Comments on: Breed-Solomon

Breed-Solomon

Rumple — Thu, 30 Jul 2015 08:58:13 -0800

Since it folds in three dimensions, we could store all of the world's current data—everyone's photos, every Facebook status update, all of Wikipedia, everything—using less than an ounce of DNA. And, with its propensity to replicate given the right conditions, millions of copies of DNA can be made in the lab in just a few hours. Such favorable traits make DNA an ideal candidate for storing lots of informations, for a long time, in a small space.

But how stable is DNA? The Reed-Solomon method, long used to error-check data transmission and duplication, is now being explored as an adjunct to the long-term archiving of information encoded in DNA. A post by Alex Riley at the PBS Science blog NOVA/NEXT.

By: leotrotsky

leotrotsky — Thu, 30 Jul 2015 09:04:45 -0800

But how stable is DNA? The Reed-Solomon method, long used to error-check data transmission and duplication Presumably the millions of copies would provide for robust error-checking, no?

By: GenjiandProust

GenjiandProust — Thu, 30 Jul 2015 09:06:41 -0800

Does this mean that we are closer to the day where I can store all of my cat .gifs on my cat?

By: James Scott-Brown

James Scott-Brown — Thu, 30 Jul 2015 09:10:01 -0800

The Angew. Chemie paper by Robert Grass et. al..

By: xarnop

xarnop — Thu, 30 Jul 2015 09:24:41 -0800

Given that is the case, it really begs the question if awareness, emotions, and consciousness couldn't exist fully formed as well or better than a humans in a minute scale that we have no capacity of understanding. How do we know there aren't bacteria or single celled organisms who aren't in fact emotionally and intellectually more competent than we are? When we think about finding life on other planets we are willing to imagine life as radically different that how we define it on earth, but are we not willing to acknowledge we may be missing things going on right in front of us?

By: xarnop

xarnop — Thu, 30 Jul 2015 09:36:39 -0800

What's more why do we assume that the most precious aspect of life itself should be used as a tool without regard for it's experience of being? Isn't it possible there is a reason why all living beings are set to PROTECT AND REPAIR THE DNA if at all possible? Perhaps a precious part of our life force lives there. Forgive us, we know not what we do.

By: lalochezia

lalochezia — Thu, 30 Jul 2015 09:50:48 -0800

xarnop: I know you are coming from a place of care, but vitalism has been discredited for hundreds of years. There have been literally thousands of experiments done to test for this idea, all coming up negative. Inanimate matter such as DNA does not have consciousness. Even if it were true, living creatures cannot function without massive continual destruction of DNA. Every biological source of calories - which is to say every living thing we eat - has DNA which is destroyed in said extraction of energy and nutrients. Inside us, as we speak, quintillions of pieces of DNA every second are being violently chopped reorganized, recycled and destroyed up by our own biological machinery. It happens in every living being. It (and it's cousin RNA) is literally both the fuel and instruction manual of life's tapestry and without it's continual destruction and reorganization life as we know it would not exist. If we are willing to eat an organic lettuce for a nice flavor (destroying DNA) - or making pigments from plants (destroying DNA) - we should be willing to taking some synthetic lab-made DNA and re-organizing its nucleotide sequence for the the preservation of the long-term cultural interests of humanity.

By: benzenedream

benzenedream — Thu, 30 Jul 2015 10:06:13 -0800

What if the spirit moves us through the pituitary gland Perhaps hard drives are sentient

By: sobarel

sobarel — Thu, 30 Jul 2015 10:06:34 -0800

How do we know there aren't bacteria or single celled organisms who aren't in fact emotionally and intellectually more competent than we are? I sometimes wonder about how many tiny insects and what-have-you I kill walking through a field, so the idea of a world where each course of antibiotics or bolus of bleach down the bog is equivalent to genocide is fairly horrifying.

By: tecg

tecg — Thu, 30 Jul 2015 10:14:27 -0800

xarnop: How do we know there aren't bacteria or single celled organisms who aren't in fact emotionally and intellectually more competent than we are? You may be interested in the work of the biophysicist Eshel Ben-Jacob on the collective intelligence of bacteria. (I learned just now that he sadly passed away last month.) This sounds less fringe-y that it actually is; he was highly esteemed in the scientific community and e.g. former president of the Israel Physical Society.

By: tecg

tecg — Thu, 30 Jul 2015 10:17:43 -0800

I forgot to add that Ben-Jacob never suggested that individual bacteria possess consciousness, but he cam close to suggested something like that for populations of bacteria.

