Friday, July 25, 2014

The Central Dogma according to Riken

You may never have heard of Riken. Here's what they say on their website [Riken] ...
RIKEN is Japan's largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Founded in 1917 as a private research foundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing a network of world-class research centers and institutes across Japan.
They've published a video on the Central Dogma. Here's how they describe it ...
The 'Central Dogma' of molecular biology is that 'DNA makes RNA makes protein'. This anime shows how molecular machines transcribe the genes in the DNA of every cell into portable RNA messages, how those messenger RNA are modified and exported from the nucleus, and finally how the RNA code is read to build proteins.

The video was made by RIKEN Omics Science Center (RIKEN OSC) for the exhibition titled 'Beyond DNA' held at National Science Museum of Japan. RIKEN OSC has published in Nature Genetics on the regulation of RNA expression in human cancer cells.
Most of you know that I have a different view of The Central Dogma of Molecular Biology but that's not what I want to discuss here. Watch the video. Do you think it's a good idea to show this process as well-designed little machines and ships? It sure gets the IDiots excited {RIKEN’s 10-minute antidote to atheism: see for yourself].



9 comments :

  1. "Do you think it's a good idea to show this process as well-designed little machines and ships? It sure gets the IDiots excited "

    Meh. I don't see any benefit to constantly second-guessing myself in the off chance some creationist is going to see what I did or hear what I said and run with it in a stupid direction. They're immune to reason, so they're pretty unpredictable - making an obviously ambiguous statement or using certain keywords (e.g. "design", "purpose") carries a higher risk of mis-quoting than lots of alternative statements, but plenty of ways of expressing concepts are not obviously well-suited to such shenanigans.

    I didn't watch the full video, just the first few minutes. I was mildly surprised by the quality, actually - it reminded me of early attempts at computer graphics from around 20 years ago. The metaphor chosen for the video, that of precision machinery in a very science-fiction kind of background, seems like a fair choice for expressing concepts like "histones" and "transcription". Certainly they could have gone in different directions but I don't fault them for showing something that looks like precision machinery.

    I try not to let my decisions be too heavily constrained by asking myself "what would an IDiot think about this?". Quote-mining creationists are dishonest, ends-justify-the-means jerks, if they don't get excited about something I say or do they'll find some other person to misunderstand.

    p.s. hopefully this doesn't come through as a double comment.

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    1. Let's forget about creationists for the moment. I agree with you that we shouldn't let our decisions about teaching biochemistry be influenced by IDiots who won't ever accept science no matter how we present it.

      Do you think this video is a good way to show to undergraduates to illustrate how transcription and protein synthesis work? I don't.

      I didn't watch the full video, just the first few minutes.

      Hmmmm .... so it's true what they say about younger generations. Your attention span is much less than 10 minutes! :-)

      P.S. Good luck with the thesis writing ... how's it going?

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    2. Thanks! The thesis writing goes slowly, but it goes. Lights and tunnels and oncoming trains and so forth.

      "Do you think this video is a good way to show to undergraduates to illustrate how transcription and protein synthesis work? I don't. "
      I agree - it's so massively oversimplified that it's just a series of empty factoids (that might not even be correct they're so far simplified) that lead to no further information or learning. Knowing something about how a transcription factor recognizes and binds to a particular sequence of DNA leads to all sorts of interesting paths of investigation, just stating "it docks" and making the DNA appear as a different colour is not helpful.

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  2. This really was exceptionally terrible to watch. One thing is to use machine metaphors when trying to educate about molecular biology, another is to make it literal and deliberately make animations with flying robots and digital sounds and what not.

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  3. First Graham2 mentions the fact that this is probably not an accurate representation of what really goes on: "EA: Im not denying any details of the process, but the machines in the video looked like nice manufactured products, complete with lettering on the sides, all proceeding in a nice, regular, stately manner, just like the machines we are familiar with.

    Ive no idea what they would look like in reality, (if they ‘look’ at all) but I presume (based on some actual images) that their motions would be extremely chaotic, completely lacking (obvious) purpose. I repeat, Im not denying the general points being made, but the appearance seems completely unrealistic. Its a perception thing.
    "

    Here's scordova's take on it (my bold for emphasis):
    "If anything, it understates the difficulty of what is going on. There is a lot of thermal and quantum noise. It is like a tornado in the cell with all the machines miraculously resisting the disordering battering of Brownian motion. Further where are the guidance and propulsion systems for these components? If Brownian motion provides some of the “propulsion”, how is guidance and timing and traffic management accomplished?

    The video said the introns are un-necessary. That’s not exactly true. They may not be used by the ribosome to code the protein amino acids, but they may have regulatory significance in coordinating the process. I consider that the one undesirable aspect of the video, it’s treatment of introns a unnecessary junk.

    >>Graham: "Ive no idea what they would look like in reality, (if they ‘look’ at all) but >>I presume (based on some actual images) that their motions would be extremely >>chaotic, completely lacking (obvious) purpose."

    They are only superficially chaotic, if they are actually chaotic with no directionality, you’d be dead!
    "

    Superficially chaotic. Miraculous resistance to battering brownian motion.

    I can think of a few bat-things to say about that.

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    1. Apparently I've never commented here? Hope y'all don't mind the intrusion.

      Anyway, I won't even try to comment on UCD.

      What I find interesting is that scordova is actually understating the level of the miracle: the "machines" are not resisting anything, they are *using* the opportunities provided by the Brownian motion to arrive at a more stable configuration, i.e. one deeper in the sea of potential wells that it's immersed in. Spontaneously and repeatedly. Because that is all biochemistry is.

      What's truly miraculous is that life has found ways to arrange boundaries and gradients in a way that rolling downhill in a potential gets something useful done a bit more often than it does not.

      Nothing there requires design, though - crystals have invented the same thing. As have stars.

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  4. It's not a very good representation of the kinetic theory. In the US it is customary in high schools for a little processed chemistry (relates to the subject roughly the way processed cheese relates to real cheese) to be dropped in somewhere around chapter four of the biology textbook. So unfortunately for a lot of students this kind of thing is not a simplification concentrating on the novel biological elements. I'm afraid it actually plants an image of the chemistry. Lots of students have a great deal of trouble grasping the kinetic theory because of static illustrations. They have even more trouble grasping the difference between chemical equilibrium and static equilibrium. Obviously the Riken graphics have serious problems.

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  5. As a high school science teacher I would not show this to my class. While I think the concepts are appropriate for the content my students need, the video is boring and way too long. Having to read the text wouldn't go over very well in class either and the music stinks.
    .
    I, too, agree that the little spaceships are inappropriate. They are cute, but foster way too many misconceptions.

    I much prefer this video, http://www.hhmi.org/biointeractive/dna-transcription-advanced-detail, in which the "machines" are referred to correctly as molecules. HHMI has more wonderful videos here: http://www.hhmi.org/biointeractive/browse?field_bio_bio_series%5B0%5D=24143

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  6. I don't understand the weird humanoid voices that seem to be emanating from loudspeakers located somewhere in the nucleus.

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