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Searching for Life's Blueprints

michael posted more than 11 years ago | from the fractals-for-fun-and-profit dept.

Science 310

Makarand writes "If the claims made by the accomplished biophysicist Andras Pellionisz hold any water, life's blueprints may indeed be in fractal patterns found in the DNA. In a human, genes constitute only around 2-3% of the total DNA (the exons). The rest of the non-genic DNA (called introns) play a role that has not yet been understood and some have even suggested that these may merely be evolutionary leftovers. Removal of this "junk-DNA", however, has been proven to be lethal. The introns, he claims, may have the "building construction blueprints" in the form of fractal patterns that the exons use to build living tissue. A patent application covering attempts to count, measure and compare the fractal properties of introns for diagnostic and therapeutic purposes has been made. He hopes his patent will help him launch his company and make it a key player in this field."

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fuck him and his patents (-1, Troll)

Anonymous Coward | more than 11 years ago | (#4732210)

patents are ruining this world. Fuck him.

so he can patent some of me (3, Funny)

Anonymous Coward | more than 11 years ago | (#4732223)

Doesn't DNA itself do this? So isn't he basically patenting all human beings that will be born after his patent is granted? Royalty payments might be something new to think about in parenthood.

Re:so he can patent some of me (0)

Anonymous Coward | more than 11 years ago | (#4732406)

Doesn't DNA itself do this?
What, "count, measure and compare the fractal properties of introns for diagnostic and therapeutic purposes"? No, no it doesn't.
So isn't he basically patenting all human beings that will be born after his patent is granted?
No, no he isn't. Try again, and think this time.

TROLL MACSLASH!!!! (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#4732224)

Please, we need your help! It's like I'm the only MacSlash troll left! http://macslash.org

- News For Turds
- aka Anonymous C0ward (on MacSlash)

Re:TROLL MACSLASH!!!! (-1, Troll)

Anonymous Coward | more than 11 years ago | (#4732316)

Im the only troll on mandrake forum [mandrakeforum.com] and wikipedia [wikipedia.org] . I need help too.

Getting to be a bit old hat (-1)

slycer9 (264565) | more than 11 years ago | (#4732225)

It just seems to me that every other day we're hearing about some new thoery. I'm all about advancing our knowledge, but it's getting to be repetitive to the point of comedy. DIdn't we go through this whole, 'chaos theory' a few years back? SHOW some progress dammit!

Re:Getting to be a bit old hat (2)

AntiNorm (155641) | more than 11 years ago | (#4732258)

but it's getting to be repetitive to the point of comedy

You mean the BS patents that the U.S. government has been issuing lately?

Re:Getting to be a bit old hat (-1, Redundant)

Anonymous Coward | more than 11 years ago | (#4732373)

No!

-- The Scientific Community

i've got him beat (3, Funny)

greechneb (574646) | more than 11 years ago | (#4732237)

I have a patent for using computers to solve anything related to the body. I'll just wait till his company gets further along, and bam, I'll hit him with the suit

Heh (4, Funny)

zapfie (560589) | more than 11 years ago | (#4732238)

Removal of this "junk-DNA", however, has been proven to be lethal.

Does this scare the shit out of anyone else?

Re:Heh (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#4732251)

Sorry, right now I'm more concerned about this... [cnn.com]

Re:Heh (0)

Anonymous Coward | more than 11 years ago | (#4732328)

Why would it scare me?

Re:Heh (0)

Anonymous Coward | more than 11 years ago | (#4732487)

In case someone removes your junk? Having said that, perhaps there'd be little left.

Re:Heh (1)

Kierthos (225954) | more than 11 years ago | (#4732370)

Nope. Read the article. Hell(tm), read the freaking intro. Some people think that it may be worthless. Not everyone in the field thinks this. It is far more likely, heck, obvious even, that it serves some purpose we don't understand yet. The fact that it is needed shows that.

Plus, it's not like there is a 'remove "junk DNA" feature' available for home weaponry or anything....

Kierthos

Re:Heh (-1, Redundant)

Anonymous Coward | more than 11 years ago | (#4732425)

Removal of this "junk-DNA", however, has been proven to be lethal.

Does this scare the shit out of anyone else?

Not really. For starters, how do we know that it is junk-DNA? Just because we don't understand what it is for, doesn't mean it isn't important.

At this stage of the game, we are a lot like the windows users who say: "Gee, there is a lot of crap on my computer, I'll just get rid of what I don't need? What's all this junk in C:\windows? I don't use that, I'll just delete it..." And of course once you do that, Windows barfs all over itself, if it even starts at all.

This isn't to say that there may not be alot of cruft in the DNA, but it will take some time before we can say: "This definatly is no longer used by anything, anywhere, and we can get rid of it without any ill effects."

Patent First: (5, Insightful)

lpret (570480) | more than 11 years ago | (#4732241)

I find it interesting that the first thing he did after theorizing a possibility is to patent that process. What has caused such a change in the scientific world? Since when have scientists become so entranced with being rich -- is that what is attracting people to science these days?

I used to think that science was the last field which blatant greed had not infested yet, and I am proven wrong yet again...

Re:Patent First: (3, Insightful)

Zutroy Of Earth (114413) | more than 11 years ago | (#4732329)

Scientists getting rich.. HA! Now *that's* rich :) Actually, It's already hard enough to get some funds to do any kind of research that some scientists must resort to such practices just to be able to continue their work.

Maybe that guy went a bit quickly to the patent office, but still... scientists don't have hats made of money [penny-arcade.com] :) Also, would you like all your research to come to halt because some other doofus patented your idea? Its a problem with the patent office, not the scientist.

Damn right (4, Insightful)

NDPTAL85 (260093) | more than 11 years ago | (#4732384)

Your kneejerk reaction to his decision to patent his idea is a most unfortunate and immature one. First of all, a biotech company is not an IT company or an internet startup. You can't start them in your garage. You need lots of expensive equipment and expensive highly trained professionals to work with it in the labs. You must also run testing trials, many of them which are also expensive. All of this takes money. Not millions, but billions.

