Xenogears in the real world.

[The Legendary Zoltan]

This is some really interesting stuff. I just read an article in the newspaper about a week ago that REALLY reminded me of Xenogears. I'll sum it up for you.

In Jerusalem, scientists have created the world's new smallest bible. Using nanotechnology the inscribed the entire Hebrew text of the Jewish Bible on a silicon surface of less than 0.5 square millimeters by blasting a particle beam at it and causing the gold atoms to bounce off. So it actually is etched in just like with a hammer and chisel. In the future they'd like to use this technology to "store vast amounts of data on biomolecules and DNA.

So why did it remind me of Xenogears? 3 reasons:

1. It relates to nanotechnology and the Jewish Bible and so does Xenogears.

2. They want to use this technology to store data in DNA. It was just one little conversation in the game but I remember there being talk of storing information or memories in one's "introns" so that their children can inherit it. Crazy.

3. I saved the best for last. The name of the dude in charge of the project is called Ohad Zohar! Is that not the coolest thing you've ever heard?!

My question about this technology is: What kind of effect will there be in inscribing stuff onto DNA? It's cool that they can do it on the molecular level, but in the end it's just like carving letters into a tree. So I wonder what the effect will be. It's pretty exciting to me. What do you think about all this?

[Robotaki]

Haha the similarities are remarkable. And yes, I do admit that guys name is pretty friggen sick. XD Towards the etching information in DNA, I really don't think it's such a good idea. Even though I have absolutely no background on this topic, I do know that the genome is a pretty delicate structure and even the slightest mutation can cause the cell to go insane (cancer and whatnot is a big one) Like you said, it's like scratching something into the bark of a tree. It can have some pretty drastic consequences. It's still pretty cool how they can cram so much information into a small space though. Sounds so futuristic! =p

[RiftDoggy]

Well, I don't know much about Xenogears or genetic science, but...if they're physically etching this thing onto DNA particles with a laser, then...the DNA itself wouldn't be changed.

Sooo...I can definitely see this as a new method for data transfer and storage--the current flash drives, and most stuff that comes after, would be rendered obsolete.

However, unless the DNA sequence itself were changed, physical etchings on a single particle would not be duplicated onto subsequent versions; i.e., kids wouldn't get this info.

Then again, if this becomes practical, then a whole new method of secret method transfer would become possible--picture spies with the DNA on, say, one of their fingernails "etched" with potential terabytes of information.

Thanks for the news post; this is really interesting!

[The Pezman]

For one thing, this wouldn't be DNA that anyone is using. It would just be DNA of some small multi-celled organisms.

Data storage would go through the roof. The hard drive as we know it has basically reached its fastest and largest capacity. In order to continue to have increases in our hard drive capacities, some breakthrough on this order is required.

[Shadow Wolf]

Inscribing something physically onto a piece of human DNA would be of little to no value, since your DNA is constantly being replaced by new bits of DNA. Not changed, but refreshed. It's part of the subcellular way we stay alive. Furthermore, cells are constantly dying, billions of them die every day and are replaced by new cells of the same kind. That's a lot of DNA loss. A physical inscription on any DNA would be lost as soon as the cell it was part of died. You could literally wash it off in the shower. As a matter of fact, the only organic tissue we are aware of that is capable of storing anything over a long period of time is the white matter of the brain, and truthfully we know almost nothing about how that works.

So we're still a long way from biomechanical storage mediums I'm afraid. It would allow for a hell of a Flash Drive though.

[I-n-j-i-n]

I don't think replacement of DNA is that big a hurdle. It's not like they're just going to put in a single cell or expect a static source of DNA information. It'll have to regenerate like all the other cells in the body.

I think the problem isn't the storage, but how you transmit the data into the brain.

[Zechs]

If it were to be used, they would use the Cell Generators to produce the DAN rich Cells, thus it would replace non-DNA cells. Or it would be applied during the conception period in order that it is applied before the cells begin to multiply.

However, this wouldn't be able to be used by the individual. It would be like keeping a genetic journal. It couldn't be applied to the individual. Because the brain develops it's own. If it understood and utilized Cellular information, then the Mitochondria within every single cell would have an opposite effect because it has been proven that the Mitochondria has distinctly different DNA. That would conflict the whole procedure, and might trigger the cell into melt down in a worst case scenario.

