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The Art, Music And Computer Science Of DNA

timothy posted more than 11 years ago | from the meeting-nucleotides-is-easy dept.

Biotech 95

Build6 writes "As part of the 50th anniversary of the discovery of DNA's double-helix structure, many news publications are writing about what has been done with the discovery so far; The Economist has a very interesting one about DNA's use in art and music. ... You can read all about it either by picking up a copy of The Economist (it's well worth the money, I've subscribed for over a decade), or online." And Clint Harris writes "As part of its series commemorating the 50th anniversary of 'the first scientific description of DNA' NPR recently aired a story comparing DNA to software (RealAudio or Windows Media). 'For many, the best analogy for the way DNA works is that it's like a computer program at the heart of every cell. Some of its programming tricks bear an uncanny resemblance to ones the human brain has dreamed up...DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.'"

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FP? (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816647)

Teehehehe :)

Let's not forget... (4, Interesting)

graveyhead (210996) | more than 11 years ago | (#5816648)

Software (and now hardware too...) that is inspired by DNA recombination [genetic-programming.com] .

First post for freedom! (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816650)

Penis birds fly in victory!
Sadam is the Goatse man!

Koo koo kajoob!

Troll? (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816698)

Bitch please, I'll show you Troll!
Troll is yo momma!

Not enough Mod points for all of us...
TROLL
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V IRII TO KARMA WHORES
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Pre-DNA Discovery DNA References? (3, Funny)

Anonymous Coward | more than 11 years ago | (#5816651)

Is it really a coincidence that a Caduceus/Kerykeion [medhelpnet.com] has a pair of intertwined snakes? (Some people say that's proof of ancient knowledge!)

Re:Pre-DNA Discovery DNA References? (2, Interesting)

nrlightfoot (607666) | more than 11 years ago | (#5816781)

The intertwined snakes on a pole symbol comes from the Bible. While the Isrealites were wandering around in the desert complaining, God got tired of it. So, he sent poisonous snakes to bite them, but also had Moses make a pole with bronze snakes on it. anyone who was bitten could look at the pole and not die. At least it was something similar to that, I might have the details a little wrong.

Re:Pre-DNA Discovery DNA References? (2, Interesting)

Anonymous Coward | more than 11 years ago | (#5816791)

Here's the explanation: http://www.medhelpnet.com/caduceus.html [medhelpnet.com]

Re:Pre-DNA Discovery DNA References? (3, Informative)

Anonymous Coward | more than 11 years ago | (#5817295)

Actually that link doesn't give all the information. While it is true that the Cadeuceus was the staff of Hermes and had two intertwined snakes, it doesn't explain why it's associated with the medical profession. Asclepius was the greek god of medicine. According to myth, he carried a staff which he used to heal. That staff had only one snake around it. Somewhere along the way, the Cadeuceus and the staff of asclepius were mixed up.

I know... (1, Informative)

Anonymous Coward | more than 11 years ago | (#5816655)

the Economist always backs this community on every financial issue. they're well worth the money.

You heard it here first... (4, Funny)

Anonymous Coward | more than 11 years ago | (#5816662)

...God's a VB kiddie :)

This amazing complexity evolved!! (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816663)

Yeah, uh huh!

DNA, as complex a creation as any program written by man.........came out of nothing.

Yup. Sure did. Boggles the mind.

Adventurers quote =) (1)

EvilSporkMan (648878) | more than 11 years ago | (#5816667)

Boggle you say? Ha, Gorilla, RIGHT THERE!

Bad Programming? (4, Interesting)

johny_qst (623876) | more than 11 years ago | (#5816672)

I'm really confused by someone equating obtuse code they can't understand as bad programming. I want more discussion on how the information encoded in genes acts. Not "This is the worst kind of spaghetti code you can imagine..." and posturing like we can't possibly understand it.

Re:Bad Programming? (2, Interesting)

Anonymous Coward | more than 11 years ago | (#5816707)

Dude, you obviously haven't taken an intro-level biology course. DNA transcription has so many stop-here, skip-here, start-here signals, that many times there's huge chains of "introns", information that just gets excised from the final product. A single mutation can change something from a regular codon (think of them as words) to a stop codon, rendering everything that follows (up to the next start) junk data.

So, that's how nature writes spaghetti code. Constantly commenting out loops, etc.

Re:Bad Programming? (1, Interesting)

Anonymous Coward | more than 11 years ago | (#5817003)

Plus the exons (the coding bits left over after you take out the introns) can be alternatively spliced. It's more like a (eukaryote) gene is a set of library calls than a program.

