, sure we will be able to see some differences between organisms, but this is already done is many studies with the control region of the mitochondria.
The problem could be if people just rely on these sequences alone to delineate species, we learnt this years ago in bacterial taxonomy that you simply cannot rely on any one particular gene (There is evidence of horizontal gene transfer in 16S genes if someone was going to counter with that).
A speciation event is driven by some environmental pressure (change in temperature say). The genes that are under selection of this pressure will change at different rates to one under no direct pressure (COI).
I could rant on but, I think this project is of some use only if combined with traditional taxonomy. The danger is that a large flashy project like this will steal research dollars away from traditional taxonomy.
"They're all animals"
Where I work, a group is using this technique to identify insect pest species.
If, for example, a group of insect eggs, or even just some parts of an insect like the legs, were found in a shipping container, then it can be extremely difficult to identify the insect species by morphology. By sampling and barcoding the DNA in the eggs or fragments then it can be determined which insect was present, and therefore whether a potential pest was present in the container.
For a country that depends on agriculture, like New Zealand does, this is a very important technology.
Maybe projects such as this one might solve some taxonomic debates such as the old chestnut about whether Megachiroptera (fruit bats) and Microchiroptera (insectivorous bats) are acutally closely related.
For those of you who don't know the debate is as to whether Megachiroptera are closer related to primates than they are to the Microchiroptera. I personally believe that fruit bats are flying monkeys. Therefore, fruitbats are the only primates native to Australia (besides Homo Sapiens obviously).
99 bottles of beer in 175 characte
I'll be anxiously awaiting them to publish the data on our own species' barcode. I'd be kewl to have one tatooded.
I am a speak english. Do you not? - Saroto
I would say that there is an effectively infinite variety of species possible as there is variation in the amount of genetic material a species uses. That is, some species have more chromosomes and more genes on each chromosome.
99 bottles of beer in 175 characte
Well one species already carries it's own barcode. It's always there on the back of their necks and grows back when it's removed. And one of them (X5-452) is a hottie as well.
99 bottles of beer in 175 characte
What DNA sequence would be considered as the base pairs of all life forms on Earth are similar?
What I don't understand is...we as humans are all different genetically as human individuals and the same must be true within the animal kingdom. Where does the intra-species DNA difference end and the inter-species one start?
Professor Karmadillo Songs of Science
barcoding.si.edu
From their DNA barcode page:
DNA barcode sequences are very short relative to the entire genome and they can be obtained reasonably quickly and cheaply. The cytochrome c oxidase subunit 1 mitochondrial region (COI) is emerging as the standard barcode region for higher animals. It is 648 nucleotide base pairs long in most groups...
Let us note however that most of our planet's biodiversity is contained in the 60% of the biomass that people don't talk much about: Bacteria. Most of them live in the soil and are difficult to study and are simply unknown. It would seem that this barcoding project does not include Prokaryota ( = Bacteria,Archaea) unfortunately.
I'll do it for cheesy poofs.
Only DNA can tell....
or maybe not.
At least in the genus Canis, DNA analysis has not lived up to its promis of identifying species. Though it does appear that the most recent research (which does incorporate findings from mtRNA and DNA analysis) that C.rufus is the same as C. lupus lycoan which should be called C. lycaon. This animal might share ancestry with C.latrans. Untill just resently all DNA studies have done more to cloud the issue then make it clearer. Unfortunatly, political conciderations and vested interests are driving most of the analysis of data.
The assignment of species status to a population of organisims is a political football. The extreem enviros would like to define every population as an unique species so they can declare it endangered and thereby use its existance to stop any project they feel like stopping. The oposite extream would like, well, the oposite.
It would be a safe bet that politics will play a more prominate roll in this project then science. And yes, I allready know I cant spel.
any clue where I can still get these for free?
OK - tell me this one thing, how are they going to fit the barcodes on the really small animals?
And a barcode on a whale would just get lost - you'd need a correspondingly large barcode (waterproof I assume). And correspondingly large readers? Attached to submarines I suppose? I think not.
They just haven't thought this through. Frikkin so called "scientists".
who wonders when, upon reading "database", what variety the database is -- e.g., MySQL?
I don't think so.
It's going to be tough to ID Chimera. It is amazing that our souls--our eternal essences, with all their hopes and dreams and visions of an eternal world--are contained within the temporal bodies. No wonder suffering is part of the human condition. --Marion Woodman from the essay Soul Moments, Handbook for the Soul edited by Benjamin Shield
RFID tag 'em all
From the BBC coverage:
"About 1.7 million species are known - we suspect there are anything from 10-30 million species on Earth," explained Dr Richard Lane, director of science at London's Natural History Museum.
Wednesday saw the announcement at the London conference of a project to get comprehensive barcode data on all known fish types - currently thought to number 15,000 marine and 8,000 freshwater species.
The current project is looking to catalogue the world's 10,000 known bird species, the 15,000 marine and 8,000 freshwater fish and the 8,000 kinds of plants in Costa Rica.
