Beta
×

Welcome to the Slashdot Beta site -- learn more here. Use the link in the footer or click here to return to the Classic version of Slashdot.

Thank you!

Before you choose to head back to the Classic look of the site, we'd appreciate it if you share your thoughts on the Beta; your feedback is what drives our ongoing development.

Beta is different and we value you taking the time to try it out. Please take a look at the changes we've made in Beta and  learn more about it. Thanks for reading, and for making the site better!

DNA-rainbow, A New Vision of Human Chromosomes

samzenpus posted more than 7 years ago | from the painting-genes dept.

Biotech 161

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."

Sorry! There are no comments related to the filter you selected.

hey... (1, Offtopic)

r3st2 (987153) | more than 7 years ago | (#17931866)

my DNA is 1337

Magic Eye? (5, Funny)

SinVulture (825310) | more than 7 years ago | (#17931870)

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

Re:Magic Eye? (0)

Anonymous Coward | more than 7 years ago | (#17932064)

Really? I can see the poor sysadmin who just got his sorry ass paged out of bed to figure out why the webserver just barfed.

Re:Magic Eye? (4, Informative)

advocate_one (662832) | more than 7 years ago | (#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.

Re:Magic Eye? (0)

Anonymous Coward | more than 7 years ago | (#17932626)

I was a bit worried when they say to stare at the circle in the middle of one of the pics, that the goatse guy was going to pop out in all his glory.

Re:Magic Eye? (0, Offtopic)

tsbiscaro (888711) | more than 7 years ago | (#17932650)

In related news, scientists discover the gay chromossome.

Re:Magic Eye? (0)

Anonymous Coward | more than 7 years ago | (#17932770)

I can do the same with random() and putpixel()

Huh - I see Skeletor (from He-Man) (1)

spineboy (22918) | more than 7 years ago | (#17933644)

And he is speaking in COBOL

Lame (4, Informative)

nacturation (646836) | more than 7 years ago | (#17931880)

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.
 

Re:Lame (1)

Yvanhoe (564877) | more than 7 years ago | (#17932070)

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 (1, Troll)

nacturation (646836) | more than 7 years ago | (#17932110)

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 (4, Insightful)

mwvdlee (775178) | more than 7 years ago | (#17932216)

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 (2, Interesting)

$RANDOMLUSER (804576) | more than 7 years ago | (#17932546)

Mendeleev notwithstanding.

Searching DNA is *hard* (1)

complete loony (663508) | more than 7 years ago | (#17932578)

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.

Re:Lame (0)

Anonymous Coward | more than 7 years ago | (#17932748)

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.
Bullshit! I've seen these patterns before during a 48 hour Quake 3 deathmatch a couple of years back. After about the 20th Jolt soda the screen went fuzzy and then I saw this pattern. It is proof that humans were designed by a Creator--to play Quake!

The major discontinuity on the second graphic ("Interesting pattern") is me sniping some poor bastard with a rail gun while camping, the third image is a detailed run through on how to rocket jump in Quake 2, and the first one is the NIN soundtrack to the original Quake.

Re:Lame (1)

hemorex (1013427) | more than 7 years ago | (#17933198)

Isn't duplication one of the most common mutations? We should see some repetition then, I would think...

Re:Lame (1, Interesting)

Anonymous Coward | more than 7 years ago | (#17932132)

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

&#928

A pattern is a patterns is a pattern (4, Insightful)

Ceriel Nosforit (682174) | more than 7 years ago | (#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.

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

sporkme (983186) | more than 7 years ago | (#17932342)

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:A pattern is a patterns is a pattern (4, Interesting)

VirusEqualsVeryYes (981719) | more than 7 years ago | (#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] ?

Re:A pattern is a patterns is a pattern (1)

VirusEqualsVeryYes (981719) | more than 7 years ago | (#17933116)

Upon further Googling (I've had enough for a couple months by now), I find it extremely interesting (telling?) that so many of these "sightings" are for sale. If it's small enough to easily ship, it's probably on eBay. Are we to believe that these people really believe their holy savior has sent them a holy sign, only to turn around and sell their very idol through a very unholy site for a couple hundred unholy bucks?

Then again, the two guys responsible for the creation of the linked story make it no secret that they're looking for a job. Come to your own conclusion, but it looks to me like there's some serious doublethink going on here.

Re:A pattern is a patterns is a pattern (1)

CaffeineAddict2001 (518485) | more than 7 years ago | (#17933926)

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."