Re:Bad Programming? (1)

etcpasswd (641551) | more than 11 years ago | (#5818365)

A better analogy is to compare the DNA to a binary executable. A decent optimizing compiler generates code that isn't easily comprehensible by humans*. The DNA and the binary executable are intended to the same job - just execute. They are not meant for humans to understand.

* Or a few C programs at IOCCC [ioccc.org] that pack LOT of functionality into a small program?

DNA software (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816685)

I've tried lots of different DNA software.

Unfortunately, there is no decent Linux DNA software. Its all VERY slow and VERY buggy.

Windows DNA software, on the other hand, is fast and a joy to use. When it comes to DNA software, stick to Microsoft - trust me on this one.

I just wish there was a viable Linux alternative.

If DNA is like programming... (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816686)

...then slashdot must be retarded.

Cool (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816695)

Fart Fart first post www.notslashdot.org

what we REALLY need... (2, Funny)

ansleybean (618941) | more than 11 years ago | (#5816696)

object oriented genes.

Re:what we REALLY need... (1)

toddhisattva (127032) | more than 11 years ago | (#5819396)

Object-oriented genes? After reading "The Selfish Gene" I'd call genes Objectivist-oriented ;-)

Bad programming? Well.... (5, Funny)

Anonymous Coward | more than 11 years ago | (#5816699)

As soon as YOUR code has had uptime of 120 years or so, then you can say nature wrote us poorly.

Re:Bad programming? Well.... (0, Offtopic)

Tim (686) | more than 11 years ago | (#5817097)

"As soon as YOUR code has had uptime of 120 years or so"

Uhm...it's more like 120 billion years, give or take.

Of course, I guess that's all considered legacy code by now, isn't it?

Re:Bad programming? Well.... (1)

orkysoft (93727) | more than 11 years ago | (#5817147)

No, it's not nearly 120 billion years, at least for Earth.

Also, you're counting the total time span for countless child processes, not the uptime of one single process.

Bad Programmer? (4, Insightful)

trotski (592530) | more than 11 years ago | (#5816705)

DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.

Wow, that sure is an arrogant statement. The chemical, physical and biological systems of nature are the most complex systems we know of. Nature is influences by a seeingly infinate number of variables. We don't understand much more than we do.

Our understanding of the world is far too small to be critiszing nature works and it's language. When humanity can create a WORKING system thats 1/1000th as complex as the natural world is when we can even start to make arrogant statements such as this. Today is not yet that day.

Re:Bad Programmer? (0)

Anonymous Coward | more than 11 years ago | (#5816719)

Wow, you are such a dork. I think it's beautiful the way nature has ended up creating us. That's not a criticism, that's an accurate summary of the mechanism nature has for evolution

Re:Bad Programmer? (0)

Anonymous Coward | more than 11 years ago | (#5816724)

"We don't understand much more than we do."
I don't know about you, but I don't know anything much more than I do.

Re:Bad Programmer? (1)

trotski (592530) | more than 11 years ago | (#5816739)

Hehehe.... oops. Had a tough day at work, sorry.

I think that was kind of the point (4, Insightful)

Trepidity (597) | more than 11 years ago | (#5816738)

Nature designs things in an incredibly complex way, because that's simply how evolution works -- there's certainly no software engineering notion of clean component separation and so on in evolution. So it ends up certainly being complex, working, and possibly even beautiful, but a nearly impossible to decipher mess of spaghetti. Sort of like an old-school assembly programming genius designing an enormous 500,000-line program in assembly -- it'll work beautifully, but nobody will have any idea what the hell is going on, or be able to modify it. Similar problems exist when trying to genetically engineer things; you're always going to mess something up.

Re:Bad Programmer? (4, Funny)

milkmandan9 (190569) | more than 11 years ago | (#5816792)

The chemical, physical and biological systems of nature are the most complex systems we know of.
Especially if these chemical, physical, and biological systems happen to be female.

Re:Bad Programmer? (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#5816864)

If you do anything with a woman, do it in an illogical manner. Be as unreasonable and illogical as possible, and you will get the results. No, it doesn't make sense.

Re:Bad Programmer? (2, Insightful)

Ieshan (409693) | more than 11 years ago | (#5817121)

Here's a quote which, at the heart, sums up *why the programmer analogy is wrong*:

Natural selection cannot play God, because it is a blind process with no goal in mind and no means to get to a predetermined endpoint.
-John Alcock, Animal Behavior, 7th ed.

