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The Emerging Science of DNA Cryptography

timothy posted more than 5 years ago | from the tight-genes dept.

Encryption 46

KentuckyFC writes "Since the mid 90s, researchers have been using DNA to carry out massively parallel calculations which threaten encryption schemes such as DES. Now one researcher says that if DNA can be used to attack encryption schemes, it can also protect data too. His idea is to exploit the way information is processed inside a cell to encrypt it. The information that DNA holds is processed in two stages in a cell. In the first stage, called transcription, a DNA segment that constitutes a gene is converted into messenger RNA (mRNA) which floats out of the nucleus and into the body of the cell. Crucially, this happens only after the noncoding parts of the gene have been removed and the remaining sequences spliced back together." (More below.)KentuckyFC continues: "In the second stage, called translation, molecular computers called ribosomes read the information that mRNA carries and use it to assemble amino acids into proteins. The key point is that this is a one way process. Information can be transferred from the DNA to the protein but not back again because during the process various details are lost, such as the places where the noncoding sequences have been removed. The new idea behind DNA cryptography is to exploit this to encrypt a message. The message is encoded in the sequence of bases in the DNA (A for 00, C for 01, G for 10, T for 11, for example) and then processed. The resulting protein is then made public. The key, which is kept private, is the information necessary to reassemble the DNA from the protein, such as the position of the noncoding regions (abstract)."

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46 comments

And when the cell mutates... (4, Funny)

NecroPuppy (222648) | more than 5 years ago | (#27244245)

My Word doc becomes porn.

Re:And when the cell mutates... (-1, Offtopic)

Anonymous Coward | more than 5 years ago | (#27244315)

Here is some porn [cowtax.com] for you. It is very cute and very NSFW.

Re:And when the cell mutates... (2, Funny)

BSAtHome (455370) | more than 5 years ago | (#27244537)

Evolutionist: A virus or other organism will evolve to decode on the fly
Creationist: God made this secret. No man shall decode it. The church shall interpret divinely for you

One of the best encryption schemes... (1, Funny)

Anonymous Coward | more than 5 years ago | (#27244327)

...is called BUKKAKE.

It uses multiple DNA streams to encrypt all data.

Re:One of the best encryption schemes... (1)

Ihmhi (1206036) | more than 5 years ago | (#27249077)

DNA DECODER V 1.92

>Decoding... [########100%########]
>Message decoded.
>Message reads as follows:
>THERE IS SOMETHING UNPLEASANT ON MY FACE STOP
>PLEASE GET ME A TOWEL STOP

organic computing by any other name... (4, Insightful)

girlintraining (1395911) | more than 5 years ago | (#27244385)

It's still organic computing. We've already demonstrated that there are some classes of computational problems that are massively parallel and can benefit from the use of organic instead of synthetic design. This is decades-old news. The problem is doing this on a mass and automated scale, and then figuring out how to reintegrate these systems into the digital ones we use now. Digital systems are very fast, but lack capacity. Organic systems are very slow, but have incredible capacity. What's needed is a bridge between these two developing systems. The good news is... Research on organic computing has been very slow... people are far more interested in silicon right now, so there's no real rush.

Re:organic computing by any other name... (-1, Redundant)

Anonymous Coward | more than 5 years ago | (#27244743)

"We've already demonstrated that there are some classes of computational problems that are massively parallel and can benefit from the use of organic instead of synthetic design."

Pfft. Frankie and Benjy Mouse figured that out ages ago.

Re:organic computing by any other name... (0)

Anonymous Coward | more than 5 years ago | (#27247251)

> "What do you get if you multiply six by nine?"

Organic computers seem to also suffer from a few precision bugs. :P

Re:organic computing by any other name... (1)

Onymous Coward (97719) | more than 5 years ago | (#27252695)

That was a result of a design flaw. They just had to build another. Some things take time. And iterations.

Anyway, the answer happened to be correct in base 13 -- that's got to count for something.

ymmv (0)

Anonymous Coward | more than 5 years ago | (#27244399)

Well I process my DNA in two stages, like that. But then I've always been a eukaryote.