Now I know in the Fantastic Land of Slashdot that making money is always a bad thing, but at some point one has to grow up and become an adult about things and approach them with some measure of maturity.

Furthermore, where the hell have you been for the past 50 years? You didn't think money and greed were factors in the field of science? Money and greed are a factor in EVERY industry. There is no "innocent" industry left. I'm also not fond of the idea that someone who brings us such a great discovery should only have it attributed to him, and not also make a fortune. If somone comes up with something that could cure thousands of ailments and help billions, then he desereves a very large fortune indeed.

Re:Patent First: (2)

Docrates (148350) | more than 11 years ago | (#4732455)

Perhaps a scientist wants tons and tons of money so that he/she can, uh, keep researching????

It's not like the medical field that has come to a point where more and more doctors see a patient and think of a yacht (not all! I do have 5 doctors in my family and about half are still pretty humble people). Most scientists still see something strange and thing of a big lab and more strange things!

Re:Patent First: (2, Insightful)

Alex Reynolds (102024) | more than 11 years ago | (#4732464)

On the other hand, if a scientist doesn't patent an idea, a corporation surely will.

Don't assume all patents are established entirely with profit in mind.

There are concepts of protecting intellectual property and the value of research in terms of both time and money.

-Alex

Re:Patent First: (4, Informative)

siskbc (598067) | more than 11 years ago | (#4732571)

I used to think that science was the last field which blatant greed had not infested yet, and I am proven wrong yet again...

Yeah...academics used to do their thing for the massive ego gratification, now they do it for profit. Don't know that it's necessarily worse this way.

It's not like scientists were ever this pure group of unbiased, purely objective people who are solely out to benefit the world and increase the knowledge of all. That's the publicity answer. Fact is, we fall to the same weaknesses as everyone else, including the great god Profit, and this shouldn't be surprising.

For what it's worth, the worst example was of a couple of guys, Ziegler and Natta, who invented a class of catalysts while working at a university. They worked really well, so they left the university (who paid for the research) and started a company, without giving the university a dime. They made millions, I believe. It happened in the 50's. So this isn't really new...though more widespread as universities have realized they can make a lot of money that way (patents) without much effort.

A good way to look at it. (4, Interesting)

-ryan (115102) | more than 11 years ago | (#4732244)

Coming from a Computer Science background I think the best analogy I can make between DNA and computers is "bytecode vs. virtual machine". DNA is bytecode and proteins are the virtual machine. Bioinformatics research can be boiled down into trying to debug raw bytecode when you don't know the structure and rules of the virtual machine. Until we understand these massive and extremely complex molecular machines called proteins, we'll never fully understand what the code of DNA does.

Re:A good way to look at it. (5, Informative)

HisMother (413313) | more than 11 years ago | (#4732411)

This is not a very good analogy. A (virtual) machine executes (byte)code. DNA is a set of instructions for creating proteins -- not a set of instructions for proteins to execute.*

Perhaps you might say DNA is code, and proteins are objects? I think DNA is like a C header file, really -- it specifies the structural information, but leaves out the mechanics, which come from physics.

In any event, the mechanisms by which DNA is used to create proteins are actually very well understood already. Understanding what proteins do after they're created -- i.e., fold up, catalyze chemical reations -- now that's another story. But that doesn't mean we don't understand how DNA is used to create them.

* Well, the purpose of some proteins is to transcribe DNA and thereby build other proteins, but that's not what most proteins do.

Re:A good way to look at it. (1)

scotay (195240) | more than 11 years ago | (#4732450)

Cool Analogy.

I was thinking more of one of those Russian dolls, with littler nested dolls inside.

I think we have virtual machines inside virtual machines.

The folding of the DNA selectively exposes sections of bytecodes that drive RNA transcription that feeds another virtual machine (the ribosome) that generates another set of bytecodes to build peptides.

Does god work for Transmeta?

Re:A good way to look at it. (2, Informative)

bfinuc (162950) | more than 11 years ago | (#4732452)

Most of the vast amount of information an organism contains is not in the genes at all. For example, ion concentrations in cells are often very far from equilibrium. If that pattern of disequilibria is messed up, it could kill the organism. Another example is the pattern of switched on and switched off genes, which varies from cell type to cell type - and is mostly controlled by proteins binding to "junk" DNA.


Because genes are so neatly digital, people tend to think of them as being all the information in a cell. Actually a cell is like a computer - some information is stored explicitly as software, and the rest is hardware, but it is really hard to tell where software ends and hardware begins. After all, floating point coprocessors work with big internal tables - so are those tables hardware or software? And think of the IBM keyboard BIOS. It started out life as hardware and ended up as software that emulate the hardware. Similarly, some proteins are taken from the same gene, but with a different set of exons.


Another thing is that biological systems love hacks, so the borders are constantly shifting. I think there's a good chance of finding introns doing unexpected stuff.

Re:A good way to look at it. (2, Interesting)

Quaternion (34622) | more than 11 years ago | (#4732514)

To use your analogy... bioinformatics research is proceeding rapidly down both the "bytecode" and "virtual machine" avenues of inquiry. Some people are actively working to uncover the structures of proteins and other relevant bio-molecules (see, for instance, this year's nobel prize in chemistry... kurt wuthrich pioneered the application of NMR to large molecules like proteins and dna, for the purpose of determining structure). Other people are trying to find the patterns in the dna itself that encode portions of the cell's regulatory apparatus. Other people are trying to characterize which genes are complicit in which pathways of the cell...

The analogy of "bytecode" and "virtual machine" is flawed anyway: it gives the impression that the cell's transcriptional apparatus is just an interpreter (highly parallelized, sure) that chugs down the DNA, reads the "code", and produces the appropriate proteins to do the cell's business. But that's misleading... for the most part, the cell's transcriptional activity is in some steady state, until outside stimuli signal it (in a complex way) to change one part of the humming machine, and then that change cascades to other portions of the cell's transcriptional activity, until the cell has reconfigured itself to handle the stimulus. There's a lot of feedback between the proteins and the dna (the transcriptional apparatus _is_ protein), etc.

