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DNA-rainbow, A New Vision of Human Chromosomes

Posted by samzenpus on Thu Feb 08, 2007 03:21 AM
from the painting-genes dept.
Biotech Science
An anonymous reader writes "Two scientists have rendered amazing pictures using datafiles from the human genome project. They assigned different colors to the DNA and rendered images showing interesting patterns and strange structures of our chromosomes. It might be a groundbreaking new idea for displaying and maybe better understanding our genes. With its fascinating pictures it is a beautiful mix of science and art."
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[+] DNA-Radio, Tune In To Your Chromosomes 77 comments
An anonymous reader writes "The folks behind the DNA-Rainbow project (discussed on Slashdot before) apparently have some time to play around with genome data. After creating amazing pictures from the human DNA code they are now transforming all chromosomes to audio and streaming them to the Internet. Every base is read and broadcasted instead converting it to a color. Seemingly this artistic project will last a while. After some math they found out that it will take them more than 23.5 years to air the whole human genome sequence."
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  • Magic Eye? (Score:5, Funny)

    by SinVulture (825310) on Thursday February 08 2007, @03:26AM (#17931870) Homepage
    No matter how hard I try, I can't see the sailboat!

    • Re:Magic Eye? (Score:5, Informative)

      by advocate_one (662832) on Thursday February 08 2007, @04:15AM (#17932068)
      for the bemused... here's the reference... [imdb.com]

      Little Girl: [looking at a Magic Eye poster] Wow. It's a schooner.
      Willam Black: Ha ha ha ha. You dumb bastard. It's not a schooner... it's a Sailboat.
      Little Boy: A schooner IS a sailboat stupid head.
      Willam Black: [becoming enraged] You know what. There is NO Easter Bunny. Over there, that's just a guy in a suit.

  • Lame (Score:4, Informative)

    by nacturation (646836) <nacturation.gmail@com> on Thursday February 08 2007, @03:27AM (#17931880) Journal
    This is the same principle as the Bible Code which has been shown [anu.edu.au] over and over to be rubbish. If you line things up in various ways you can find just about any pattern you want given sufficiently long input.
     
    • The article is slashdotted so I can't say for sure. But isn't this representation aiming at helping recognize and differentiate two genomes instead of finding information in it ?

        • Re:Lame (Score:5, Insightful)

          by mwvdlee (775178) on Thursday February 08 2007, @05:03AM (#17932216) Homepage
          Sound like they're claiming they made nice pictures using the genome data to generate them. Nothing more. Humans tend to see patterns in everything, it's in our nature. So no wonder we see patterns in those pictures. We'd probably see patterns in them if the input was purely random data.
    • It doesn't matter what the pattern is, nor what it means. If the pattern is there, then the pattern is there. What does matter is what you DO with the pattern, and maybe why it is there.

      Any pattern can be modeled in an algorithm, and from this algorithm it can be extrapolated. A set of data without any patterns is noise; random data. An algorithm found in a dataset speaks of a function, and understanding functions in the human genome leads to better understanding of what we truly are.

      • Re:A pattern is a patterns is a pattern (Score:5, Insightful)

        by sporkme (983186) * on Thursday February 08 2007, @05:34AM (#17932342) Homepage
        Referencing the earlier mentioned movie, Pi:
        Sol Robeson:

        Hold on. You have to slow down. You're losing it. You have to take a breath. Listen to yourself. You're connecting a computer bug I had with a computer bug you might have had and some religious hogwash. You want to find the number 216 in the world, you will be able to find it everywhere. 216 steps from a mere street corner to your front door. 216 seconds you spend riding on the elevator. When your mind becomes obsessed with anything, you will filter everything else out and find that thing everywhere.
        Just that a pattern exists does not give meaning to the pattern. The Golden Rectangle [wikipedia.org] was applied to the human body by Da Vinci and others, but no great significance can be discerned except that vertebrates tend to be symmetrical. The heavens did not burst forth as our creator revealed himself. The DNA pattern is more of the same - searching for patterns tends to yield them eventually.

      • Re: (Score:3, Insightful)

        by radtea (464814)
        An algorithm found in a dataset speaks of a function, and understanding functions in the human genome leads to better understanding of what we truly are.

        An algorithm found in a dataset speaks of imperfect compression.

        As to "what we TRULY are", we are everything that we are, neither more nor less, in all our messy complexity. Reductionism generates epistemological convenience, not metaphysical revelation. Although Platonists in reductionist clothing have been overstating their case for centuries.

    • Re:Lame (Score:5, Insightful)

      by Anonymous Coward on Thursday February 08 2007, @06:30AM (#17932534)
      Well, no, it isn't.

      The Bible Code people claimed that their ability to find patterns in a particular text of a particular religion both validated the truth of that religion and also allowed predictive ability on world events.

