storage See the first movie uploaded to DNA of living cells

[captain_to_fire]

Primary Source: Nature

Secondary Source: CNET

 

ABSTRACT:

Quote

DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro^{1, 2, 3, 4, 5, 6}. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1–Cas2 integrase, the CRISPR–Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity⁷. When harnessed, this system has the potential to write arbitrary information into the genome⁸. Here we use the CRISPR–Cas system to encode the pixel values of black and white images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We also uncover underlying principles of the CRISPR–Cas adaptation system, including sequence determinants of spacer acquisition that are relevant for understanding both the basic biology of bacterial adaptation and its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.

 

Shipman, S. L., Nivala, J., Macklis, J. D., & Church, G. M. (2017). CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature. doi:10.1038/nature23017

I'm probably the only one geeking out to this but storing a movie into DNA is awesome. The scientists worked on bacterial DNA instead of mammalian DNA for a couple of reasons like bacterial DNA is circular with a single origin of replication and it's much simpler to work with. 

Quote

A team at Harvard University's Wyss Institute for Biologically Inspired Engineering led by George Church has built the first so-called "molecular recorder" using the well-known CRISPR gene-editing system.

 

The aim is to be able to record data in the genomes of living cells that can be accessed later, providing insights that could help fight disease and deepen our understanding of biology.

To prove such a seemingly far-out thing is possible, the team successfully encoded complex information -- including an image of a human hand and a sequence of a galloping horse taken from one of the first motion pictures ever made -- into the DNA of bacteria cells.

Prior to CRISPR, genetic engineering is a hit or miss by using restriction enzymes to snip a portion of DNA and insert a desired gene or remove an unwanted gene into bacteria. But CRISPR changed all that with extreme accuracy and precision. CRISPR (Clustered regularly interspaced short palindromic repeats) is how prokaryotic cells defend themselves from virus attacks. A bacterial enzyme snips a portion of viral DNA and inserts it to their own genome so that once the virus attacks again, the bacteria becomes immunes. This has the potential to end life threatening diseases like cancer and HIV, reverse aging, or even make real life Captain Americas which the idea creeps me a little.

 

But at this moment, the Harvard scientists were able to save a small video into bacterial DNA. 

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This doesn't mean you're going to be watching the latest season of "Game of Thrones" via your parakeet or whatever genetically modified pet you choose to store your video files on in the future, though it does technically make such a future possible. Never doubt that truth is stranger than fiction, folks. Church is also behind an effort to sequence the genome of the woolly mammoth to reintroduce the species to the Siberian tundra as part of a long-shot gambit to fight climate change. Church and his team want to give living cells the biological equivalent of the "black box" found in aircraft that records all sorts of key data.

So I don't think anyone for the next ten years people would be making computers with DNA as a means of storage and run Windows 20. DNA is harder to maintain than NAND cell of a SSD. But according to the researchers...

Quote

"We want to turn cells into historians," explained neuroscientist Seth Shipman, Ph.D., a post-doctoral fellow working with Church, in a statement. "We envision a biological memory system that's much smaller and more versatile than today's technologies, which will track many events non-intrusively over time."  Being able to then tap into cells' internal data recorders could become an invaluable tool for scientists.

"We could potentially use them like a recipe to engineer similar cells," Shipman said. "These could be used to model disease -- or even in therapies."  

Ultimately, the same technology that today is being demonstrated with vintage images of a galloping horse could be used to unlock one of the great remaining mysteries of human biology: the workings of the brain. "We want to use neurons to record a molecular history of the brain through development," Shipman said. "Such a molecular recorder will allow us to eventually collect data from every cell in the brain at once, without the need to gain access, to observe the cells directly, or disrupt the system to extract genetic material or proteins."  

This could either be a life saver for patients with debilitating degenerative neurological diseases like Alzheimer's to kids in school who wanted to excel and remember better. It's kinda like taking steroids or doping but instead for competitive sports, it can be used to beat every other kid in school when it comes to academics. This proof of concept isn't new exactly as Linus even pointed it out on a Techquickie episode.

There's so many factors to consider just yet when will human genome be our own mass storage. Immune system cells (NK and T_c cells specifically) might recognize these edited cells as foreign and kill it in the process. What would happen if those CRISPR edited cells containing instructions how to assemble a gaming PC becomes mutated or cancerous? Another concern is that gene edits are permanent. One mistake like a single random deletion, insertion, substitution can result to something fatal or nasty. It raises the question, it it worth it to tamper with the human genome using CRISPR just to store data or we just need to make solid state drives more efficient like NVMe and Intel Optane? 

