Early press coverage on FractoGene [As of January 6, 2003]
Introduction by inventor Dr. András J. Pellionisz
[January 6, 2003]
From November 21 to 28, 2002 a leading daily, San Francisco Chronicle, ran on it's server (SFGate) an Article by Hal Plotkin "Junk DNA Revisited. A Silicon Valley startup claims to have unlocked a key to the hidden language" on a Provisional Patent Application FractoGene, submitted on July 31, 2002 to USPTO by András Pellionisz. Excerpts from the Article are color marked.
Pellionisz' Silicon Valley startup company HelixoMetry, Inc. at this point explicitly invites Private Funding. The journalist emerged from a "pool" of top high-tech and biotech writers, carefully selected, and independent of the inventor. The journalist did a brilliant and impeccable job with this very difficult subject. Still, potential investors may wish to rely more directly on the inventor's statements. Therefore, in effect indemnifying the journalist from the responsibility of advertising an Investment Opportunity, please find below some clarifications of the text in the Article. By editorial policy, the manuscript was not seen, thus the inventor had no control over its contents, only key data were asked for double-checking. The inventor highly appreciates the excellent work of all contributors, but reserves the right of providing clarified information for potential investors.
Clarifications may be warranted, especially because immediately after the appearance of the 2,241 word Article, spirited discussions broke out in close to a dozen "internet discussion groups" worldwide. Slashdot.org posted almost 300 entries in the first 24 hours alone! Moderators of such discussion groups (again, independent of the inventor) "summed up" the Article typically in just one long paragraph. Given the nature of the Provisional Patent Application nobody saw the actual Text and Figures of FractoGene (Patent Pending). Therefore, it is inevitable that there may be some distortions in color marked casual opinions by some contributor(s) to color marked discussion groups (hyperlinks), compared to the actual Patent Application.
In a "reverse order", let's start from one of the most recent points raised about the Article:
Yale University Law School
First business-method patents, now scientific-method patents
Ernest Miller on Tuesday, November 26
Petersuber writes: "Andras Pellionisz is seeking a patent on a scientific research program (the study of DNA introns to see whether they represent fractal patterns). Patents must describe a non-obvious technique. In this case, the patentability of the research program depends on the fact that most biologists are not familiar with fractal mathematics.
Yale University Law School has a point - but is incorrect on another issue. It is true, that the patentability is based on the non-obvious nature of fractals to "Mainstream Academia". However, this is a problem of Academia, beyond control of the inventor. Whenever technology leapfrogs an impressive, but concensus-seeking (therefore by definition slow) or perhaps otherwise imperfect system, such phenomena are bound to occur. Weakness in knowledge of fractals of biologists (or in a larger sense, weakness in mathematics) is not something this inventor is responsible for. In fact a similar phenomenon has been experienced before. When Pellionisz' information geometry approach in biology, Tensor Network Theory, leapfrogged Mainstream Academia, it took 20 years - about this time - to eliminate major gaps caused by a disruptive approach. In general, it is noteworthy that in different continents, similar "disruptive technologies" not once leapfrogged Academia in the past. One example is quantum mechanics, that that was beyond "Mainstream Academia" when it became known that technology might release awesome amounts of nuclear energy both for peaceful as well as for decisive geopolitical purposes. Even the USA "Mainstream Academia" was caught embarrassed by the appearence of a disruptive technology of Sputnik in 1957. Such phenomena are therefore distinctly "non-unique" and a principal question is if those leapfrogging Academia should be punished, or rather, quickly rewarded/embraced. (The Copenhagen group created quantum mechanics in a hurry, rewarded by several Nobel Prizes, and the USA Academic system went through a major re-vamping, with many tens of billions of dollars poured into the system after the Sputnik was launched). If there is any truth in the Yale Law School comment (and I strongly believe, that there is) the present USA Academia may be in need of a major revision in view of disruptive breakthrough technologies appearing with the "Genome Revolution".
