Dna Computers

[Maine farmer]

For some reason, I found myself thinking about the potential for using DNA in computing today.  I came across this https://www.technologyreview.com/s/534721/what-can-dna-based-computers-do/  and found it interesting, but leaving me wanting to know more.

 

I think there are far more possibilities than those discussed in the article, and I wonder if we could develop biological computers that can reproduce and evolve.

 

Any thoughts?

[BrainJackers]

DNA computing is a fascinating topic. It is quite a departure off our current standards, and will have little benefits (in the short term, possibly even in the long term if current computing devices continue to advance).

 

They reason species evolve is mutations. These mutations persist as the organisms with the best set of genes, live into the future. Just a review of basic Darwinism there.

 

Biological computers (on the scale of organisms) will fail in this sense. Mass production will have variations which will destroy a standard. We could make sure they all had the same genes yet that will be impossible to guarantee if we let them reproduce. As they evolve, they might not evolve towards favorable usage by us humans, and it would take so long, it is more of an annoyance than a good thing.

 

Some work into organism computers have been done. Kevin Warwick used rat brain cells to make a robot (very basic, https://singularityhub.com/2010/10/06/videos-of-robot-controlled-by-rat-brain-amazing-technology-still-moving-forward/). This isn't on a DNA level though and doesn't face the issues stated above as it was trained as an individual, not a species.

 

Beyond these factors, there is also ethical complications. Do these devices count as true, living, beings (thereby protected by animal abuse laws)? Do they have sentience? Can they make proper decisions? Is this right to do at all? Tamper with life put here by something (either a God or a randomness factor in the universe, that isn't actually random, but appears such)?

 

I think while interesting, they are not worth the time. I also believe they could be used to create a complete organism, tampering with life (which is bad to do on a mass scale, in my opinion), and could cause mass abuse of sentient beings. Also, if they are sentient, why should they listen?

 

These arguments become quite void if you move back down to the DNA scale yet it would take forever to design even just one proper cell. You could mix existing DNA strains but then we're just playing Frankenstein.

 

Given our current level of computers, it is unworth it do it on a small scale (as I've said). Therefore, I find this thing interesting, yet something to make a footnote of, nothing more. Feel free to prove me wrong, anyone.

--@Kayaba

[CraigD]

I’ve been fascinated by the idea of DNA and other chemical computers since it first began to be discussed seriously the 1990s, but find it a difficult subject to understand in detail.

 

On a high level, it’s just an approach to very massively parallel computing. DNA computing is very slow compared to electronic computing – a typical “compute cycle” for a DNA computer is from 30 minutes to more than a day – but can potentially have a huge number of “processors” – on the order of 10²⁰, assuming there’s some sort of limit of about 0.01 kg on the amount of DNA that can be part of a single “computer”, much greater if that limitation can be overcome.

 

This paint a high-level picture of a DNA computer as being very good at tasks that take electronic computers a long time but can be broken down into many pieces that can be run on many computers, like simulating the atmosphere, but unusable bad for tasks that must be completed quickly, like controlling a motor.

 

I had to be careful reading about DNA computing to distinguish between arrangements that are

• “true computers” in the way an ordinary digital computer is – a machine made of simple logic gates that can do AND, OR, and NOT operations on single 0 or 1 bits, allowing it to do arithmetic and if-then logic –
• artificially built arrangements of DNA that can do very useful things, like quickly recognize specific proteins
• systems that use DNA to store digital data, but not read, write, or change it.

As best I can tell, the state of the art in DNA “true” computers is playing tick-tak-toe (like MAYA-II, described in this 2006 article)and calculating the square root of a small number (for the one described in this 2011 article, integers up to 15)

 

Understanding how any of these biochemical computers work, though, is hard, because they use a lot of complicated biochemistry to what in an electronic computer is a single simplest transistor. To really understand, you have to be good at both molecular biology and computer engineering!

