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DNA Strands as Semiconductors
Dyslexic writes "ABCNews is reporting that strands of DNA can act like semiconductors. After seeing "The Matrix" this makes me only fear the future." The research is coming from two researchers in Basel, Switzerland. Essentially, this research is saying that while DNA makes a good semiconductor, it does not conduct as well as, say, copper. It's real usefulness comes from the fact that "...he knows of no metallic wires that can be
made as small or as regular as DNA strands. A strand is 2
billionths of a meter thick, or one-forty-four-thousandths
of the diameter of a medium-size human hair ". Uber-thin. I like it.
My brain-pc at least doesn't crash when it
encounters a situation it can't handle. In the
worst case it produces some stress but afterwards
the error always gets fixed in only a matter of
time without the need of interference from
GOD/Root
The problem I see would be that a lot of these really cool sorts of technologies are developed by private industry which means that private industry also gets first crack at them. It's also private industry who wants to random shotgun sequence the entire human genome and patent whatever they want (e.g. Craig Venter's Celera, who shows the most chance to do so).
I seriously wonder how the publicly funded labs can get this kind of stuff, since they're working entirely on government grants. Anyone care to build a GNU gene sequencer?
The double-stranded nature of DNA would probably prevent this as you would get interference not only from the hydrogen bonding but from the complementarity of the bases themselves.
However... If you could denature a fragment (that did not contain any inverted repeats) and end up with a single stranded section, then you could possible use scanning tunneling electron microscope to actually distinguish the different bases. Such microscopes have already visualized the DNA helix itself but without the resolution to determine different bases.
Perhaps some variant techniques of PCR fragment analysis combined with this sort of technology would work out better. (Way off in the future of course.)
We all have Watchdog timers in our brain that reboot when we lockup. ;-)
Actually I think that would work. At the very least the purine pyrimidine bases will have different signatures. I would suspect with a fine enough resolution on detection the differences within the classes of base should be detectible as well.
;-) ) would the resonance be affected by a base that is bonded to the one you're searching for? I mean the would the complement base cause any sort of interference?
I was wondering (caveat my background is genetics and biology, not electronics
Other potential problems lie in the methylation of bases and those bases that have transient forms.
I was just supposing that single stranded DNA (which is all you really need anyway) would be easier to work with.
Any info would be great.
Interesting question... If we're building DNA wire, does the actual sequence even matter?
Would certain bases, or sequences of bases provide more efficiency?
And as was pointed out above... DNA is not stable unless it is compacted and stored. Which would make it useless for these purposes. Not to mention the size of a strand for any length. The E.coli genome measures about a milimeter.
As far as using microscopy to sequence. I'm willing to be we get there. After all, a great deal of research goes into visualizing various molecules (even nucleic acids) for observational determination. The tech may not quite be there but I'm guessing it will come.
(If you synthesize it, they will come)
Didn't take long for the Starr Warriors to discover a way to use these DNA wires to track people's sex lives:
Sexprinting: Using Electrical Gene Resonance to Track Sexual Activity
That's what it is. Here's Webster's definition:
Marko
You will address "that guy" as Mr. William Gibson!
Noteworthy in regards to DNA computing, with four base pairs, the opportunity is there for multiple calculations at one time. A natural branch prediction so to speak. Also, the source is the executable ... now that's open-source !
Posted by JoeyRamone:
:), I'm happy. This is exiting, only hope Intel doesn't run of with it or, heaven forbid, kills the technology, just like the car-industry is doing with hydro-propulsed (is that right?) cars.
Yes boys and girls the star-trek future comes closer and closer
Posted by F.A.N.G.:
I see nothing describing DNA chains as semiconductors, only as poor conductors.
For the love of mike, please tell me you know the difference.
Posted by jclanfear:
It is crap. I can't remember what it actually referred to, but it wasn't general brain function.
(It's also several decades old, so I wouldn't bet on it being correct for anything.)
(Neurons that aren't utilized tend to die as part of the brain's optimizations. AFAIK I'm not missing 90% of my brain (of course I don't check it all that often).)
