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Biotech Science

Touching Molecules With Your Bare Hands 125

Posted by Zonk from the jurassic-park dept.
FiReaNGeL writes "Researchers at the Scripps Institute just devised an incredibly interactive way to manipulate complex molecules, such as proteins and DNA, with your bare hands. Combining 3D printed hand-held objects with sophisticated computer displays & cameras, this technology allow more natural and intuitive interactions with biological molecules - you can manipulate them with your hands and visualize the results on the computer in real time. Don't miss the incredibly cool movies and images illustrating the 3D printing process and augmented reality interaction with diverse proteins, viral self-assembly simulation and HIV-1 protease folding. A detailed press release is available."
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Touching Molecules With Your Bare Hands More

Touching Molecules With Your Bare Hands

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  • A classic in the making. (Score:3, Funny)

    by Anonymous Coward on Saturday April 09, 2005 @05:32PM (#12189384)
    It's gonna be a hit!
    Chorus


    I want you
    I don't want anybody else
    And when I think about you
    I touch molecules
    Ooh, oooh, oooooh, aaaaaah


  • Eh? This is something new? (Score:4, Funny)

    by rice_burners_suck ( 243660 ) on Saturday April 09, 2005 @05:34PM (#12189400)
    Touching Molecules With Your Bare Hands

    Newsflash!! Anytime you touch anything, you're touching molecules with your bare hands! In fact, your hands are made of molecules, too!

    • Newsflash!! Anytime you touch anything, you're touching molecules with your bare hands! In fact, your hands are made of molecules, too!

      Informative?!!!? I think not. Mod down and here is why: What the article has to do with is how to interact with molecules to see how they interact at the very hard to appreciate scales that one works with. Van der walls, intramolecular and intermolecular forces are critically important for many molecular reactions such as covalent bonding and enzymatic activity. Under

      • Comment removed (Score:5, Insightful)

        by account_deleted ( 4530225 ) on Saturday April 09, 2005 @05:58PM (#12189515)
        Comment removed based on user account deletion

        • Re:Indeed (Score:5, Funny)

          by tukkayoot ( 528280 ) on Saturday April 09, 2005 @06:22PM (#12189615) Homepage
          Seeing these posts makes me wonder what kind of molecules are neccessary to construct a sense of humor.

          • Re:Indeed (Score:3, Insightful)

            by DaoudaW ( 533025 )
            Seeing these posts makes me wonder what kind of molecules are neccessary to construct a sense of humor.

            Amen!
            Mostly the OP was simply making fun of the headline. My first thought when I saw it before I RTFA was "I'm doing that right now!" Then I took my hand off the mouse and thought for a moment that I wasn't Touching Molecules With My Bare Hands(tm), but then I remembered the O2, CO2, et al that I was still touching. I just started laughing at the really bad choice of headline made by Zonk [slashdot.org], but was r
          • HUMoR obviously has to be a compound of Hydrogen, Uranium, Molybdenum and a yet unknown element which has the R as it's symbol. It might be easier to use HUMoRh, althoughRhodium isn't a good substitute for "R".
            Replacing our mysterious "R" element with Rhodium might result in a damaged sense of HUMoR (a "sense of HUMoRh"), the most common symptom of which is the tendency to moderate HUMoRous posts down using "Overrated".

            Perhaps including more Rhodium in the jokes might make them appeal to people with a se
      • (Apart from what the poster above me says about touching being a macro-level thing, ) in my opinion, your parent is right: Anytime you touch anything, you're touching molecules with your bare hands! The article should have been titled "Interacting with molecules with your bare hands", as "touching" molecules just makes no sense.
    • Comment removed based on user account deletion
    • Unless you're touching something made of pure elements that is..
      • No, even if you are. All matter is made of molecules, even that made of "pure elements". A molecule does not have to have atoms of more than one kind to be called a molecule. Molecules of hydrogen, for instance, are made of two hydrogen atoms. A molecule doesn't even have to have more than one atom -- it's a mono-atomic molecule, if it has only one atom.
        • Answers.com gives

          molecule (ml'-kyl') n. The smallest particle of a substance that retains the chemical and physical properties of the substance and is composed of two or more atoms; a group of like or different atoms held together by chemical forces. A small particle; a tiny bit.

