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Biotech Science

DNA-rainbow, A New Vision of Human Chromosomes 161

Posted by samzenpus
from the painting-genes dept.
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-rainbow, A New Vision of Human Chromosomes

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  • Magic Eye? (Score:5, Funny)

    by SinVulture (825310) on Thursday February 08, 2007 @04:26AM (#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 @05:15AM (#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.
      • by spun (1352)
        I love Kevin Smith, but am I the only one who thinks every line of dialogue in his movies sounds like something Kevin Smith would say? I watch his movies, and even as I'm laughing my ass off, I can't help but be reminded of the scene in Being John Malkovitch where John goes inside his own head. To me, the dialogue sounds like this:

        Kevin: "Kevin Smith? Kevin smith kevin smith!"
        Mr. Smith: "Kevin kevin smith smith, kevin smith kevin smith."
        Kevin: "Smith, kevin. Smith kevin smith smith kevin kevin smith."
    • And he is speaking in COBOL
  • Lame (Score:4, Informative)

    by nacturation (646836) <nacturation@@@gmail...com> on Thursday February 08, 2007 @04:27AM (#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.
     
    • by Yvanhoe (564877)
      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: (Score:1, Troll)

        by nacturation (646836)
        Check out the article on MirrorDot [mirrordot.net] -- quoting from the page:

        We took the genetic code from huge data files and assigned a color to every of the four bases. Then we rendered these fascinating pictures, showing the genetic code of humans in color. You can see crazy structures and strange patterns in the images, best viewed when shutting your eyes just a little bit. Click on a link to a chromosome above and use your imagination to get a new view of your genes.

        Sounds like junk science to me.

        • Re:Lame (Score:5, Insightful)

          by mwvdlee (775178) on Thursday February 08, 2007 @06:03AM (#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.
          • Re: (Score:3, Interesting)

            by $RANDOMLUSER (804576)
            Mendeleev notwithstanding.
          • DNA is very very very difficult to search and index effectively, especially since scientists are very interested in finding sections that don't quite match.

            A good friend of mine (hi Paul [google.com]) has been working on hardware and / or software searching algorithms for a couple of years now. I used to live over his back fence, and he's talked me through a couple of his ideas.

            <surprise> Oh, I see he filed a patent. </surprise> Well I can't say any of that was obvious.

          • We'd probably see patterns in them if the input was purely random data.

            The input is random, so we are seeing patterns. A chromosome is linear. These guys wrapped that single long line into a box. Where they put the line breaks is completely arbitrary. Any patterns that you see must be formed by interesting "stacking" of lines together, and that effect is arbitrary. Pretty pictures, but utterly meaningless.

            Kinda simple, too. Besides downloading the 40GB or so of genomic data from NCBI, all they needed were l

          • by COMON$ (806135) *
            If you want cool genetic pictures you should check this out. http://www.dna11.com/ [dna11.com]

            I would love to get something like this done for my wife. Of course I would need to remove my tinfoil hat and not think about how they could just be gathering dna samples for the genetic superarmy.

            • by x-caiver (458687)
              My wife and I got one of these made. My side is red, orange and black, her side is orange, red and black. The walls in our kitchen are red, and the cabinets are black - it looks really cool in my personal opinion. A side bonus is that we were 2 of the first hundred people to get them made!

              It was really pricey, so its the only piece of art we've bought for our house, but it looks cool and is unique so I think it was worth it.
              • by COMON$ (806135) *
                glad to hear you thought it was worth it. I wanted to do something similar for an anniversary then subsequently for each kid. Given the prices of artwork that I have in mind for our house to collect throughout the years this didn't seem too pricey, great conversational piece I would think though!
          • by hyc (241590)
            Agreed it's lame, but not just for those reasons.

            There are 4 bases, yes, but they can only form in specific pairs. Adenine can only pair with Thymine, and Cytosine can only pair with Guanine. So there's really only two values. In other words, the two possible base pairs can be represented as the two possible values of a binary digit - a bit. Instead of using 4 colors to represent the DNA, only two are actually needed, assuming you use one base-pair per pixel. But really, looking at a 100 million bit long bi
    • Re: (Score:1, Interesting)

      by Anonymous Coward
      Ever seen the movie pi? [imdb.com]
      Unfortunately Slashdot will not render:

      &#928
    • by Ceriel Nosforit (682174) on Thursday February 08, 2007 @06:04AM (#17932220)
      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.
      • by sporkme (983186) * on Thursday February 08, 2007 @06:34AM (#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.
        • by VirusEqualsVeryYes (981719) on Thursday February 08, 2007 @09:17AM (#17933050)
          That [ebay.com] can [bbc.co.uk] be [riverusers.com] applied [cbsnews.com] to [wkyc.com] sightings [nbc10.com] of [bbc.co.uk] many [optusnet.com.au] other [snafu.de] things [nbcsandiego.com].

