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Science

Searching for Life's Blueprints 310

Posted by michael
from the fractals-for-fun-and-profit dept.
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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Searching for Life's Blueprints

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  • by Anonymous Coward on Friday November 22, 2002 @12:03PM (#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.
  • by greechneb (574646) on Friday November 22, 2002 @12:05PM (#4732237) Homepage Journal
    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
    • by mhackarbie (593426) on Friday November 22, 2002 @01:18PM (#4732742) Homepage Journal
      Yeah, and I've got a patent for using non-linear equations and bifurcation theory to describe molecular activity. If anybody uses my brilliant patented idea, they have to PAY!

      Seriously, this patenting nonsense is completely antagonistic to the spirit of scientific inquiry. There are so many extremely difficult problems to be solved in molecular biology. How can we predict protein folding? How does morphogenesis produce perfectly formed organs? How do neural networks store and retrieve memories? It's a fascinating challenge and to solve it we need to maintain an open scientific environment with the free flow of ideas.

      As others have noted [tuxedo.org], the Open Source software movement has drawn upon the paradigm of scientific research for its extraordinary growth and success.

      What Pellionisz is doing is just the opposite. He's promoting the 'Proprietary Corporate Control' paradigm for scientific research.

      Newton stood upon the shoulders of giants to make his great discoveries. These days people like Pellionisz use the boots of greed to trample science into the mud.

      mhack

      • There are so many extremely difficult problems to be solved in molecular biology.

        Precisely the reason patents on such things can be a good thing. There is a lot of very hard work that needs to be done, and one really good way to get them done is to let people make money off of the work they do.

        However, I'd like to consider the option of requiring any entity which uses patent protection for inventions to release all details of the production of patent protected products when the patent expires.

        I don't like the idea of discoveries being locked away as secrets for much longer than it takes for a company to turn a good profit on them. I'd just hate to see useful technology lost because the few people who know how to do it got hit by a low flying airliner.

  • Heh (Score:4, Funny)

    by zapfie (560589) on Friday November 22, 2002 @12:05PM (#4732238)
    Removal of this "junk-DNA", however, has been proven to be lethal.

    Does this scare the shit out of anyone else?
  • Patent First: (Score:5, Insightful)

    by lpret (570480) <lpret42NO@SPAMhotmail.com> on Friday November 22, 2002 @12:06PM (#4732241) Homepage Journal
    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...
    • 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 (Score:4, Insightful)

      by NDPTAL85 (260093) on Friday November 22, 2002 @12:26PM (#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:Damn right (Score:4, Insightful)

        by OeLeWaPpErKe (412765) on Friday November 22, 2002 @01:27PM (#4732840) Homepage
        *ahum*

        get your lazy bum out of your chair and check WHO actually discovered things.

        ALL (not some, ALL) medicines currently known against aids were first researched at a university

        same for virtually any other disease.

        You seem to think that competition (= not cooperating, but working to kill off, or at least bancrupt, your collegues) works, it doesn't.

        Even the simplest of molecules used in the human body has thousands and thousands of possible incarnations. WAY to much for even multinationals to research.

        In universities, where researchers are given a free hand in research, they occasionally stumble upon new medicines. Eg. someone is researching some ancient plant and discovers a poison the plant uses to kill of insects that helps against a disease.

        Understand that we don't understand even the energy production in a cell, transport systems haven't even all been identified.

        The processes we're talking about are not only VERY sensitive, but also play on a very small scale (transport systems in a cell for example, work by merging, melting, mixing, breaking, etc molecules that contain thousands of atoms, and each and every one of those atoms has a function. Determining the composition of a single of the molecules is a work that takes years with the most advanced tools available.

        Keep in mind that the biggest thing that happened last year in biotech was the succesful analysis of ONE enzym involved in energy production in the cell (out of more than 10.000 different enzyms).

        That analysis took 5 years of intensive communication between a lot of different universities. With competition (that means without communication) you don't stand a chance.

        Most, if not all biotech startups fail, promise great things, but deliver none. And these are the things you want to stimulate ?
        • Re:Damn right (Score:2, Insightful)

          by Hecubas (21451)
          *ahem*

          Before you go all holier-than-thou with academia, I would suggest to you that with out the finanical support of the biotech firms much of that research would not be funded or possible. Lets not forget that those biotech students often have the desire to graduate and take home a paycheck. You can't have one without the other.

