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Using Bacterial DNA For Data Storage
NPV writes "January ACM Communications has an article on the use of DNA in genetically modified bacteria to store information. This is an attempt to achieve the ultimate in archival storage (one of the modified bacteria can tolerate 1000X more radiation than a human being). Now just suppose that the "junk DNA" in the human genome is the documentation package for the machine code. Who wrote that manual?" Here's the article abstract.
I mean these bacteria have evolved for millions of years to be as streamlined as possible and yet i a few short years we can figure it all out and more. Also we can make it better of course.
unzip; strip; touch; finger; mount; fsck; more; yes; unmount; sleep
Who wrote that manual?
I think the important question is... who has IP rights over it?
The Raelians, duh! That's how come Clonaid is so far ahead of other human cloning efforts... they read the documentation.
Java: the COBOL of the new millenium.
So when one of these engineered bacteria wipes out the human species, and some alien species comes along and ganders a look, the bacteria will be carrying a precise record of how we humans fscked ourselves.
--- Grow a pair, liberals... stop letting the Republicans bully you!
so much for P2P networks, if anyone wants the new Apache release, I just sneezed.......
(one of the modified bacteria can tolerate 1000X more radiation than a human being).
I haven't read the article (don't have access to where I am) nor have I thought about this subject much, but one question I have is how the authors keep the sequences under selective pressure. DNA sequences are only conserved over many years if evolution needs them. Non-coding regions (So called "junk-DNA", poor choice of words, btw) would easily mutate into other sequences. One could imagine sequencing many cells, and infer the original sequence, but this gets more expensive as time goes on (as the number of sequences you need to sequence goes up).
-Sean
Scientist have discovered that humans and all life on earth was just a discarded bacterial disk drive from a geek with pimples living in his mother's basement 5 million light years from the solar system.
...and making backup organisms would be more pleasurable than waiting for a tape unit to finish whirring
That keeps four copies of it's DNA in rings and error checks constantly. They're probably using one of these, as it happens to be very radiation resistant, I'm guessing they used these, and so the mutation rate would be very, very low. So it wouldn't keep forever, but would for a very long time.
You could also put error checking (parity, checksums, etc) so once you found some bactera you could check to make sure they had the right version and not a mutation
autopr0n is like, down and stuff.
Just to be clear, no non-coding segments have been found in bacteria yet (last I heard). So putting data in as 'junk-DNA' in humans is quite a bit different from interrupting a fully functional bacterial DNA segment with the data to be stored.
Also note that the introns in eukaryotes are highly mutable (look up 'tandem repeats' if you have the inclination), so the fidelity of the data would be sacrificed by putting it there. The longest lifetime for the data would be achieved by tricking the replication machinery into thinking the segment was an exon, which would involve tying it to a functional protein that would be absent were the sequence to be mutated.
Duplication of the data would also work, but it would only hammer down the probability of mutation, since the probability of a point mutation of a base at the same location in two widely separated sequences is roughly 10^-18 to 10^-17 per year for exons.
Don't you people watch the outer limits?
I'll probably write this code in sometime in the future. Human cloning is stealing and I will sue your ass for infringement.
You can't judge a book by the way it wears its hair.
Scientists have concluded that they can use a bacteria's DNA to store the complete description of... a bacteria. Revolutionary.
What I really want to know is, can the same be done with the DNA of a bug? Because if it can, I'm going to buy some MSFT shares...
RMN
~~~
I think that you may have your terms a little mixed up. An intron is the DNA between exons (coding regions) in a gene. i.e.
o n- --junk---junk---junk.
junk---junk---junk---exon-intron-exon-intron-ex
The junk DNA often referred to is mainly intergenic DNA, and this is where most of the non-coding DNA is found. This also makes up the majority of the eukaryotic genome. Prokaryotes (bacteria) do contain intergenic DNA, but no introns.
You just ate the entire sum of human knowledge. Nice work Sparky. Now you might want to go looking for a Tums and start polishing up your resume.
KFG
...if only the machines had used the humans for data storage!
Morpheus coulda pointed to a SAN/NAS box!
Instead they make a duracell commercial and mumble about the "human body generating more bio-electricity than a 120-volt battery and over 25,000 BTUs of body heat."
Ok I'll quit ze bitching... it was spiffy anyway.
Interactive Visual Medical Dictionary
Just to be clear, no non-coding segments have been found in bacteria yet (last I heard).
My first impluse was that this is way off. I'm used to working with plasmids where frequently like 60% of the sequence is junk. They use E. Coli and D. radiodurans in the study mentioned in the article. A brief survey of E. Coli K12 (the parent of most common lab strains) sez that about 5-10% of it is non-coding. The old initial reference claims about 11% is non-coding, but a good chunk of that may be regulatory. The radiodurans genome is about 9% non-coding. The up shot is that there is actually a fair amount of 'junk-DNA' in (at least the Coli) bacterial genomes. Not a lot by human standards but enough to be able to squeeze in a chunk here or there if you're careful.
Another impulse was 'gad... that made it into Nature!?' (the journal, the article cited is a self congratulatory summary of their Nature paper). A lot of it follows a well duh kind of reasoning. 'Well duh' science is often the really good kind, but I wasn't particularily amazed by this. The DNA manipulation methods are beyond standard now, the only really clever thing was proposing the use of radiodurans as the host. Even that was sort of obvious (a blazingly well studied organism that is transformable). The DNA -> text using a 6 bit space? Well if you've ever designed linker regions in proteins I'm sure you were at least thought about spelling out you name or something in amino acids (unless your name is BOB). In part this is because every one learns the amino acids by doing stupid things like spelling out their name. Few people actually do this, mind you, as it usually would have some deleterious effect, but the point is I'm sure they weren't the first ones to try something like this, probably just the first to get funded to do this explicitly. Their big addition was to come up with a 3-letter code that includes all the letters and, ooo, punctuation. Then they spelled out bits of 'It's a small world.' My point is that it's not that far fetched and a bit surprising (to me) that it made it to Nature.