A better analogy might be... well, I'm not sure there's a decent analogy at all. Maybe the "cell is a virtual machine," and outside stimuli are a form of programming language... Bleh, that's no good at all either.

At any rate, your post makes it seem like bioinformatics researchers have made a universal choice to put their research priorities in the wrong order... but that's certainly not the case. Working to decode the cell's apparatus in different ways simultaneously makes everyone's research more productive and useful.

So think of me (-1, Offtopic)

slycer9 (264565) | more than 11 years ago | (#4732247)

When you think of a Beowulf cluster of these....(heh, yeah.....um........ok)

Oh Joy, another patent on genetics. (3, Insightful)

EQ (28372) | more than 11 years ago | (#4732248)

We can now wait 17 years before anyone gets to freely reap the fruits of this basic scientific discovery.

Patenting the method, as long as its not the only method? Thats fine. Patenting the discovery? Thats absurd.

Re:Oh Joy, another patent on genetics. (1)

HyperMind (628041) | more than 11 years ago | (#4732323)

Please re-read the article: "A patent application covering attempts to count, measure and compare" They arent looking to patent the method or the discovery - merely the ATTEMPT to count, measure, and compare. Can I now get a patent for my attempt to tie my shoes? FWIW, I wear sandals - mostly.

Not 17 years. Only 7 1/2. Don't forget BIOPAT (-1, Troll)

Anonymous Coward | more than 11 years ago | (#4732405)

We can now wait 17 years before anyone gets to freely reap the fruits of this basic scientific discovery.

Actually, 7 1/2 years, due to the recently voted "BIOPAT" rules [cnn.com] that apply to patents in the medical and biological areas.

Re:Oh Joy, another patent on genetics. (1)

ryanvm (247662) | more than 11 years ago | (#4732644)

Considering that you probably won't be reaping the fruits of this discovery until after 15 years of R&D, where's the harm?

No Big Surprise (3, Insightful)

Inexile2002 (540368) | more than 11 years ago | (#4732256)

Seems that every few years someone figures out that something in nature that was perviously though to have no function or a trivial function to particular process is actually critically important. "Junk genes" was another way of saying "I don't understand this so I'm going to pretend that it doesn't matter."

No surprise that the "junk genes" in one of the most complicated structures in nature - DNA - that has been fine tuning itself for billions of years, turn out to have a function and a critically important one. True insight will always come from people with enough courage to say, "I don't know."

Re:No Big Surprise (1)

Evil Adrian (253301) | more than 11 years ago | (#4732395)

Come on now... we all know that evolution is a hoax!

"Our God is an awesome God." O:-)

In programming terms... (3, Insightful)

Cap'n Canuck (622106) | more than 11 years ago | (#4732257)

Maybe a programming analogy for the introns (non-genic DNA) is that they are subroutines. The exons (genes) use different subroutine calls, resulting in different executables (people).

So I guess mankind is just self-evolving code. Cool!

He hopes his patent will help him ... (2, Funny)

C.U.T.M. (595268) | more than 11 years ago | (#4732259)

He hopes his patent will help him launch his company and make it a key player in this field. ... and take over the world!

Sounds pretty interesting, I just hope there isn't something deeper seeded in this guy, like wanting to take over the world... *plays pinky and the brain music*

Obligatory response (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#4732442)

Andras Pellionisz and Co. to world:
- All your intron base pairs are belong to us.

Whew! Glad that's out of the way...

Of course a simpler explanation... (5, Insightful)

Jonathan (5011) | more than 11 years ago | (#4732272)

...for the lethality of removing introns is simply that this may mess up gene regulation. The amount of mRNA transcript produced by each gene has to be carefully regulated for all parts of the cell to function properly. Having junk of the appropriate length in a gene is one way of slowing down the production of a transcript that the cell may not need a lot of. But, hey, that explanation just isn't as sexy as something involving fractals, now is it?

We're losing sight of what's really important... (-1, Offtopic)

HarveyBirdman (627248) | more than 11 years ago | (#4732273)

And this helps me get laid more how?

This gets me closer to a completely immersive VR pr0n experience how?

I wish the brains of the world would turn their minds to dealing with what is truly important and useful.

Junk DNA (2, Interesting)

Anonymous Coward | more than 11 years ago | (#4732275)

It actually makes a lot of sense to me that there would be huge amounts of useless cruft. In fact, I think about it as if there were large segments of the sequence to which 'execution' never branches.
Imagine looking at the source code of a program generated essentially at random to do something or other. It might work, but the source would show little sign of design and large sections could be commented without effect.
Don't know what to make of the notion that removing seemingly useless sections affects anything. Removing all the useless sections should reduce disease caused by gene-copy errors.

Re:Junk DNA (2, Interesting)

fstanchina (564024) | more than 11 years ago | (#4732581)

If a program was evolved in a semi-random way and not designed, then apparently useless code might in fact be significant. Just not in a way that we understand. Maybe it just slows down the CPU (or DNA production, as another post says) for a while and avoids a race condition that would otherwise break the useful part of the code.

Oh, by the way, if it was useless, how could errors in it affect our health?

programming? (2, Interesting)

chef_raekwon (411401) | more than 11 years ago | (#4732281)

kind of like programming, in a way.

from what is explained, exons would be the 'linkers', the introns the actual data. this actually is a very likely concept, which explains the extra dna stuff. in java, (for those who dont know) one makes a 'reference' to an object. the references take very little space, (about 2-3%)compared to the actual data in memory. the reference 'points' to an actual object. the exons may be doing this 'pointing' to the introns....

hmmmm
maybe i'll apply for a patent.....