          You need to foster that learning environment and you need the application of the technology to keep the cycle going.

          What needs to happen is a balance to keep everyone on track and honest, having that patent keeps the control with the idea maker. I can see where it would be in the best interest of the professor to patent his ideas, lest you have biotech firms run with his idea, make billions, and never return the favor back to the university with grants, scholarships, etc.

          Don't think though that the university system can be solely creditted with all the great achievements. In order to have the luxury of time devoted entirely to research, somebody has the pay the bills, buy the equipment, pay the profs, fund the grants.

      • Re:Damn right (Score:3, Insightful)

        by mhackarbie (593426)
        Sorry, but you're flat wrong about billions of dollars being required in this field. This work is in the area of theoretical biology. With large amounts of genetic sequence data and 3D structure data out there in PUBLIC FREE NON-PATENTED databases like Genbank [nih.gov] and the Protein Data Bank [rcsb.org], cutting-edge research can be done using a PC and molecular biology software. Biology and IT are merging into Bioinformatics. There's a lot of exciting and important work to be done. People can even make MONEY doing it, nothing wrong with that. The problem is GREED, which is an excessive desire for money at the expense of more important things. That's what Pellionisz is guilty of.

        mhack

      • by FreeUser (11483) on Friday November 22, 2002 @01:59PM (#4733169)
        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.

        Your kneejerk reaction to defend the privatization and monopolization of human knowledge is unfortunate. Government entitlements in general are antithetical to free markets, government monopoly entitlements particularly so.

        1) Biotech and pharma companies routinely exaggerate their R&D costs, often by orders of magnitude, rolling standard corporate costs of doing business into the sum total.

        2) most bio and pharma research is done with a mixture of private and public capital, yet those donating money to (e.g.) AIDS research are not given a portion of the "ownership" once the patent is granted. Indeed, that same patent prohibits, by force of a government gun, the donator from persuing research along the very same lines his or her donation helped to initially fund.

        3) Patents stifle research. This has been demonstrated historically time and time again. The Wright Brother's patent led to the United States falling a generation behind in aircraft technology, stifling improvements so much so that with the advent of World War I the US government, in an unprecedented move (and a tacit admission that patents do in fact stifle progress, no surprise since they are antithetical to competition which unlike patents actually does promote progress) seized their patent, opened it up to all comers to promote competition, and granted the Wright Brothers an arbitrary 1% royalty so that the technology would be improved and we'd have a fighting chance against the much more advanced German aircraft (whose builders had not been hamstrung by such patents).

        More recently, several lines of research into potential cures for breast cancer and AIDS have been stopped, in response to Cease and Desist letters sent by patent holders very similiar to the person you so blindly laud.

        Your anti-slashot ranting and raving aside, monopolies are antithetical to competition, antithetical to free markets, and antithetical to progress. Yes, they enrich the inventor (sometimes, often they do not, they enrich instead the inventor's employer), but even in the best case (such as the Wright Brother's invention of the airplane, or perhaps this case), all further improvements on the technology will only come from a very limited group: the patent holder themself, or those few they license to use the patent. Vast numbers of researchers are thus excluded, and a vast number of improvements essentially left unexplored for at least 20 years.

        With fundamental science like this, that's a lot of research, a lot of unrealized cures or treatments, and a lot of dead people as a result. Not in Fantastic Land, in the real, hard world.

        There are other methods to funding research besides granting government entitlements to 20-year monopolies, and almost all of them are vastly better than the patent system we are employing today.
        • by runderwo (609077)
          Nice post. One question:
          There are other methods to funding research besides granting government entitlements to 20-year monopolies, and almost all of them are vastly better than the patent system we are employing today.
          Do you have any links or information regarding alternative methods of research funding and their effectiveness across different fields? That was the only thing missing from your post that I could see.
          • For example the IT industry in the near past (not 100% but to an important degree)). They say that it was more important than patents the secrecy and time2market.

            After that was gone, most of the game is getting patents so that you can have a nice deck of cards (patent portfolio) so you can "play" with your competitors. If you don't have patents, you can't play (can't play without cards).

            Patents are a way to divide the pie, not to promote technological advance. YES, the promote "this particular advance" and thus delay all related advances 20 years. They "kill a line" or way of doing something, so more research is needed to find an alternative way of doing the same (this is usually common when the monopoly patenty doesnt want to license the patent for a logical price, which is ... MOST OF THE TIME. And when they do offer it for a resonable price is because economically that makes sense to them, specially in applications where it is not hard to use an alternative techology - read: there are competing technologies. If there are no competing technologies because the PO granted them with a monopoly on the ONLY way to do something, then....).