 

The possibilities are endless at the moment since the technology as at its infancy stage. What would be more exciting other than a fully automated restaurant is how would a computer read DNA. At the moment, in order to know how a DNA segment works is by transcribing the DNA segment by an enzyme RNA pol into a single stranded RNA segment which goes into the cell's ribosome for translation into protein.

Scientists are able to replicate transcription process by PCR or Polymerase Chain Reaction involving an enzyme Taq polymerase

 

I would love to know how the scientists encoded the video from that DNA segment. I would love to read the actual journal article and provide my own comments on it especially on the methodology but unfortunately, it's behind a paywall of $200 which I am not paying. This will just keep getting better once other scientists be able to reproduce this experiment. Who knows, maybe Apple would be selling movies and have them stored in our DNA to watch after payment.

 

 

Edited July 13, 2017 by hey_yo_

[goodtofufriday]

How is this crap even possible. Ive never been able to wrap my head around how rocks and lighting make computers. 

[SCHISCHKA]

as with any new technology the pornography industry will be early adopters. think about this...

[captain_to_fire]

1 minute ago, goodtofufriday said:

How is this crap even possible. Ive never been able to wrap my head around how rocks and lighting make computers. 

Just imagine the future where office documents are stored in DNA samples while immersed in Tris-acetate EDTA buffer inside a test tube connected to a computer. Or in a more dystopian future, the US government mass producing genetically enhanced super soldiers from the US army going to battle against China's genetically enhanced super soldiers. The latter is way more creepy.

[captain_to_fire]

1 minute ago, SCHISCHKA said:

as with any new technology the pornography industry will be early adopters. think about this...

Saving 4K porn video on a person's skin cells. But unfortunately, the person is always at the beach without sunscreen and the person developed metastatic melanoma and the cancer cells came from the edited cells with porn on it. Will the person become a porn mongering pervert since those mutated porn containing cells are dividing so fast? 

 

I don't know. Only time will tell but probably in that future, cancer will be treated like strep throat. Take this CRISPR shot and rest and you'll be okay. ¯\_(ツ)_/¯

[Drak3]

14 minutes ago, hey_yo_ said:

This has the potential to end life threatening diseases like cancer

Anyone that believes this does not know how cancer comes to be. It's a genetic mutation that alters cell grown, and one that can be influenced by many things, from radiation to simple probability occurring during the mitosis/meiosis stage of cell division. Not something that can be cured with an absolution. It has always, and will always, exist as a disease (in strict definition, not the connotative meaning). The best we can do is revise our tools of detection and treatment/removal/prevention.

[goodtofufriday]

6 minutes ago, hey_yo_ said:

Just imagine the future where office documents are stored in DNA samples while immersed in Tris-acetate EDTA buffer inside a test tube connected to a computer. Or in a more dystopian future, the US government mass producing genetically enhanced super soldiers from the US army going to battle against China's genetically enhanced super soldiers. The latter is way more creepy.

The latter is the most likely unfortunately. 

[captain_to_fire]

Just now, Drak3 said:

Anyone that believes this does not know how cancer comes to be. It's a genetic mutation that alters cell grown, and one that can be influenced by many things, from radiation to simple probability occurring during the mitosis/meiosis stage of cell division. Not something that can be cured with an absolution. It has always, and will always, exist as a disease (in strict definition, not the connotative meaning). The best we can do is revise our tools of detection and treatment/removal/prevention.

I know. It's just an oversimplification of the new method. Cancer cells have high genetic variability. If a woman with breast cancer is responding to methotrexate, doxorubicin, and tamoxifen now, some of her cancer cells are mutating to be resistant. Not to further derail the OP, it's an overview of the researchers who are hard at work in making it close to reality and that includes storing data on bacterial DNA. 

 

[Misanthrope]

Those damn, clever, internet pirates always finding new ways to redistribute copyrighted work!

[iRileyx]

This both interests me and confuses the crap out of me at the same time. 

 

We need a tech quickie episode on this

[captain_to_fire]

9 minutes ago, goodtofufriday said:

The latter is the most likely unfortunately. 

That's why it's a dystopian future. An army of real life Captain Americas vs an army of real life Super Russians or enhanced North Koreans if you prefer that.

[ARikozuM]

I love Kurzgesagt, but this was one of his longer "short-tellings".

 

I'm all for this. I wouldn't mind seeing viruses being easily removed even when latent. 