    • good book, but not as good as Snow Crash
    • "Newsflash!! Anytime you touch anything, you're touching molecules with your bare hands!"

      Err I thought I heard somewhere that molecules don't ever actually touch each other. There's a lot of space between them.

      Oh.. wait.. that might have been Honey I Shrunk the Kids.
    • Makes me think of the eternal question raised by They Might Be Giants:

      Particle man, particle man
      Doing the things a particle can
      What's he like? It's not important
      Particle man

      Is he a dot, or is he a speck?
      When he's underwater does he get wet?
      Or does the water get him instead?
      Nobody knows, Particle man

  • Saw this already (Score:4, Funny)

    by Mr. Arbusto ( 300950 ) <.theprimechuck. .at. .gmail.com.> on Saturday April 09, 2005 @05:35PM (#12189409) Journal
    In the first Jurrassic Park between the advertisments for Thinking Machines(TM) Supercomputers and Silicon Graphics(TM).

  • In the post Michael Jackson world... (Score:2, Funny)

    by Anonymous Coward
    ...Molecules touch you!

  • Opposite (Score:3, Insightful)

    by LiquidCoooled ( 634315 ) on Saturday April 09, 2005 @05:41PM (#12189440) Homepage Journal
    I assume you could expand on the principal and have an entire galaxy at your fingertips.

    Sure would be cool to have hanging around.

    • Re:Opposite (Score:3, Insightful)

      by jessecurry ( 820286 )
      this is a very cool technology that seems to have applications for anything that is either too large or too small to directly interact with. One of the limitations that many people have when learning is that they cannot visualize the concepts, this sort of evens the playing field for those people that have trouble.

    • Only that you would have to wait 100000 years for feedback from the edge of the Galaxy, as nothing can go faster than light!

  • Sugar molecule - $5.99 $4.99 when you buy with paypal!

  • HIV (Score:1, Funny)

    by ximenes ( 10 )
    I tried this out, specifically touching the HIV molecules. Now I'm infected. This technology really works!

    • Re:HIV (Score:3, Insightful)

      by wideBlueSkies ( 618979 ) *
      The other night I kissed the cheek molecules of one of my dear friends, and I saw the molecules of her lips form into a smile. :)

      Technology is great.... firendship is better.

      wbs.

      • Re:HIV (Score:1)

        by ximenes ( 10 )
        Thanks for reminding me that the furthest I can go now is kissing. The Scripps Institute has ruined my sex life.

  • Cool! (Score:5, Interesting)

    by kyle90 ( 827345 ) <kyle90@gmail.com> on Saturday April 09, 2005 @05:43PM (#12189454) Homepage Journal
    Tactile interaction with molecules is the first step towards understanding them well enough to create working nanotech. Right now all we have are descriptions and equations, and it's a lot harder to work from a statement like "the force between these two atoms is such-and-such Newtons" than it is to actually feel the force (appropriately scaled up, of course)
    • United Devices has received over a half a million years of cpu time devoted to studying the interaction of ligands with protein stuctures associated with cancer(autodock). I do not think they can claim saving even one person's life. The program has been running now for close to 4 and a half years without too much positive results. At least none that they are willing to publicize. I keep hoping that programs like this will help but my hopes are fading.

    • Oh-o (Score:1)

      by Hsien ( 864759 )
      Just dont mistake them for jaffas and break them between your teeth...listerine would have nothing on the freshing action of an atomic exlosion in your oral cavity.

  • QUICK (Score:5, Funny)

    by Xeo 024 ( 755161 ) on Saturday April 09, 2005 @05:44PM (#12189462)
    everyone get out your gloves! You wouldn't want molecules on your hands, would you?

  • Haptic interfaces (Score:5, Informative)

    by G4from128k ( 686170 ) on Saturday April 09, 2005 @05:49PM (#12189481)
    In preslashdot days, there was a segment of the VR community working on force-feedback (haptic [northwestern.edu]) interfaces. In one application, a 6-DOF, 3-D mouse let a researcher "hold" a simulated molecule and "feel" how that molecule fit into a receptor site of an enzyme. Computing the forces required high-end equipment at the time, but should be very doable today if one had the specialized interface hardware [northwestern.edu].