I have looked very deeply into the field of "molecular wires" and found several flaws. The published journal articals on this that I know of all use a high level of congugated pi bond interaction as the mechinism for the transport of electrons. Although this produces a remarkable increase in electrical conductivity compared to a "normal" molecule, the ability to conduct electrical current still drops off exponentially as a function of distance. Or, in other words, unless the whole circut is only a few ~30 atoms long, it would require enough juice to totally distroy it to get any electrical flow across it!
Now, there is the possability of "bundleing" these systems, maybe using something such as carbon nanotubes (maybe several of them built one on top of each other) to overcome this, but the fabrication process for doing something like this is more science fiction right now than science. Maybe that's what they are trying with the DNA stuff, but from what I know, it's not possable.
But, AGAIN, I point to a possability that is realistic. If you look at some of the work done in IBM labs, specifically The Almaden Lab and the one in Zurich (don't have the URL on hand, but there is one), you can see something that would be superior on TWO counts. Actually using indivual atoms insted of full molecules. Positioning highly conductive METAL atoms (not carbon molecules) on a semiconductor surface (carbon), it might be possable to create a circut that would stand a much higher chance of working, AND be much smaller. Right now, I believe that IBM is using this technology to try to work towards data storage at an atomic level, which, in theory, could fit the Library of Congress on a postage stamp. ;-) But even this work is limited, AFAIK, to very low temperature (like 10K?) and is not truely practical.
But, this shows more hope, as I have seen a few research groups position molecules (buckyball) with STM on a surface at almost room temprature. To me, at least, this is much more realistic, and much much more exciting research.
The potential to rapidly get the sequence of a DNA strand is a very hot field, and very heavily government funded. Based primarily in the Human Genome (spelling?) Project, I believe. So, I don't doubt there is a lot of work on rapidly "reading" DNA.
But, this begs the question, how are you going to accurately build long strands of DNA, sequenced exactly as you would like them to be, in order to store data on them? And, why DNA? Potentially, you could use something easier to detect (cool tagged or marked base pairs if DNA, or something totally diffrent), and easier to build?
Not a limitation, but a new field of investigation. Classically, electronics is something that has been looked at very one dimentionally. Consider the switch set to off, and not only are you stoping flow in a liniar direction and influancing one data point, your have a flow of electrons tunneling into bulk, and influancing the behaviour of the whole circut.
Yes, it's not a classical model. But, I don't believe it's an unusable consept. Gates and switches have a much wider base from which to be developed. And, the actual movement of an atom from the tip of an STM is one of the first examples of something with known physical mass actually tunneling! Wahoo... think, this is not as we know it, this is new, and of course it's not classical, by any sence, but, that also means it's not subject to classical limitations.
So I wouldn't worry.
--
--
Umm .. you already have a computer in your brain.
otherwise known as "bucky tubes" make better wires, etc...
I'm working on rod logic computers right now, actually, in between all my other classes. (yay 20-unit load!) designing a computer from the groun up has never been so much fun!
check out ralph merkle's stuff too... he's got GREAT stuff, and is absolutely dominating the field. bistable logic, anyone?
www.merkle.com
Lea
You could fairly easily identify a *very* short sequence, say 4-10 base pairs by NMR spectroscopy. Longer sequences require far too much effort, and would likely have to rely on multi-dimensional NMR. The biochemical method of sequencing (using gel assays, etc.) is far superior and faster, which is why scientists use it. :)
Microscopy for sequencing is out of the question I think. Way too involved, expensive, and time consuming. The only way I can see that a DNA wire could be useful is if you could grow them in situ on some kind of support. DNA is a fairly fragile biomolecule and you can't deposit it in any way even resembling solid state techniques.
The problem with atomic scale systems is that you will run into quantum mechanical effects. While this may be desirable in quantum computing systems, it is NOT desirable in the classical regime.
now someday I can have a computer in my brain, can't wait...
This should be called "microsoft" like the guy who wrote Neuromancer called it.
"I control the Mouse, the Mouse controls me."
