On 01/12/2010 11:01 PM, D103 wrote:

> This may be of little consolation now, but maybe in 20 years or so...
>
> http://www.tech-faq.com/dna-computer.html
>
> Imagine a computer with a CPU about the size of a coin, capable of 66 Gigaflops
> and having 700 Terabytes internal memory AND a power consumption of ~
> 0.0000000001 watts (minus the screen and interface devices, of course).
>
> That should speed up rendering!

While I'm not disputing the factual content of your statement, the 
article linked to is... well, essentially it's dumbed down so much that 
they might as well be talking about computers powered by Pixie Dust.

"[T]here is a limitation to how small, fast and compact silicon computer 
chips can be. DNA computers show promise because they do not have the 
limitations of silicon-based chips."

O RLY?

"For one, DNA based chip manufacturers will always have an ample supply 
of raw materials as DNA exists in all living things; this means 
generally lower overhead costs."

And you understand that silicon chips are MADE OF SAND, right? You know, 
as in "worthless as sand"? Given planet Earth's gross elemental 
composition (60.2% silica, 15.2% alumina, >5% everything else), I 
suspect that silicon is rather more abundant than DNA. And let us not 
even get into the fact that DNA for computers would be utterly different 
in sequence to DNA from living organisms.

It's like saying "people all over the world have windows made of glass, 
therefore we can easily make silicon chips". The stuff in a modern IC 
isn't very much like window glass.

"Secondly, the DNA chip manufacture does not produce toxic by-products."

Riiight. So because the end product is DNA, a molecule that already 
exists in nature, therefore you can produce it with no toxic by-products?

And the DNA itself wouldn't be toxic, no?

"Last but not the least, DNA computers will be much smaller than 
silicon-based computers as one pound of DNA chips can hold all the 
information stored in all the computers in the world."

Current computers are much, much larger than strictly necessary mainly 
due to issues of heat dissipation. You can already make RAM chips that 
hold absurd quantities of information; it's just that they tend to melt 
when you switch them on.

Besides, just because a strand of DNA can /store/ a lot of information, 
it does not necessarily follow that you can build a working 
/computational device/ which is only slightly larger.

"a DNA computer the size of a teardrop will be more powerful than 
today's most powerful supercomputer."

Possibly. But if you want it to do something /useful/, the teardrop by 
itself won't be much help. You still need I/O devices, for example.

"The capacity to perform parallel calculations, much more trillions of 
parallel calculations, is something silicon-based computers are not able 
to do."

I beg to differ. It would be more accurate to say that nobody has come 
up with a way of structuring computer programs as trillions of 
independent steps. We could totally build really parallel silicon chips. 
For example, recent GPU designs involve executing several hundred 
computations in parallel. There's no particular reason why you can't 
scale that up to thousands or millions - it's just that the extra R&D 
work probably wouldn't pay off in extra sales, because the software to 
utilise that much parallelism is lacking.

"In the current technology of logic gates, binary codes from the silicon 
transistors are converted into instructions that can be carried out by 
the computer."

This is a highly questionable and very muddled statement. It's hard to 
read something like this and continue to believe that the writer has any 
clue what they're talking about.

"though it may be very fast in providing possible answers, narrowing 
these answers down still takes days."

This rather suggests that the operation of a DNA computer is 
non-deterministic (and hence, applicable to a much smaller set of 
problems than a Turing-complete machine).

I won't hold my breath for this happening any time soon. :-P

Post a reply to this message

On 12/2/2010 3:37 AM, Invisible wrote:

> "[T]here is a limitation to how small, fast and compact silicon computer
> chips can be. DNA computers show promise because they do not have the
> limitations of silicon-based chips."
>
> O RLY?

Of course there's a limit. And there's likely a limit on how small/fast 
a DNA-based machine could be as well. The higher the clock frequency, 
the more susceptible it is to external influences such as EMI. The 
faster the clock, the more limitations on the actual circuit design 
there are, but you knew that.