    • Not so (Score:5, Insightful)

      by exp(pi*sqrt(163)) ( 613870 ) on Saturday April 09, 2005 @06:51PM (#12189780) Journal
      Computing the forces required high-end equipment at the time, but should be very doable today
      I wasn't doable on high end equipment then, it still isn't doable today. I spent 2 years working in computational chemistry and I've never seen such voodoo in my life. Yes - there are formulae for computing forces. But no, they don't bear much relation to reality Any simulation running anywhere near realtime is likely to be a purely classical simulation - balls and springs. This bears no relation to reality. Someone will run a simulation a few hundred times and after much tweaking of spring stiffnesses and so on they'll get results that vaguely approximate something measured in a lab. In the next simulation they'll need different parameters with no way of predicting what that change should be. Basically people in computational chemistry are doing post hoc fitting of models with close to zero predictive power. I've seen it happen over and over again and from time to time other people will also confess this is what they are doing. Occasionally someone will even run a quantum simulation - often a single electron model that is about as representative of a full quantum model as an elephant's dung is about its trunk.

      Unfortunately, with the advent of fancy graphics workstations came the belief that these methods worked - after all, people could see pictures, on a computer at that. These new methods make things even worse, people will feel forces generated by a fictional simulation and be even more convinced that what they are experiencing really does reflect reality. If you care to check you'll find very few cases of a drug discovery, say, resulting from a theoretical prediction about receptor binding. And when you do, you'll find plenty of people questioning that interpretation. After all, drug discovery is largely about dumb luck, and every so often the next randomly suggested compound for testing comes from a computational chemistry lab, even if a bunch of fortune tellers using the I Ching to predict drug designs might score just as well.

      Sometimes I worry if atmospheric sims used to predict global warming are just as bad - not not having worked in atmospheric science I've no evidence to back it up. The tricky thing is that anyone who works with sims is likely to have a vested interest in maintaining their use.

      • Re:Not so (Score:3, Interesting)

        by G4from128k ( 686170 )
        I wasn't doable on high end equipment then, it still isn't doable today.

        Thanks for the insight. I'd always suspected that they were using gross approximations for the field force calculations. Its one thing to compute the forces on a point charge in a uniform field. Its another thing to compute all the quantum mechanical effects of interacting electron shells in a real molecule.

        Unfortunately, with the advent of fancy graphics workstations came the belief that these methods worked - after all, peopl
        • More preaching to the choir, but you don't even know how bad it truly is. The "point charge in a uniform field" bit actually isn't working all that well these days. . .when you try to represent water with a continuum dielectric the standard approximations that are fast enough to use in a motional simulation (generalized Born) have something like 50 percent error when applied to a protein. . .that 50 percent error really kills you when you're trying to propose a thesis. It's no wonder the drug industry is

      • Yes - there are formulae for computing forces. But no, they don't bear much relation to reality Any simulation running anywhere near realtime is likely to be a purely classical simulation - balls and springs.

        You are preaching to the choir and any computation chemist worth his salt will tell you how far we have to go. The Merck force field actually performs better at generating bio-active conformations when electrostatics is turned off, mainly because the electrostatics of the protein completely masks the

      • Your criticisms may be more valid for computational chemistry, but they are certainly not as valid for biomolecular modeling. Modern interactive molecular dynamics simulations have become very useful for investigating complex sequences and interactions between biomolecules. They don't necessarily require high accuracy forcefields or QM methods to discover features such as hydrogen bonding patterns, steric clashes and distance constraints. It's true that having the accuracy will help, and modern forcefields
        • Well, there's a big difference between "useful for limited sets of problems" and useful to biology in general. I'll point out you don't even NEED molecular dynamics if all you wanted was a static h-bonding pattern, steric clashes, and distance contraints. Rasmol and a structure file will do fine. The force fields are getting better but with the current machinery in place, we can never even hope in our wildest dreams that MD is going to tell us the mechanistic details of catalysis or protein-protein recog
    • The current haptic devices include the Phantom OMNI [sensable.com]. This is the only system, I've had the chance to use with 3D software. It gave good feedback on the virtual models, but it would probably be much better if you could combine it with atomic force microscopy.
    • I seem to recall Neal Stephenson used the idea in The Diamond Age. There's a sequence where a guy is using a sort of glove with force feedback to manipulate individual molecules and atoms - as in literally manipulate real molecules, not just manipulate in a simulation, because the whole culture the book is set in revolves around nanotech. Whether The Diamond Age predates your VR wossname, I don't know, but it doesn't stop it being immensely cool.