Wow...think of the Beowulf Cluster I could make with my body...
(sorry)
pooptruck
Electronic and photonic systems will always be faster than mechanical systems, but initially, mechanical systems may be easier to get working.
WWJD for a Klondike Bar?
I wonder if the strands could be "read" by electrical means.?. After all, DNA is ultimately a biologically evolved four-state memory device.
One method: If each base has a unique resonant frequency (or set of frequencies, like little tiny antennas - akin to spectroscopy), and you "modulate" a strand at each resonance set, would you be able to extract an RF profile or "image" of the strand's sequence? Scanning Capacitance Microscopes might do the trick.
Just a thought...
--The more you know, the less you know.
The complementary nature of the bases should actually work in your favour. My proposal/idea does depend on uniquely identifiable RF signatures for each base, relative to the other three. If this is the case, you apply each signature in sequence and watch/scan for the resonance. The existance of one pair over the other would strengthen that pair of RF signatures; orientation would show up via the scanning action, maybe some phase variation/difference.
:-)
I would expect the hydrogen bonding interference to be relatively easy to filter out; treat it as (average) background noise and filter with a little signal processing. You would have four sets of data (one per base) to work with, making it that much easier. Apply some sort of "helix transform" to account for differences in base-pair oriention from one to the next...
I guess we'll just have to wait and see!
(caveat: my background is in electrical engineering, semiconductors and mathematics, not biology and chemistry, so apply holes in my logic as you see fit.)
--The more you know, the less you know.
Would resonance be affected? Most likely. Like an antenna, I would expect a base-pair (v.s. individual bases) to be "de-tuned" by their close/attached proximity. A difference in behaviour should manifest itself as some sort of "polar" RF signature for the pair.
:-) If the two types of base-pairs have "sufficiently different" signatures, the task is easier because it's like being able to automatically distinguish between a N-S/S-N magnet and a W-E/E-W magnet by their shape.
Analogy time:
Think of it as a magnet with four possible orientations. You're looking at the difference between N-S, W-E, E-W and S-N orientations with an unmarked (no N/S/E/W markings) compass. You can determine the orientation of one magnet relative to another by watching and recording the relative changes on the compass when you bring it near each. Compare that to a set of known samples, and the actual orientations fall out of the measurements.
eg. You measure: abd-cdd-aba. You then bring calibrate your compass with some known samples and discover that a=NS, b=EW, c=SN, d=WE. From your measurements, you get: (NS)(EW)(WE)-(SN)(WE)(WE)-(NS)(EW)(NS)
Grossly over-simplified, but hopefully a little more clear.
eg. You already know that (a,c) forms a pair of measurements and (b,d) forms another pair. Calibrate to differentiate between a and c, and between b and d.
Plenty of research potential, eh?
--The more you know, the less you know.
We only use 10% our brain for thinking process, or conscience thinking. Everything else is use for memory or involunetary process. Am I right on this?
I ate my tag line.
-=Ellis (D)25=-
Not to mention what happens when you put too much current through a strand of dna. Personally, I wouldn't want to fry my dna. Next thing that will happen is that I'll start to grow a microsoft symbol on my forehead.
-?-
Never mind all the other goodies we could get with nano-machines! ;]
Herbert von Kammerstein
Herbert von Kammerstein
Nosferatu Hacker extraordinaire! Well, I wish, anyways...
If DNA strands work for semi-conductors make me into a cyborg!!!
either we are networking or we areNT networking
I think there is an inherent fear that comes with mixing technology and our body. Even though the matrix was not exactly related to using DNA as a semi-conductor, it was a movie that showed us a possiable end scenario of man vs. machine. I believe this is what the author of the post meant when he said he fears the future of this.
I personally would be scared of integrated technology with my brain. It gives viruses a whole new meaning. Although the thought of having computing power inside your mind is fascinating, I still think it is way far off from what you and I would consider cool.