> "For one, DNA based chip manufacturers will always have an ample supply
> of raw materials as DNA exists in all living things; this means
> generally lower overhead costs."
>
> And you understand that silicon chips are MADE OF SAND, right? You know,
> as in "worthless as sand"? Given planet Earth's gross elemental
> composition (60.2% silica, 15.2% alumina, >5% everything else), I
> suspect that silicon is rather more abundant than DNA. And let us not
> even get into the fact that DNA for computers would be utterly different
> in sequence to DNA from living organisms.

The advantages of living on a planet with a primarily silicate crust: 
Lots and lots of silicon to go around. Not sure what the ratio is of 
silicon to carbon, but I imagine its not hard to find a rock containing 
some sort of silicate.

>
> "Secondly, the DNA chip manufacture does not produce toxic by-products."
>
> Riiight. So because the end product is DNA, a molecule that already
> exists in nature, therefore you can produce it with no toxic by-products?
>
> And the DNA itself wouldn't be toxic, no?

Not unless it codes for something that could cause illness or kill you, 
but who's paying attention anyway. Organic compounds are some of the 
most toxic to us, because they are the most likely to interact. To be 
sure, there are a lot of extremely toxic inorganics as well.

> "Last but not the least, DNA computers will be much smaller than
> silicon-based computers as one pound of DNA chips can hold all the
> information stored in all the computers in the world."

Storage is not the same as computation. No mention as to how fragile 
that pound of DNA is. UV light or any form of ionizing radiation? 
consider your data hopelessly corrupt. so much for DNA computers in the 
space program. Other chemical and even physical processes could degrade 
it. If it happens to get contaminated by bacteria, they'd certainly 
enjoy the amino-acids that used to compose your photos from your latest 
family vacation to Hawaii. Not stable in the least!

> Current computers are much, much larger than strictly necessary mainly
> due to issues of heat dissipation. You can already make RAM chips that
> hold absurd quantities of information; it's just that they tend to melt
> when you switch them on.

I believe the bigger limitation on the amount of information that RAM 
can ultimately hold is more about the lower limit on the size of a 
transistor, rather than heat. What generates heat is the act of 
switching. If a latch is held, then there isn't much switching going on, 
though I'm sure there is some power consumption leading to some heat. 
Processors get burning hot because they constantly switch. RAM gets hot 
because of the way its state is maintained and how its accessed, at very 
rapid rates nowadays. Flash memory is obscenely high density, yet 
generates very little heat, unless it's accessed at its full bandwidth 
for an extended period of time, and even then its not nearly as much as 
a processor. Its also a few orders of magnitude slower than RAM.

>
> Besides, just because a strand of DNA can /store/ a lot of information,
> it does not necessarily follow that you can build a working
> /computational device/ which is only slightly larger.
>
> "a DNA computer the size of a teardrop will be more powerful than
> today's most powerful supercomputer."
>
> Possibly. But if you want it to do something /useful/, the teardrop by
> itself won't be much help. You still need I/O devices, for example.
>
> "The capacity to perform parallel calculations, much more trillions of
> parallel calculations, is something silicon-based computers are not able
> to do."
>
> I beg to differ. It would be more accurate to say that nobody has come
> up with a way of structuring computer programs as trillions of
> independent steps. We could totally build really parallel silicon chips.
> For example, recent GPU designs involve executing several hundred
> computations in parallel. There's no particular reason why you can't
> scale that up to thousands or millions - it's just that the extra R&D
> work probably wouldn't pay off in extra sales, because the software to
> utilise that much parallelism is lacking.

You'd need the pipelines to do it in the chip die. You'd need to build 
very small computational units to get that massively parallel.

I don't get how DNA can compute anything. DNA is essentially a coding 
for proteins. What would your end result of a computation be? A glob of 
proteins that mean some sort of result?

> "In the current technology of logic gates, binary codes from the silicon
> transistors are converted into instructions that can be carried out by
> the computer."
>
> This is a highly questionable and very muddled statement. It's hard to
> read something like this and continue to believe that the writer has any
> clue what they're talking about.

The statement doesn't seem to make a lot of sense. The instructions, 
encoded in binary do tell the computer what to do, yes? But it's 
essentially flipping a bank of switches to route the data from the input 
of an ALU to one unit or another....

> "though it may be very fast in providing possible answers, narrowing
> these answers down still takes days."
>
> This rather suggests that the operation of a DNA computer is
> non-deterministic (and hence, applicable to a much smaller set of
> problems than a Turing-complete machine).