 

I think there are far more possibilities than those discussed in the article, and I wonder if we could develop biological computers that can reproduce and evolve.

Nature is already full “biological computers” or a sort – not what I called “true computers” above – that do that – every biological organism there is, from bacteria to blue whales.

 

Your question brings to my mind an awe-striking possibility concerning computer manufacturing: if you can make a useful DNA computer, then encode it and gene for the biochemical machinery it needs to run in the genome of some cell, you can manufacture them just by feeding the cells and having them to divide. What takes hundreds of factories to do with electronic computers could be done in a few petri dish for DNA computers. DNA computer could be made in numbers many powers of 10 greater than electronic computers.

[Maine farmer]

 

Your question brings to my mind an awe-striking possibility concerning computer manufacturing: if you can make a useful DNA computer, then encode it and gene for the biochemical machinery it needs to run in the genome of some cell, you can manufacture them just by feeding the cells and having them to divide. What takes hundreds of factories to do with electronic computers could be done in a few petri dish for DNA computers. DNA computer could be made in numbers many powers of 10 greater than electronic computers.

 

Exactly!  Just think about all the toxic chemicals and heavy metals used in manufacturing computers that we may one day be able to do without.  

 

I also recently read an article about how someone recently created synthetic dna, and  I know that in the dairy business we are already using genomics to select for specific genes in our breeding program, so if we now have the ability to identify the functions of genes and create genes, we should some day be able to guide and accelerate an evolutionary process that could be used to "grow" virtually anything we want.

 

How crazy does that sound?

[Maine farmer]

Now I have a completely insane idea.  We will not just live in our homes, but our homes will be biological entities that we will have a symbiotic relationship with.  The homes will grow and maintain and repair themselves.  They will filter our air and water and use our waste products as building materials, and they will be able to produce our food.  

 

Our homes will be able to network with other homes, and we will be able to grow a biological internet and we will be able to grow our own network connections directly in our brains.  No more need  to carry electronic devices of any kind!

 

I better stop now before someone tries to commit me to an asylum .

[CraigD]

Now I have a completely insane idea. We will not just live in our homes, but our homes will be biological entities that we will have a symbiotic relationship with. The homes will grow and maintain and repair themselves. They will filter our air and water and use our waste products as building materials, and they will be able to produce our food.

While there’s no such technology now, I don’t think this is a crazy idea.

 

It’s been showcased in science fiction for at least 33 years. In 1984, Harry Harrison built his West of Eden 65,000,000 year alternative history world around the idea of genetic engineering being such a mature technology that machines – water wheels, pumps, steam engines, etc – are never invented, and everything from microscopes to ocean going vessels are genetically modified animals.

 

I think Harrison would have been surprised how quickly our molecular biology has advanced. He imagined a science that took millions of years to mature, that slowly modified animals found in nature over many generations, similar to how we humans selectively bred wild animals into our present menagerie of domestic ones. We’ve now reached the point of having made completely new organisms by synthesizing DNA from scratch. We’ve not made giant fish that can replace mechanical ships, but we may do things even more amazing, proving the old adage about fact being stranger than fiction.

 

Personally, I’d like to have clothing made of a living plant that cleans, heats, and cools me, and doesn’t wear out for 100 years. It might not be able to stream video from the internet, or run any sort of computer program, but it would be immensely practical. :)

 

Our homes will be able to network with other homes, and we will be able to grow a biological internet and we will be able to grow our own network connections directly in our brains. No more need to carry electronic devices of any kind!

As I stressed in my previous post, DNA computers are limited in the computing task they can do, high-speed network hardware being one of the things they just can’t do. DNA is part of a system that’s very good at building proteins, but very slow at it. Trying to make a DNA computer into a network router is akin to trying to make a television image out of rapidly growing plants – it’s just not something biological systems like these can do.