~pearcec
Mechanical computers are one of the worst nanotech ideas. They are a "proof of concept" thing to demonstrate that nano-scale computers are possible, because in absence of experiment it is easier to convince people that bumpy nanosticks can compute than that the quantum effects can be dealt with. Drexler needed something possible to point at, I doubt even he seriously thinks mechanical computers are the way of the future.
They are definitely way slower than an equivalent-scaled electronic or light-based design. They are indeed theoretically a bit faster (about 1 GHz and 1000 MIPS) than your current average production chip (when "Engines of Creation" came out, the gap was much wider), but it is a theoretical high estimate which conventional electronic designs have already overtaken.
Realistically, do you think it's more efficient to move around hundreds of whole atoms or a few electrons or photons? (the concept of single-particle signalling is a very exciting one to me)
Incidentally, I have a copy of Nanosystems on my lap as I type this. I've read it, but I don't have the expertise to check his work. It is very thorough and quite interesting if you like theoretical engineering.
Gotta agree with you on the internal computer bit; I would be hestitant about it... early adopter does not have my name on it. Instead, why not try to find the means to unlock and use that substantial amount that is already there. I mean, if we can do the activities and such that all of us do, and only use 10-15% of the brain, imagine the computational capacity if just 50% was used. Or even higher... Then, we might scoff at internal computers, knowing that it was a foolish I idea for the lazy, but then, I ramble...
I think it would be neat if we could develop a game/simulator that allows you interact with basic elements found in nature such as rocks, dirt, trees, etc on a physical level. To build a house you would first have to put together the tools you need. Everything would rely on what you wanted to do and what you could figure out how to do with the basic elements. It would be the ultimate civilization game.
It would be very impratical and hard to program because you need to model the world to a great level of detail. It also wouldn't sell to well to today's action/WWF obsessed gamers, but if done right it would be totally immersive, and I would have fun playing it.
That may be all well and true.
Although we do have computers in our brains, in the form of our brains, the problem with human thought is that it's not quite 'linear' or 'computatational'.
Human beings lend themselves well to solving 'fuzzy' problems, but stuff like 2+2 and matrix muls eats time. Most of us have to count it out in our heads in some way.
Now if we could reverse engineer our brains and engineer in our own ALUs to our own cortexes, that would be very handy. I could delegate computational processing to that computer-like part of my brain, and leave the rest of my brain and consciousness free to deal with the more pressing fuzzy problems human beings are so good at - like abstraction, problem solving, decision making and model building.
What I'm saying is that if we harness this innovation, and use it for the good of humanity, all well and good. It could equally be used to control people. Usual hacker disclaimers/restrictions apply, but from a hacker p.o.v, I like the idea of having more control over my own brain. If I could engineer new computational functionality into it, leaving the rest of my brain free to do the important things, that would be great.
See the difference between 'arithmetic' and 'mathematics'. One isn't really a subset of the other. Arithmetic is what computers do. Mathematics explains why and how they do it.
Bruce M. Simpson Unix/Network Bod & Win32 Developer
I know that thermal runaway at the molecular level could ruin your day (Can you say spontaneous combustion). Better to make Organic machines than to incorporate an inherently unstable electromagnetic field into your own body.
Live your life as you will wish you had on your deathbed.
First of all, children, adaptation is built into the body without actually being built into the body as a module as opposed to the way our brain "suppossedly has it's different centers.
:)
We do not need this technology. We can do it ourselves and maintain flexibility.
Every cell is (in terms of the model of the thing not the thing itself) like a plastic bag. Ever have someone tighten a knot in the opening of the bag so tight only GOD/root could open it and you didn't have a knife nor a pair of scissors? If you push in slightly on the plastic it returns to its original form. If you push harder eventually it begins to stretch. If you push in far enough it breaks.
Here comes the magic (no it's not designed into the body):
Most pragmatists, efficiency experts and altogether too-lazy-to-rearrange-the-pieces-before making-a-judgment scientists would say the above covers everything. Reductionism Knows All...
That's like saying all you need to know about driving is the brake pedal and the gas pedal. That's like saying that you don't need to develop a sense not just a reflex of how you control your speed around a curve (this is where fuzziness is a gold mine!). Going too slow around a curve can be just as deadly as going too fast.