      These guys are saying, "Hey look, if you display a bitmap representation of genomes, they look pretty."

      I am sure that you can see the difference between these two claims.

      • Re: (Score:3, Interesting)

        by Angst Badger (8636)
        Well, it's a bit more than that. It's plainly structured data, and that's what's interesting. If you plot random data in a graphic, it looks very different than if you load a program or a structured datafile into video RAM. These plots, or at least parts of them, look very much like programs. Now, I wouldn't read anything more into it than that it is indeed structured, any more than I could distinguish between a graphical representation of a word processor versus a billing package, but it is definitely not,
      • Amusing aside:

        Using the Bible Code method, you can find a 'prediction' of the death of Princess Diana in the book 'Moby Dick'

        Also, Genesis contains the phrase "Darwin got it right"

    • Re: (Score:3, Informative)

      by gnalle (125916)
      The two scientists have invented a nice way of visualizing repeated sequences in DNA, but the results are hardly controversial. They are doing something along the following lines: pixel(x,y) = getcolor(DNAsequence(x + 256*y))
    • They're not claiming otherwise. They made it clear that the structures depend on the width of the rendered image, and only touched upon the idea that information might be modulated in genetic code, a theory which has been about for much longer.

      Ever seen a few "maps" of the Internet [opte.org]? Completely pointless, but it helps people to visualise the scope of the whole thing, even though they can't do anything useful with it. It's mainly art, but it also shows us something we can't understand in a way that is more hu
    • He who defines the scale(x and y axis), defines the patterns.
    • I thought the whole point of the "Bible Code" was that they found certain patterns that went away with, say, the same amount of text taken from the hebrew translation of "war and peace", or the old testament with every 1000'th letter swapped around, and lots of other collections of 250k hebrew characters. None of them had this certain series of patterns in them (I will personally verify this at some point, but for now I'm not strongly defending it because they could just be lying.)

      Ok, so they could just hav

  • Your chromosomes... (Score:5, Funny)

    by Riktov (632) on Thursday February 08 2007, @03:34AM (#17931910) Journal
    ...are heavily fragmented. This could degrade performance in creating offspring.

    Would you like to optimize your chromosomes?

    [Yes] [No] [Cancel]
    • Actually your chromosomes do fragment as you get older. It's possible that in some distant future we will contain nanobots to "defrag" our chromosomes.
        • They try, but don't do a very good job at it. Ever heard of cancer?

          • Or just plain aging. [wikipedia.org] Slowly, but surely our telomeres (the junk tails on the ends of our DNA) get eroded, and eventually the chromosomes themselves begin to degrade. Since most of our cells are not meant to divide frequently, most don't express telomerase to repair the damage.

  • Hey, baby. . .. (Score:5, Funny)

    by gardyloo (512791) on Thursday February 08 2007, @03:35AM (#17931916)
    Taste the rainbow!
  • Only a white page with nothing on it...

  • Oops (Score:5, Funny)

    by tehSpork (1000190) on Thursday February 08 2007, @03:51AM (#17931970)
    It looks like the DNA has been Slashdotted.

    Hopefully the next version will have developed a natural defense mechanism to handle the strain Slashdot puts on servers. :)

  • Arrgh! (Score:3, Funny)

    by Anonymous Coward on Thursday February 08 2007, @03:59AM (#17932006)
    My genes! They've been slashdotted!

    I need tissues!

  • Good Science/Art websites? (Score:2, Interesting)

    by Anonymous Coward
    Actually, does anybody have other good Science/Art websites they can share? I remember having a book, "On the Surface of Things" I think, that basically had lots of colorized/slightly manipulated images from science and technology. Some the shots were magnificient, surprising,and intriguing all at once. I had always thought that sort of thing would be a good tool for educators to get children (or adults) more interested in science. On a side note, I also wanted to set up a website community to bring to
  • Piet is an 'esoteric' (useless) programming language that reads bitmaps as source files.

    http://en.wikipedia.org/wiki/Piet_(programming_lan guage) [wikipedia.org]
    http://www.dangermouse.net/esoteric/piet.html [dangermouse.net]

    It'd be nice to be able to load the chromasomes up into the piet interpreter, and see what comes out!

    Wouldn't it be interesting, though, if it turns out that the genome could be understood as a 'program', and a specially coded interpreter could process it... ... what would the binaries do?

    • Re: (Score:2, Insightful)

      by Neeth (887729)
      Wouldn't it be interesting, though, if it turns out that the genome could be understood as a 'program', and a specially coded interpreter could process it... ... what would the binaries do?

      The genome is a program and children are it's binaries. But please do tell me more about that interpreter stuff, that seems, uhm, nice.
  • I've seen that before... when my TV was on an unused channel and someone started blow-drying their hair.