Programs are tools for a purpose. DNA is not.

Re:Bad Programmer? (1)

Alsee (515537) | more than 11 years ago | (#5819903)

Out of context the quote you used looks like a creationist argument that evolution can't reach the "goal" of complex life. I almost replied to you based on that misreading. I just had to delete an entire post, lol.

You're actually saying that DNA is "spagetti-code" because it's created at random. No objections here :)

-

Re:Bad Programmer? (1)

Ieshan (409693) | more than 11 years ago | (#5820589)

Right - and it's so random that it has no ultimate purpose. All programs have a purpose, DNA doesn't. Long-term changes in DNA happen because of changes in the immense system that DNA is a part of.

For instance, cheetahs didn't get faster in able to catch prey - one day, a faster cheetah was born who had the potential to survive longer, and he mated more, and spread his "fastness" through DNA - these individuals had greater potential than the rest of the individuals in the population, and the DNA changed in the long term. But at the outset, the faster invdividual wasn't biased-to-win, he was a fluke of nature, a mutation.

That's how DNA ultimately changes - mutation. Fluke things that end for better or for worse.

Re:Bad Programmer? (1)

brrent (129448) | more than 11 years ago | (#5817948)

Agreed. I suspect that nature uses a
lot of goto's as well. Goto's produce
'code' that is hard for us to
understand. Perhaps the only efficient
way to grow the 'wiring' that
constitutes a human brain is organically
without concern for complication. I suspect (I
do not know, I'm not an expert) that as
long as AI researchers look for an elegant
solution, they are destined to miss the
goal. Nature's designer doesn't seem to
share the human passion for regular
polygons, straight lines and clearly
stated theorems. Physicists may dismiss such
thinking, I don't know that biologists
would.

Brent

Re:Bad Programmer? (1)

Alsee (515537) | more than 11 years ago | (#5819805)

We don't understand much more than we do.

I love that sentence. Yep, and I don't have much more money than I have either.

Our understanding of the world is far too small to be critiszing nature works and it's language.

We shouldn't criticize nature works and it's language? OOOooo! OOoo! NATURE! It's arrogant to talk about NATURE! LOL. Could you possibly be thinking "god's works and god's language"? Why else would you be offended? Well if you mean god then why not come out and SAY god?

When humanity can create a WORKING system

Chuckle. There are numerous articles reporting we'll be building our first synthetic minimal cell soon. Check google.

I've written various genetic algorithm programs and watched evolution in action. Evolution goes with whatever happens to work better than it's last random attempt. It is filled with garbage and inefficencies and errors and lousy "spagetti code". Oh wait, something tells me you don't think random evolution explains nature's works. It would be arrogance to criticize nature's works by pointing out that DNA spagetti code sometimes results in two-headed babies. That's obviously part of nature's wisdom. It's arrogant to criticize two-headed babies :D

-

Re:Bad Programmer? (1)

brahms3 (668893) | more than 11 years ago | (#5823378)

The bad programmer paradigm is probably intended to infer our inferiority and nature's superiority in this arena. Ever get a programmer nut whose code you couldn't fathom? Well we all thought he was a nut but turned out he was a genius. The spaghetti code method he used was appropriate because he could handle the complexity. The rest of us are taught OOP and the like in an attempt to simply our own complicated and misunderstood minds and program something useful and maintable by us (when we've forgotten how we wrote the code) and our peers (who have no clue how individual minds wrap themselves around things.)

I met a GIRL today (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#5816708)

Hey guys I met a real girl today and I think she likes me.

She gave me her phone # and it doesn't start with 555! I'm so
excited, I met get to score!

Anyhow, I just had to tell someone. I'm going to go call her
right now!

Wish me luck!

Re:I met a GIRL today (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#5816743)

Good luck!

Uh Oh... (0)

Anonymous Coward | more than 11 years ago | (#5816710)

DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer

For craps sake don't let BillG's company let rip on it... the genetic horror of it (plus the EULA wouldn't be fun).

Re:Uh Oh... (1, Funny)

Anonymous Coward | more than 11 years ago | (#5816954)

(plus the EULA wouldn't be fun)

Agreed. I'm sure it would include a passage about duplication and reproduction without a license from MS. Well thank god, finally a reason to have MSDN site licenses.

Had a comment... (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816711)

But was moderated into an Overrated Troll

Soooooooo..........

IN SOVIET RUSSIA...
You make your OWN genes and prefer spaghetti code!