            There should be some other way to reward research, for example, with beign the first to market, or with having a good brand and a good image, or a grant up to certain limited amount of profit from the research, or maybe....that you can keep the invention in secrecy for your own use untill somebody else finds about it be it by coincidence or whatever.

            Also, let's not forget that 99% of the usefull inventions are ever patented, and the people patenting stuff never pay a dime for them, and usually use that knowledge to lock people that truly contributed to society and facilitated this very research that is being patented.
      • Example #1: The guys who manufactured the polio virus from scratch earlier this year said everything was "off the shelf".

        Examples #2: There are now several gene manipulation projects being submitted to the Intel National Science Fair. I know 15-year old geniuses are smarter than me :-), but usually dont have industrial resources.
    • 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: (Score:2, Insightful)

      by Alex Reynolds (102024)
      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: (Score:3, Informative)

        by FreeUser (11483)
        On the other hand, if a scientist doesn't patent an idea, a corporation surely will.

        Not necessarilly, and even if it were true, if the scientist publishes first, that is prior art and the corporate patent won't hold up in court. Indeed, if the USPTO were not being criminally negligent in its fudiciary duties under the constitution, it wouldn't even grant the patent in such a case.
    • Re:Patent First: (Score:4, Informative)

      by siskbc (598067) on Friday November 22, 2002 @12:52PM (#4732571) Homepage
      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.
  • by -ryan (115102) on Friday November 22, 2002 @12:06PM (#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.
    • by HisMother (413313) on Friday November 22, 2002 @12:30PM (#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.

      • by Gumber (17306) on Friday November 22, 2002 @01:33PM (#4732911) Homepage
        Protiens are what turn DNA into other proteins. Those new and existing proteins then interact with eachother, so the VM/bytecode analogy works better than you think. I would suggest that the protiens might be analogus to instantiated objects. They intract with eachother in a manner that is not necesarily dependant on the underlying bytecode or VM.

        Of course, the idea of the virtual machine isn't necessary, since the machine is real.

        DNA is less like a C header file than it is like a C program.

        The basic mechanisms by which DNA is used create proteins is well understood on one level. What isn't well understood is all the regulatory mechanisms that interact with that process.

        Why is a given stretch of DNA transcribed into mRNA? Why is it that only particular pieces of a stretch of DNA end up in the mRNA. What determines how long that mRNA transcript exists in a cell, and how many times it is translated into a protein?

        These are all open questions before you even get to the question of protein folding and catalysis, and you have to assume that all the proteins in a cell have some involvement in gene regulation. How does a muscle cell know that it is time to stop producing myosin. Somehow, there is a feedback loop.

      • by mhackarbie (593426) on Friday November 22, 2002 @02:43PM (#4733632) Homepage Journal
        It's true that DNA is not a set of instructions for proteins to execute. However, it is a set of instructions for CELLS to execute. At this level, the idea of a virtual machine might make more sense.

        If you're really interested in this sort of thing, you might want to check out something called OOOP [ooop.org], which is a intriguing combination of biology and OOP.

        mhack

    • 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.

    • 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.
  • by EQ (28372) on Friday November 22, 2002 @12:06PM (#4732248) Homepage Journal
    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.
  • No Big Surprise (Score:3, Insightful)

    by Inexile2002 (540368) on Friday November 22, 2002 @12:07PM (#4732256) Homepage Journal
    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."
  • by Cap'n Canuck (622106) on Friday November 22, 2002 @12:07PM (#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 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*
  • by Jonathan (5011) on Friday November 22, 2002 @12:10PM (#4732272) Homepage
    ...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?
  • Junk DNA (Score:2, Interesting)

    by Anonymous Coward
    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 (Score:2, Interesting)

      by fstanchina (564024)
      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?
      • Oh, by the way, if it was useless, how could errors in it affect our health?

        like this img src=. there. a blank image tag.it's useless. now if I make an error in it, like give it an incorrect URL, it'll sit there for awhile trying to execute the code and eventually fail. same thing with your DNA. coded in a certain way, it might not do anything, but once there's an error that changes it from "useless" to "harmful" we've got a problem.
  • programming? (Score:2, Interesting)

    by chef_raekwon (411401)
    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.....