When you have a hammer (5, Insightful)

NickFusion (456530) | more than 11 years ago | (#4732336)

every problem looks like a nail.

Why should DNA act anything like computer code?

Let's look at it objectively, and see what it has to teach us, instead of straight-jacketing it into familiar metaphors.

Re:When you have a hammer (1)

chef_raekwon (411401) | more than 11 years ago | (#4732424)

dna should act like computer code because:
a - computer code is relatively logically.
b - our bodies are relatively logical
c - everything scientific thus far in the world has been explained by mathematics or logic.

in deciphering DNA, we need to "reverse-engineer" the "code" in order to understand its composition.(sounds like computer code to me).

does this look like a nail to you?

Re:When you have a hammer (2)

david duncan scott (206421) | more than 11 years ago | (#4732563)

I think your last point -- "everything scientific thus far in the world has been explained by mathematics or logic" -- is tautological, inasmuch as we define as scientific those things that can be explained by mathematics or logic. It's a bit like saying that "everything we've been able to measure is measurable" -- one can't argue the point, but one hasn't really learned anything from the statement either.

Re:When you have a hammer (0)

Anonymous Coward | more than 11 years ago | (#4732573)

How can you look at anything, except through some sort of metaphor? Are you the first person in the world who's been able to cut through his own metaphor and see only the unvarnished truth?

Please. There are plenty of reasons why "computer code" is a pleasant (if occasionally wrong or misleading) analogy for DNA. You could also think of DNA as containing assertions in some logical language, assertions that say something about the state of the cell, the state of other genes, the state of external stimuli from the "outside," etc. You can think of genes and their regulatory apparatus as gears in a machine, blank puzzle pieces, etc.

These have all been fruitful metaphors for interesting research. No one who posits them claims to have reached the final truth... but everyone admits their utility.

You can only interact with the world through metaphor anyway. Buy some sophistication.

introns affect DNA folding (3, Interesting)

aok (5389) | more than 11 years ago | (#4732284)

I learnt this in undergrad so it can't be that amazing of a discovery, except the part about fractal patterns...

The DNA bases in the introns affect how the DNA is folded, and that determines whether or not the exons in that folded region are exposed enough to be translated or not.

At least some regulatory mechanisms manipulate the folding/unfolding to turn on or off the production of various enzymes/proteins.

and that's why introns are important (1)

aok (5389) | more than 11 years ago | (#4732306)

...forgot to say this in the parent post.

Re:and that's why introns are important (0)

Anonymous Coward | more than 11 years ago | (#4732325)

i'm no scientist, but that's kind of what i was thinking - not exactly junk if removing it's lethal.

Math in Nature (3, Interesting)

SomeoneGotMyNick (200685) | more than 11 years ago | (#4732291)

I have long held the belief that EVERYTHING in nature has an underlying mathematical basis.

It's just that we haven't figured out the formulas yet. Once we do, such as in this fractal theory, we will understand the behavior of life and can reap the benefits.

The tough research will become easy (when applied through a function or formula).

And once and for all, we'll finally see if the answer is really 42!!!

Re:Math in Nature (0)

Anonymous Coward | more than 11 years ago | (#4732327)

>And once and for all, we'll finally see if the answer is really 42!!!

You moron. We all know it's 56.

Re:Math in Nature (2, Funny)

product byproduct (628318) | more than 11 years ago | (#4732418)

EVERYTHING in nature has an underlying mathematical basis.

Possibly. But if we ever come up with a mathematical theory explaining female behavior, it will make heavy use of imaginary numbers.

Re:Math in Nature (2, Funny)

kin_korn_karn (466864) | more than 11 years ago | (#4732534)

No, it'll be based on games theory. Or maybe chaos theory.

Re:Math in Nature (1)

Docrates (148350) | more than 11 years ago | (#4732492)

That's exactly the oposite from what Stephen Wolfram is saying: that everything in nature has an underlying ALGORITHM, not a mathematical formula. Check out this light news.com article [com.com] , or just read his wonderful book [wolfram.com] : A new kind of science.

Re:Math in Nature (3)

SomeoneGotMyNick (200685) | more than 11 years ago | (#4732596)

Algorithms and mathematical formulas aren't opposites.

Wolfram's statements may show that scientists don't need to look any deaper that the 'formulas' to get an understanding of everything in nature.
That may be good for a while, but scientists will get bored quickly. Anybody who got as far as understanding the formulas without going any further may be nothing more than 'wannabe' scientists. The true scientist will still look for the formulas.

It's kind of like someone saying they are a programmer because they got a Word macro to format their text a certain way.

Re:Math in Nature (1)

DrTrogg (586983) | more than 11 years ago | (#4732532)

I have long held the belief that EVERYTHING in nature has an underlying mathematical basis. Isn't that a line from Pi?

Re:Math in Nature (1)

porn*! (159683) | more than 11 years ago | (#4732536)

I think it may be true that we can find a mathematical way to interpret everything in nature, but I'm not sure I believe that math or science is the underlying basis of life, the universe, and everything. Think of math and science as a lens through which we view nature. Our knowledge colors our perception.

I do agree we could figure out a way to apply mathematics to a natural 'function' so that we could more easily understand the origin and outcome of said function.

Saw a very interesting talk about fractal geom. at siggraph one year where the lecturer could map fractal relationships to a vast array of images, music and other qualitative forms of expression. He had a specific fractal ratio(I believeit was 1/f?) that could be used to programatically create art and music that was pleasing to the eyes and ears, respectively. I'm too lazy to look it up at the moment.

I will concede, however, that the answer is 42.

porn*! - counting with my fingers since 1968
Is there a patent for that?

Another scientist who thinks he knows the answers (3, Flamebait)

Jon Erikson (198204) | more than 11 years ago | (#4732293)

Gah, every time I read one of these stories I'm rendered speechless by the hubris of these scientists who think that somehow they have a right to own part of the very building blocks of life. And appalled at a government that is happy to let people lock away such vital information for the sake of a few measly dollars in kickbacks, sorry I mean patent applications.

