Living the Scientific Life (Scientist, Interrupted)

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I still remember when I learned how DNA (Deoxyribonucleic Acid) replication occurs, and it was like a lightning bolt from the sky: it changed my view of the world and a molecular biologist was born. This video uses the latest research to create an animation of how DNA is replicated in a living cell [1:54]

DNA replication is a fundamental process underlying biological inheritance that occurs in all living organisms to accurately copy their DNA. This process occurs through a “semiconservative” mechanism where each strand of the original double-stranded DNA molecule serves as template for the production of a new complementary DNA strand. As the result of DNA replication, two identical DNA molecules are produced from a single double-stranded DNA molecule, each strand containing an original strand of DNA from the parental molecule and a new complimentary “daughter” strand that is bound to it. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication, making less than one error per one billion bases — one thousand times more accurate than the best computer.

Comments

  1. #1 IBY
    August 18, 2009

    I can’t believe how complicated the replication from the 5-3 side is (was it 5 to 3 or 3 to 5, don’t remember, whichever one needs the Okazaki’s fragments) and the overall structure of the protein complex.

  2. #2 biobot
    August 18, 2009

    I think this is the coolest video I have ever seen in my life. Thank you!

  3. #3 Chris Farnet
    August 18, 2009

    Thanks for bringing us this amazing video- the results of over 30 years of elegant research captured in a 2-minute film! I was mesmerized by the “knit one, purl two” movements of the replication complexes.

    Video provides a powerful way to communicate complex scientific ideas to the public. I just included a link to your blog on the Darwin Facebook group so our members can enjoy it as well.

    Chris
    Volunteer, Darwin Facebook Campaign
    On our way to 1 million, help us get there:
    http://www.facebook.com/group.php?gid=53320310123

  4. #4 Phil Terry
    August 18, 2009

    This is a great video for the mainstream American adult – who may not have had a science course in 20 or 30 years but is looking to understand some of the big ideas in biology.

    Thank you!

    Phil
    Darwin150 – 150th Anniversary Lecture Series
    It’s free! Interact with E.O. Wilson, Sean Carroll and others
    http://showsupport.typepad.com/odyssey/darwins-150th.html

  5. #5 Ian Calvert
    August 18, 2009

    It is very impressive, but what do you mean by this:

    “Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication, making less than one error per one billion bases — one thousand times more accurate than the best computer.”

    Computers certainly make less than 1 error per million bits, even if you’re transferring data across many systems. If they didn’t we wouldn’t be able to transfer large amounts compressed data reliably.

  6. #6 Nate Sulli
    August 18, 2009

    In reply to Ian Calvert:

    Remember a bit is just a one or zero, and a nitrogeneous base is composed of over fifteen atoms each. Bits are the simplest part of a computer, and atoms are the simplest part of DNA. Not only does the system have to be near flawless in its replication it also has to deal with bases, which are more complicated than binary. Sure what they said is a shot in the dark, but it holds truth. The process of replicating is more complex than anything a computer can produce. However, you do have the right to believe the sky is purple, even if it’s wrong.

  7. #7 steave
    August 19, 2009

    I think this is the coolest video I have ever seen in my life. Thank you!!

  8. #8 Purschy
    August 19, 2009

    Random accident or Intelligent design? You be the judge.

  9. #9 Takophiliac
    August 19, 2009

    In replay to Purschy:
    Did you see how the there are no mechanical parts? The whole system is nothing more than a self replicating chemical reaction. The idea that an all powerful being would design such an elegant, yet obviously flawed process is preposterous. Even you could improve on it given the opportunity, i’m sure.

    In reply to Ian:
    1 million bits is 1/8th of a megabyte. The statement of one error in 1 million bits being the average error rate of computers is preposterous. In media format alone that would result in at least 32000 errors on a DVD. In processing terms, assuming a computer that processes data in 64-bit chunks at modern speeds (~2.5 ghz) could make more than 150,000 errors a second if I didn’t do my math wrong. This web page alone would have several. So, i agree, definitely computers are far more accurate than a 1 per million error rate. GrrlScientist should either elaborate on this figure or correct it.

    In reply to Nate Sulli:
    You need to think about the fact that the animation you saw was handled by a computer. Meaning…, you guessed it, a computer can handle the complexity of replication. Its also important to note that DNA replicase does not create bases, they are already present in solution. The enzyme merely provides a docking site for the appropriate base to insert itself from the solution.