[captain_to_fire]

1 minute ago, ARikozuM said:

I love Kurzgesagt, but this was one of his longer "short-tellings".

 

I'm all for this. I wouldn't mind seeing viruses being easily removed even when latent. 

I love their videos too.

 

On the topic of DNA storage, do you think malware in the future would be biological viruses? Since data can now be stored inside the DNA of a cell, real life viruses can corrupt it like how HIV butchers a Helper T cell.

 

Oh crap, I just gave cybercriminals an idea!!! 

[ARikozuM]

21 minutes ago, hey_yo_ said:

On the topic of DNA storage, do you think malware in the future would be biological viruses? Since data can now be stored inside the DNA of a cell, real life viruses can corrupt it like how HIV butchers a Helper T cell.

I'm sure that when DNA is used as storage the DNA itself is hidden/encrypted unless an agent can successfully draw the proper sequence in much the same way that your ribosomes read RNA with their numerous STOP sequences.

 

Hopefully, that Terminator 2 movie I stored mutates to make the T-101 grow his arm back rather than having him die...

[captain_to_fire]

1 minute ago, ARikozuM said:

unless an agent can successfully draw the proper sequence in much the same way that your ribosomes read RNA with their numerous STOP sequences.

 

I think it would mostly be physical breaches then. They have to physically steal the DNA sample and put in a real time quantitative PCR.

[ARikozuM]

Just now, hey_yo_ said:

I think it would mostly be physical breaches then. They have to physically steal the DNA sample and put in a real time quantitative PCR.

Don't know if you've ever done an ELISA, but I'm assuming that would be one way for someone to find popular stored data. 

Spoiler

Pirating has never been so scary.

 

[captain_to_fire]

9 hours ago, ARikozuM said:

Don't know if you've ever done an ELISA, but I'm assuming that would be one way for someone to find popular stored data. 

  Hide contents

Pirating has never been so scary.

 

Isn't ELISA done to verify the presence of an antigen like in serology? So if a cybercriminal wanted to steal data, the only thing ELISA would do is verify the presence of the stored data but they still can't read it. But yes it could be used for piracy.

 

Btw, I hated doing ELISA back in college. I prefer doing SDS-PAGE and AGE.

[ARikozuM]

1 minute ago, hey_yo_ said:

Isn't ELISA done to verify the presence of an antigen like in seology? So if a cybercriminal wanted to steal data, the only thing ELISA would do is verify the presence of the stored data but they still can't read it. But yes it could be used for piracy.

Verifying the presence, yes. But I mean for FBI or law enforcement. Imagine them being able to find that you've hidden something with a $2 kit. 

Spoiler

Not considering the cost of the anitgen.

 

[snpr1992]

So on the basis of this kind of technology, I can only assume that bio-computers are the next logical step.  We have our storage device, now its a matter of making it work and being able to do many processes at the same time rather than one at a time like our silicon dinosaurs.  

 

Will be fascinating to see where this technology ends up.  More info on Bio computers and bio computers vs quantum computers.

 

[tlink]

6 hours ago, SCHISCHKA said:

as with any new technology the pornography industry will be early adopters. think about this...

i love pornography so much i literally have it in my genes.

[SCHISCHKA]

6 minutes ago, tlink said:

i love pornography so much i literally have it in my genes.

Levi does recommend you dont wash your jeans

[captain_to_fire]

10 hours ago, Misanthrope said:

Those damn, clever, internet pirates always finding new ways to redistribute copyrighted work!

Why would they want a pirated movie embedded to their cells' genes? It's like having a tattoo but unlike a tattoo that can be removed painfully, gene edits are permanent. 

[Misanthrope]

3 minutes ago, hey_yo_ said:

Why would they want a pirated movie embedded to their cells' genes? It's like having a tattoo but unlike a tattoo that can be removed painfully, gene edits are permanent. 

I guess it depends on the movie. You know me I'd go for Jodorowsky (And I'm sure he'd go for it as a poetic act) but I doubt there's many volunteers to be a walking copy of sharknado.

[Sauron]

Genetically engineering babies is dangerous territory, one thing is eradicating stuff like Alzheimer's, another is changing active brain parts. Stuff like Gattaca and Bioshock come to mind.

[AHaskin14]

Interesting thought. The "read" picture is certainly different from the original with a few darker pixels here and there. This is essentially an unplanned mutation no? Imagine what sorts of problems can occur down the road when this technology is used for things other than data storage. Really cool, but really scary.