    • by NickFusion (456530) on Friday November 22, 2002 @12:20PM (#4732336) Homepage
      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.
  • by aok (5389) on Friday November 22, 2002 @12:13PM (#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.
    • by roystgnr (4015)
      Is it just the length of the intron sequences that's important, or is it their contents as well? I thought it was just their length that mattered, but that should be a testable hypothesis: instead of removing the "junk DNA", replace it with "white noise" patterns of the same length and see what happens.

      If the contents are really important, that kind of throws a monkey wrench in the works of some of the fields that study this stuff, doesn't it? I think scientists are using junk DNA to study cladism and human population movements, for example, because they thought they could be sure that natural selection isn't biasing the results.
      • Unsurprisingly, each amino acid has a slightly different bond with a different stiffness.

        The DNA coil doesn't curl exactly the same way everywhere; it curves more sharply in some places and less sharply in other places.

        Mostly this averages out, and in many places it doesn't matter, but like every other imaginable property, sometimes evolution has taken advantage of this.

  • Math in Nature (Score:3, Interesting)

    by SomeoneGotMyNick (200685) on Friday November 22, 2002 @12:14PM (#4732291) Journal
    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!!!
    • 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.
    • Speaking as an expert in the field of genetics and information science, I can honestly tell you all that this whole "fractals in the exons" crap is just that: crap. There are a few basic problems with the article posted here:

      1. There are many names for the stretches of DNA in our cells. The genome is made up of more than exons and introns, as the article would have you believe. Exons are the part of a gene that gets translated into protein. Introns are the parts of the gene that get "spliced" out by our bodies' natural processes. (they are not just "everything left over")
      2. It's long been known that non-gene portions of the genome play important roles. Genes contain the information to make proteins, but other DNA around the gene dictates things like: "where", "when", and "how much"
      3. There's 6 gigabits of information in the human genome. Some genes cluster together, other genes have huge stretches of non-coding DNA between them. If you look hard enough, you can make any mathematical formaula apply somewhere.
      4. There's plenty of stuff left in our genome left to discover. Sure, we know most of the genome, and we need new methods to discover what different sections of it mean. But using fractals? Come on, we have more specific and more well-trained methods of searching the genome that trusting our discoveries to pure guesswork. What basis is there for using fractals, other than it sounds really cool?
  • by Jon Erikson (198204) on Friday November 22, 2002 @12:14PM (#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.

  • 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.
    • 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.
    • by gorilla (36491) on Friday November 22, 2002 @12:44PM (#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.

    • Fractals in biology (Score:3, Interesting)

      by abhinavnath (157483)
      Well... I don't think that the morphology of the human body is in any way a fractal system.

      However, in 1997, West, Brown and Enquist (Science 276:122-126) showed that vertebrate circulatory systems are space-filling fractal networks and this in turn could explain the scaling relations between mass and metabolic rates etc. If BMR scaled with volume, we would expect 1/3 exponential scaling; however, since BMR scales with a "four-dimensional" fractal network, BMR = a*M^(3/4).

      The West et al paper is mathematically somewhat involved - there is a good summary by Williams (Science 276:34).
  • What took so long? (Score:2, Insightful)

    by fciron (619458)
    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.
    • It's not a new idea. In fact, if the guy has a truly new idea, it's very well hidden, not apparent in the article.

      See for instance the 8 year old research in:

      CA Chatzidimitriou-Dreismann, RMF Streffer, D Larhammar (1994), "Are there any fractals in DNA of living organisms"

      ...and

      RF Voss (1994), "Long-range fractal correlations in DNA introns and exons", Fractals, 2(1):1-6.

  • psuedo-science (Score:5, Insightful)

    by paulbotto (628486) on Friday November 22, 2002 @12:32PM (#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!
  • That with a pair of Levi's and my old Commodore 64 Mandelbrot generator, I can create life? *bwhahahahahahahaha* ;-)

    -psy
  • 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
  • Junk (not likely) (Score:3, Insightful)

    by Red Rocket (473003) on Friday November 22, 2002 @12:39PM (#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.
  • 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?)
  • by goombah99 (560566) on Friday November 22, 2002 @12:43PM (#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.

  • 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?
  • by fferreres (525414) on Friday November 22, 2002 @12:49PM (#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).
  • by Nintendork (411169) on Friday November 22, 2002 @12:59PM (#4732609) Homepage
    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.
  • by girl_geek_antinomy (626942) on Friday November 22, 2002 @01:02PM (#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.