You made me but you can't mod me out of existence BEYATCH!

Anyone else....? (2, Offtopic)

slulovic (636452) | more than 11 years ago | (#5816712)

Anyone else find it funny that most gene sequences are proprietary, and hence even DNA isn't Open Source? --Scott

Re:Anyone else....? (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816717)

I find that you are an Overrated Troll!

-1 Overrated
-1 Troll
-1 Flamebait
-1 Offtopic

Troll Troll Troll Troll Troll Troll

Re:Anyone else....? (0, Offtopic)

Uber Banker (655221) | more than 11 years ago | (#5816747)

SUrely you are the troll?

The parent post hasn;t even been modded yet.

You are a sad sad sad troll troll troll. loser.

Re:Anyone else....? (1)

etcpasswd (641551) | more than 11 years ago | (#5818347)

I thought genes are under GPL: You can fuc^H^H^H^Hork as many times as you want to modify and distribute the code.

Genetic Programming (4, Interesting)

CBNobi (141146) | more than 11 years ago | (#5816746)

DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.

How ignorant of you to say that. There was an article in the Feb. 2003 issue of Scientific American about genetic programming - the creation of new devices and electronic circuity by computer.

It basically involves starting out the core components (resistors, inductors, capacitors, etc) and a design (for a voltage-current converter, perhaps). A supercomputer is able to rewire the circuit through basic evolutionary processes including crossover, copying, and extinction, and come up with a much more efficient circuit.

The resulting circuitry is so effective and original that there have been designs that earned approval from the patent office. They're so complex, much like nature's genetic code.

Sure, it might look like spaghetti code - but you mean to tell me, nature is a bad programmer? Heh.

Google search on genetic programming [google.com]
Everything2: Genetic programming [everything2.com]
What is Genetic Engineering? [genetic-programming.com]

Re:Genetic Programming (1)

CBNobi (141146) | more than 11 years ago | (#5816755)

The last link is about genetic programming; I just typo'ed 'genetic engineering'.

Carry on...

Re:Genetic Programming (2, Informative)

Saeger (456549) | more than 11 years ago | (#5816998)

The resulting circuitry is so effective and original that there have been designs that earned approval from the patent office.

And, IMO, it's a very bad idea to hand out patent monopolies for designs that no human invented, especially if no one can even understand how the damn thing works!

It's not that patents on evolved solutions -- which are both computationally expensive to produce, and to manufacture physically -- wouldn't necessarily promote progress (unless we're talking software algorithms), but that we'll end up with the richest corporations going for another huge IP landgrab with their "patent invention machines" [slashdot.org] set to 'Ludicrous Speed'. Isn't it bad enough that they've already squatted on our genes?

--

Re:Genetic Programming (1, Funny)

Anonymous Coward | more than 11 years ago | (#5817213)

You misspelled "ludacris"

Re:Genetic Programming (0)

Anonymous Coward | more than 11 years ago | (#5817280)

A milliondollar supercomputer isn't necessary to run a genetic algorithm; you can get amazing results [poznan.pl] with only 2GHz to play with.

Re:Genetic Programming (1)

graveyhead (210996) | more than 11 years ago | (#5817058)

Good point, you have elaborated fairly well on my frost pist.

I have tried to point this out on multiple occasions, but slashdot readers are hung up on the fact that some people seriously abuse patents. Not everyone does.

In this case, the patentability of an invention provides a direct comparison between genetic programming (or in fact, any AI that purports to be able to design or invent software or hardware) and human intelligence.

With such a yardstick, we can directly measure the progress that genetic programming is making as a science.

Other than that, John Koza (the inventor of GP and [less known fact] scratch-off lottery tickets) doesn't seem to me to be the type [genetic-programming.com] to hold patents over peoples heads.

James Watson. (3, Informative)

I'm a racist. (631537) | more than 11 years ago | (#5816751)

I've been pleasantly surprised by all the attention the 50th anniversary of the discovery of DNA has gotten.

It got to be the Google logo [google.com] . Cold Spring Harbor Laboratories [cshl.org] has been very active in celebrating this. Among a few other things, they've had a really nice lecture series to commemorate the event.

I'm a little bit closer to the whole thing since I've done some genetics work (mostly at the Columbia [columbia.edu] Genome Center [columbia.edu] ). My current work involves some genetic manipulation, but that's not the main focus.