Reductionism Knows Shit. If you use two fingers the stretched section shapes itself like two fingers. If you apply a flame to the plastic it melts. Now before flaming me that all this is obvious please tell me where is it programmed into the plastic that two fingers cause the plastic to stretch around two fingers and that plastic melts.
It isn't programmed anywhere. Programming means not only specifying a feature of a thing but designing that feature out of basic actions all microprocessors do, namely move memory values around and around. With all due respect to Lara Croft, what we call a picture is just a bunch of dots.
With physical objects such as a rock, we have no way of programming the things. The lowest level of physics is in theory. We can spend a ludicrous amount of resources to isolate one subparticle from the rest of the universe, but we cannot design subparticles with our own features. Features such as adaptation cannot be assigned to any one thing.
There's two environments we're talking about here.
One is an environment where feedback loops do not exist. This is the case of objects being out of the range of natural forces (ie. zero gravity).
Here all you have is cause and efect.
When you have intelligence, there is a feedback loop. Cause and effect are no longer separated and neither are the objects they apply to. There is only adaptation. An example of this is military mobilization or as I like to call it the mushroom that comes before the mushroom cloud. (To think humanity is doomed to screw itself over and over again unless we keep some of our runaway adaptatiopns in check. Not turn them off but in check.)
The fact of the matter is all our senses are learned and depend on adaptation. Everything we see, taste, touch, smell, feel, and hear is a reconstruction of the world outside. I believe through the right training neurons can be organized in handy sets of logic gates that can be organized into ALU's. And don't get me wrong, despite my reservations, H.R. Geiger rules. Let's face it. Interfacing a spaceship to the human brain raises space travel to the glory of snowboarding, skying, roller-blading, hang-gliding or what have you.
But integrating machines inside your brain permanently? Yech! No thank you. Besides what mostly likely would happen if you even tried to train the brain, it would happily transfer all your efforts to create rigid structures into fuzzy structures that you wouldn't be able to differentiate from the rigid structures you intended to create, except under special conditions. This again is not a magic feature cleverly designed into the brain but a feature gained from experience that fits the nature of the universe and the fact that the universe invariably presents fuzzy problems to be solved.
And don't even think of suggesting early training
in linear thinking, you would take away the one thing that allows an organism to survive.
And yes I do believe cellular phones are part of a corporate government plot
The ship sank. Get over it. (This sig was cut out from another's shirt and painstakingly hand-posted)
What we call thinking is actually us listening in on the actions of our brain, modeling it, and controlling it. Learning theory says that in order to pick up new information, you must not attack your brain with data, but let it settle and "cook" a little. The language center of our brain by nature not by design or miracle also has the capacity to function as a internal laboratory.
Just as dreams contain sounds, images, smells, we can recreate those things inside our heads voluntarily. (Sure, we can't always get certain tunes Out of our heads.) Or we could set our brain to work on a problem without necessarily watching every neuron fire. We call that kind of obsession paranoia, or stage fright.
So I don't think consciousness is some complicated that exists because of some esoteric property of the universe. I pretty much think it's as simple as plumbing.
The ship sank. Get over it. (This sig was cut out from another's shirt and painstakingly hand-posted)
DNA denatures above 40 C. Moreover,
300 MHz will frie the molecule
beyond recognition...
A few people are making devices to attempt to do faster, mass sequencing. Lydia Sohn's group at Princeton has assembled two-probe platinum devices which, at the present, only detect a change in capacitance when the DNA strand spans the gap b/w probes. Obviously this is pretty far from being able to sequence anything. The thing people forget about though is that human DNA is pretty huge (>~30 microns in length) and has been scanned succesfully by atomic force microscopy (AFM) in solution at room temperature (e.g. work by Lindsay's group at ASU >5 yrs ago). The big stumbling block in sequencing using electronic transport is an extremely sketchy knowledge of the electronic states one should expect as well as the inherent thermal (Johnson/Nyquist)noise at the temperature range that would not destroy the molecule.