  • I cant say I know the answer. Both the distribution of sub-units in human language- sounds and words- and the DNA signal are power-law fractal. These represent the tradeoff between novelty (the message) and redunacy (communicate through noise). EE people know better coding systems for puhing signal through noise, yet nature seems to have settled on fractal.

    On the other hand fractals occur everywhere in nature, usually as result of simple processes. A very simple case is to sum the heads of coin tosses- the resulting curve is fractal. Nothing too profound about randomness.
  • Actually God holds the patent on that and all DNA, but he doesnt have any Lawyers available to back up the claim.
  • by Hythlodaeus (411441) on Friday November 22, 2002 @01:35PM (#4732937)
    From the article, "It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue." This is a very wild claim with nothing to back it up. The concept of "gene" is a leaky abstraction in this case. There's DNA, and there are proteins. Their high level interaction is called a gene, but the work in the cell is done by proteins, not the abstraction.

    Just what is this guy proposing the fractals do? What is the mechanism for reading these fractals?
    Until this guy can propose a specific biochemical pathway using his fractals that can't be explained on the basis of protein and transcription regulation, I won't take him seriously.

    One of the fundamental problems in genetics is deciding whether a particular streach of DNA is or is not part of a gene. There are a number of very effective statistical methods for identifying genes, but they are not 100% accurate. Part of the reason is "alternative splicing" wherein a particular sequence might be an intron sometimes and an exon at other times. The whole gene, introns and exons intact, is transcribed to mRNA, then proteins splice out the introns, but in many cases, different parts may be left in or taken out, so that a single gene produces a number of related proteins. If somone tried to remove all the introns from any sort of eukaryote, it's exceedingly likely that they'd cut out something important unintentionally.

    As for prokaryotes, they don't have alternative splicing, but they have very few introns to begin with. The most time-consuming step in cell division is DNA replication, so prokaryotes whose survival strategy is exponential growth are under a lot of evolutionary pressure to minimize junk DNA. It seems they don't need it, anyway. Higher organisms, however, are full of so-called "transposable elements" - essentially proto-viruses. They are genes that encode proteins that then act on the original gene, spliciing it out of the chromosome and putting it back somewhere else. The genome is full of these, along with non-functional truncated or mutated versions of them. These are mostly just parasitic.

    Finally, there are the "highly non-conserved" portions of DNA. These are areas with extremely high variablility between members of a species, meaning that there is no evolutionary pressure to conserve the function. The best explanation for this is that there is no function.

    Non-coding sequences can however play structural roles, since the chemistry of the nucleotide bases can introduce "kinks" into the DNA strand. These form the basis of many protein recognition sites for regulation, duplication, splicing, error correcting, etc.

    We have all these ways for accounting for a lot of the DNA, but it sounds to me like this guy said to himself "Wouldn't it be cool if all this DNA were like, a fractal or something!" This would be a tremendous discovery if it were true, but the article shows no evidence that he has any clue how it might work or what it might accomplish.
    • Saying DNA sequences is a 'fractal' (really self-similar) is nice, but not that profound, yet.

      In fact if it were a uniform fractal then it would have VERY LITTLE evolutionary mechanistic importance. Only if the law were sufficiently different that physical mechanisms translating DNA patterns into phenotypes (expression of organisms) could account for observed differences in organisms would something behind the fractal law matter.

      Indeed, most of the thinking on the introns is involved in eludicating the mechanisms of the "fractal pattern" but this is all in the mechanisms of replication and crossover. There is little science showing mechanistic (and not just correlations) translations back.

      As far as patenting "all methods of observing fractal patterns" I point out this prior art:

      R Roman-Roldan, P Bernaola-Galvan, J. L. Olivier, "Sequence compositional complexity of DNA through an entropic segmentation method." Physical Review Letters, V80, p1344 (1998).

      Here is its introductory paragraph:

      "The analysis of sequence correlation structure, in both the spatial and the frequency domains, resulted in the finding of short range[1] and long-range[2] correlations in nucleotide sequences, thus uncovering a complex fractal structure of DNA."

      Both[1] and [2] refer to a large number of references each.

      The paper then goes on to discuss an information theory based statistical approach to derive an automated algorithm for hierarchical partition of DNA sequences in to succesively more homogeneous regions. The obsevations is that the breakups are self-similar and thus roughly fractal.