Also, I happen to personally know James Watson. I first met him when he spoke at my commencement. But, I shouldn't tell that story, because it has some racist (and very amusing) content... which would only get me modded as a troll. I've kind of worked with him a bit since then, and he's really a very nice, down to earth, intelligent guy. He hasn't really let this whole thing go to his head.

Anyway, it's very nice to see the general public taking a little bit of interest in science. Maybe this will help to turn some of the scientific illiterates into elites [phds.org] ...

Re:James Watson. (1, Interesting)

Anonymous Coward | more than 11 years ago | (#5816825)

Also, I happen to personally know James Watson. I first met him when he spoke at my commencement. But, I shouldn't tell that story, because it has some racist (and very amusing) content... which would only get me modded as a troll. I've kind of worked with him a bit since then, and he's really a very nice, down to earth, intelligent guy. He hasn't really let this whole thing go to his head. Well, if your work was based on the (alleged) theft of someone else's work (Rosalind Franklin), wouldn't you be a little modest?

Re:James Watson: Theif, Fraud. (2, Informative)

stanwirth (621074) | more than 11 years ago | (#5817955)

Not alleged theft, but well established, and admitted. Maurice Wilkins gave Watson and Crick the keys to Franklin's lab, and the locked drawer where she kept her X-ray photos. Of the DNA that she grew. Using the X-ray camera she designed and built herself .

In their own defence, they tried to dismiss her as a mere "lab tech" (with a Ph.D. and several publications? I don't think so!) and then put her down in their book The Double Helix by wondering repeatedly, in print, whether she'd look any more attractive if she did "something more interesting with her hair."

READ ABOUT IT HERE [amazon.com]

Re:James Watson: Theif, Fraud. (0)

Anonymous Coward | more than 11 years ago | (#5818444)

Not alleged theft

Alleged as in a legal sense.

Re:James Watson. (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5816957)

You, my good sir, are a jizz-guzzling cock-monger with a penchant for anally intrusive gratification modalities. May your racist shitcakes of like-minded circle-jerkers all get sars and infect each other again through semen-ingestion and get treated with caustic enemas by burly nurses.

Dumb nigger. (-1, Troll)

Anonymous Coward | more than 11 years ago | (#5817226)

Awww... the poor nigger feels threatened. Gee, what a fucking shame!! Maybe you dumbasses should've thought about what people would think of you before you sold yourselves into slavery...

That's right! Niggers sold themselves into slavery. Do you really think the Europeans would go running through the jungles with nets to catch some porch monkeys? Fuck no! They'd just trade some cheap manufactured goods (often guns) to one tribe who had recently captured their neighbors. Then, the tribe with the guns could catch even more jungle bunnies.

For this, niggers have no right to be indignant about their enslavement. Nor do they have any right to get all uppity over their treatment. If they weren't such fucking filth, then they wouldn't be considered as equivalent to walking shit.

Finding DNA solutions (4, Funny)

teamhasnoi (554944) | more than 11 years ago | (#5816754)

I don't see why the scientists don't just look at the REM statements...they'd have that stuff figured out in no time.

"Geez, it says here that the next 24,000 lines of code are wholly dedicated to picking one's nose!"

I'm sure that they would find that politicians are the result of millions of unreturned GOSUB commands.

Re:Finding DNA solutions (0)

Anonymous Coward | more than 11 years ago | (#5816845)

Naw its all decompiled code not the sourcecode we the life compiler left out the REM statements.

Re: Finding DNA solutions (1)

Black Parrot (19622) | more than 11 years ago | (#5818304)


> "Geez, it says here that the next 24,000 lines of code are wholly dedicated to picking one's nose!"

Yes, but it's just a mutation of the scratch-your-arse code.

Think of it as OOP-style inheritance in action.

I suppose DNA could be like computer software, if. (1, Funny)

Anonymous Coward | more than 11 years ago | (#5816762)

...I could mate Microsoft Office with Star Office and crossbreed an office suite that is both free and feature complete...

Can anyone explain this to me? (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#5816765)

DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.

English is not my first language. Can anyone please explain why the word "like" is in brackets, and what this means? Thank you.

Re:Can anyone explain this to me? (1, Informative)

Anonymous Coward | more than 11 years ago | (#5816785)

It means that the word "like" wasn't in the original quote, it was instead added by the writer/editor.

The original quote said, "DNA is spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer."

The writer and/or editor added the word "like" because they felt it corrected a grammar problem with the sentence, captured the tone better (which may have gotten lost when writing down the sentence), or it made the sentence more clear.