          The [ebay.com] problem [ebay.com] is [farshores.org], how [metro.co.uk] does [wkyc.com] one [jsonline.com] determine [goldenpalaceevents.com] which [pittsburghlive.com] patterns [local6.com] indicate [nbc5.com] something [nbc5.com] and [nbc5.com] which [nbc5.com] patterns [nbc5.com] are [nbc5.com] just [nbc5.com] convincing [wtol.com] illusions [reuters.com]?
          • by x-caiver (458687)

            That [ebay.com] can [bbc.co.uk] be [riverusers.com] applied [cbsnews.com] to [wkyc.com] sightings [nbc10.com] of [bbc.co.uk] many [optusnet.com.au] other [snafu.de] things [nbcsandiego.com]. The [ebay.com] problem [ebay.com] is [farshores.org], how [metro.co.uk] does [wkyc.com] one [jsonline.com] determine [goldenpalaceevents.com] which [pittsburghlive.com] patterns [local6.com] indicate [nbc5.com] something [nbc5.com] and [nbc5.com] which [nbc5.com] patterns [nbc5.com] are [nbc5.com] just [nbc5.com] convi

        • Aww man, you forgot the best part of that quote:
          "As soon as you discard scientific rigor, you're no longer a mathematician, you're a numerologist."
        • The Golden Rectangle 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.

          I'm not sure why parent post did not cite the Golden Ratio [wikipedia.org] instead, since that is what Da Vinci was mostly working with. BTW, the original expression was more along the lines of "the smaller part is to the larger part as the larger part is to the whole", which implies a much broader application than the algebraic presentation in the Wikipedia article. Also, note the use of G.R. in grecian architecture and sculpture predates Leonardo by about 1500 years.

          There is certainly significance in the G.R. in that

      • 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.
    • by Logopop (234246)
      Nah, not lame, since they don't really try to put a lot of interpretative meaning into it. Maybe someone should make an app to take the dataset and vary the line length (width of the images) to look for more vertical patterns (which also will only have artistical meaning)? I would also like to play the data as a wav with different pitch. Endless possibilities...
    • Re:Lame (Score:5, Insightful)

      by Anonymous Coward on Thursday February 08, 2007 @07:30AM (#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,
      • Re: (Score:3, Interesting)

        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
      • by Fred_A (10934)

        I mean, you can see a human as a bitmap image, that's gotta be cool, hasn't it?
        Aftar all, bitmaps of human images are among the most popular kind of content found on the network.

        Um. Or did you mean something else ?
    • by SengirV (203400)
      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
    • by X0563511 (793323) *
      So, somebody attaches a visualization to an incredibly complex natural system. Surprise surprise, the image appears fractal.

      Wake me up when they find the differential equations governing DNA.
    • by ukyoCE (106879)
      Are you trying to suggest that there ARENT really patterns in DNA? DNA is not random data that people are "making up" patterns out of. It is also not structured data (like the bible), that people are trying to find sub-meaning within. DNA is essentially byte code for creating and running entire organisms. It's highly structured, and we understand relatively little about it.

      Visualizing this data allows us to use our eyes to search for patterns. Which is actually a great idea, considering how good our ey
    • by AaronStJ (182845)
      Did, you, by any chance, actually look at the pictures? The patterns they refer to (and that appear on the first page of TFA) are pretty clearly more than just random patterns. Sure, much of it is noise, but there are long sequences that repeat, and the pictures make it clear. The overall "color" (literally and figuratively) of some of the crops also make it clear some one chemical dominates the others in many parts of the DNA sequence.

      Sure, I agree that any time someone purpose to find a special pattern
  • I dunno... (Score:1, Funny)

    by Anonymous Coward
    I tried banging the side of my computer, but all I see is static. Something must be wrong with the rabbit-ears on my modem.
  • by Riktov (632) on Thursday February 08, 2007 @04:34AM (#17931910) Journal
    ...are heavily fragmented. This could degrade performance in creating offspring.

    Would you like to optimize your chromosomes?

    [Yes] [No] [Cancel]
    • by pubjames (468013)
      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.
      • Well, they do that pretty well themselves, being self repairing and all, don't they?
        • by juhaz (110830)
          They try, but don't do a very good job at it. Ever heard of cancer?

          • by kypper (446750)
            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.
  • by gardyloo (512791) on Thursday February 08, 2007 @04:35AM (#17931916)
    Taste the rainbow!
  • Only a white page with nothing on it...
  • Oops (Score:5, Funny)

    by tehSpork (1000190) on Thursday February 08, 2007 @04:51AM (#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. :)
    • by empaler (130732)
      Hell, it's fast. It already evolved to being up, and now it wants authentication before allowing stuff in. That's even stronger than AB positive immune defenses!
    • by sa1lnr (669048)
      "It looks like the DNA has been Slashdotted."