On the issue if FractoGene is a "patent on a scientific research program", the Yale University Law School is simply less than fully informed. If one would come forward with a diagnostic system to count the discarded bear cans in the garbage, and where one regularly finds an excessive number of cans (say, more than a dozen per day), would flag the house as a likely home of an alcoholic, nobody would brand such a practical suggestion a "scientific research program" - would they? USPTO patent laws do not require either "scientific" or "research" background for an innovation to be patentable. It is enough if the disclosed invention is new and potentially useful. Even for a drug-patent, the only requirements are that the medicine must be effective and safe. (The scientific knowledge how the medicine works, is not required, and sometimes simply not available). One may add, that the Yale University Law School is not privy to the exact details of the contents of provisional patent application.
The implication of the Yale Law School posting is, that the FractoGene patent application might indeed trigger massive "scientific research program" (by providing a mathematical explanation for the excessive, self-similar DNA basepair sequencies) is in fact quite likely. However, should that happen, it will be an extraordinary bonus and one hopes it will not be held against the inventor. While it is obvious from the posting below, that the Patent Application is part, perhaps even a trigger to a trend of the Genome Revolution becoming highly mathematical (see MCT Physics discussion group below), that patent application itself is not a "scientific program":
MCT Physics - A Technology Journal For Geeks!
November 25, 2002
DNA = Fractal? A patent has been filed by Andras Pellionisz, who expects to be able describe "junk" DNA as fractal pattern.
It's interesting to see biology being put into a more rigorous mathematical footing. If this trend continues it could be very beneficial to biology's growth. Just look what math did for physics. Without a standard and universally understood language, physics would be nowhere near where it is today. It's amazing to think how flexible numbers are at describing the world. It's mind-blowing that something so simple can even begin to describe what we see around us everyday.
Not 17 years. Only 7 1/2. Don't forget BIOPAT
by Anonymous Coward on Friday November 22
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 that apply to patents in the medical and biological areas.
With the above in mind, one would read the Article in a rather different manner than the Yale University Law School contributor did.
When the human genome was first sequenced in June 2000, there were two pretty big surprises. The first was that humans have only about 30,000-40,000 identifiable genes, not the 100,000 or more many researchers were expecting. The lower -- and more humbling -- number means humans have just one-third more genes than a common species of worm.
The second stunner was how much human genetic material -- more than 90 percent -- is made up of what scientists were calling "junk DNA." The term was coined to describe similar but not completely identical repetitive sequences of amino acids (the same substances that make genes), which appeared to have no function or purpose. The main theory at the time was that these apparently non-working sections of DNA were just evolutionary leftovers, much like our earlobes.
But if biophysicist Andras Pellionisz is correct, genetic science may be on the verge of yielding its third -- and by far biggest -- surprise.
In addition to possessing an honorary doctorate in physics, Pellionisz is the holder of Ph.D.'s in computer sciences and experimental biology from the prestigious Budapest Technical University and the Hungarian National Academy of Sciences respectively -- institutions that together have produced nearly a dozen Nobel Prize winners over the years.
In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human.
Another way to describe the idea: The genes we know about today, Pellionisz says, can be thought of as something similar to machines that make bricks (proteins, in the case of genes), with certain junk-DNA sections providing a blueprint for the different ways those proteins are assembled.
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.
Other investigators are also looking into introns from a variety of perspectives. A group at UC Berkeley, for example, recently won $14 million from the National Institutes of Health to study the role introns might play in cardiovascular disease. Other researchers have begun looking at similar questions, with most focusing on intron strands located near genes whose functions are better understood. Scientists at UCLA, for example, recently made a promising association between what appears to be an intron abnormality and spinocerebellar ataxia, which is similar to Huntington's disease.
What makes Pellionisz' approach different is his suggestion that fractals will be found to play a critical role not only in these conditions but also in tens of thousands of others that have not been studied yet. His patent application covers all attempts to count, measure and compare the fractal properties of introns for diagnostic and therapeutic purposes.
"It's certainly possible that such a patent could be granted," says C. Anthony Hunt, Ph.D., a holder of nine patents who heads the Hunt Lab in the Department of Biopharmaceutical Sciences and Pharmocogenomics at the University of California at San Francisco.
To win a patent, Hunt notes, all an inventor must do is describe or teach some new skill that is not obvious.
"And this would certainly qualify as non-obvious," he says. "If it works, [fractal intron analysis] could become a very important tool."
Hunt adds that most biologists simply don't know enough about fractals or the advanced math behind them to understand how they might apply to the field of genetic medicine.
