DNA-rainbow, A New Vision of Human Chromosomes

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."

Comments

Magic Eye?

[SinVulture]

No matter how hard I try, I can't see the sailboat!

Re:Magic Eye?

[advocate_one]

for the bemused... here's the reference...

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

[nacturation]

This is the same principle as the Bible Code which has been shown 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.

Re:Lame

[mwvdlee]

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:Lame

[Anonymous Coward]

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:Lame

[$RANDOMLUSER]

Mendeleev notwithstanding.

Re:Lame

[gnalle]

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))

Re:Lame

[Angst Badger]

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, as some skeptics here have suggested, random in its appearance.

Re:Lame

[Conspiracy_Of_Doves]

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"

Your chromosomes...

[Riktov]

...are heavily fragmented. This could degrade performance in creating offspring.

Would you like to optimize your chromosomes?

[Yes] [No] [Cancel]

Hey, baby. . ..

[gardyloo]

Taste the rainbow!

Oops

[tehSpork]

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!

[Anonymous Coward]

My genes! They've been slashdotted!

I need tissues!

Good Science/Art websites?

[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 together artists and scientists to see what how they might collaborate. Never got around to it of course, but has anyone seen anything similar?

Re:Good Science/Art websites?

[vonmeth]

http://antwrp.gsfc.nasa.gov/apod/archivepix.html

Re:Reminds me of the Bible Code

[QuantumG]

Great, now I'm gunna be on that site trying to find a Flying Spaghetti Monster.

A pattern is a patterns is a pattern

[Ceriel Nosforit]

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

[sporkme]

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 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:A pattern is a patterns is a pattern

[VirusEqualsVeryYes]

That can be applied to sightings of many other things.

The problem is, how does one determine which patterns indicate something and which patterns are just convincing illusions?

Re:A pattern is a patterns is a pattern

[radtea]

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:Dirty secret of HGP

[Adam Hazzlebank]

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!

Hey, it looks like piet source code!

[MrTrick]

Piet is an 'esoteric' (useless) programming language that reads bitmaps as source files.

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

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:Hey, it looks like piet source code!

[Neeth]

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 pattern before

[bl8n8r]

It's what the data segment of your app looks like when you accidentally dump it to vga video memory.

Genetics

[worst_name_ever]

I don't even see the genes anymore - just blonde, brunette, redhead...

Hmmmm...

[flajann]

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 will not really be elucidated by mapping them on a 2-dimensional grid. It is a curio, but not likely to yield much of anything useful.
3. I would think it would be much better to do this with codons than with base pairs. Since it is codons that code for amino acids, we might actually see some really cool patterns that way. Some of the codons are polymorphic and that can be taken into account with the color assignments.
4. I wish the site were a bit more interactive. Basically, I want to be able to dynamically manipulate the data in real-time, in 3 or 4 dimensions, and be able to fly through it. OK, this would call for much more than just a mere website. Perhaps I am trying to inspire someone to crate an OpenGL project that would do this!!!

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! See From Brain Dynamics to Consciousness to see what I mean. Applying his neural darwinistic approaches to DNA would not only reveal many surprises, but would be referentially cool, applying neural evolution to what was the result of biological (and memetic) evolution!

OK, so you think I am mad as a hatter. Perhaps. Perhaps not.

Heroes

[kalirion]

So, which colors represent superpowers?

Completely pointless

[glwtta]

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

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