[Shadow Wolf]

The point is that what they've done here has absolutely nothing to do with genetics or biology in any way, shape, or form. They just learned how to write really small. The only reason anyone has thought of applying it to DNA is because DNA is really small. Blasting DNA with a particle beam would KILL IT. Which in turn would FUCK YOU UP at a subcellular level.

The only way we will ever transmit messages through DNA is if we figure out a way to create a code using naturally occurring GCAT (Guanine, Cytosine, Adenine, Thymine) recombinance. Thymine always binds with Adenine, and Guanine always binds with Cytosine. DNA is designed that way, and it is IMPOSSIBLE to change that. The GOOD thing there is that in a bonded double helix, you only have TWO possible types of pairs, and TWO is the magic number of computing. Or more accurately, zero and one. But there are only TWO different states any computer is capable of recognizing, and everything a computer does is built off that. Zero means there was no electrical impulse, and one means there was. So then, if you can give a computer data in a format that only has two different options, you can speak its language.

So basically, the code you wanted to transmit would have to be contained in a very long helix in which AT and CG pairs were bound in a certain order. If you could get a computer to read through a helix and recognize bonded pairs as ones and zeroes, to see a CG pair and send an electrical impulse through the circuit board, to see an AT pair and withhold that impulse, THEN you could potentially start working on biomechanical storage mediums.

The problem that would be presented then is, DNA is constantly 'zipping and unzipping' changing its order dynamically to adapt to cellular needs, etc. You would have to learn to create a static double helix, and I'm not even gonna theorize how you would do that.

But the point of all this is that you can't store code on DNA by blasting it with lasers.

[Necrotic]

The first practical post in this thread.

Keep in mind that DNA unzipping isn't prompted by magic. Enzymes and other molecules are responsible for that process, and that's generally prompted by the cell's need to divide as it is. I mean, if we're talking strictly about keeping DNA molecules as a form as storage outside of the body then I think what you said could work.

The practicality of writing small on the other hand, I wonder if there's some sort of application to this if it becomes cost effective. Like someone said, the need for storage capacity in hard drives is becoming greater and greater and we're reaching our limits.

Actually shadowolf, quite fascinating is the fact that scientists speculate that memories are stored as molecular information sort of like DNA, although I have no idea how far we've come on this concept. My biology teacher just brought it up one day and I began thinking of the sorts of things our bodies are capable of. Imagine if we started to discover how memories were stored, and wouldn't have to deal with the issues of DNA being so delicate.

[Shadow Wolf]

There is definitely huge application for being able to store data in a form that small, but not as far as standard hard disks go. Standard hard disks never physically modify the disc surface, they magnetize and demagnetize parts of it. To make it rewritable you would have to develop a new type of surface to write it on. The closest thing we have right now is a CD-RW, because optical discs have microscopic holes physically burnt into them to store the data, and to erase them, the writing medium is simply melted by the laser, closing all the holes so you can write it again. The problem with that is that the more times you melt it, the less reliable it becomes. Flash memory won't work either, because it uses a very mechanically oriented gating system, which is much better explained right here.

So in order for this to be useful in computing application, we need to develop a surface that can be physically modified, and completely restored to its original state on command. I know of nothing like that right off the top of my head, although I'm sure the scientists are working on it.

But yes, if we ever figure out how the brain stores memories, then we'll be getting somewhere. My largest concern at that point would be that if we know how memories are stored then we know how to erase them, and that's a little too "The Matrix" for me.

[The Legendary Zoltan]

Man, you guys suck. I want to talk about Xenogears!

Xenogears Xenogears XENOGEARS!!

Hahaha. But yeah, I should have realized it as soon as I read it. As Pezman wrote, they didn't mean DNA that's still in a person. Which means that, as Shadowolf wrote, they just thought of using DNA because it's really small.

Blasting DNA with a particle beam would KILL IT.

Maybe they're planning to do it with something other than a particle beam. They must have some kind of idea of a way to do it without killing it since they expressed that they'd like to do it.

[Robotaki]

I think this technology would allow vandalism go to a completely new stage...e.g. drawing a penis that's the size of 1 fucking nano. I like, hehe

[RiftDoggy]

I think this technology would allow vandalism go to a completely new stage...e.g. drawing a penis that's the size of 1 fucking nano. I like

But...how would anyone ever know?