"We need someone to tap us on the shoulder and explain it to us," he says. "But if it clicks as a tool, we would be more than happy to use it."
"Overall, we know very little about what is referred to as 'junk DNA,'" he adds. "But every year that goes by, there are more insights into the possible role they might play."
Some misunderstanding popped up in the discussion groups when the precise statement of the Article saying Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself got a little bit distorted by quick readers. For instance, a major discussion group Slashdot.org introduces the Article by saying among others, that the Provisional Patent's claims may contain that "life's blueprints may indeed be in fractal patterns found in the DNA". From this, one may jump into a conclusion that FractoGene has claim on "life" itself. One has to firmly state that the Article did not say anything of this sort, moreover Provisional Patent Applications according to USPTO rules can not contain any claims at all - let alone the absurdity that "life" itself would be patentable. Again, the Article crystal clear what the Provisional Patent Application wishes to accomplish:
Staking His Claim
Pellionisz hopes his patent application will help him launch his company and make him one of the field's key players. The provisional application lets him put the words "patent pending" on any related creations for one year, after which he must file a complete application. Like other inventors, he's also free during that time to disclose his concept through other means, such as in professional journals or at scientific gatherings.
While they remain generally cautious, a number of top biomedical researchers and other scientists say Pellionisz might be onto something really big.
Experts generally agree that a breakthrough in figuring out the role junk DNA plays, if any, would represent a spectacular advance in our understanding about how DNA in general turns inanimate matter into living organisms. If that happens, humanity would take a giant leap toward gaining control of the machinery of life itself, which would open up a wild new frontier in medicine and science that could lead to everything from growing new organs designed for specific patients to preventing and curing any health- or age-related problems that have a genetic origin or component.
Pellionisz says his main goal is to set the stage for the next and even more promising generation of research into genetics. Given the fact that he may be the first person to assert a patent on intron fractal counting and analysis, it's also conceivable that Pellionisz could wind up with related commercial rights worth billions of dollars. If he's wrong, of course, any patent he might receive will be worthless. (The inventor would like to clarify for the sake of investors, that this is not necessarily the case. "Post it" emerged when an invention of an adhesive proved to be a "failure" as it did not stick strongly enough - and now it generates a huge portion of revenue of 3M. "Tea bags" were invented to distribute samples of tea - but became a huge success when by mistake someone used it for "instant tea". Even a "better mousetrap" can still be used e.g. for a doorstop, if it does not catch a single mouse. Just look at the early patents on airplanes or automobiles how "off" they were even on some essentials, yet they unquestionably helped launch the airplane- and automobile industries) And even if he's right, he could have to contend with other inventors who may also have recently filed similar patent claims that, like his, have not yet been fully disclosed. (The truth in this remark is the justification for the investors of the extreme urgency behind the "first to market" attitude, rather than sticking to the dance card of peer reviewed academic journal publications. Every modern industry has to contend with "submarine patents" and the best known strategy is to launch an as robust effort as possible that can ride out storms with the highest likelihood of survival).
Meanwhile, Pellionisz has several additional patent applications in the works that he says will build on and further protect his original claims. At the same time, he's also looking for the investments he says he needs to move forward more quickly, including completing his formal patent application by the deadline, as well as ramping up his company's first commercial applications, which other researchers would use. (A clarification for the investors is to include applications for directly to the "end user" of the health care system, which happens to be the most immediate and easiest use)
Wary of all the startup horror stories Pellionisz has heard, he's hoping to avoid working with a traditional venture-capital company. Instead, he says he's looking for a single "angel" investor, ideally someone knowledgeable and connected in the biosciences and database worlds who can help him develop his patent portfolio and formulate a business plan that links his efforts with those of some larger organization in a related field. Pellionisz even has a short list of names of specific people who he thinks would be ideal partners at this stage. He is, he says, more interested in building a successful company than in selling the idea for a quick buck. Given the stakes, additional competitors seem certain to join the fray.