Re:Can anyone explain this to me? (2, Informative)

Namaseit (668654) | more than 11 years ago | (#5816798)

its in brackets because it wasnt said in the quote but was implied.

no analogies allowed (3, Interesting)

hachete (473378) | more than 11 years ago | (#5816830)

Well I guess the problem with the posting is the analogy. Comparing genetic "code" to software implies that there's a writer - in this case "nature" - who is either "good" or "bad" in the works that it perpetrates. The aesthetic and/or moral values of "good" or "bad" don't exist in the evolutionary process, only what works. If a sequence works, then the sequence survives. If it doesn't it dies. Consider Linus when he talks of DRM and Linux: he wants Linux to survive so he won't object to DRM being inserted into Linux; he doesn't want Linux's chances of surving limited. OTOH, RMS is a moralist and an idealist. He doesn't want DRM in Linux - in fact, he sees Linux as a weapon *against* DRM. If he succeeds in pre-empting DRM from Linux, then he will have closed off a route of survivability for Linux - in evolutionary terms, a major no-no.

Of course, this pulls the analogy apart from the inside: no aesthetic or moral judgments, no writer-figure ghosting in the background. What we have is a an autonomous, self-organising system - a far more interesting prospect if you ask me.

Of course, calling it "spaghetti-code" enables you to insert that programmer-figure into the argument. All spaghetti-code needs re-factoring right? Tweaking to make it "right" make it work "better"? I dunno; the self-autonomous self-organising model has worked quite well up to now...and, lets face it, when has trying to make something "better" produced less bugs than you first started with? Particularly with something you barely understand in the first place and are desperately trying to portray with ill-thought out analogies.

h.

Like a bad programmer? (2, Interesting)

Anonymous Coward | more than 11 years ago | (#5816842)

Spaghetti code is only dangerous because it's hard to follow and thus understand, a barrier to maintenance and sharing with others. Perhaps the "programmer" simply has the capacity to know and understand the implications of each piece of the code at once - and perhaps also doesn't wish to share the code with other developers.

Microsoft Take note (1)

Papa Legba (192550) | more than 11 years ago | (#5816856)

Even though it is composed of major spaghetti code and is attributed to a bad programmer hacking away at it for billions of years, DNA has not suffered a root level exploit yet! Stick that in your trustworthy computting pipe and smoke it.

Uh - what about EBOLA and other viruses? (0)

Anonymous Coward | more than 11 years ago | (#5816970)

There is left over viral DNA from millions of years ago still left in our junk dna areas.

Re:Microsoft Take note (0)

Anonymous Coward | more than 11 years ago | (#5817044)

DNA has not suffered a root level exploit yet!

Except for sexually transmitted viruses.

Re:Microsoft Take note (1)

Dynedain (141758) | more than 11 years ago | (#5817093)

AIDs?
Black Plague?
Smallpox?
Polio?
Ebola?
. .. ...

Re:Microsoft Take note (1)

jonhuang (598538) | more than 11 years ago | (#5818056)

Maybe.. but as they say, with physical access you can break anything. Viruses actually insert in extra code.

A better example of an exploit would be telling someone to take their right hand and pat their head, take their left and rub their tummy.. and then laugh as the buffer overflow makes them fall on their arse.

Re: Microsoft Take note (1)

Black Parrot (19622) | more than 11 years ago | (#5818317)


> Even though it is composed of major spaghetti code...

Well after all, it implements the control program for a machine that makes spaghetti. What kind of code were you expecting?

> ...and is attributed to a bad programmer hacking away at it for billions of years

Well, code does tend to become more spaghetti-like the longer it is maintained.

> DNA has not suffered a root level exploit yet!

Viruses exploit it all the time.

correction (3, Informative)

NotAnotherReboot (262125) | more than 11 years ago | (#5816876)

It was not the 50th anniversary of the discovery of DNA, it was the 50th anniversary of the publication of Watson and Crick's paper saying that DNA possibly has a double helix.

It's kind of funny, everyone seems to be making this mistake, I heard the vice president of Clonaid talk just yesterday, and he said the same thing. Not that Clonaid is a legitimate company. :p

Re:correction (1, Informative)

Anonymous Coward | more than 11 years ago | (#5817021)

No, it's more like the 50th anniversary of the paper saying that all DNA possibly has a particular double helix structure. Many people prior to this thought a double helix was possible, some of Franklin's X-ray data (insert Adelaidian plug for Bragg family here) strongly suggested a double helix for one of the forms of DNA (she in fact misunderstood some of her data on the other form so she didn't think it was a double helix, iirc).