      Not only that but the trend towards greater 'complexity' with organism complexity is also observed here.

      Note that traditionally fractals are defined on a continuous geometrical space, and since there is a minimum breakpoint size (one base pair) in sequence analysis this is not a true fractal---there will only be self-similarity in some "scaling range".

      Note I am a physicist in nonlinear dynamics and happen to know a little bit about information theory. I am not a biology or genetics expert.
  • Its been two years since Clinton & Venter & Collins announced the human genome had been "sequenced" yet they dont even have a firm gene count yet. Of course that was just the "first draft", with the final draft now about 94% completed. [nih.gov] I know its a very complex problem. These MicroSoftian "vaporware" announcements make me very skeptical about bold claims by other researchers.
    • Remember that the "rough draft" took some 20 years to complete. Do you really expect everything it tells us to be completely understood in less than 1/10 of that time? How is this draft "vaporware" in any way whatsover? It is what it claims to be, and has been incredibly useful to researchers, particularly those locating disease genes. As far as not yet having a complete gene count, it would help if you could provide a complete and accurate definition of a "gene". The full sequence has raised more questions on this front than it has answered. Can you really call something a "gene" just from looking at the sequence? Does an open reading frame really mean something is actually transcribed? How do you separate out the psuedogenes from the real ones? What about alternate splicing to create alternate proteins--does this count as one gene or several? You're dealing with 3 billion bases and a highly variable definition of what you're looking for. Why do you expect a final answer to be that easy?
  • If genetic material is called exons, shouldn't junk DNA, that which serves no purpose, be called Enrons?
  • Structural Genes (Score:3, Informative)

    by xener (71427) on Friday November 22, 2002 @02:20PM (#4733415)
    The mechanisms by which genes code for structure
    are reasonably well understood. There's no need
    to invoke mysterious fractal magic to explain
    it.

    A good non-technical book on the subject
    is:

    "The Art of Genes: How Organisms Make Themselves"
    by Enrico Coen

    The fact that he wants to invoke fractals in
    introns to explain structure suggests that
    he dosen't know the molecular biology very
    well.


  • Having space in genetic code not used by anything would not be a huge disadvantage. If life was formed by random chance and evolution, it just means that the circumstances that brought about man were made off of a large slate, with different parts that happened to connect well across that genetic slate. It also makes sense that removing or altering seemingly meaningless parts of that slate would mess up indexing methods (skip ahead X number of A's, start reading, etc.)

    Having a very large set of non-referenced entries in a genetic set would also be an advantage in itself. You have a large set of potential mutiations that can be subtly linked to to find advantages, and plenty of room to sort things out genetically. You can also have things like children who are genetically designed to be born to die to save their siblings.

    Large-scale life itself is built on the idea that gross inneficiency is acceptable if it allows food and access to mates to be found at the larger scale. So simple bacteria has tight genetic code, fruit flies have fast-mutating genetic code, and large animals have inneficient code with different portions that mutate at varying rates. It's life competing with itself to explore all corners of possibility. Semmingly inneficient aspects are just another legitimate part of the process.

    Ryan Fenton
  • by eyefish (324893) on Friday November 22, 2002 @02:40PM (#4733610)
    After having read Stephen Wolfram's A New Kind of Science [wolframscience.com], I see more and more how amazing his book is. This DNA-fractal mechanism is exactly what he talks about in his book when he explains how all this complexity we see in life and the universe itself actually arise from much simpler structures which simply apply a simple computation over and over again (in this case, like a Fractal Computation) to obtain complex behavior.

    If such patterns are indeed found in DNA, it will only provide more evidence to support Wolfram's theories (and I trully hope a Nobel prize is waiting for him).
    • I am still reading the book you reference, and as I am reading it and seeing things like this, I have to say it is becoming very interesting. Some of the diagrams and math are going over my head, but I am trying to gain the fundamentals about what he is talking about - which I think was his goal.

      By the way, it seems as though Wolfram is most interested in the non-fractal systems the CA produces - the fractal-like systems (can't remember the rule numberes off the top of my head, but many look like Serpinski's (sp?) triangle) were repetitive, always continuing, even after many iterations - on the whole never evolving.

      The more dynamic rules seem fundamentally random, almost chaotic - but all seem to point to an organization of some sort. I do agree that there is something interesting going on with DNA - I think in some manner, it is going to end up being a simple Turing-like machine, with a very limited and simple ruleset, acting like a simple CA, and after having run for such a very, very long time - gaining an extreme level of complexity based on Wolfram's ideas.