Re:A pattern is a patterns is a pattern (2, Insightful)

radtea (464814) | more than 7 years ago | (#17933098)

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 (1)

Logopop (234246) | more than 7 years ago | (#17932478)

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 (5, Insightful)

Anonymous Coward | more than 7 years ago | (#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:Lame (3, Informative)

gnalle (125916) | more than 7 years ago | (#17932702)

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 (1)

LordVader717 (888547) | more than 7 years ago | (#17932724)

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 human than a set of repetitive characters spread over pages.

I mean, you can see a human as a bitmap image, that's gotta be cool, hasn't it?

Re:Lame (1)

SengirV (203400) | more than 7 years ago | (#17932838)

He who defines the scale(x and y axis), defines the patterns.

Re:Lame (1)

PatrickThomson (712694) | more than 7 years ago | (#17933212)

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 have done a thousand patterns until they found one unique to the torah, but that's not what the common detractors say, which is the ignorant response of "oh, if you randomise it enough anything'll fall out."

Oh, and in the original book about it, they specifically denied the ability to predict the future.

Reminds me of the Bible Code (0, Redundant)

Fred Ferrigno (122319) | more than 7 years ago | (#17931890)

If you put enough random data together, you're bound to see patterns every once in a while. I bet you didn't know God scribbled pictures [bible-codes.org] in the Bible, too.

Re:Reminds me of the Bible Code (2, Funny)

QuantumG (50515) | more than 7 years ago | (#17932142)

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

I dunno... (1, Funny)

Anonymous Coward | more than 7 years ago | (#17931904)

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.

Re:I dunno... (1)

p3lvicthrust (663089) | more than 7 years ago | (#17932570)

Whoa, looks like those things need a serious de-frag.

Your chromosomes... (5, Funny)

Riktov (632) | more than 7 years ago | (#17931910)

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

Would you like to optimize your chromosomes?

[Yes] [No] [Cancel]

Re:Your chromosomes... (1)

pubjames (468013) | more than 7 years ago | (#17932086)

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.

Re:Your chromosomes... (1)

Loke the Dog (1054294) | more than 7 years ago | (#17932244)

Well, they do that pretty well themselves, being self repairing and all, don't they?

Re:Your chromosomes... (1)

juhaz (110830) | more than 7 years ago | (#17932380)

They try, but don't do a very good job at it. Ever heard of cancer?

Re:Your chromosomes... (1)

kypper (446750) | more than 7 years ago | (#17932948)

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. . .. (5, Funny)

gardyloo (512791) | more than 7 years ago | (#17931916)

Taste the rainbow!

Re:Hey, baby. . .. (-1, Redundant)

Anonymous Coward | more than 7 years ago | (#17932138)

Just don't spill your skittles all over her.

DNA-rainbow (0, Troll)

Anonymous Coward | more than 7 years ago | (#17931932)

DNA-rainbow
I didn't RTFM-- did they just find the gay gene or is this a dupe about finding the flamboyant gene?

Re:DNA-rainbow (0)

Anonymous Coward | more than 7 years ago | (#17932358)

This isn't a troll, it's a social commentary on the whole idea of a "gay gene."

Mod parent up.

I see no patterns! (1)

Bob54321 (911744) | more than 7 years ago | (#17931946)

Only a white page with nothing on it...

Re:I see no patterns! (1)

cepler (21753) | more than 7 years ago | (#17932828)

Stop looking at MY chromosomes!

Oops (5, Funny)

tehSpork (1000190) | more than 7 years ago | (#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. :)

Re:Oops (1)

empaler (130732) | more than 7 years ago | (#17932324)

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!

Re:Oops (0)

Anonymous Coward | more than 7 years ago | (#17932544)

Hopefully the DNA will also develop a resistance to strained humor.

:-<

Re:Oops (1)

sa1lnr (669048) | more than 7 years ago | (#17932598)

"It looks like the DNA has been Slashdotted."

Does anyone else see a pattern forming here? ;)

Worthless (0)

Anonymous Coward | more than 7 years ago | (#17931972)

This is about as useful as assigning a different colour to every ASCII character and then viewing the works of Shakespeare, arbitrarily wrapped at 3500 characters. It's not beautiful, it's not insightful, and it's not worth anyone's time.

Arrgh! (3, Funny)

Anonymous Coward | more than 7 years ago | (#17932006)

My genes! They've been slashdotted!

I need tissues!