Re:ymmv (0)

Anonymous Coward | more than 5 years ago | (#27246613)

rotflcopter, mod parent up

Sounds stupidly brittle... (1, Insightful)

nweaver (113078) | more than 5 years ago | (#27244401)

This sounds amazingly,stupidly brittle. When it comes down to it, it looks like some variant of a substitution cypher. Now I'm not a cryptographer, but I'm pretty sure blowing this thing out of the water would be a good exercise for a grad-school Crypto class.

Re:Sounds stupidly brittle... (3, Insightful)

Anonymous Coward | more than 5 years ago | (#27244491)

I'm pretty sure that "blowing this thing out of the water" would constitute solving the protein folding problem. Good luck with that! (No seriously: please figure this out).

Re:Sounds stupidly brittle... (5, Informative)

reverseengineer (580922) | more than 5 years ago | (#27246395)

You would not need to solve the protein folding problem in order to crack this form of cryptography. It is not as though data is encoded in protein conformation using this technique. In fact, this technique would be unlikely to generate well-formed proteins at all. According to the paper, the method does not actually use real nucleic acids or proteins, or even very accurately simulate their properties in biological transcription or translation. The paper is even titled "A Pseudo DNA Cryptography Method." The author is using transcription and translation as a model for the general data flow present in this scheme, but the author points out that strictly hewing to the biological splicing scheme would introduce extra vulnerabilities, since it would be possible to identify from the final protein sequence places where splicing occured.

On the subject of vulnerabilities, this method, as admitted in the paper, is a symmetric substitution cipher. You still need a secure channel to perform key exchange (the key here contains the locations and lengths of spliced out introns). If an eavesdropper gets ahold of the protein (ciphertext), a simple lookup of codons gets the eavesdropper back to the post-spliced RNA. The unique challenge of this cipher is to determine where splicing occured in order to get back to the pre-spliced RNA (which is a simple complement of the DNA sequence, which in turn is an easy substitution cipher away from the plaintext). While a clever way to implement it, the intron splicing in this method is really no different than the mechanisms used to confuse plaintexts in block ciphers like DES, and it is subject to the same vulnerabilities like differential attack.

technology review completely wrong (1)

ean (179878) | more than 5 years ago | (#27244407)

They are not using DNA to perform cryptography (or any thing else).

from the original abstract:
In this project, We do not intended to utilize real DNA to perform the cryptography process; rather, We will introduce a new cryptography method based on central dogma of molecular biology. Since this method simulates some critical processes in central dogma, it is a pseudo DNA cryptography method.

Re:technology review completely wrong (2, Funny)

edittard (805475) | more than 5 years ago | (#27244527)

Do you come here often?

Re:technology review completely wrong (1)

cicuz (1414125) | more than 5 years ago | (#27245899)

yes, he right away knew that nobody read TFA and that another abstract was nothing but in place here (:
btw, I didn't think they were doing cryptocells..

Self promotion (4, Informative)

ShadowRangerRIT (1301549) | more than 5 years ago | (#27244443)

Every link related to this is apparently owned by this group/person arxiv. The details are far too sparse to make much sense of, but as far as I can tell, the approach is:

  1. Alice write a message as "DNA" (really, just two bit blocks which happen to be designated as ACTG)
  2. Using a transcription algorithm, bits of the message are chopped out and produce a protein (really, just a subset of the message).
  3. Magic happens (specifically, Alice manages to send the information for reinserting the chopped out sequences in some unspecified manner)
  4. Bob reproduces original message

I have to assume some additional manipulation of the transcribed message so you aren't just giving Eve large segments of your message for free, but even then, it seems like a hell of a lot of work to disguise yet another scheme to protect data via the magic transmission of additional secret data.

Anyone see where I misread this? Even if we assume that the "DNA" is the key and not the message, I'm still not seeing how you avoid the "magic" step.