It could be years, even decades, before the dust settles and Pellionisz learns whether his patent application has any real merit, as well as whether someone else beat him to the punch with an earlier enforceable patent claim. (Clarification for the investor: you can win a war against adversaries, such as diseases, by "brute force", or better yet, "algorithmically", by deciphering and thus reading the code of the adversary. If you can even "patent" the utility of deciphering the code, it is an extra bonus - though e.g. the H-bomb was never patented. However, the name of the game in our case is "winning the war" against diseases. One may collect "war compensation" on top of victory, or may just barely win in the struggle, while sustaining terrible losses, however, a slim winning is still victory)
"All I know is that I'm in a race," Pellionisz said last week. "And the clock is already ticking."
It is clear from the Article that the Patent Application does not dismiss or replace traditional means of Academia (peer reviewed publications, participation in conferences, lecturing, etc.). The strategy of "business first" only responds to the extreme "urgencies" and "pressures" of our time. It merely does "Business first, Academia later". While the Article was clear enough about this, in view of the ensuing debate the rationale should perhaps be elaborated further. Especially, since some mistakenly thought that this modern agenda is dictated by personal preferences. Fortunately, several commentators point out below that this novel sequence is necessitated by priorities of our time:
Gotta Be More To This...
by Anonymous Hero
This is very interesting and I've got to read more about this guy and his ideas but offhand it seems a little screwy.
I guess the point is that science progresses by new and startling insights that go against the common dogma like that I've outlined here...hope he IS on to something, but the patents seem to be a greedy way to announce it...
Who is greedy?
by Anonymous Hero
I think those might be greedy who approach Helixometry with the right "sophisticated angel" whom they will take (if it has not happened already). It may already be too late, although the "too late for investment?" link is still active on their website. Most "match makers" do this kind of "searching for the right angel" - not for fun but for a fee. The patentor took the time for his discovery, and the "smart angel" provides the funds for a risk in hope of an easy tenfold revenue within a year or two. If Fractogene takes only $1 mil, the "matchmaker" can fetch a decent yearly salary (if the fee is a typical 5%) just for a couple of well-placed phone calls. If he/she gets it in shares, such an easy and quick "matchmaking" could yield a pretty penny. If anyone is bothered by *others* making money, why don't you think with the head of these guys and call ahead those Venture Capitalists (whom the article says the inventor will not take), but it is widespread knowledge that a lot of VC partners are very rich and some are very knowledgable in the subject - and some of these VC partners do "angel investments" out of their own pocket. They first make their *own* money on the "new next big thing" and later help doing the round A with the VC company in which they are a partner already, and in the next stage wrap such investments together with those pharma- and/or information technology company that they also finance already. All this is completely legal, widespread practice, simply called "leveraging". Get over your envy, get into the act. Companies are meant to be "win-win" for a *lot* of people.
I think it is disgusting that anyone can patent a process so important for the future treatment of disease and inherited illnessess. Gerry Michaud Roslin, Ontario
The Ethics of Patenting
There are certainly a lot of ethical issues regarding patenting anything related to medicine or genetics. But the unfortunate truth is that medicine and biotechnology are businesses like anything else, and it's difficult to disallow patents for particular areas of research. I don't begrudge some physicist or software developer patenting an invention that radically changes our world, and which may have taken years of research, because without that patent they may never see a dime--they'll do all the work, publish the results and then watch as some big corporation uses their results to create products that make them a fortune. It's not only unfair, but it would result in less innovation and entrepeneurial initiatives. The inventor deserves to reap the rewards.
But what if the invention is intended to aid people's health? Or what if it wasn't originally intended for that reason, but wound up being used in medical devices? Should patents no longer apply? If we don't allow biologists to patent their research, then we're forcing them to be unwilling altruists.
As much as I dislike the pharmaceutical industry, the same rules must apply. Big corporations will not invest the time and money on creating new drugs that their competitors can start duplicating and selling immediately without paying royalties. That said, just because you have a patent, does not mean you have to charge a fortune for its use. Pharmaceutical companies can use the patent defensively, to prevent competitors from benefiting, but still choose to sell the drugs at a reasonable price. Or they could choose to allow other pharmaceutical companies to cheaply manufacture their drugs for third-world nations that desperately need them.
Patents basically give the inventors the right to choose what is done with their invention. It's when the owners of patents act unethically, that the system breaks down. I don't have the answers to how the system could be improved, but I don't think simply disallowing patents for anything that could aid human health is the correct approach.