Huh? Computers can very quickly give exact answers to a wide class of 
problems. Modeling complex systems, however, is a different story. I 
don't see DNA helping with that. Often performing calculations much 
quicker than our organic brains can. That cluster of neurons may be 
massively parallel, but it's still not very fast at doing things like, 
say, computing a Fourier transform. In fact, before the silicon-based 
machines of today, the Fourier transform was regarded as largely useless 
because it was so difficult to compute. And still, until FFT was 
discovered it was regarded as simply a novelty.

> I won't hold my breath for this happening any time soon. :-P

If you do that, you may cause a catastrophic failure of your DNA-based 
system.

I haven't read the article, just adding my commentary to your 
selections, but based on what I've seen this sounds like massive 
speculation and nothing more. What is needed, really, is more 
improvements on existing algorithms to allow them to operate in parallel 
on simpler computational units. Once a high degree of parallelism is 
met, then we'll see some huge jumps in how fast these silicon machines 
can really work.

-- 
~Mike

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On 12/2/2010 7:34 AM, Mike Raiford wrote:

> I haven't read the article, just adding my commentary to your

as a further aside, tech-faq.com is considered naughty by our stupid 
censoring filter. Dumb piece of equipment. I hate that thing

-- 
~Mike

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>> "[T]here is a limitation to how small, fast and compact silicon computer
>> chips can be. DNA computers show promise because they do not have the
>> limitations of silicon-based chips."
>>
>> O RLY?
>
> Of course there's a limit. And there's likely a limit on how small/fast
> a DNA-based machine could be as well.

In reality, the nature of matter (and quite possibly time and space 
itself) is quantum. Therefore *every* technology has limits.

Now a DNA computer could potentially be very much smaller than current 
silicon ones. This is not the same statement as "DNA computers do not 
have the limitations of silicon-based chips".

>> "Secondly, the DNA chip manufacture does not produce toxic by-products."
>>
>> Riiight. So because the end product is DNA, a molecule that already
>> exists in nature, therefore you can produce it with no toxic by-products?
>>
>> And the DNA itself wouldn't be toxic, no?
>
> Not unless it codes for something that could cause illness or kill you,
> but who's paying attention anyway.

A virus is nothing more than a stand of DNA or RNA (in some cases coated 
with proteins, but not always). Now, it's highly unlikely that the DNA 
sequence used by a computer would /just happen/ to code for viral 
activity within human cells. It's /completely plausible/ though that if 
some of that stuff gets inside you, it will make the cells it enters 
synthesize endless amounts of some useless protein until they 
prematurely die as a result.

A chemical that kills living cells it touches? Yeah, I'd call that 
pretty toxic. (Still, you presumably don't need to make that much of it...)

> Organic compounds are some of the
> most toxic to us, because they are the most likely to interact. To be
> sure, there are a lot of extremely toxic inorganics as well.

To be sure, there are lots of organic compounds which are "designed" to 
be toxic to us. But even ones that aren't sometimes end up 
"accidentally" being toxic. (E.g., the black widow's venom isn't 
supposed to kill mammals, it's meant to kill insects. And, indeed, it's 
completely harmless to cats and dogs - yet just happens to be lethal to 
humans...)

>> "Last but not the least, DNA computers will be much smaller than
>> silicon-based computers as one pound of DNA chips can hold all the
>> information stored in all the computers in the world."
>
> Storage is not the same as computation.

Agreed.

> No mention as to how fragile that pound of DNA is.

Also agreed, since DNA is very, very definitely biodegradable. (In fact, 
human skin is coated in enzymes designed to snip up RNA, as a protection 
against viruses composed of RNA...)

>> Current computers are much, much larger than strictly necessary mainly
>> due to issues of heat dissipation. You can already make RAM chips that
>> hold absurd quantities of information; it's just that they tend to melt
>> when you switch them on.
>
> I believe the bigger limitation on the amount of information that RAM
> can ultimately hold is more about the lower limit on the size of a
> transistor, rather than heat.

I still suspect that if you weren't worried about heat, you could 
"stack" layers of silicon on top of each other, producing 3D circuitry 
which takes up a fraction of the space.