Like, if one night some drunk scientists broke out their lasers and started drawing on the Mona Lisa, and the next morning all of her teeth were covered with macroscopic penises (peni?), how would we know?

Or if some nerd knocked his friend out the night before April Fool's, went crazy, and the next morning:

Nerd: Pfhahhahahaha--*coughs.*

Friend: What?

Nerd: Oh, nothing.

Friend: ...You're weird.

Nerd: *Laughing again.*

Friend: Okay, seriously, what?

Nerd: *Cracks up.* I--hahahah--I drew--hahahhahahahah!--I drew a penis on a cell on your face! *Laughs hysterically.*

Friend: D=!

[Fusion2004]

shadowolf: Everyone you said, though, is based on the assumption that we need the ability to rewrite over what has already been inscribed. Although that has been a standard of computing for a long time, there was a time when my father wrote programs on punch cards for use at the room-size computer at his university. What if we simply make the storage medium big enough that we wouldn't absolutely NEED the ability to rewrite data, we could simply write a new copy of it.

I'm thinking an external USB drive that has slabs, not discs, of which you can buy at the sizes of one terabyte, ten terabytes, and one hundred terabytes. Sound good?

Obviously it's not practical in the long run, but for us peoples that just want a crapload of storage space RIGHT NOW, it would work in the short run.

[Shadow Wolf]

That actually had not occurred to me, and it seems logical unless you have a really good grip on how operating systems actually store data. As I've said before, a hard disk represents 1s and 0s by magnetizing and demagnetizing sectors of the disk surface. Even when you're just copying or moving a file on your hard disk, it's changing its location on the physical disk surface.

With a hard disk today, when you delete a file, its contents remain on the drive. What you're really doing when you delete a file is earmarking the sectors it's written into for overwriting. Then, the next time you create any type of file whatsoever, new file data is written into the sectors that "deleted" data resides in, wherever they happen to be found on the disk surface. That's why you have to defragment your hard drive, because files are written into whatever empty sectors are found, and don't necessarily get written all in order to one spot on the disk, and as a result, the disk has to spin and search longer to find the whole file. If you etch data permanently into the disk surface, you lose that capability, which means you can never truly delete a file or clean your hard disk.

Data storage would be like writing a book with a Sharpie pen... you go from the top of the page to the botttom, and you can't change anything. It would, however, mean that you would never have to defragment your hard disk again. But eventually simply using your computer would fill the disk, and you would have to start using a new disk. The question would then become, can you give me an etching surface large enough to allow me to write on it for the standard lifecycle of a computer (3 to 5 years) without having to replace it? If they can get the bible on a .5 mm or whatever it was silicon chip, that may be entirely possible. But scarier yet would be that since you can't delete anything, there is a complete record of every keystroke, click, and command ever given to that computer etched into the surface.

I like this thread. I could go for a long time yet.

[The Legendary Zoltan]

Wow, Shadowolf. Thanks. I totally learned a lot about computers from that.

I can totally see the microscopic penises on the Mona Lisa becoming a movie plot. Hahaha!

[I-n-j-i-n]

I think it'd be both hilarious and extremely annoying if you meet someone who is a total evil clone of you and says he is your father and he's the same age as you.

[ifirit]

That actually had not occurred to me, and it seems logical unless you have a really good grip on how operating systems actually store data. As I've said before, a hard disk represents 1s and 0s by magnetizing and demagnetizing sectors of the disk surface. Even when you're just copying or moving a file on your hard disk, it's changing its location on the physical disk surface.

With a hard disk today, when you delete a file, its contents remain on the drive. What you're really doing when you delete a file is earmarking the sectors it's written into for overwriting. Then, the next time you create any type of file whatsoever, new file data is written into the sectors that "deleted" data resides in, wherever they happen to be found on the disk surface. That's why you have to defragment your hard drive, because files are written into whatever empty sectors are found, and don't necessarily get written all in order to one spot on the disk, and as a result, the disk has to spin and search longer to find the whole file. If you etch data permanently into the disk surface, you lose that capability, which means you can never truly delete a file or clean your hard disk.