Now this guy comes along and you can be sure that even before he proves anything he'll have signed up for the 97% of the genome he's talking about, "just in case". And what can anyone else do about it? Nothing.

There should be no price on scientific advance. People who do this sort of things are not scientists, they are nothing more than minions of Satan out to prevent us from evolving and taking our rightful place at God's side.

Re:Another scientist who thinks he knows the answe (1)

stratjakt (596332) | more than 11 years ago | (#4732367)

>> I'm rendered speechless by the hubris of these scientists who think that somehow they have a right to own part of the very building blocks of life.

No, they want to own the rights to the methods they use to understand and manipulate those building blocks.

Noone is trying to patent the gene that gives someone blue eyes - but they are trying to patent the methods and devices they used to discover and manipulate that gene.

And frankly, a financial incentive that a patent provides is the only thing to drive the research at all. If you want to do it for free - go right ahead.

Re:Another scientist who thinks he knows the answe (0)

Anonymous Coward | more than 11 years ago | (#4732490)

"There should be no price on scientific advance."

If there was no monetary gain in science, then there would BE no scientific advance.
And rest assured, niggers and zipper heads would take over the world. Then we would be fucked for sure.

Junk is Important (1)

HumanXX (625059) | more than 11 years ago | (#4732299)

My girlfriend keeps telling me that I should get get rid of all that nasty computer junk in my study, and I have been resisting so far. Now I can point to the role played by these introns, to show her that getting rid of the so called junk is lethal. Nature proves ua all winners again, I can keep my lovely pcbs and stuff, girlfiends man stays alive, yup everyone is a winner.
---------
Human Experimentation [humanexperimentation.com] its music, just not as we know it.

blueprint? (0)

Anonymous Coward | more than 11 years ago | (#4732305)

In geekspeak we call it "life's source code".

Humans as fractal creatures? (2, Insightful)

Bonker (243350) | more than 11 years ago | (#4732310)

I've always been fascinated by the fact that mammals have five major appendages... and five major digits on four of those appendages and five major sense organs (tounge, lips, ears, eyes, nose) on the fifth one. Of course, it's pure conjecture that this might be a reflection of a lower-level self-symmetry, but it's still interesting conjecture.

Re:Humans as fractal creatures? (1)

BoojiBoy0 (596932) | more than 11 years ago | (#4732363)

Dude mammals all have these wonderful symmetries? WHALES are mammals, even horses seem to be symmetry breaking by your criteria.

Re:Humans as fractal creatures? (2)

jellisky (211018) | more than 11 years ago | (#4732437)

Um, not to burst your little bubble, but felines and canines tend NOT to have five major digits on four of those appendages. If you count dewclaws, many will have five on the forelegs, but none have five on the back legs. Felines and canines have only four toes on their back feet.

'Course it /is/ interesting that four and five seem to show up the most. 'Course that's probably just the "Law of Small Numbers" showing up... or something dealing with the innate symmetry that backbones tend to give (bilateral symmetry). It's just all in how you look at the problem, I guess.

Re:Humans as fractal creatures? (0)

jck2000 (157192) | more than 11 years ago | (#4732489)

It is because we are made of starfish.

Re:Humans as fractal creatures? (4, Insightful)

gorilla (36491) | more than 11 years ago | (#4732517)

Most mammals have 6 appendages, 4 limbs, tail and head. Digits vary a lot, though 5 is the usual maxium. You're 5 sense organs is quite contrived. Why are the lips an organ, but the skin isn't? Other mammals have extra organs that we don't, for example whiskers.

Basically, if you force something like this, then you can make a connection. Doesn't mean the connection is real.

Re:Humans as fractal creatures? (1)

Wyatt Earp (1029) | more than 11 years ago | (#4732603)

My head isn't an "appendage", nor is anyone elses.

It's one of the three divisions of most arthropods bodies.

Head, Thorax, Abdomen.

I'm not sure what you do, but most people I know don't use thier lips as a sense organ.

The tounge and nose work togeather on taste. The nose does smell, the ears hearing, the eyes sight, the skin and hairs sense touch and other environmental changes.

My lips pretty much hang out, not used much in day to day activities.

What do other mammals use the lips for? Blue Whales for instance.

Great!!! (0)

Anonymous Coward | more than 11 years ago | (#4732317)

Yet another Stupid Patent.

fractal dna (0, Troll)

jack torrence (521339) | more than 11 years ago | (#4732331)

Wrong and wrong! The spare dna IS mathematically required, but it is NOT fractal in nature, I assure you. It is compressed under a completely unassociated lossless compression method. So screw you and your pathetic patent.

What took so long? (2, Insightful)

fciron (619458) | more than 11 years ago | (#4732335)

I have been assuming for the last ten? years (since I read James Gleik's "Chaos") that blood vessels, tree branches, fingerprints, etc. were following fractal patterns. I am surprised that no one had been looking for these patterns in the Genome Project. The introduction of this new research project on the internet and already patented is an interesting twist. I thought from the article that he had patented his computer analysis pattern, but there are certainly plenty of very scary biological patents out there. I can understand the need to look outside of the traditional biological circles for this research, but going straight to the internet instead of the math department is way out of the academic research paradigm.

SLASHDOT MODERATION (-1, Troll)

Anonymous Coward | more than 11 years ago | (#4732346)

This is it, I am so fucking disgusted with idiots being allowed to moderate with abandon that I am leaving this site for good.

Re:SLASHDOT MODERATION (-1, Offtopic)

Anonymous Coward | more than 11 years ago | (#4732397)

I'm with you bub.

But instead of leaving, I'm going to stick around and troll.

Ever notice how much linux sucks? And how bad it's users smell?

Hi there (-1, Troll)

stratjakt (596332) | more than 11 years ago | (#4732347)

I'm a slashdot reader, and I havent read the article, and know absolutely jack-shit about molecular biology.