By: doctornemo

doctornemo — Thu, 30 Jul 2015 10:26:27 -0800

place these glass beads in the dark at –0.4˚ F, the conditions of the Svalbard Global Seed Bank on the Norwegian island of Spitsbergen, and you could save your photos, music, and eBooks for two million years. I'm still thinking about this.

By: xarnop

xarnop — Thu, 30 Jul 2015 10:48:44 -0800

I am aware of research into bacterial intelligence as well as slime molds and quorum sensing. Just because I'm an animist doesn't mean I don't read science. It just means I cringe in horror at how unwilling humans are to consider that other forms of sentience might exist. Reading up on elephant intelligence, despite that they appear to mourn their dead, exhibit empathy for other elephants AND non elephants we find that "Scientists often debate the extent that elephants feel emotion." This kind of crap is why I don't trust "ethics committees" of scientists to actually favor the possibility of sensing or emotion over the pressure to plow ahead and presume there is no feeling if at all possible or if there is any doubt of certainty there is emotion/sensing present. I do think it's possibly other forms of energy than just life can sense, in fact I wonder if life isn't the manifestation of an already sensing universe fighting as hard as it can to get to the locations and experiences it desires despite the difficulty of exerting any will against either the order or the chaos defined by the physics of this world.

By: qcubed

qcubed — Thu, 30 Jul 2015 11:02:33 -0800

"other forms of energy"? What exactly do you mean by that?

By: Rumple

Rumple — Thu, 30 Jul 2015 11:04:59 -0800

Speaking of elephants, from the same blog

By: b1tr0t

b1tr0t — Thu, 30 Jul 2015 11:16:38 -0800

In another decade or two, we will discover that blue-green algae is actually some Alpha-Centaruian teenager's weird porn stash.

By: happyroach

happyroach — Thu, 30 Jul 2015 11:19:39 -0800

It just means I cringe in horror at how unwilling humans are to consider that other forms of sentience might exist. Nonsense. Humans have always been more than willing to believe that other forms of sentience exist. In fact many of them orient their lives around that belief, and what they think those sentiences want. They've sacrificed goods and animal and people to those sentiences. They've slaughtered people of differing ethnic and cultural backgrounds in the name of these sentiences. And currently, evidently these sentiences are obsessed with the sexual morality of humans. So what you ought to be asking is not "why don't people believe?", but "How can I make money and power off of this exploit in human cognition?" Play your cards right, and you can probably get followers who will enact a crusade against people who don't believe in Our Sentient DNA buddies, or the Will of the Cosmos, or whatever.

By: Mitrovarr

Mitrovarr — Thu, 30 Jul 2015 11:20:59 -0800

There are lots of good ways of storing huge amounts of data, if you don't worry about trivialities like storing or retrieving it in a reasonable amount of time, doing a random seek, or the physical robustness of it all.

By: Mitrovarr

Mitrovarr — Thu, 30 Jul 2015 12:07:24 -0800

xarnop: Isn't it possible there is a reason why all living beings are set to PROTECT AND REPAIR THE DNA if at all possible? Perhaps a precious part of our life force lives there. Actually, they aren't. Living things will generally destroy any DNA found outside a cell. It's an important safeguard against viruses. It'll also happily sacrifice cells for the good of the whole, destroying the DNA inside, as part of apoptosis. This happens to huge numbers of cells all the time. Anyways, there are obvious good reasons to protect the DNA in a living cell from damage. It's essential for life, and cells that mutate can cause cancer, etc...

By: maryr

maryr — Thu, 30 Jul 2015 12:34:06 -0800

*reads thread, shrugs, returns to the bench to create and destroy DNA again and again and again and again* PCR, DNase, PCR, DNase, PCR, DNase, bleach bleach bleach.

By: atoxyl

atoxyl — Thu, 30 Jul 2015 12:44:58 -0800

Given that is the case, it really begs the question if awareness, emotions, and consciousness couldn't exist fully formed as well or better than a humans in a minute scale that we have no capacity of understanding. You know, I'm relatively well-disposed, in a purely speculative way, to the notion that on some level consciousness is an inextricable attribute of matter. But I've always thought the obvious conclusion is that there's not so much special about "life" versus "not life" after all, and little significance on a grand scale to the continuity of any particular "experience of being."

By: atoxyl

atoxyl — Thu, 30 Jul 2015 12:51:29 -0800

Anyway this is really cool. Definitely strictly an archival format for now though.