Twenty years ago... (4, Interesting)

jazzbazzfazz (600773) | more than 11 years ago | (#5816917)

Douglas R.Hofstadter discussed very similar ideas in his book Godel, Escher Bach, an Eternal Golden Braid. It was published in 1979, won a Pulitzer Prize and is virtually certain to change the way you look at pattern recognition and AI, genetics, musical innovation and a host of other areas of human intelligence.

If you haven't ever picked it up, give it a try. You can read it on a very superficial level and enjoy the dialogs among the characters, flip through it for the Escher prints...but eventually you'll start digging deeper and see things in the same words that you didn't see before. Highly recommended!

Re:Twenty years ago... (1)

jpkunst (612360) | more than 11 years ago | (#5820623)

I second that. I do have to say that the Godel part of the book is more interesting and enlightening than the Escher and Bach parts, though. Only after reading GEB I actually understood what Godels Theorem was about.

JP

(I wonder why I can't use ö? Now I have to spell Godel's name wrong.)

Not the only musician composing w/ DNA... (4, Informative)

Zanthany (166662) | more than 11 years ago | (#5816918)

The "Sonic Gene" mentioned in the Economist article is not the only one. I attended university where one of the piano professors has been working on a project like this for many years now.

His name is Brent D. Hugh, and he has downloadable .mp3s here. [mp3s.com] This has been a pet project of his, and it's definitely worth checking out. His personal site is available here [mwsc.edu] as well.

Happy listening!

Ahhh (3, Funny)

Timesprout (579035) | more than 11 years ago | (#5816947)

Now you tell me. I just hired nature last week. She told me she had loads of experience coding on big projects.

Source code for a bacterium (2, Funny)

theCoder (23772) | more than 11 years ago | (#5816965)

#include <unistd.h>

int main(int argc, char** argv)
{
while (1) fork();
return 0;
}
So, you think if I run this long enough it'll evolve into an AI? :)

Re:Source code for a bacterium (0)

Anonymous Coward | more than 11 years ago | (#5817111)

Are differences inserted by computational bugs merely genetic mutations?

like a bad programmer (1)

shadowbearer (554144) | more than 11 years ago | (#5817089)

No, more like a poorly programmed AI with a limited rule set.

SB

Re:like a bad programmer (1)

etcpasswd (641551) | more than 11 years ago | (#5818372)

Did you ever wonder who put the "I" in "AI"?

A variation on the theme... (2, Interesting)

unique13 (668835) | more than 11 years ago | (#5817120)

Perhaps DNA is more akin to highly optimised compiler output, as opposed to the source code.
It doesn't matter how elegant your implementation is, once an optimising compiler has done it's business the results aren't going to be very pretty to look at (or easy to understand).
As soon as a talented group of software engineers develops a useful decompiler/dissassembler for them, the geneticists will start to be freed from the low level detail overload and some of the elegance of the design will no doubt become more apparent.

Spaghetti Code == Bad? (0)

Anonymous Coward | more than 11 years ago | (#5817623)

While the DNA code has been likened to spaghetti code, keep in mind it's only had one developer working on it since life began. This developer is pretty adept at manipulating the code, even if only at a slow rate.

I wonder how stable the code will be when we patch it with our changes (given the past behavior of our scientists this seems inevitable). If genetic programming is ever allowed, maybe testing should take generations to complete rather than receive the relatively light review of the FDA.

After all, the current maintainer seems to have a knack for working out the bugs... er..

basta! (1)

coloth (630330) | more than 11 years ago | (#5817872)

Everybody knows only bad programmers write spaghetti code. Nature clearly writes fusilli lunghi code. Just look at it!

spaghetti code? (1)

oohp (657224) | more than 11 years ago | (#5818081)

Maybe it's just like obfuscated C and we're to stupid to understand it.

Molecular music (2, Informative)

zoeblade (600058) | more than 11 years ago | (#5818185)

Dr. Linda Long had been doing something similar [molecularmusic.com] with Music of the Plants and Music of the Body.

Comparing DNA to software (1)

oddityfds (138457) | more than 11 years ago | (#5818194)

NPR recently aired a story comparing DNA to software (RealAudio or Windows Media).

Does that mean that Men are from Real, Women are from Microsoft?

Billions of Years? (2, Insightful)

pantropik (604178) | more than 11 years ago | (#5818227)

'For many, the best analogy for the way DNA works is that it's like a computer program at the heart of every cell. Some of its programming tricks bear an uncanny resemblance to ones the human brain has dreamed up...DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.'