So a way to then
Martha, I've been bitten by a snake!
Hang on Frank, let me get my barcode reader out..
*eh* *eh*
Dang it, frank, hold its head still. Can't get a read.
*bleep* *bleep*
There we go.
Good news Frank, its only a black mamba
Martha, how is that "good"? I thought they were deadly.
Frank, the life insurance is all paid up!
----- LoboSoft specializes in Digital Language Lab
Ummm....isn't this like taking a database of animals and then just printing the primary key out as a barcode?
Coder's Stone: The programming language quick ref for iPad
Do you think this will allow me finally to identify the species of my mother-in-law?
Shouldn't we wait for the SETI program to succeed? We wouldn't want our data to be incompatible with the aliens.
People studying drug metabolism in your lab? Can I be a test subject?
I'll turn into a supernova and burn up everything. Well I'll turn into a black little hole and you'll turn into string.
You wouldn't try to understand your Ramen noodles by looking at its barcode, but the barcode does help the computer to identify the noodles.
As far as I can tell, that's all they're proposing here, as well. This would allow a student researcher (or other less educated researcher) to help a more experienced biologist by figuring out whether an animal actually is species X or whether it just looks like species X to a relatively untrained eye. And, in this case I imagine the experienced biologist will be very interested when called over for a "price check" when the animal does not match any species in the database (after the database is "complete" of course).
Ben Hocking
Need a professional organizer?
Now with evolutionary theory we have the 'tree of life' model of speciation, which is a tree. Why do we still use the Linnean table structure? You can tell it's out dated because people are making it more tree-like by adding sub-classes, sub-orders, etc. Of course, I understand the use of having a universal naming system, but the linnean table structure is now being used to point out divergence from a common ancestor , which is wasn't designed to do.
One alternate proposal is this: for each species, pick a unique, descriptive, Latin-like name, and reference that to divergence from a common ancestor with other speciie[s]. What do you think?
Computers are useless. They can only give you answers.
-- Pablo Picasso
...but isn't the point the converting genetic information into a number in a database, and not the barcode? I mean, the barcode itself is of utterly no value except as a shorthand for transmitting numeric data.
They take a sample.
They convert the genetic information to numbers.
* they convert the numbers to a barcode *
They send this data to the database
* it's backconverted from barcode to numbers *
The information is checked against what's in the database.
arent the "*" lines redundant?
I mean, the 'barcode' is simply a way to reduce (not eliminate) the human error factor in transmitting long numbers. They might as well say that they are "Identifying the world's species with RFID" if that's the method they use to transmit the data to and from the database.
Frankly, barcoding seems rather dumb, because a barcode is not inherently readable to a person - if Joe Biologist gets the data, he can't do anything with it unless he has electricity, a reader, probably a laptop, AND knowledge of what barcode standard they're using. That doesn't seem a very efficient replacement for a PENCIL.
-Styopa
Well, I guess this will make my grocery shopping simpler.
www.timcoleman.com is a total waste of your time. Never go there.
Wait, I saw this movie already!
...
*beep* Ring-tailed Skink.... $4.95ea
*beep* Warthogs............... $1.50/lb
*beep* Rodents (misc)....... $0.50/lb
"Your total is $46.72"
"Thanks for shopping Manny's Mammals, pls come again."
The barcodes are coming! The barcodes are coming!
Scientist scans picture of "Kangaroo" DNA Computer says "Dustmite" Scientist "Dog" Computer "Dustmite" Scientist "Dustmite" Computer "Amoeba"
I can see it now... drop a piece of hotdog into a scanner, and your PC starts scrolling out DNA matches.
70% Cow
10% Pig
5% Chicken
3% Rat
2% Cockroach
2% Mealworm
1% Quagga
1% Housefly
6% Other
On second thought, maybe we'd be better off not knowing...
Anyone remember the end of Titan AE when they discover the ship with the genetic code for every living thing on earth?
Insert Sig Here
Both platypus and monodelphus are being sequenced as we speak. Yay!
Does anybody remember Kevin Kelly's All Species Foundation? Within the last month or so the website has gone down.
Thank you.
Are there any net resources you can point to for amateurs in need of taxonomy?
I've done a flora on 40 acres of wildland -- some 300+plant species, keyed out (Jepson's California flora) and a few of the native grasses characterized with gross DNA fingerprints (extract, Western blot).
The botanist who did the flora trained several local highschool kids -- all of whom got into college, perhaps helped by the summer job.
So -- I wish you WOULD go on and on about this, in a thread here or on a website somewhere.
Willy Ley once remarked that analysis is all very well, but you can't tell how a locomotive works by melting it down and analyzing the mess. DNA barcodes seem much the same to me, interesting but not enough information, and as you say enticing people away from the real work that's needed.
-- Search is going mobile.
... or does it bug other people that mitochondria have their own DNA and reproduce asexually? It's like we have this second species living inside our cells. We're utterly dependent on them, but they're just coasting along, evolution wise. I predict trouble, 4 billion years from now. Ok, maybe 5.