  • I've seen that pattern before (Score:3, Insightful)

    by bl8n8r (649187) on Thursday February 08 2007, @06:55AM (#17932606)
    It's what the data segment of your app looks like when you accidentally dump it to vga video memory.
  • Seeing structure where there isn't any Quote :

    Strange structures (close your eyes just a little bit to see more details)
    • Longer repetitive sequences can absolutely be visualized by something like this. Those patterns are already known. There are logical reasons (like histone length) for certain stride lengths to be more prevalent. There is nothing to see here, please move along, but this doesn't mean that all of the actual patterns are bogus. Karyograms [wikipedia.org] have also been used for a long time to identify matching regions between species, and chromosomatic defects, and that's also partly related to studying GC/AT ratios to find th

  • Genetics (Score:4, Funny)

    by worst_name_ever (633374) on Thursday February 08 2007, @07:32AM (#17932762)
    I don't even see the genes anymore - just blonde, brunette, redhead...
  • The DNA molecule and the basepairs are essentially a one dimensional pattern, i.e. series of letters or codes or symbols. The pattern they see depends on how many pixels you choose per line. Now if you rearrange the same data in 3D like a cloud of dots in a box or in 4D an animation of a cloud of dots in a box you can see even more interesting stuff. But all of it happens in the brain, you could probably get the same effect by encoding the telephone directory's list of names or the letters served up by goog
  • While I find the DNA rainbow interesting, I do have a few criticisms.
    1. I think that speaking of "information" in the DNA is a bit misleading. It is not "information" in the sense we normally think of information. The DNA sequence is the result of millions of years of evolution. One might even say that the DNA sequence is a "phenotype of evolution". It is as much a phenotype of evolution as the organism is a phenotype of the DNA itself.
    2. The relationship between arbitrary base pairs is multidimensional and w
    • "OK, so you think I am mad as a hatter. Perhaps. Perhaps not."

      No, I just think you've unloaded a bunch of big words (some not used correctly, by the way) and linked to a video of a dry low-level lecture with graphics that are no more sophisticated than these guy's in order to appear cool.

      "Overall, I think this is wicked cool, but amateurish from the standpoint of science. Actually, I'd like to see a Gerald Edelelman approach to handling and analyzing the DNA -- which would be wicked cool!"

      Wicked cool -- the
  • I've been doing this for years with large contigs to help visualize repeats. You'd be amazed at how good we humans are at picking out patterns visually.
  • proof [slashdot.org]

    (and it's also more artistic than linux)

  • Heroes (Score:3, Funny)

    by kalirion (728907) on Thursday February 08 2007, @09:35AM (#17933778)
    So, which colors represent superpowers?

  • Completely pointless (Score:3, Interesting)

    by glwtta (532858) on Thursday February 08 2007, @12:09PM (#17935728) Homepage
    So, they gave each base-pair a color? What on earth is the point? 98% of that sequence doesn't do anything. And why is a virtually random sequence of pixels of 4 different colors "beautiful"?

    I can understand if they took two different genomes from the same species and did some kind of comparison: different colors for matches, indels, translocations, silent/synonymous/non-synonymous SNPs, etc. Or translated the sequence and colored by hydrophobicity/charge/polarity/whatever. Or showed haplotype conservation between species.

    At least that would tell you something, this is just a bunch of pixels with no meaning. A vaguely similar thing I've done was to plot plot SNP density (as color intensity) over the genome - but that was for a specific project, I didn't realize such things are "new visions".

    There are definitely prettier visualizations out there too: http://acg.media.mit.edu/people/fry/genomevalence [mit.edu]

    Even this [visualcomplexity.com] is a lot more informative (I think www.visualcomplexity.com was mentioned on slashdot a couple of years ago).

    • Human genome project scans just the 'upper level'
      Yea, it's real hard to get at that 'lower level' DNA hidden right on the inside, geez.

      Things are much more complicated there. It's like their binoculars captured upper boundary of the mountain range underneath.
      I... I... don't even know how to respond to your rambling misinformed bullshit. Just No!!! That's not it! That's not it at all!
    • "We share 99% of DNA with the shimp right (now)."

      We share a large (not 99%) of our DNA with shrimp (and shimp, whatever those are) because most of it is involved with cellular functioning, you idiot.
    • Do you use a special keyboard for the completely retarded?
    • "I had a paper published about how DNA SNPs seem to follow a Poisson process in their distribution."

      Isn't that pretty much what we would expect as the null hypothesis? It seems like the deviation from poisson would be the interesting phenomenon in this case....

      More specifically: if point replication errors occur randomly and without mechanistic bias (i.e. they're unrelated to chromatin structure, or some other higher-order biological process), it seems like a poisson model would be the simplest descriptio

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