Data storage would be like writing a book with a Sharpie pen... you go from the top of the page to the botttom, and you can't change anything. It would, however, mean that you would never have to defragment your hard disk again. But eventually simply using your computer would fill the disk, and you would have to start using a new disk. The question would then become, can you give me an etching surface large enough to allow me to write on it for the standard lifecycle of a computer (3 to 5 years) without having to replace it? If they can get the bible on a .5 mm or whatever it was silicon chip, that may be entirely possible. But scarier yet would be that since you can't delete anything, there is a complete record of every keystroke, click, and command ever given to that computer etched into the surface.

You make a number of valid points about the incapabilities of using DNA as a mechanical/electrical data-storage-medium. However, you're ignoring the biological logistics of DNA.

DNA can exist in a static state. When not in the presence of chromatin (a protein within chromosomes that regulates DNA), DNA does not replicate, express, or mutate. Simply having DNA does not mean having life, as our DNA can long exist after our deaths in its original order, e.g. dinosaur DNA preserved in amber. A chain of nucleotides could be used to store a particular sequence of information, yes, but again we come back to the problem of how to modify and revert this sequence of nucleotides. For this, you should consider the process by which DNA replicates itself.

Within the chromosomes, chromatin proteins trigger various stages of the DNA's replication process, such as unwrapping the DNA, unwinding the helix and pulling the helix apart, in addition to copying the DNA structure and reassembling the helix. Various chemicals control each of these stages and can also repair or "activate" sequences of DNA. So, by monitoring and controlling these stages of DNA replication, the structure of a DNA molecule can be modified and remodified on the molecular level. However, to be able to modify individual base pairs would require incredible amounts of precision and control of the DNA's environment.

Still, one method of marking individual base pair for modifying would be to damage that pair and initiate the chromatin to repair the damage. By using the appropriate chromatin proteins, you can utilize the naturally-occurring DNA repair processes to rewrite an A-T pair as a G-C pair or vice-versa. The information could also be modified by undergoing DNA replication to unravel the helix and make changes. Then stored, and even copied, by completing the DNA replication.

However, these processes are still not completely understood and incredibly complicated. Still, there comes a problem of how to physically store the DNA and its modified chromatin without a cell or nucleus. But, I suppose you could use viruses or other nanomachines for that purpose.

[Shadow Wolf]

Yeah, I realized shortly after I posted that that you could simply control the enzymes that cause DNA to replicate and such. Nice to see there's someone with more intimate knowledge of the other end of the idea here. I don't see us developing the precision to use biological material for storage anytime soon, and even then, we may well have mechanical technology small enough at that point to make it not worth doing. It could have huge applications in the fields of organ replacements and prosthetics though... If you could grow and transplant a biomechanical organ, and place it into a human body to such a degree that you could actually get the thing to analyze and emulate the DNA of the original, you theoretically wouldn't have to deal with rejections anymore. If you could design prosthetics that tie into the stump of an arm on a DNA level while still creating viable connections with machinery, there is the potential for prosthetic arms that function as exactly as a real one. Bio/nanotech is an exciting field. I can't wait to see where we are in 20 years.

[ifirit]

You may not have to wait that long. The reason is because of a discovery made in 2007, which makes it possible to have cells undergo cellular "reprogramming."

Cellular reprogramming seems almost like science-fiction. You see, by extracting the nucleus of a developed cell and implanting it in another developed cell with the nucleus removed, the cell will revert to the stem-cell state, allowing it to be developed into any other type of cell within the genetic makeup. Cellular reprogramming can be implemented very economically compared to other reprogramming techniques and has a much higher success rate.

Apparently, cellular reprogramming is such a breakthrough in cellular research that many of the world's universities are switching gears away from cloning and other embryoic stem cell technologies. And according to the Wall Street Journal, even Ian Wilmut, the researcher who lead the development of the first full clone (Dolly), has apparently abondoned his research on cloning in favor of cellular reprogramming.

However, this is more of an ethical breakthrough compared to a biological one, since embryoic stem cells are no longer needed for regeneration research. This could accellerate genetics research and technology here in the US and, once fully developed, allow for cheaper and safer alternatives to organ and tissue donation.

[Shadow Wolf]

Which is all to say: YAY! The nice thing is that we're pretty good at getting stem cells to turn into nervous tissue, but the trick is getting the body to accept implantation. Now if we could get as good at turning them into cardiac tissue, we'd be set, since those are the only 2 types of cells in the body that can't repair themselves.