  • TFA is a lie (Score:4, Insightful)

    by mrRay720 ( 874710 ) on Saturday April 09, 2005 @05:52PM (#12189491)
    That's no more "touching molecules" than owning a copy of playboy is having a girlfriend. It's touching a solid immitation of one.

    (Ignoring the obvious complaint that most stuff is made of molecules.)

  • Augmented reality... (Score:4, Insightful)

    by FireballX301 ( 766274 ) on Saturday April 09, 2005 @05:55PM (#12189502) Journal
    I skimmed the article, and apparently, what happens is that they have a machine that will manufacture molecules out of plaster and such. That model can then be manipulated, and the manipulations will occur on the computer. A camcorder feed records your hands and the molecule, and will display it, along with the computer's own overlay. Thus, the pictures are all CG, and the weird effect is simply an overlay of a normal molecule model.

    IMO, not as impressive as a video I saw, where there was a desk that had virtual (i.e. you could put your hand through them) objects moving around and interacting with some real objects (a plug outlet). Also had a guy turning his mic into a rose. I forget the link.

    • Re:Augmented reality... (Score:4, Informative)

      by NSObject ( 250170 ) on Saturday April 09, 2005 @08:45PM (#12190370)
      IMO, not as impressive as a video I saw, where there was a desk that had virtual (i.e. you could put your hand through them) objects moving around and interacting with some real objects (a plug outlet). Also had a guy turning his mic into a rose. I forget the link.

      The company is Total Immersion [t-immersion.com]. The video you're talking about can be seen here [gprime.net].

      • Thanks for the links.
      • There is a similar technique developed in the Netherlands, but it still depends on 3d-glasses: http://homepages.cwi.nl/~robertl/pss/pss.html This looks much more crude than the video, but although the thing shown in the video here is nice for demostrations etc, for work like practicing operations the most important thing is that the one who's doing the movements actually sees a virtual reality that is coupled to his/her movements, not just the public on a separate screen. I thought there was one similar d

  • Blue Gene (Score:3, Insightful)

    by karvind ( 833059 ) <karvind@NoSPAM.gmail.com> on Saturday April 09, 2005 @06:01PM (#12189526) Journal
    I am not sure if I understand this completely (I read the Press Release).Blue gene [ibm.com] does protein folding computations which requires hours of CPU time. How can you understand these molecular interactions in real-time ? Article doesn't give detail about how they implemented the time-consuming computation.

    • Re:Blue Gene (Score:2, Insightful)

      by t35t0r ( 751958 )
      The fold of the proteins in question are already known. That's how they know how to construct them physically using the magnets or 3d printers. It's how the protein will interact with other molecules that makes this approach useful.

    • Re:Blue Gene (Score:3, Insightful)

      by tfoss ( 203340 )
      First, Blue Gene's aren't yet up to the task of true de novo protein folding simulation (and there is debate about when/if we'll be able to actually do that with the knowledge we have now). Molecular interaction calculations on the other hand, aren't nearly so challenging, and many can be done in real-time (there are obviously many caveats to that, but...).

      Second and more importantly, that isn't what this does. This setup is mainly to help in teaching about molecular interactions by providing an enhance
      • Pass on my admiration to Art, this system is fantastic. I cannot understand why the slashdot crowd seem so dismisive. The more protiens that IBM fold the more this system will be usefull as a research and teaching tool. You could eventually have a model of a whole virus in one hand and see how various drug candidates could attach to it with the other. Perhaps they could borrow an idea from the game industry and implant a vibrating device inside the models to represent the forces. Actually that sounds more l
    • Er. No. Batch protien folding is expensive, because you're folding 10^preposterous possible protiens. Folding one protien is relatively trivial; you could do it realtime on a z80. Amusingly, that means that the Classic Gameboy has enough horsepower to pull it off.