As to the utility of these things for information carriers... Mutation would be a problem in the long term. Sure radiodurans would survive nuclear war (these guys put cockroaches to shame) but they do it using lots of mismatch repair and recombinatorial repair methods. These are not perfect repair systems, they can and frequently do introduce many errors, especially in non-essential DNA space. Tying it to a functional protein isn't a bad idea, but unless the added sequence adds some survival advantage it won't enhance the lifetime of the measage (ie. if uncorrputed data gives an advantage then it is statistically less likely to propagate). Also, as you mentioned, the bacterium might notice long chunks (they're using 100 characters here) of useless DNA and excise it. For that kind of text, it might be better to just etch it into stone or something, at least you have some hope of seeing it intact in 2000 years.
"All right. Which one of you bastards put the penicillin in my hard drive?"
Reminds me of that Star Trek episode The Chase, in which Dr. Galen, Captain Picards old Archaeology professor, found genetic data-blocks from various species around the galaxy stored in the junk portion of each species DNA, including our own. When a sufficient number of these data blocks were put together it completed a stellar map, identifying the precise location of the original origin of life on out planet and countless others. The jury is still out on the Panspermia Theory, but my own hunch is that there is lots of intelligence out there vastly older and greater than we are.
Planet P Blog - Liberty with Technology.
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IAAB too (not the same one as above), and I have to say, sorry, you're wrong. Yes, adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C), but bases are not restricted to one strand of a double stranded DNA- A and T or G and C can be found in the same strand. In fact, there are some regions where sequences consisting of A's and T's or C's and G's together play a critical role, like a sequence of TATAAT (or similar) called the TATA box, which is recognized by RNA polymerase, and leads to initiation of transcription. Usually, all 4 bases are present in each of the two strands, and since there are three bases in each codon, 4^3, or 64, possible different amino acids can be coded for from a single codon. Now, there are only actually 20 amino acids that are coded for (there are a few exceptions to this that depend on specific context), so a few of the possible codons can be used to code for a stop in protein translation, and there is a redundancy built in called "wobble" that allows correct translation despite certain slight mutations.
Now, although there are two strands in most DNA molecules, only one actually codes for proteins- the two strands are sometimes referred to as sense and nonsense (or antisense) strands. Both are involved in replication, however- a DNA helicase splits the two strands, each acts as a template for a new complementary strand. And both can and usually do contain all four bases, with the concentration of each base in either strand being totally independent. Since the two strands in a double helix are complementary, the amount of adenine must equal the amount of thymine and the amount of cytosine must equal the amount of guanine in both strands . In fact, recognizing this relationship led to the realization that complementary base-pairing occurs. The original IAAB is correct though- the genetic code is indeed base 4- although nature has chosen to not use it to its full potential (i.e. code for 64 different amino acids) in favor of building in some redundancy.
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."
Just had to throw in that there *are* non-coding intergeneic sequences (akin to introns) and bunches of other non-coding goodies in prokaryotes including bacteriophages such as T4 (look back to the mid-80's).
:-)
And if you consider RNA editing (where the wacking out or modification of nucleotides prior to translation), you gain a tremendous amount of flexibility in the smaller genomes of these bugs.
Of course, the long term storage they're looking at is best done by the spores of gram positive bugs, like Bacillus subtilis. When they're in this non-replicative stage, there is little chance of sequence alteration. And by having, some 10^8 spores around, even if there were a few mucking things up, the majority would maintin the original sequence.
But engineering a bug to not alter sequences is much more difficult than knocking out RecA.
Nobody believes in 'junk DNA'. It's a stupid media buzzword. Ask any geneticist, any at all, whether they consider 'junk DNA' to be a misnomer or not. If the unknown equaled "junk", there would be no scientists. Go figure.
This has to be the 434340930493rd article where the presenter considers himself clever because he sees an insight... that everyone else does, too. Give it up. The abstract is interesting, if lacking in news or useful information, but its presentation is nothing but annoying.
The easiest way to disprove the "junk DNA" is to remove the "junk DNA" and see if the organism still works. Take for example a computer program where "junk code" is removed. If the program still runs then the code might not be important. However, the "junk code" could be comment code not removed by the compiler, error checking code (which will not activate unless the program hits an overflow then all heck breaks loose), or even just graphic data which would allow a program to run (but with a corrupted image display).
The basic truth of "junk DNA" is that unless somebody has a "decompile into a higher level language" device then removed code could case all sorts of things to go GOOEY later on when certain conditions are met. Heck, if we look back at the early days of BBS protocols you'd remember the FOO junk padding code at the end of many ZIP files just to compensate for buggy data transmission protocols. That padding allowed a certain amount of send errors at the end of a file to be tolerable while keeping the important parts of the file intact.
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/* I know, I know, I should write more unit tests, but I've only got six days until my long vacation on the 7th and I'm not taking homework with me. Oh well, if I missed anything, it'll evolve. */
The perfect match between biological weapon and porn collection... puts a whole new meaning to the phrase "Infected by Anna Nicole Smith" don't ya think?
Open Source software downloaded by a simple handshake or sneeze!
Then, when Microsoft gets in on the new industry (2 years too late as usual) all life on earth will be wiped out by an unchecked buffer overflow in blank bacteria media as it is sequenced by default when accessed by any device.
Seriously though, I wonder what the maximum storage capacity of something like that would be? How much data could be packed into a bacteria sequence? Would there be a really high read/write time to sequence the DNS? What about seek time? "Godammit come back here you bug!"