Re:Self promotion (4, Informative)

ShadowRangerRIT (1301549) | more than 5 years ago | (#27244525)

I should also point out that what makes this "magic" rather than just another private key encryption scheme is that the secret data you need to transmit is:
  • Different for every message
  • Substantially longer than the message (assuming you don't want to give away too much in the "public" part of the message)

If you've gone that far, you may as well use a one-time pad. At least then you only have to deal with magically transmitting an amount of data equal to the message. In addition, you could bulk transmit a whole bunch of pads, while this technique prevents you from coming up with the secret until you already have a message ready to send.

Re:Self promotion (2, Informative)

PotatoFarmer (1250696) | more than 5 years ago | (#27244681)

I'm not seeing the actual encryption part, either. It sounds more like message signing to me, with transcription being a hashing function to produce the "signature" protein.

Re:Self promotion (1)

Zerth (26112) | more than 5 years ago | (#27245351)

arxiv is a scientific prepublishing server. Scientists put papers up there for reference/review.

The method does seem rather "a biologist's first try at encryption".

Drat... (3, Funny)

imamac (1083405) | more than 5 years ago | (#27244463)

For a minute I thought I was hoing to be able to encrypt/decrypt my hard drive by my computer taking a sample of my blood...

I got something just as good (1)

jonaskoelker (922170) | more than 5 years ago | (#27252971)

For a minute I thought I was hoing to be able to encrypt/decrypt my hard drive by my computer taking a sample of my blood...

<Deep, dark voice> You can have even better protection against the RIAA goons if you give up just a small sliver of your soul...

Poorly written/defined article (0)

Anonymous Coward | more than 5 years ago | (#27244611)

The person who wrote the original article obviously understood nothing of basic molecular biology or cryptography. If he or she did, they might have noticed that viruses break this type of coding all of the time by bypassing several stages of the cellular machinery. Granted they use a blunt force attack (the equivalent of a substitution cypher)and not something more ingenious, but it works. If a virus is only successful on its final attempt (the best case scenario), it can crack the code after about 3x10^50 iterations. Now imagine if a virus was intelligently designed (I'm not getting into that discussion here) and had the ability to complete an iteration (or operation) in a billionth of a second - how long do you think it would take for it to find the correct "RNA sequence" and bypass the "ribosome machinery" stage altogether?

Interesting, but not too exciting (5, Insightful)

Laxitive (10360) | more than 5 years ago | (#27244723)

Couple notes for people who haven't read the paper:

1. Their scheme is not in-vivo (they're not actually working with DNA and proteins). It's a computational process that is based on the information transformations that occur inside a cell.

2. It's kind of cute and nifty, but not particularly applicable. They discuss weaknesses in the attack, but in a pretty handwavey way. The core problem is that their "encrypted text" will include their entire plain text, just split up into pieces. Secondly, it doesn't seem to offer anything particularly new when compared to traditional block ciphers.

3. Mathematically, this has nothing to do with biology. It's just loosely based on biological processes, and it's not really clear that these biological processes have anything particular to contribute to development of encryption. Transcription is just a mapping (from genomic DNA to mRNA), and translation is just a lossy mapping (from 3-tuples of mRNA to peptides). Mathematicians and cryptographers have been aware of generalized versions of these functions these for a long time (homomorphisms and reverse homomorphisms). There's not much new being introduced here.

-Laxitive

snake oil (2, Informative)

0ptix (649734) | more than 5 years ago | (#27252355)

At least as far as the crypto is concerned the original arxiv file is basically a fake.

Choice example quote:

Little information needed to be communicated through a secure channel (only the keys). The key size is proportional to the size of the plaintext with a small ratio.

If key size is already proportional to ciphertext size then why not simply do OTP. That already gives provable information theoretic security. Then you don't need any extra privacy provided by the "DNA Encryption". All you need to do is transmit the ciphertext. The proposed scheme is at best a steganographic technique. Calling it in encryption is down right false.

The author basically proposes the following code. Write down your message as a bit string. Translate the bit string from binary to base 4. (interpret it as DNA). Remove random chunks at random positions from it (i.e. the introns), and express the remaining DNA it as a protein. The encryption "key" are the introns and the position of the introns.

Sounds pretty much like BS to me.