>> "The capacity to perform parallel calculations, much more trillions of
>> parallel calculations, is something silicon-based computers are not able
>> to do."
>>
>> I beg to differ.
>
> You'd need the pipelines to do it in the chip die. You'd need to build
> very small computational units to get that massively parallel.

True. But, as I understand it, transistors are /already/ "very small". 
The reason that people like Intel and AMD build chips containing several 
thousand million transistors which only comprise two or three "cores" is 
because nobody has really figured out how to make use of lots of cores. 
(Let's face it, Cray have been making vector machines for decades...)

> I don't get how DNA can compute anything. DNA is essentially a coding
> for proteins. What would your end result of a computation be? A glob of
> proteins that mean some sort of result?

If you read some website which actually *explains*, in technical detail, 
what a DNA computer is, you will discover that the DNA is just the 
storage medium. Essentially the DNA is your RAM, and enzymes are your 
computational hardware. So some DNA goes in with the input data encoded 
on it, and new DNA comes out with the result coded on it. (Wikipedia 
indicates that the enzymes function something like an actual Turing 
machine, with the DNA as the "tape".)

>> "In the current technology of logic gates, binary codes from the silicon
>> transistors are converted into instructions that can be carried out by
>> the computer."
>>
>> This is a highly questionable and very muddled statement.
>
> The statement doesn't seem to make a lot of sense.

Indeed.

>> "though it may be very fast in providing possible answers, narrowing
>> these answers down still takes days."
>>
>> This rather suggests that the operation of a DNA computer is
>> non-deterministic (and hence, applicable to a much smaller set of
>> problems than a Turing-complete machine).
>
> Huh? Computers can very quickly give exact answers to a wide class of
> problems.

I'm saying that this description implies that DNA computers aren't 
Turing-complete.

According to Wikipedia, actually they can be. It's just that each 
"computer" is a single molecule, so typically you run millions of them 
at once, in parallel. The slow part, presumably, is synthesizing the 
reactants, and then analysing the reaction products to get your answer 
back afterwards.

> What is needed, really, is more
> improvements on existing algorithms to allow them to operate in parallel
> on simpler computational units. Once a high degree of parallelism is
> met, then we'll see some huge jumps in how fast these silicon machines
> can really work.

I agree.

Post a reply to this message

"D103" <nomail@nomail> wrote:

>
> This may be of little consolation now, but maybe in 20 years or so...
>
> http://www.tech-faq.com/dna-computer.html
>
> Imagine a computer with a CPU about the size of a coin, capable of 66 Gigaflops
> and having 700 Terabytes internal memory AND a power consumption of ~
> 0.0000000001 watts (minus the screen and interface devices, of course).
>
> That should speed up rendering!
>
> D103

After posting this I realized that most of my info (apart from the link) was 7
years old, and while perhaps not out of date, it was only hypothesis.

Also, I have yet to finish high-school so my knowledge of computers and how they
work is somewhat limited.

D103

Post a reply to this message

D103 wrote:
> Also, I have yet to finish high-school so my knowledge of computers and how they
> work is somewhat limited.

Back in high school I found in the library a wonderful text. It was a huge 
hardback book about 3 or 4 cm thick.  It started with vacuum tubes, tube 
diodes and triodes, then went into semiconductor tech, including what a 
semiconductor *is*, how the doping affects its behavior, how a diode works, 
an LED, a transistor, a thermistor, etc. Then into chips, how to make 
transistors on a chip, how the doping is done, then gates from that.

I wish so much I remembered what that book is called. It taught me 90% of 
what I know about hardware.

After that, the SAM'S book on the 8080 pretty much taught me the basics of 
computer architecture, instruction sets, etc.

It's a shame in some ways that everything has gotten so complicated that you 
wind up with either a quantum physics textbook or a "Teach Yourself 
Microsoft Word in 24 hours" sort of book, and nothing really in between that 
I know of.

-- 
Darren New, San Diego CA, USA (PST)
   Serving Suggestion:
     "Don't serve this any more. It's awful."