      Molecular interactions are simple. The problem with batch protien folding is the sheer number of foldings which need to be addressed.

  • Manipulate DNA? (Score:1, Funny)

    by Anonymous Coward
    I dont need no special gloves to manipulate DNA. I manipulate DNA with my bare hands several times a day!
  • ... Physical.

    Lemme hear your molecules talk. Yeah, lemme hear your molecules talk...

  • Science Fiction (Score:5, Insightful)

    by Qwerpafw ( 315600 ) on Saturday April 09, 2005 @06:14PM (#12189582) Homepage
    Once again, we see a real advancement predicted by a science fiction author.

    In his work The Diamond Age (which was published, I believe, in 1995), Neal Stephenson predicted that nanotech engineers would manipulate molecules by hand, maneuvering them into position to create microscopic engines, rod-based logic elements, and other devices. John Percival Hackworth, one of the semi-protagonists of the novel (Stephenson has a nasty tendency to complicate his writing with multiple protagonists who follow divergent paths), is such an engineer, an individual who creates 'bespoke' nanotech designs.

    The central conceit of the novel is that Nanotechnology has entirely replaced conventional manufacturing through the use of a "feed"--a dedicated line of raw materials which couples with computers to create almost any object desired. How long until such things become reality? Only time will tell. Obviously though, we're on our way.
    • This is a visualization technology, and not actually connected to the idea of moving around literal molecules. That is to say, the technology on display here allows you to move around molecules in a computer model, but those molecules are computer constructs and don't actually exist.

      If someday we find a way to manipulate single molecules with such precision that we can mechanically and specifically control their movement freely, then we could of course use a technology such as this one to specify those mov

      • This is a visualization technology, and not actually connected to the idea of moving around literal molecules. That is to say, the technology on display here allows you to move around molecules in a computer model, but those molecules are computer constructs and don't actually exist.

        Right, but it's on the way towards creating actual molecule manipulation. If they work on the physics of the molecule interactions (the current system doesn't really allow for this, but perhaps more dynamic future developmen

      • No, the cool bit is that you could conceivably build a self assembling system out of these macroscale parts which works the same way as an equivalent microscale system. Much easier to design something when you can work with it. In fact, I bet if you were to give 1000 of these parts to a bunch of 5th graders and teach them the concept of self assembly they could come up with a working system in a day.
      • Yup. However, there is research into things sort of like what Stephenson described. One example:

        TeleNano Project: Augmented Reality User Interface for Atomic Force Microscopes (afm) [cmu.edu]

        With this 3D computer simulation coupled with realtime force feedback, an AFM can become a nanomanipulation tool where a user can interact with nano-size particles as easily as if they were lagre objects on the desk in front of them. This expands the utility of the AFM from simply a scanning device to a manufactuing tool wit
    • I'm pretty sure Neil got beat by some prior art on that subject...no disrespect to him, of course, but I don't think he originated the idea.
    • Once again, we see a real advancement predicted by a science fiction author.
      Don't forget that they've also predicted thousands of inventions that have not yet been invented, or are actually impossible by the laws of physics. (There's also inventions that are possible, but aren't practical or particularly useful in light of other inventions.)
  • Don't miss the incredibly cool movies and images

    And that's exactly how you shall write in a Slashdot article to be sure people will miss them. :-/
  • I am sure the Rubic cube came about due to Mr. Rubic making/inventing a 'moving model' to show his students how atoms moved around in a bound molecule.
    • Rubik was a sculptor and architect, not a chemist or physicist. He invented an interesting puzzle [answers.com]. Its motion works identically to dynamics of "group functions", which some physicists realized works like a model of quark/antiquark combinations that compose several subatomic hadrons.

    • Re:Rubic Cube (Score:4, Informative)

      by TapeCutter ( 624760 ) on Saturday April 09, 2005 @10:59PM (#12190993) Journal
      I was about 25 when Rubik's cube came out and was facinated as to why the corners didn't fall off. A couple of days after buying a cube I was a my parents house and dear old dad was fiddling with a cube. He had been a mechanical engineer most of his life so I asked him "why don't the corners fall off" - "Oh it's just got keys that fit into channels on a ball". I still had to pull the cube to bits before I could "visualise" how it worked.