      Does anyone else see a pattern forming here? ;)
  • Arrgh! (Score:3, Funny)

    by Anonymous Coward on Thursday February 08, 2007 @04:59AM (#17932006)
    My genes! They've been slashdotted!

    I need tissues!

  • 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
  • I demand royalties
  • I don't think there are any meaningful patterns to be found in a two-dimensional projection of the data. Maybe there can be found something interesting if the data is arranged in three or more dimensions.

    I used to think of the DNA as a kind of a programming language for the physical laws that exist in the universe. DNA in its very basic function is a mechanism to assemble complex organic molecules from simpler molecules and / or atoms, so I'm not sure wether we can extract any information from it using a
  • 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.
  • This will certainly have put the authors' gizzajob plea in front of many eyeballs, and that may be its primary value. A more interesting approach to the harnessing of our pattern recognition abilities to spotting significant sequences in the chromosomes would be to display the genetic code [ebi.ac.uk] in colours relating to, e.g. the hydrophilic/hydrophobic nature of the encoded amino acids. I agree with earlier posters; anything you spot in an arbitrarily-wrapped 4-colour mapping of bases is so far separated from a
  • by bl8n8r (649187) on Thursday February 08, 2007 @07:55AM (#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)
    • by cnettel (836611)
      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 @08:32AM (#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
  • If you stare at a graph long enough, you can make it have any pattern you want.

    There is, of course, much ongoing research in finding mathematical patterns in DNA. I had a paper published about how DNA SNPs seem to follow a Poisson process in their distribution. Does someone know a good way to visualize Poisson processes? When graphed as they do, it just looks like a sequence of randomly spaced dots.
    • by Tim (686)
      "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
  • Hmmmm... (Score:2, Funny)

    by flajann (658201)
    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.
  • It's not really much different to dumping binary data to screen memory. Some old home computers used to use screen memory as a temporary store (e.g. when loading a large programme, prior to relocating it elsewhere in memory), and you sometimes saw interesting patterns in it (ignoring graphics data).

    [Happosai]
  • proof [slashdot.org]

    (and it's also more artistic than linux)
  • Those patterns look like random data in video memory, with the default color palette of VGA's mode 13h. Ten years ago I wrote some x86 assembly code with quite similar results! :)
  • ...the difference between geeks, artists and art lovers is clearly illustrated. Those images do not look beatiful to anyone outside of the geek/scientific community. And I'm sure that even within that community there are those who had the same reaction I did. "Hmmm... just looks like the noise filter from Photoshop or the GIMP". Which brings up an interesting question. If we took one of the noise filter outputs and translated it back the other direction, would we wind up with any genomes? ;P
  • This publicity-stu^H^H^H^H^H^H^H^H^H^H^H^H^Hexperiment is teh crap because:

    • They need to provide a slider or a dedicated viewer so that we can adjust the dimensions of the picture. Some patterns may only appear at certain widths and lengths. For example, if a pattern is 100 bits wide, it will not overlap itself in an obvious way if the picture frame is 140 pixels wide.
    • Although human brains are neural networks that specialize in pattern detection, so much so that we even see non-existent patterns (conspi
  • Heroes (Score:3, Funny)

    by kalirion (728907) on Thursday February 08, 2007 @10:35AM (#17933778)
    So, which colors represent superpowers?
  • They chose the rendering and display parameters, such as a line size of 3500 pixels, for the computing & display ease, or culteral bias, not because of relation to genetic structure. This is too simplistic. Does anyone really think that significant or important genetic patterns will show up when rendered as:
    • 2 dimensionally
    • 3500 points per display line
    • left to right
    • top to bottom

    Sheesh. How about 3 dimensional spiral rendering or spherical or (for the "flat worlders") a cube? Granted, even with

  • Looks more like my early attempts at programming in mode 13h in DOS.
  • What would happen if you just displayed four random colors? I wonder how many patterns you'd see. Anyhow, I doubt that at the level of the four basic ACGT elements, there is any obvious information
  • Looks like they've finally found the gay genes.
  • However, it might just be their frontpage that's hammered.
    You can get 'deeper' pages at http://www.dna-rainbow.org/chromosomes/X.html [dna-rainbow.org] where X is the chromosome number (1-22) or x or y (lowercase).
  • Completely pointless (Score:3, Interesting)

    by glwtta (532858) on Thursday February 08, 2007 @01:09PM (#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).
  • Maybe if we have them represent base-4 numbers, nibbles of ASCII, or some other numeric base, we'll find a circle, or just a stereo-optic starfish image to cross your eyes over.

    Then, this would will be irrefutable proof of something, some sort of README.first, or just random gibberish for monkeys to type out.

    Contact.

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