Post a reply to this message

Darren New <dne### [at] sanrrcom> wrote:
> Back in high school I found in the library a wonderful text. It was a huge 
> hardback book about 3 or 4 cm thick.  It started with vacuum tubes, tube 
> diodes and triodes, then went into semiconductor tech, including what a 
> semiconductor *is*, how the doping affects its behavior, how a diode works, 
> an LED, a transistor, a thermistor, etc. Then into chips, how to make 
> transistors on a chip, how the doping is done, then gates from that.

> I wish so much I remembered what that book is called. It taught me 90% of 
> what I know about hardware.

> After that, the SAM'S book on the 8080 pretty much taught me the basics of 
> computer architecture, instruction sets, etc.

  Do you really need to know how a vacuum tube works in order to know how
a modern computer works?

  I mean, it may be interesting knowledge in a historical sense, but is
there any practical application to this knowledge? (In computing science,
that is. In guitar amps vacuum tubes are quite popular, although for a
slightly different reason.)

> It's a shame in some ways that everything has gotten so complicated that you 
> wind up with either a quantum physics textbook or a "Teach Yourself 
> Microsoft Word in 24 hours" sort of book, and nothing really in between that 
> I know of.

  I'm sure there are in-between books as well.

-- 
                                                          - Warp

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Warp wrote:
>   Do you really need to know how a vacuum tube works in order to know how
> a modern computer works?

Well, at the time, TVs still ran on vacuum tubes. I guess with the death of 
CRTs, only people running medical equipment care about how they work now. 
But that's why it was a 1200-page tome. It went all the way from vacuum 
tubes to TTL and CMOS circuits. You could probably drop the first half of 
the book and it would still work.

You didn't have to know it, but it might be a little easier to understand 
semiconductor transistors if you can make an analogy to vacuum tubes, perhaps.

>   I'm sure there are in-between books as well.

College text books, I guess, sure. They're just not common. Do a search on 
"computer hardware textbook" and you get "how to use Windows 7" and 
"Understaning Access" as the first hits. :-)

http://www.amazon.com/Principles-Computer-Hardware-Alan-Clements/dp/0199273138/ref=sr_1_fkmr0_1

I mean, look at the TOC of this, the first book on amazon for the search of 
"computer hardware textbook". Nothing in the TOC obviously about the 
semiconductor level. Gates, yes, bits, yes. 100 pages talking about gates, 
zero talking about semiconductors.

The "computer architecture" goes from page 205 to 209, followed by 50 pages 
about the instruction set. Nothing actually gets all the way down to the 
*hardware*. From what I can tell of the TOC, nothing there tells you how 
many pins a transistor has, for example.  As I go on, I see chapter 7 looks 
like it might address some of the same stuff the SAM's book I referred to 
addressed. But still no hardware. Actually, other than that, it looks like a 
really good textbook. :-)

That said, *this* one sounds pretty good, but without looking into it it's 
hard to say:

http://www.amazon.com/Semiconductor-Devices-How-They-Work/dp/041258770X/ref=sr_1_1

I guess everything just got complexer, to the point where it doesn't make 
sense to put it all in one book.

-- 
Darren New, San Diego CA, USA (PST)
   Serving Suggestion:
     "Don't serve this any more. It's awful."

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>
http://www.amazon.com/Principles-Computer-Hardware-Alan-Clements/dp/0199273138/ref=sr_1_fkmr0_1
>
> I mean, look at the TOC of this, the first book on amazon for the search 
> of "computer hardware textbook". Nothing in the TOC obviously about the 
> semiconductor level. Gates, yes, bits, yes. 100 pages talking about gates, 
> zero talking about semiconductors.

Maybe because this area is more covered by electronics textbooks?  In my 
courses everything from electrons up to simple logic circuits like 
bistables, adders, counters etc were handled in the "electronics" courses. 
The "computing" courses started off assuming you knew what logic gates did - 
even if you couldn't remember exactly how they did it or how to wire one 
up...

Post a reply to this message

scott wrote:
> Maybe because this area is more covered by electronics textbooks? 

It's entirely possible I'm looking at the wrwong search terms. :-)

-- 
Darren New, San Diego CA, USA (PST)
   Serving Suggestion:
     "Don't serve this any more. It's awful."

Post a reply to this message