It is a similar "changed priorities" of our times, that in the 21st Century Internet assumed predominance not only in communication, but also in organizing the public, e.g. for for Public Investments. "Ivory Towers" were never very good at connecting "ideas" to "business", while it is a major strength of the "New Internet Media". There is quite a debate on this "Internet first, Academia second" topic, as well:
In a move sure to alienate some scientists, 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. (Clarification for the investor: the strategy was not picked by one's fancy, but was enforced by business conditions). Most mainstream scientists usually blanch at such approaches, preferring more traditionally credible methods, such as publishing articles in peer-reviewed journals. Scientists who don't follow that tradition are usually treated with suspicion.
But Pellionisz' credentials and prior accomplishments make him much harder to dismiss than the average cyberspace sci-fi wacko.
(Clarification for the investor: see 35 years of accomplishments here of Dr. András J. Pellionisz in Academia, Government and Industry - this author did his homework in the last third of the 20th Century to earn the right of doing business in a novel manner required in the brave new World of our 21st Century)
A biophysicist by training, the 59-year-old is a former research associate professor of physiology and biophysics at New York University, author of numerous papers in respected scientific journals and textbooks, a past winner of the prestigious Humboldt Prize for scientific research, a former consultant to NASA and holder of a patent on the world's first artificial cerebellum (a part of the brain), a technology that has already been integrated into research on advanced avionics systems. Because of his background, the Hungarian-born brain researcher might also become one of the first people to successfully launch a new company by using the Internet to gather momentum for a novel scientific idea.
by paulbotto on Friday November 22
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!
It is particularly interesting that superficial readers overlook the "Fractal Model of a Purkinje Neuron" by Pellionisz 1989 (one of over hundred publications he disseminated the "old fashioned way") - although could look up his "Summary of the One Third of a Century Path" that led to the discovery contained in the FractoGene Patent Applicaton.
by Anonymous Coward on Friday November 22
Hey, who said that this was a scientific claim? Looks like it is a patent-application eyeing usefulness in industry.
Would anyone say that the Wright-brothers were in pseudo-science? No, they laid out the foundations of the airplane industry. (Did contribute to science, though, as they ruined the "nice scientific theory" of some starchy academics who pontificated that "nothing heavier than air can ever fly").
If the fracto-thing will be useful to diagnose or cure some diseases, so be it. (Placebo is no science at all, still occasionally helps). Aspirin can even be used, in a very non-scientific manner, as a contraceptive (if a woman holds it between the knees) - and the argument of pseudo-science is just ridiculous. If the fracto-thing will help, shareholders will get rich. If in addition will be proven as a great scientific breakthrough that might be an extra bonus (most shareholders will not care much about it).
by Anonymous Coward on Friday November 22
Of all the people who have commented so far, this is the first one who actually knew what he was talking about.
What took so long?
by fciron on Friday November 22
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
Re:What took so long?
by Anonymous Coward on Friday November 22
Fractals have been suspected to play some role with the DNA. There is certainly much academic research about the DNA. But if something pops up that could be directly useful in e.g. pharmaceutical industry (repeat, not only in academic research but in health care industry) patent applications seem to make a lot of sense. Don't they?
by Anonymous Coward on Sunday November 24
This one makes the most sense to me. Sutble changes in the algorithm, vastly different outcome. As a byproduct we have gotten the philosophy of individualism, in spite of genetic determinism.
What a silly idea!
by Anonymous Coward on Friday November 22
Ok this is a case for computer and scientific intelligence 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
Re:What a silly idea!
by gacp on Friday November 22
>If they are so important how come the gene products from bacteria minus introns is the exact same as plus introns.
Well, that's why you can't build metacellulars in a test tube. Proteins is all you usually can build, virii at the very best. And often even that does not work without twiking (e.g. removing introns), as you pointed yourself.
No, the guy has a point. We have known this for quite a while, but the mainstream biology silences this kind of research.