Good Science/Art websites? (2, Interesting)

Anonymous Coward | more than 7 years ago | (#17932056)

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? (1)

rkaa (162066) | more than 7 years ago | (#17932734)

Don't know about "good", but the old bomb project came to mind: http://draves.org/bomb/ [draves.org]
The Really Paranoid Reader might wish to investigate which piece of music created this [draves.org] one.

On a related note (all pun intended), it would be interesting to synthesize the chromosome images to sound.
Perhaps fragments of interesting music might be lurking there. Something to listen to while jaywalking with your iPod anyway. It would add that extra dimension to a Darwin award :)

Re:Good Science/Art websites? (1)

winterlens (258578) | more than 7 years ago | (#17933122)

My cousin has a friend who does science art: http://www.kevinvanaelst.com/art.html [kevinvanaelst.com] is the site.

forget RIAA (1)

Fist! Of! Death! (1038822) | more than 7 years ago | (#17932146)

I demand royalties

password needed?! (0, Offtopic)

probain (206453) | more than 7 years ago | (#17932208)

not much use to have a slashdot story that is password protected.
just my two cents

Re:password needed?! (-1, Troll)

Anonymous Coward | more than 7 years ago | (#17932218)

I am a gay nigger from outter space and I just had to get that off my chesticles which are hard from watching gay niggers hump each other and produce large ammounts of gay nigger sperm.

Re:password needed?! (0, Offtopic)

albyrne5 (893494) | more than 7 years ago | (#17932760)

What's a chesticle?

Re:password needed?! (0, Offtopic)

rucs_hack (784150) | more than 7 years ago | (#17932224)

its probably to halt the slashdotting.

Retard (-1, Troll)

iliketrash (624051) | more than 7 years ago | (#17932260)

How many mistakes can one poster put per line?

The link needs a password.

"groundbreaking new" is redundant.

"Anyways" is, what, Canadian?

"it's" is a fuck*ng contraction, not a pronoun. Kids, let's get this right just once, OK?

Re:Retard (0, Offtopic)

Gabrill (556503) | more than 7 years ago | (#17932500)

I dont know what yer talkin about, eh? ARe ye just trollin for the grammr coppers, or di d you just think that yer postage would actally put the fear o' God inter the submiter's braain? Braains. . . Brains . . . .

Mirror here ... (1)

foobsr (693224) | more than 7 years ago | (#17932310)

Re:Mirror here ... (1)

Irish-DnB (161087) | more than 7 years ago | (#17932658)

They're pretty underwhelming alright !

Dirty secret of HGP (-1, Troll)

AnnuitCoeptis (1049058) | more than 7 years ago | (#17932388)

Human genome project scans just the 'upper level' of the DNA and not the entire DNA sequence. We share 99% of DNA with the shimp right (now). Things are much more complicated there. It's like their binoculars captured upper boundary of the mountain range underneath.

Re:Dirty secret of HGP (3, Insightful)

Adam Hazzlebank (970369) | more than 7 years ago | (#17932404)

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!

Re:Dirty secret of HGP (1)

Oligonicella (659917) | more than 7 years ago | (#17933294)

"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.

Re:Dirty secret of HGP (1)

sholden (12227) | more than 7 years ago | (#17933344)

Do you use a special keyboard for the completely retarded?

Why 2D? (1)

cookie_token (1048774) | more than 7 years ago | (#17932450)

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 (2d/3d) spatial arrangement like in these images.

Maybe a tree-dimensional approach reveals more details / information about the structure of our genes, maybe we even need four dimensions (i.e. include the flow of time in our considerations).

Meanings in randomness (1)

gavink42 (1000674) | more than 7 years ago | (#17932508)

Even if it doesn't mean anything, putting false colors onto DNA images (or, for that matter astronomy pics) could have a positive result of attracting interest in the field.

And sometimes, they're just nice to look at!

Hey, it looks like piet source code! (2, Interesting)

MrTrick (673182) | more than 7 years ago | (#17932518)

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:Hey, it looks like piet source code! (0)

Anonymous Coward | more than 7 years ago | (#17932646)

The genome can be interpreted as a program, the interpreter would be the minimum cell that can use the genome. The binaries would provide you with whatever output youd want from such a simulation. Perhaps the entire stochastic simulation of a cell cycle under particular conditions or just the secreted products in a iron-poor environment.

Re:Hey, it looks like piet source code! (0)

Anonymous Coward | more than 7 years ago | (#17932936)

They would make more binaries.
The process you refer to is known as "life".