      While I have seen a lot of criticism here on /. about Wolfram, CAs, Mathematica, lawsuits involving everything, references to this book as being a doorstop - I think he is on to something, and I hope he is vindicated - something tells me he didn't write such a large book and sell it so cheaply for nothing. The book would be cheap (book price wise, if nothing else) at three times what it cost - he spent $15.00 a copy, and it is only selling in bookstores for $40-50.00 a copy - so you know he isn't making much money on each copy - and no one spends that much time and money on writing that large of a book on such a topic for a mere "vanity press book" - not unless he is completely nuts, which I don't think he is...

    • I too am reading Wolfram's book, and it is excellent (and very interesting). But Wolfram takes a great deal of credit which IMHO ought to go to Fredkin, who originally proposed and explored this idea.

      No slight against Wolfram intended, but we ought to give some credit where it is due.
  • First of all his patent is overly broad. It applies to any attempt to measure and compare introns. How can that be unless he tells us every concievable way to measure and compare introns. That's patently silly ( pun intended )

    Secondly, a heart could be thought of as a three dimensional picture made of atoms which are analogous to pixels. The genes that define how to make a heart and keep it functioning are merely a coding scheme ( like jpg ). While there are 'fractal' compression algorithms, they are not radically better than conventional coding schemes except maybe in some special instances. They may be faster or slower or better at compression or worse. There are tradeoffs. The 'formula' for the psychedelic fractals you see on posters may look complicated for having been drawn by a formula like x1 = x^2 + c but they actually are simple ideas repeated ad infinitum.

    A heart has some repetitive features ( like cells ) but there is alot of innate complexity in the structure that can not be factored out easily. It has in information theory terms a certain entropy that means it can only be compressed just so far. The compressed heart code ( ie it's fractal formula ) may be very complicated and have as many bytes( or codons ) as other algorithms for encoding biological information.

    it is even possible that we have evolved many different coding algorithms and that different introns and exons are in different 'file formats' so to speak.

  • Hmm... maybe my application for a patent covering measuring the height of trees for botanical purposes has a chance, then?
  • [netspace.net.au]
    This is the first chapter of greg egan's book, diaspora, which describes a simulated neurogenesis in software, the technique of which was reverse engineered from the fractal patterns of human DNA.

    Although this is science fiction, and art in only the literary sense, would it not qualify as prior art?
  • by vga_init (589198) on Friday November 22, 2002 @07:41PM (#4736051) Journal
    Being a member of a local biotechnology program at my school, I have attended several biotechnology courses, this already being my third year. When first learning about DNA, I laughed at the idea of "junk DNA," basically rejecting the whole idea from the start.

    It shouldn't take anyone very long to realize that the scientific field of genetics is in such an infantile state, and all the biotech buzz going around so far (to me personally) seems to be rather much ado about nothing. Albeit, we can make insulin, clone sheep, and poke the human genome, but really, other than the recombinant DNA technology we've developed to use with bacteria and a few crop-altering techniques, I really don't find biotechnology to be a very applicable science, or even practical for that matter.

    Now, I'm not going to claim the theory, because I come up with many hairball theories about stuff all the time, not really having proof behind any of it, however, I always did suspect that this "junk DNA" was good for something, and I found it rather peculiar that fractitions (made the term up myself ^^) have found correlations between certain morphological structures and fractals. I actually attributed the fractal behaivor to be the result of some abstract physical phenomenon resulting from the cells themselves, not DNA, but this guy's theory holds a lot of weight with me as he is much more highly educated and obviously knows what he's talking about. I advise everyone to pay heed to this theory, because it has great potential to change the face of the WORLD as we know it. ;)

    While on the subject of biotechnology, I would like to defend the genetecists' position against religious fanatics. From my studies, I have concluded that genetics is a subject of absolutely no spiritual/religious/moral import whatsoever. The moral dilemas in biotechnology can be considered very minute in comparison to that of other situation that politicions engage in. Obviously, anyone can agree that risky human experimentation is immoral (which is the same for any field of science), but other than that, I don't see any other relevant issues that are practical at the same time.

    Also, just to set the records straight, cloning is a science that is centuries old. It brought us the Irish Potatoe Famine, and yet it also saved the wild orchid. I always hope to believe the benefits outweigh the losses.

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