But that's not going to stop me from acting like I do!

DNA is just like C++. Only 2 to 3% of it is used because god is like Microsoft, and theres lots of code bloat.

This guy seeks to patent stuff, and thats bad. Even though I couldn't comprehend the patent applications if I was bothered to look them up, I can say confidently that this is another greedy fat-cat with plans of world domination.

DNA should be open source, free as in beer. That way all the thousands of lifeless kernel hackers can develop new and creative medicines. Because knowing how to properly implement a System V semaphore is just like creating a syrum to combat parkinsons disease at the DNA level.

patent... (0)

Anonymous Coward | more than 11 years ago | (#4732349)

Using patent to earn money - patent pending

This is a great discovery! (-1, Flamebait)

Anonymous Coward | more than 11 years ago | (#4732369)

We can finally hunt down and eliminate the nigger dna sequence and rid the world of the biggest disease carriers since the plague.

Re:This is a great discovery! (0, Offtopic)

Slaveway (562761) | more than 11 years ago | (#4732403)

You are truely a COWARD. /. needs a new moderation option: Idiotic

Junk DNA script (1)

FungiSpunk (628460) | more than 11 years ago | (#4732382)

Removal of "Junk DNA" is lethal? Now if I can just find some way to transmit my "Junk_DNA_Rem" script to the morons that call mine and other helpdesks, I might just have a winning product to sell...

not a big leap (1)

rendermouse (462757) | more than 11 years ago | (#4732383)

I am no genetics expert, I'm not even a big math whiz. I have read a bit about fractals, and actually wondered about the relationship between fractals and DNA. I'm sure a HUGE number of actual fractal mathematicians have, too.

I guess his patent is specific enough, involving the application of fractals to introns, for this to go through, but I doubt this is a completely original idea.

Protect these blueprints (1, Funny)

jmcwork (564008) | more than 11 years ago | (#4732409)

No matter what, they should not give them to Greg Brady. He is sure to lose them.

Gene expression regulation (1)

HighTeckRedNeck (538597) | more than 11 years ago | (#4732422)

Some writers once said that humans only use 5% of their brain because the scientists could only explain the 5% that directly created a recognizable effect when they poked it with a stick. This is like saying a computer uses only 1% of its ability because they can only understand what's on the phosphors in the video tube. Any language needs support functions like comma's and gerunds or the sentences would be nothing more than a jumble of concept words. For instance take the last sentence and remove everything but the "important" words and then mix them up and you get. Support gerunds functions nothing concept jumble language. Hardly understandable. The rest of the genetic language probably has to do with regulation of ontological development, phenotype expression, and such. Antibodies generally have an RNA segment attached how difficult would it be to use something similar on non-protean coding sequences to regulate transcription. Wouldn't you expect that as the number of genes increases and their interactions exponentially explode that the percentage of code necessary for regulation would come to dominate the portion coding for the proteins.

Do unto others as you would have done to yourself, don't let America become like Israel. It is un-American to support human rights violations, support justice in Palestine.

psuedo-science (5, Insightful)

paulbotto (628486) | more than 11 years ago | (#4732428)

First, why is it that only fringe scientists get publicity when it comes to certain research areas? I'm a molecular biology/genetics student who seems to know more about DNA and genetic informatics than this biophysicist. Everyone makes comments about DNA and its functions and regulations, but these comments are oversimplified and greatly generalized. Biologists are still learning about DNA and have much to find out. Intron are nothing new to science. They have been known for years and some of their functions elucidated. Additionally, junk DNA is a misappropriate phrase that has remained in popular use. Non-protien coding sequences are not necessarily junk. RNA itself plays an important role in cellular functions. Additionally, the DNA itself must fold, coil, and commpact at incredible ratios during specific portions of the cell cycle. This compaction can be highly sequence specific. So this "junk DNA" may be very important and not junk at all. Yet to argue that fractal patterns shape gene expression is pseudo-science at best, especially without critical peer-review in journals. Publish, repeat, verify...all together now! PUBLISH, REPEAT, VERIFY!

Interesting possibilities (0)

Anonymous Coward | more than 11 years ago | (#4732430)

I hope that something like this will come to pass. I always thought the "junk DNA" conclusion was a rather supercilious and unscientific one - they do not know what 90% of DNA is for, and they just conclude it is rubbish. Very scientific indeed.

I recall that a few months ago Craig Venter mentioned something along those lines - i.e. he acknowledge to our complete ignorance about that so- called "junk DNA."

So you're saying? (2)

psyconaut (228947) | more than 11 years ago | (#4732447)

That with a pair of Levi's and my old Commodore 64 Mandelbrot generator, I can create life? *bwhahahahahahahaha* ;-)

-psy

Prior Art (2)

SniffleBear (604984) | more than 11 years ago | (#4732453)

A patent application covering attempts to count, measure and compare the fractal properties of introns for diagnostic and therapeutic purposes has been made

I don't mean to ruin Mr. Andras Pellionisz's patent party, but I think the exons probably already does that...

The introns, he claims, may have the "building construction blueprints" in the form of fractal patterns that the exons use to build living tissue

You have got to be kidding me.... (0, Flamebait)

dlimona (628479) | more than 11 years ago | (#4732467)

Does anyone belive in God anymore? Does everyone belive in evolution now? What the hell is this garbage... 'left over' DNA? Sigh, the ignorance is just SCREAMING from this jibberish. Give God some credit...

Re:You have got to be kidding me.... (1)

lhbtubajon (469284) | more than 11 years ago | (#4732562)

Who is more ignorant, the one who, for lack of an obvious answer, presents an educated guess, or the one who bellows out the same supernatural answer to every new question?

and in other news: (1)

dandelion_wine (625330) | more than 11 years ago | (#4732653)

Georgia School Board Bans 'Theory Of Math'

COGDELL, GA--The Cogdell School Board banned the teaching of the controversial "Theory Of Math" in its schools Monday. "We are simply not confident of this mysterious process by which numbers turn, as if by magic, into other numbers," board member Gus Reese said. "Those mathematicians are free to believe 3 times 4 equals 12, but that dun [sic] give them the right to force it on our children." Under the new ruling, all math textbooks will carry a disclaimer noting that math is only one of many valid theories of number-manipulation.

patenting nature (1)

six11 (579) | more than 11 years ago | (#4732469)

To win a patent, Hunt notes, all an inventor must do is describe or teach some new skill that is not obvious.