Re:snake oil (1)

Laxitive (10360) | more than 5 years ago | (#27259067)

I had the same impression, except I didn't want to say it in quite the direct way you did. I'm not in crypto.. I just have a math/cs degree and work in biotech. The whole thing seemed kind of hokey to me, but I don't have the expertise to dissect it properly from a crypto perspective.

seems normal enough (0)

Anonymous Coward | more than 5 years ago | (#27244901)

In Soviet Russia, DNA encodes you!

wait.. what?

I'm using my DNA, to crack your DNA! (2, Insightful)

Hurricane78 (562437) | more than 5 years ago | (#27244915)

At least that of those who run the secure system.

Seriously. Nowadays it's far easier to just do a little social engineering (partially scripted) than to try to break any encryption scheme. Even the highest security company has some stupid grunts and drones.

They should fix the weakest link in the chain first.

I learned something important, when I programmed my first GUI program for a large client: If they can do something wrong, they *will*.
The only solution, is to not give them any functionality that they could mis-use. Build your UI and your backend API like a deep packet inspecting firewall.

Then, when that works, start to think about other ways to strengthen it.

Yeah, right BBQ (0)

Anonymous Coward | more than 5 years ago | (#27245043)

The "emerging science of DNA cryptography", my ass. See Laxitive for an informative post that should have scored a 5.

Already Done (1)

joeflies (529536) | more than 5 years ago | (#27245253)

Star Trek Next Generation, Season 6, "The Chase"

Message encrypted using DNA (actually the message was encoded in DNA.

Still one of my favorite scenes when the Klingons express their disappointment to find out that the result of all their work is a new age message of peace.

Re:Already Done (1)

maxume (22995) | more than 5 years ago | (#27246275)

Please don't describe things that didn't happen as having been done. It makes everybody dumber.

This is stupid (3, Informative)

graft (556969) | more than 5 years ago | (#27245875)

The suggestion to "encrypt" things in proteins, suggesting that they're a one-way code, is absurd. We've been able to sequence proteins since the 1950s by Edman degradation. From which you can relatively easily back out possible DNA sequences. Enumerating the possible mRNAs leading to a given protein sequence is a trivial task for any Perl programmer with three minutes to spare. Either the people who came up with this scheme know nothing about cryptography, or nothing about biology. As for the "massively parallel" computing DNA allows, true, it does, but since you're dealing with physical systems, it quickly becomes impractical. If you have to synthesize and mix bathtub-sized quantities of DNA in order to perform even modest calculations (that you can likely do faster and more easily on a desktop computer anyway), this method becomes expensive and cumbersome long before you reach the point where you can actually crack keys that are interesting.

Maybe this idea isn't new. (2, Funny)

Max Threshold (540114) | more than 5 years ago | (#27247053)

Maybe somebody already did it, a long time ago. Maybe we should be looking for secret messages from space aliens in our own DNA. Maybe...

Ask... (1)

Yaa 101 (664725) | more than 5 years ago | (#27247867)

Ask a Down Syndrome patient or another person with some problem or sickness caused by DNA how well cells behave in every day life.

This story is very shaky.

Re:Ask... (0)

Anonymous Coward | more than 5 years ago | (#27250317)

The fact that people with trisomy 21 (Downs) are viable at all is a testament to the resilience of our genetic makeup.

DNA cryptography... (0)

Anonymous Coward | more than 5 years ago | (#27250393)

... the key is in your privates!

Let's get it over with... (1)

evilviper (135110) | more than 5 years ago | (#27252931)

which threaten encryption schemes

The threat of "quantum computers" seems to be the way to justify any crazy thing you want to do, these days. Even though, in reality, it's no threat at all.

There are plenty of theoretically secure encryption algorithms out there, even now, which aren't threatened by quantum, or any other kind of theoretical computer. Let's just all switch to using Lamport signatures [wikipedia.org], so that we can ignore the next 100 million stories posted on /. that offer status updates on the most elementary of quantum computers, and what it means for the nude pictures you're e-mailing to someone you've never met in person...

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