By: clawsoon

clawsoon — Thu, 30 Jul 2015 14:06:03 -0800

By: lucidium

lucidium — Thu, 30 Jul 2015 15:00:51 -0800

> Does this mean that we are closer to the day where I can store all of my cat .gifs on my cat? 22 million years in the future, whiskered scientists jostle around a display. "Wait, that section that keeps repeati-" "It's noncoding junk, full of random mutations." "Just, bring it up again. Reverse it. Okay, try losing this outside part?" "This is a waste of time." "Wait, run it in parallel lines instead." As one, their heads slowly tilt to the side. "My god, it — it looks like a face!" "It looks like a message, and it looks... grumpy."

By: atoxyl

atoxyl — Thu, 30 Jul 2015 15:18:44 -0800

Someone who knows Reed-Solomon well: Is it localized enough for the possibility of a single protein (or ribonucleoprotein) to use the correction codes during replication? I.e. are the "checksums" (or whatever is used in Reed Solomon) placed right next to the data, so that a modified DNA polymerase could use, say, every 4th base to check on the accuracy of the previous 3? It's not something I know well (it's something I learned once upon a time in CS school) but I think it would depend on the exact scheme chosen? A message N symbols long (a symbol could be more than one DNA base if you wanted) is encoded in blocks of K symbols and can withstand the corruption of (K-N)/2, which is to say you do need to be able to look at the other (K+N)/2.

By: atoxyl

atoxyl — Thu, 30 Jul 2015 15:27:38 -0800

Note that it's not a checksum and there are not particular "redundancy" data points. The beauty of it is that any combination of (K+N)/2 symbols from a block is sufficient to reconstruct the message.

By: atoxyl

atoxyl — Thu, 30 Jul 2015 15:34:48 -0800

N being the number of message symbols encoded per block, not the total length of everything you are encoding. That's probably clear from context but my wording was poor.

By: Jpfed

Jpfed — Thu, 30 Jul 2015 19:40:43 -0800

Given that is the case, it really begs the question if awareness, emotions, and consciousness couldn't exist fully formed as well or better than a humans in a minute scale that we have no capacity of understanding. How do we know there aren't bacteria or single celled organisms who aren't in fact emotionally and intellectually more competent than we are? This is fun and you should read it

By: ymgve

ymgve — Thu, 30 Jul 2015 20:46:12 -0800

Is it possible to read back DNA-stored data in a fast, cost-effective way yet? If not, magnetic and optical storage will still be king and queen.

By: maryr

maryr — Thu, 30 Jul 2015 21:48:37 -0800

so that a modified DNA polymerase could use, say, every 4th base to check on the accuracy of the previous 3? This is kind of the opposite of cousin wobble.

By: en forme de poire

en forme de poire — Fri, 31 Jul 2015 00:16:57 -0800

Actually, they aren't. Living things will generally destroy any DNA found outside a cell. There are also organisms that regularly jettison large parts of their genome (the one I'm thinking of actually also has two nuclei and over 15,000 "nanochromosomes"...Oxytricha, never change, you little weirdo!).

By: en forme de poire

en forme de poire — Fri, 31 Jul 2015 00:19:39 -0800

(Also most papers about bacterial "intelligence" or information processing that I'm aware of have focused on properties of populations of bacteria, not on single individuals. But that's kind of a derail here.)

By: flabdablet

flabdablet — Fri, 31 Jul 2015 04:27:05 -0800

Ben-Jacob never suggested that individual bacteria possess consciousness, but he came close to suggested something like that for populations of bacteria Speaking as a population of bacteria, I endorse this notion.

By: flabdablet

flabdablet — Fri, 31 Jul 2015 04:36:22 -0800

As one, their heads slowly tilt to the side. "My god, it — it looks like a face!" "It looks like a message, and it looks... grumpy." http://www.youtube.com/watch?v=wSYAZnQmffg

By: flabdablet

flabdablet — Fri, 31 Jul 2015 05:00:35 -0800

Is it possible to read back DNA-stored data in a fast, cost-effective way yet? As I understand it, full-genome DNA sequencing gets done by massively replicating it, then breaking it into pieces that are short enough to sequence directly, sequencing those, then working out where the breaks were by matching end pieces to the middle parts of other pieces. If I were to design a digital storage system that relied on this kind of thing, I would build my archival molecules as data-bearing blocks with embedded error correction codes, separated by cleavage regions, using a group code recording scheme inside the data blocks so that data can never look like a cleavage marker; then I'd store all the data in the form of Merkle trees, allowing for easy data reassembly after a massively parallel sequencing step. With enough parallelism in that sequencing step, it ought to be possible to make large reads very fast.

By: en forme de poire

en forme de poire — Sat, 01 Aug 2015 14:55:20 -0800

There are also newer technologies that give much longer but somewhat more error-prone reads (this describes PacBio, at least last I checked -- they may have gotten the error rate down since then) but they are not as common yet compared to e.g. Illumina-style 100bp reads.