Re:Hey, it looks like piet source code! (2, Insightful)

Neeth (887729) | more than 7 years ago | (#17933380)

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.

Seen it Before (1)

camperdave (969942) | more than 7 years ago | (#17932566)

I've seen that before... when my TV was on an unused channel and someone started blow-drying their hair.

Near miss (1)

The Cornishman (592143) | more than 7 years ago | (#17932580)

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 meaningful biological message that the site as it stands is just a bit less interesting than zooming in on bits of the Mandelbrot set. FRACTINT, anyone?

I've seen that pattern before (2, Insightful)

bl8n8r (649187) | more than 7 years ago | (#17932606)

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

Paradoelia (1)

aepervius (535155) | more than 7 years ago | (#17932634)

Seeing structure where there isn't any Quote :

Strange structures (close your eyes just a little bit to see more details)

Re:Paradoelia (1)

cnettel (836611) | more than 7 years ago | (#17932804)

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 the origin of sequences.

Well... no symbol there... (1)

denzacar (181829) | more than 7 years ago | (#17932680)

Who's ever those genes are - he or she is not on the list. Move along.

But nice to see that they have upgraded Prof. Suresh's software to do colours.

Genetics (3, Funny)

worst_name_ever (633374) | more than 7 years ago | (#17932762)

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

Re:Genetics (0)

Anonymous Coward | more than 7 years ago | (#17933690)

pay no attention to these 'hypocrites'

YUO FA1L IT? (-1)

Anonymous Coward | more than 7 years ago | (#17932792)

Be a cock-sucking Don't walk around of the old going Dying' croWd - gave the BSD

Why 2D? What happens in 3D? (1)

140Mandak262Jamuna (970587) | more than 7 years ago | (#17932820)

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 google on a particular search term.

If they kept the 1D data in 1D and enoded it as music or sound we could use all the technology developed in Digital Signal processing and come up with even more bizzarre stuff. For example the DNA mole could actually sound "Om bhur bhuvasuvaha, Om tats vidhuvareNyum, Bhargo dhiivasya dheemahi, Diyoyona prasaadayaad". Just have to select proper notes and pitches.

As we statisticians say (1)

dorpus (636554) | more than 7 years ago | (#17932844)

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.

Re:As we statisticians say (1)

Tim (686) | more than 7 years ago | (#17933016)

"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 description. If the poission wasn't your null hypothesis, what was?

Note: I am not an expert in this field, so it's a serious question.

Re:As we statisticians say (1)

dorpus (636554) | more than 7 years ago | (#17933100)

If "point replication errors occur randomly and without mechanistic bias", that would imply a uniform distribution. A uniform distribution looks very different from a Poisson process (note I said process, not distribution).

Hmmmm... (2, Funny)

flajann (658201) | more than 7 years ago | (#17932860)

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 [urlbit.us] 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.

Re:Hmmmm... (1)

Oligonicella (659917) | more than 7 years ago | (#17933248)

"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 new definition of sophisticated science.

See if you can explain to everyone here just how using his approach (with which I am familiar and just watched your pretty useless link) would be different from what's being done in DNA research now. You don't think folks already understand that genes do or do not survive?

Neural evolution is the result of biological evolution.

This isn't a new idea (1)

FellowConspirator (882908) | more than 7 years ago | (#17932888)

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.

Binary data (1)

Happosai (73708) | more than 7 years ago | (#17932894)

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]

windows is more artistic than our dna (1)

circletimessquare (444983) | more than 7 years ago | (#17932932)

proof [slashdot.org]

(and it's also more artistic than linux)

mov ax,13h; int 10h (1)

dmbasso (1052166) | more than 7 years ago | (#17933026)

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! :)

And Thus... (1)

eno2001 (527078) | more than 7 years ago | (#17933638)

...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 is teh crap (1)

inviolet (797804) | more than 7 years ago | (#17933664)

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 (conspiracy theory anyone?), computers are better at this particular kind of detective work. Tell folding@home to crunch the data for a few hours and see if there are any repeats. Or just sic the LZW algorithm on it... LZW long ago mastered the art of finding patterns in large blocks of data.

cheap gibe (1)

Floritard (1058660) | more than 7 years ago | (#17933718)

if they had used Tom Cruise's DNA the resulting rainbow pattern would probably approah a visual singularity.

Heroes (2, Funny)

kalirion (728907) | more than 7 years ago | (#17933778)

So, which colors represent superpowers?
Load More Comments
Slashdot Login

Need an Account?

Forgot your password?