That isn't very efficient. Microsoft did the same thing with the Windows codebase in only 20 years ...

Seriously, though, I don't think this statement is as arrogant as some of the posters before me claim. Nature IS a bad programmer. Its arsenal consists of trial-and-error and brute force.

Given the scale nature works on (billions of years) it's not a bad way to go about things. A few million years testing out a given design seems slow and ponderous to us but from the point of view of evolution itself it's no big deal. Plenty of time to try again.

There's apparently been plenty of time for nature to develop a sense of humor. [pl.atyp.us]

ack (1)

drik00 (526104) | more than 11 years ago | (#5818312)

DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.



I dont know that I could imagine a worse metaphor. Anyone that has ever studied the tendencies of human beings to be insanely ethnocentric and myopic should appreciate what I mean. To make an analogy that the simplistic beauty of DNA is anything like "spaghetti code" is hilarious. You're comparing a bad algorithm method with an incredibly complex (yet very beautiful in its simplisitic design) and far more brilliant system. Most programmers cant write code to do one simple task without having some sort of bug or malady arise, whereas DNA is able to manipulate individual molecules and chemical reactions in order to create a system magnitudes above anything the most brilliant human could think to design. Its like comparing apples to books if you ask me.



J

Re:ack (1)

FallLine (12211) | more than 11 years ago | (#5818678)

I dont know that I could imagine a worse metaphor. Anyone that has ever studied the tendencies of human beings to be insanely ethnocentric and myopic should appreciate what I mean. To make an analogy that the simplistic beauty of DNA is anything like "spaghetti code" is hilarious. You're comparing a bad algorithm method with an incredibly complex (yet very beautiful in its simplisitic design) and far more brilliant system. Most programmers cant write code to do one simple task without having some sort of bug or malady arise, whereas DNA is able to manipulate individual molecules and chemical reactions in order to create a system magnitudes above anything the most brilliant human could think to design. Its like comparing apples to books if you ask me.
All of this may be true, but I think you're missing the point. The comment is not to slight its design, but to point out that its interface is such that it lacks the abstraction that would allow us humans to manipulate it directly, without experimenting a lot and seeing if we like the results. I highly doubt that we'll ever be able to know how to tweak bit X to get result Y and nothing else--it just doesn't work that way.

Biology is a hack, albeit a very successful one (2, Informative)

dexter riley (556126) | more than 11 years ago | (#5819665)

Most programmers cant write code to do one simple task without having some sort of bug or malady arise, whereas DNA is able to manipulate individual molecules and chemical reactions in order to create a system magnitudes above anything the most brilliant human could think to design.

As a molecular biologist/computer progammer, I think you are giving DNA too much credit. Just as a single error in a piece of code can cause it to crash, a single base mutation in an organism's DNA can either a)cause it to abort during development or b) give it any of a thousand different diseases, from the annoying (myopia) to the deadly (Cystic Fibrosis, Huntington's, Cancer, and so on). The genetic code is a hack; a hack developed over 4 billion years that works just well enough to keep making more copies of itself.

This doesn't mean that life isn't incredible. Biological systems may be kludges, built off the remnants of older versions of itself, out of countless imperfect parts (like DNA which accumulates mutations, or proteins which can be misfolded or poisoned), but it has produced organisms that live in every concievable niche, including one that's trying to figure out how it works!

Computer science is still in its infancy. Right now, we're just learning how to make redundant, parallel systems that don't have to work perfectly with a 100.0% uptime to do their job. My guess is that if we someday develop artificial intelligence, it will use many trillions of small programs, none of which will work perfectly, but which will work in tandem with each other to make amazing things happen.

Realsoft and Microsoft (1)

GQuon (643387) | more than 11 years ago | (#5818531)

NPR recently aired a story comparing DNA to software
(RealAudio or Windows Media). 'For many, the best analogy for the way DNA works is that it's like a computer program at the heart of every cell. Some of its programming tricks bear an uncanny resemblance to ones the human brain has dreamed up...DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.


Did anybody else read this and think:
"Realsoft and Microsoft might not be too happy being called bad, spaghetti code programmers!"
Eh?

Then I understood that it meant "You can listen to it in RealAudio or Windows Media." But I think my version is more interesting....

An open source solution? (0)

Anonymous Coward | more than 11 years ago | (#5819276)

Some things you just have to recompile as root:

# gdna -O3 -pedantic-errors -Wall -Werror HumanGenome.dna
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