  10. #10 Mike Olson
    August 19, 2009

    I’m currently reading a lot of pop sci stuff on genetics and cellular function. I’m at a library now and can’t really sit back and completely absorb the info from the video. I’ll get on the machine home and check it out. On a different note, good luck in getting to the Antarctic. While in the Navy I’d hoped to go on operation Deep Freeze. I was, however, a single parent and my son came first. I’d think it would be the trip of a lifetime in many ways. More unusual, unbelievable adventure then fun loving relaxation I’m sure. Good luck again.

  11. #11 amphiox
    August 19, 2009

    Hmm. . . 8 posts before the argument from personal incredulity rises, zombie-like, yet again from the grave.

    Cue the countdown to the inevitable “molecular machine” post, 3. . . 2. . . 1. . . . (channeling the ghost of Charlie Wagner. . . )

    But to answer Purschy’s question. Neither. The system evolved under the influence of natural selection, which is neither random, or intelligently designed.

  12. #12 Jonathan Taylor
    August 21, 2009

    I think the statement GrrlScientist makes about replication fidelity is simply a reversal of the description in the youTube video. The video describes CD burning as having 1 error in 1 billion (bytes?), while DNA replication after proofreading of having a fidelity 3 orders of magnitude better.

  13. #13 Alex Besogonov
    August 22, 2009

    Re: Nate Sulli:

    “Remember a bit is just a one or zero, and a nitrogeneous base is composed of over fifteen atoms each.”

    DNA bases are binary. Each base encodes exactly two bits, so comparison is fair. It’s also true that DNA replication is _way_ more reliable than burning raw data into a CD.

    However, real computers use _error_ _correction_ _codes_ which can ‘fix’ most of errors so you won’t even know they were there. Particularly, on CDs errors correction codes take about 30% of the disk’s physical area.

    Nature doesn’t have ECCs (The Intelligent Designer was not so intelligent, was he?), so it has to use more precise processes.

  14. #14 PCR Music Video
    August 24, 2009

    nice video, i like it quite a bit. here is another good one with a different flavor: DNA polymerase used for the PCR reaction. Simpler mechanism; cool video.

    http://www.youtube.com/watch?v=oCRJ4r0RDC4

  15. #15 L505
    September 20, 2009

    “Nature doesn’t have ECCs (The Intelligent Designer was not so intelligent, was he?), so it has to use more precise processes.”

    Right, so something precise is less intelligent than say some idiot that makes errors and then corrects them later? Are you sure you are intelligent?

    Now I’m an agnostic and not a believer myself, but your argument is so lame that it isn’t even funny.

  16. #16 L505
    September 20, 2009

    “In replay to Purschy: Did you see how the there are no mechanical parts? The whole system is nothing more than a self replicating chemical reaction. The idea that an all powerful being would design such an elegant, yet obviously flawed process is preposterous. Even you could improve on it given the opportunity, i’m sure.”

    An intelligent designer would use mechanical parts that wore down and failed like engines that stop after 300,000 miles? Are you that stupid? The fact that a designer could avoid mechanical parts and just use atoms at a micro/nano scale is exactly intelligent.

    Now I am not a believer myself, I personally am agnostic. But your argument is lame and ridiculous, and shows that you are not intelligent. If you can’t visualize a machine without stupid gears and human made abstractions (which easily break, fail, and wear out) then I don’t think you should be here arguing about what intelligence is.

    Imagine an intelligent designer creates a car engine or electrical motor without metallic parts and dirty oil, and without things that break and bend, such as crankshafts or pistons, or valves. Stupid designer? I think not – I’d congratulate a designer if he could put together that masterpiece. Once again, as an agnostic I’m not a believer myself – so I’m not saying it came from an intelligent designer. Just the fact that you are arguing out of ignorance and stupidity does not help. What do you see that is so stupid about a machine without metal, oil, and other parts that cause tremendous problems? Are you arguing that are silly machines that we stupid humans produce, are much better than the one shown in this video?

    In fact machines without parts that can break easily are the exact opposite of “stupid”. If this machine that you describe is not from an intelligent designer, which as an agnostic I fully give possibility to, then it is still intelligence through accident, but not a designer. Understand? Or do you actually think that this machine is really stupid (and if so, why does it work, with such a low error rate?).

    If you can’t admit that this machine is marvelous, and you actually think that it is stupid, then you sir or madam, are completely ignorant, and a moron for not recognizing and appreciating the absolute stunning and amazing molecular machine being discussed. Yes, if you actually think that this molecular machine is “stupid” then you truly are stupid yourself.

  17. #17 L505
    September 20, 2009

    By the way, considering that there are obviously some extremely intelligent people here who know better than DNA knows, please do offer a solution that is better since you think this machine is elegant but not very good. In other words, some of you people claim that this machine is good, but not so good – do offer your alternatives and the design and proof that you have a better more intelligent machine since you obviously have intelligence but evolution over time does not.