Bezos agrees.

Now, I'm not one of those raving anti-patent people, but it seems to me that when it comes to patents that are based on discoveries of natural phenomena, those awarding the patent have to be very, very careful. It reminds me of the pharmaceutical companies receiving patents on some exotic plant that only grows in Brazil, and then sending their lawyers south to prevent the natives from using the plant that the Company owns.

Junk (not likely) (3, Insightful)

Red Rocket (473003) | more than 11 years ago | (#4732474)

I love how all these geneticists keep referring to the bits of DNA code they don't understand as "Junk DNA." It reminds me of the ancient Egyptians who, when mummifying a body, would carefully remove and preserve the organs in jars . . . except for the brain. The brain, to them, was just a bunch of gooey junk in the skull to be thrown away because it didn't serve any purpose.
The same geneticists now have the ability to tinker with the code of life and release their monstrosities into the environment that we depend on for our very lives. "Here let's see what happens when I do this! Don't worry, I'm a geneticist and I understand DNA completely and all the ramifications of releasing this new creation into the wild." And we thought nuclear (or is that nuke-u-lar) weapons were how we were going to destroy ourselves.

Great! Patent anything! (2)

evilpenguin (18720) | more than 11 years ago | (#4732481)

Admitting up front an almost complete ignorance of the science involved here (since when has that stopped any of us on Slashdot?), I think it is absolutely amazing that one can patent a hypothesis now...

(Did I mention that I was also completely ignorant of the details of the patent application?)

Re:Great! Patent anything! (0)

Anonymous Coward | more than 11 years ago | (#4732529)

Did I mention that I was also completely ignorant

No, you didn't mention it, but your posting history shouts it.

All DNA information (-1)

Anonymous Coward | more than 11 years ago | (#4732507)

should be Open Source

or is that open sores?

A primer on DNA structure (5, Informative)

goombah99 (560566) | more than 11 years ago | (#4732512)

Starting with the caveat that science reporters tend to miss present sceintists ideas let me try to heap some ridicule on this article.

first it's well known that DNA is not merely a double helix but this ribbon also coils on itself (super coiling) and can be would in complex patterens around the biological equivalent of tape reals (called histones). And that there even larger hierarchies of organization like chromosomes.

When a gene is "expresses" (read) from the DNA, that portion of the DNA has to be exposed, thus from square one the mobility and ease of exposure of a structure regulates its expression. Additionally, in order for some of the portien moelcules that trigger expression as well as those that do the expressing to bind to the DNA the DNA often has to have a characterisitic kink or lack of a kink. Binding in biology is --unlink the interaction of simpler molecules--inherently recognition of another structure.

so point 1 is that whoop-tee-do structure of DNA organization is important to expression. We all knew that already.

The second point is that as far as binding goes these specific events are almost excusively local. that is proteins and other molecules that bind to DNA are small (relative to the size of DNA), sort of like a fly landing on an aircraft carrier. At the scale of the dimensions of binding we are takling about atomic interactions and as the word "atomic" suggests, there is no notion of fractal subdivsion of space available. In other words patterns that exist distantly elsewhere in the DNA have no relevance to a binding event.

The third point to make is that the are many useful properties of "useless" sections of DNA. For example, at various times in its lfe DNA breaks the double helic and becomes two complimentary strands over sections of the DNA. Sometimes the one strand from won pair will go bind with a strand from another pair. This mainly happens when the two strand-swapping sections of DNA have nearly comlimentary chemical (base or nucleotide) patterns. At this chemical interaction level, whether or not the DNA section in question is "codeing" (and exon) or non-coding (an intron) is moot. DNA is DNA. thus non-coding regions can facilitate strand pairing and strand swapping activity. In other words useless DNA has a purpose of structure-structure interaction. TO the extent that this is already known this patent issue is silly.

Now What about those introns are they really useless DNA? some may be, some are not. Its a little tricky to exaplain in a few words but you have to imagine DNA like a hard disk with streams of consecutive bits. the word size of reading this is 3 bits. however, one has a slight problem when you go to read it, where do you start reading? if you are off by one bit then each word contains 2 bits from one word and one bit from the next word. this is called a frame shift, and obviously there are three possible frames on could read words in. Amazingly enough, not only can the cell figure out which frame to read, but sometimes all three frames contain a valid message!!! its a lot like the winnowing and chaffing encryption scheme. (indeed sometimes the messages can be read backwards and in a different frame to make sense too, much like a palindromic sentence, except that the reverse sentence may be different but still make sense). One purpose of introns is to create frame buffers and other signals to guide the readin mechaism to get into the proper frame.

Another purpose of introns is what is known as alternate splicing. Sometimes as (or after) a message is read off, sections of the dna get skipped over, like jumping a track on a vinyl record, and discontiguous portions of a the message are joined together. The decision to skip or not to skip can be regulated. Thus he same nominal section of DNA can produce slightly different edited messages. Thus introns sort of multiply the number of gene variations.