      To be able to do the same sort of thing with molecules to explore self-assembly seems (to me anyway) a fantastic development. I wonder if furniture places like "Ikea" have heard of this. They could pour the tiny pieces in a box and let the vibration of home delivery assemble the furnitue.

  • Stephenson wins again (Score:2, Informative)

    by Sairret ( 786685 )
    I always knew Diamond Age had it right.
  • Chorus:

    I believe in molecules
    Where you from
    You sexy thing
    I believe in molecules
    Since you came along
    You sexy thing

    Oh yaa.. dj spin that record
  • ... but don't you touch molecules everytime you wave your hand in the air or in the water? The next thing these eggheads will be saying is that the Earth is round instead of flat. :P

  • Nice learning tool (Score:4, Insightful)

    by InternationalCow ( 681980 ) <mauricevansteensel.mac@com> on Saturday April 09, 2005 @06:27PM (#12189646) Journal
    But nothing more. I agree with other posters. Now, if you could get some kind of force feedback that would tell you if one molecule can dock to the other in a particular orientation, or whether a, say, DNA molecule will accept a transcription factor and bend in the right direction, or.... - that would make a really useful tool for research. As it is now, this is a nice way of helping students to visualize the spatial properties of complex molecules. Useful, but hardly revolutionary in any sense.
    • I'm most interested in the fabricating machine.

      For the molecules, as you said, it would be more valuable to have a force-feedback system that could give us an intuitive idea of the forces involved in molecular structure. I've seen robotic-arm type structures that allow a person to "interact" with something on the computer screen in a way that makes it feel like something is actually "there".
    • Yes, unfortunately if you've ever run molecular dynamics simulations you know that water is a crucial ingredient in determining the ultimate behavior of multiple protein / nucleic acid / docking simulations.

      So unless we can model protein - water - protein - NA interactions physically in realtime (There are programs which do this somewhat already VMD visual component + NAMD molecular dynamics + IMD (interactive molecular dynamics), then what you are referring to will be possible. But we are well on our way
      • Heh. You work for Klaus, don't you. .

        More on topic, IMD actually does have support for force-feedback joysticks. You can, for instance, use the joystick to stretch a muscle protein out, and feel its resistance to the stretch.
  • Why waste all that money when you can touch some molecules of your own! Your hand!
  • look, i'm touching molecules with my bare hands!
  • The word you apparently were struggling to come up with when composing the article's title, but failed, was "individual". Better luck next time.

  • Previous Work (Score:2, Informative)

    by IronicCheese ( 412484 )
    You REALLY have to give a tip of the hat to the folks at UNC who've been doing this sort of work for YEARS.

    Their GRASP system was a force-feedback molecule-docking simulation driven by a motorized WALDO arm. Very impressive. Nice to see that others are following in their footsteps.

    http://www.cs.unc.edu/Research/nano/cismm/

  • ... if you pantomime a jerking-off motion, you can recombine [wikipedia.org] DNA into Jimmy Kimmel [tvtome.com].
  • The hard part about protein and molecule manipulation is getting in a pure form and obtaining the data about the molecule. For a single protein, it might not only take years to get the protein pure enough to work with, but once it is crystallized, you may get different versions of the data depending on crystallization conditions. For a given protein, you get at least two pieces of angle information for the phi and psi angles of the amide bond, plus any degree of rotation for the side chain. DNA can have
  • If you are wondering, how fingers positions tracked by camera, pay attention to small black and white squares on the end of the fingers. Those are square-shaped markers used in the ARToolkit [washington.edu] - Open sourced [sourceforge.net], multiplatform Augmented reality [uni-weimar.de] library. ARToolkit is esy to use and with camera connected to PC and having camera SDK you can esily write your own augmented reality application. There are augmented relity libraries for cellular phones and pocket pc in development.
  • In any case, I can't browse to those links you provided. "Connection was refused" by www.scripps.edu ....

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