 

This is not to say that we might not be able to engineer organisms that use DNA to build electronic or mechanical, or even neurological computers, just that such computers wouldn’t be DNA computers.

 

There’s been a lot of speculation that future high speed computers won’t necessarily be electronic. Contending alternative technologies include photonic – computer that use light, without always transforming it into electricity – and mechanical – things like the “rod logic” machines Drexler described in his speculative nonfiction (here a recent web article about them), and Neal Stephenson’s IMHO excellent 1995 novel The Diamond Age.

[Turtle]

While there’s no such technology now, I don’t think this is a crazy idea.

 

It’s been showcased in science fiction for at least 33 years. In 1984, Harry Harrison built his West of Eden 65,000,000 year alternative history world around the idea of genetic engineering being such a mature technology that machines – water wheels, pumps, steam engines, etc – are never invented, and everything from microscopes to ocean going vessels are genetically modified animals.

Imagine your microscope catching the flu! Or you getting rabies from your ship! :lol:

 

There’s been a lot of speculation that future high speed computers won’t necessarily be electronic. Contending alternative technologies include photonic – computer that use light, without always transforming it into electricity – and mechanical – things like the “rod logic” machines Drexler described in his speculative nonfiction (here a recent web article about them), and Neal Stephenson’s IMHO excellent 1995 novel The Diamond Age.

Interesting. I was somewhat surprised that Drexler didn't mention the MIT Tinker Toy computer.

This computer, built from Tinker Toys, always wins at tic-tac-toe. Danny Hillis and Brian Silverman began building it as MIT sophomores; the full story is described in the October 1989 issue of Scientific American in an article by A. K. Dewdney. It was displayed at the Computer Museum in Boston and is currently at the Boston Museum of Science. A community member writes that it "is a powerful illustration that technology is not only about Electronics." Photo by gribley used under Creative Commons Attribution Noncommercial Share Alike license.

[OceanBreeze]

Now I have a completely insane idea.  We will not just live in our homes, but our homes will be biological entities that we will have a symbiotic relationship with.  The homes will grow and maintain and repair themselves.  They will filter our air and water and use our waste products as building materials, and they will be able to produce our food.  

 

Our homes will be able to network with other homes, and we will be able to grow a biological internet and we will be able to grow our own network connections directly in our brains.  No more need  to carry electronic devices of any kind!

 

I better stop now before someone tries to commit me to an asylum .

 

 

And what, pray tell, do these homes eat? :shocked:

[OceanBreeze]

Imagine your microscope catching the flu! Or you getting rabies from your ship! :lol: 

 

 

But Honey, I swear I caught it from my laptop!

[Maine farmer]

And what, pray tell, do these homes eat? :shocked:

They would build carbon structure using photosynthesis, and they could pull minerals out of the soils.  They could even use nitrogen to build proteins that could be used to grow muscles so doors could be self closing.  You wold fertilize such homes much as you would a garden, adding whatever minerals or nutrients that might be needed.

 

While there’s no such technology now, I don’t think this is a crazy idea.

 

Personally, I’d like to have clothing made of a living plant that cleans, heats, and cools me, and doesn’t wear out for 100 years. It might not be able to stream video from the internet, or run any sort of computer program, but it would be immensely practical. :)

 

As I stressed in my previous post, DNA computers are limited in the computing task they can do, high-speed network hardware being one of the things they just can’t do. DNA is part of a system that’s very good at building proteins, but very slow at it. Trying to make a DNA computer into a network router is akin to trying to make a television image out of rapidly growing plants – it’s just not something biological systems like these can do.

 

 

I think the time will come when someone figures out some revolutionary method of computing to break the limits of what we now think is possible.  We just aren't smart enough.

[CraigD]

And what, pray tell, do these homes eat? :shocked:

They would build carbon structure using photosynthesis, and they could pull minerals out of the soils. They could even use nitrogen to build proteins that could be used to grow muscles so doors could be self closing. You wold fertilize such homes much as you would a garden, adding whatever minerals or nutrients that might be needed.