Finally, because of the way DNA makes mistakes when it copies it self or repairs damage, what offen happens is that a chunk of DNA gets copied to a new place on the DNA and the old one is not completely erased. This is infact exactly like a fragmented hard disk. Image a hard disk in which you have copied the smae files many times, and deleted the ones. At this point the FAT table fets lost and you have to use norton disk recover to try to find files. Wll you find lots of complete files and also fragments that look like old versions of parts of other files. This is what DNA looks like. So these self-similar patterns actually emerge accidentally. Since the chunk size varies the sel-similar patterns can be multi-scale and hence are fractal like. This is all accidental! Now its possile to imagine that what was once accidental is now being exploited by the body for a new puprose. For example, recombination plays a role in the immune system. But I doubt that the fractal nature of this is important. One reason to doubt it is that it is simpler to imagine that this happens beacuse there is no penalty for it happening. In higher organisms having wad's of extra DNA does not harm the cell since higher orgnaism have lots and lots of error correcting mechanisms to deal with DNA damage, dealing with extra DNA is small potatoes. Conversely, single cell organisms have a preimum on efficiency and thus minimize the saize of their DNA. Bacteria for example dont have introns, and have very little junk DNA. Viruses almost never have any junk dna at all bacause space is at a premium. Thus biology shows that when there is a reaosn to do so organisms chuck extra DNA.

so in conclusion I think this idea is cute but really nothing new or special, and is probably mostly hokum.

What a silly idea! (0)

Anonymous Coward | more than 11 years ago | (#4732513)

Ok this is a case for computer and scientific intelligence is overdone in a biological field. Modern cloning techniques require the removal of introns from genes in order to express them in bacteria. If they are so important how come the gene products from bacteria minus introns is the exact same as plus introns. I think this guy is about to flush several million dollars down the toilet

In Theory.. (2)

xchino (591175) | more than 11 years ago | (#4732530)

I'm a little confused here.. so his theory is that the extra genetic material is in the form of fractals, which are supposed to represent some sort of blueprint for DNA? How can a fractal be a representation of something else? Isn't a fractal just a non smooth geometric shape? Is he saying the blueprint is in the specific arrangement of the fractals?

fractal organs (1)

wiggys (621350) | more than 11 years ago | (#4732546)

I'm convinced that we posesss certain organs in our bodies which can only be explained as having been grown in a fractal way. The first thing which springs to mind is our lungs... just as we have fractal formulae to generate shapes which look like clouds, there must be a fractal which can generate lung-like shapes/tissue.

Possibly the most exciting thought is that our own brains are fractal-based. Very very minor changes in starting conditions can lead to the variety of brains we have today - and all that goes with it.

Another useless patent on the way... (1)

Kindaian (577374) | more than 11 years ago | (#4732552)

Just wait... the patent itself isn't useless... because with lots of money he can start pushing DMCA's and the like over it's competitors...

Patents should go to ... (3, Insightful)

fferreres (525414) | more than 11 years ago | (#4732555)

God, I won't acept any other patent regarding my DNA as well as my relatives DNA (going back to Adan and Eva or whatever you call them). If anyone has a patent on this issue, and certainly doesn't need us to recognize it is god (be it aliens or a more stylized one like in religion).

How can any asshole claim to have a patent restricting me what I can do with my DNA and how to process is? This is just intelectual violence. We should find a different way to reward these scientists when and if their contributions to society are proven to be worthy.

I'm kind of stating to get bored about raping of the humans by other humans. You can't fit everything under the free market schema with hacks like patent law or copyright. It can help in certain cases, but generalized like this, they turn into a pie divider of societies gains through time which happens to be unacceptable (to me).

Just Read Blood Music (3, Interesting)

Nintendork (411169) | more than 11 years ago | (#4732609)

Greg Bear's 85 novel, Blood Music [amazon.com] starts with a mad scientist using introns to store data. Make's me wonder what we will find out about ourselves as we disect and expore our DNA.

I'm quite skeptical about this... (5, Interesting)

girl_geek_antinomy (626942) | more than 11 years ago | (#4732634)

And here's why... A few things in that article set alarm bells ringing in my head:

The notion that at least certain parts of junk DNA might have a purpose appears to be picking up steam. Many scientists, for example, now refer to those areas with a far less derogatory term: introns.

They've been introns for ever and ever. I don't know what the author of the article Hal Plotkin's biological credentials are, but they're not looking great... 'Junk DNA' is almost universally a Pop-Sci term.

(...)Other researchers have begun looking at similar questions, with most focusing on intron strands located near genes whose functions are better understood.

Yes, intron patterns are used as markers in genetic testing, because a particular pattern is associated in space with a particular version of a disease-gene, and because intron repeats are easier to recognise in standard gene profiling techniques. There's no magic, and no one is suggesting the intron pattern itself is significant.

Pellionisz has chosen the unorthodox route of making his initial disclosures online on his own Web site. He picked that strategy, he says, because it is the fastest way he can document his claims and find scientific collaborators and investors. Most mainstream scientists usually blanch at such approaches, preferring more traditionally credible methods, such as publishing articles in peer-reviewed journals.

This is pretty bad. Intentionally avoiding peer-review is, um, well, not great for his credibility, shall we say? The article also spends an awful lot of time jumping up and down about just *how* good this man's credentials are. C'mon folks, methinks the lady doth protest too much...

Fractals are a way that nature organizes matter. Fractal patterns can be found in anything that has a non-smooth surface. (...) If junk DNA really is junk, some of it is certainly organized in a pretty peculiar pattern, one that looks amazingly like a fractal.

So if it's a generalised effect of non-smooth data, why is it so surprising that it's present in intron DNA? After all, the way DNA replicating machinery works in cells, it's much more prone to accidentally copying bits of self-similar code - it's more likely to get stuck to itself in the wrong place, and similar effects.

Just as knowing the radius of a circle lets one create that circle, understanding the more complicated fractal-based formula that nature uses to turn inanimate matter into a heart might -- in theory, at least -- help us learn how to grow a living heart, or simpler structures, such as disease-fighting antibodies.

We already understand how antibodies are put together, and have a pretty good idea how cells assemble themselves into organs! We don't need fractal dark magic to explain the protein synthesis in antibody production, it's just protein, and protein is coded directly by gene exons.


Hopefully that gives a flavour of the problems with this, anwyay. There are dozens bore things I could quote and argue, but I can't be bothered.

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