I was gonna’ say “sunlight, air, and poop.” But now that you mention “as you would a garden”, I should add compostable trash, or, as I assuming these GM wonder house plant/animals have sophisticated chemical systems to decompose practically anything, all trash.

 

Once you assume bioengineering has solved every chemical challenge of civilization, you can pretty much imagine artificial organisms like a House doing everything our civilization does to support the input and output of a house full or humans now. Give it enough area, and it could make food. Give it a protective shell, and it could do it in space.

 

It’s just a matter of writing the right genes. So far (ca 2010), the biggest synthetic organism we’ve made is a microscopic simplified/streamlined bacterium, which was mostly an exercise in throwing out genes that looked useless, keeping the useful ones without completely knowing what they do, but it’s a start. :)

 

I’d also guess the “carbon structure” of choice these things’ll build will be chemically along the lines of (C_xH_yO_z)_n, known more commonly as wood.

 

I think the time will come when someone figures out some revolutionary method of computing to break the limits of what we now think is possible. We just aren't smart enough.

I think the history of computer engineering has been a succession of such revolutions, often when people, often the people actually doing it, didn’t think we were smart enough.

 

Many – I’d say most – people around the turn of 1990 imagined that massively parallel electronic computers would be the thing by now, but surprisingly, most computing is doing well on just 4 to 8 CPU cores, not the millions or billions we thought would be common by now, or even the few thousand late some late 1980s machines sported, and aside from some specialized super computing, massively parallel machines aren’t much to be found.

 

I wouldn’t count massive parallelism out yet, since despite the challenges of writing general purpose software for them, the approach still make a lot of sense. I’m almost completely certain future successful massively parallel computers will have much faster working parts than DNA, though.

 

DNA is the best (some would note the only know) for growing and managing plants and animals, but I think is has some insurmountable drawbacks that will mean faster substrates – electronic, photonic, or mechanical – will always have an important place in computing.

[Maine farmer]

I was gonna’ say “sunlight, air, and poop.” But now that you mention “as you would a garden”, I should add compostable trash, or, as I assuming these GM wonder house plant/animals have sophisticated chemical systems to decompose practically anything, all trash.

 

Once you assume bioengineering has solved every chemical challenge of civilization, you can pretty much imagine artificial organisms like a House doing everything our civilization does to support the input and output of a house full or humans now. Give it enough area, and it could make food. Give it a protective shell, and it could do it in space.

 

It’s just a matter of writing the right genes. So far (ca 2010), the biggest synthetic organism we’ve made is a microscopic simplified/streamlined bacterium, which was mostly an exercise in throwing out genes that looked useless, keeping the useful ones without completely knowing what they do, but it’s a start. :)

 

I’d also guess the “carbon structure” of choice these things’ll build will be chemically along the lines of (C_xH_yO_z)_n, known more commonly as wood.

 

 

Of course, a living organism can also build with calcium, as in bones and shells, and you could conceivably grow a frame or protective covering using iron and copper, and other metals.

 

 

DNA is the best (some would note the only know) for growing and managing plants and animals, but I think is has some insurmountable drawbacks that will mean faster substrates – electronic, photonic, or mechanical – will always have an important place in computing.

Well, I have come to believe that humanity is on the verge of completely blurring the lines between the biological and mechanical.

 

I may need to go back to school!

[Turtle]

Of course, a living organism can also build with calcium, as in bones and shells, and you could conceivably grow a frame or protective covering using iron and copper, and other metals.

 

Well, I have come to believe that humanity is on the verge of completely blurring the lines between the biological and mechanical.

 

I may need to go back to school!

The shell/bone grown house also crossed my mind. It would only need to be live for as long as it took to complete the structure. Turtle shell -as if! - might better withstand acid rain than bare bone or sea shell, although a skull house has a je ne sais quoi.