Re:What a silly idea!
by Anonymous Coward on Tuesday November 26
To Academia, "silly" equals to anything officially "unaccepted". The clear pattern that Academia is petrified of "unaccepted" axioms proves the point that there is something basically wrong with running science in the USA as a "maffia" of the initiated. If there was no such avenue as patenting something that is useful (aeroplanes, electric and electronic technologies), the USA R&D would probably be totally dead by now. Where are the "peer reviewed journal articles" to let Intel develop a new, breakthrough generation of chips? Academia is clearly dominated by some control freaks who would like to absorb all taxpayer money meant for the betterment of human kind, and some are plainly scared shitless when there is a major breakthrough in which they are found flat footed. The more "control freak" an academic would like to be, the more pathetic and miserable he/she appears. Academics predicted that horse drawn carriages will be impossible in London by the turn of the 18/19 Centuries, as with the predicted escalation of traffic, horse manure will raise to a level that it would be impossible for any horse to cut through the horseshit. Academics need some "reality check" every once in a while, and this patent will help them to sober up. I predict, that in order to escape a potentially deadly embarrassment, they will rapidly embrace the breakthrough concept by saying "we have always been advocated the very same thing, just slightly in more formal and precise academic statements". When it comes to hypocrites, Academia has a brazen and ample supply of them. It is an old (and true) saying "Those who can do, those who can't, teach".
Well, the last one is probably unduly harsh, and the decorum is less than fully civilized even for the normally cut-throat environment of investors, but may be typical of the emotions that the debates stirred. Fortunately, immediately after pondering the potential of the paradigm-shift to yield billions of dollars, much ado was played at the issues of Business first versus Academia first, and Internet first versus Academia first isues. Surprisingly, there was hardly any question about the concept itself that considering formerly "junked" genetic basepair sequences fractals could well be "a big thing". Of course, there is much need for a quick crash course on fractals:
The Hidden Fractal Language of Intron DNA
To fully understand Pellionisz' idea, one must first know what a fractal is.
Fractals are a way that nature organizes matter. Fractal patterns can be found in anything that has a non-smooth surface (unlike a billiard ball), such as coastal seashores, the branches of a tree or the contours of a neuron (a nerve cell in the brain). Some, but not all, fractals are self-similar and stop repeating their patterns at some stage; the branches of a tree, for example, can get only so small.
Because they are geometric, meaning they have a shape, fractals can be described in mathematical terms. It's similar to the way a circle can be described by using a number to represent its radius (the distance from its center to its outer edge). When that number is known, it's possible to draw the circle it represents without ever having seen it before.
Although the math is much more complicated, the same is true of fractals. If one has the formula for a given fractal, it's possible to use that formula to construct, or reconstruct, an image of whatever structure it represents, no matter how complicated.
Basically, Pellionisz' idea is that a fractal set of building instructions in the DNA plays a similar role in organizing life itself. Decode the way that language works, he says, and in theory it could be reverse engineered. 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. At a minimum, we'd get a far better understanding of how nature gets that job done.
The complicated quality of the idea is helping encourage new collaborations across the boundaries that sometimes separate the increasingly intertwined disciplines of biology, mathematics and computer sciences.
Thinking about whether junk DNA has a purpose "is a rather obvious question for scientists to ask," says ... a world-renowned expert on fractals. ..
"This is a fractal form of nature that must stop at some stage," ... adding that the fractal pattern looks exactly like others that appear in nature....
"I'm not sure he has the right answer," ... "but he is asking a very important question."
Pellionisz has been working on understanding the possible linkages between math and physiology since his earliest days as a college student in Hungary, when he first decided to devote his life to understanding how the brain works. It's that pursuit that has helped lead him to his latest ideas, he says.
"When you consider how the brain tells the fingers to pick up a pencil -- all the many different muscles involved, the senses, vision, touch, the distances involved, and how it is all managed by the brain -- you quickly realize there has to be some form of math involved to coordinate everything," he explains. "I always knew from my earliest days that it had to be math, and I knew it wasn't calculus, because of the distances involved [e.g. from the brain to the tip of the finger]. So it had to be a form of geometry, but it had to be a very special kind of geometry."
This "regular Academic research, yielding a rather large number of peer reviewed scientific journal articles, book chapters, and a co-authorship in one of the most "required reading", a Textbook in any University Course on Neural Networks from Bulgaria to Belgium to Boston, only took Pellionisz a mere 35 years of his adult life. Of course, it also yielded a patent on an "artificial cerebellum" - that was assigned to New York University, and later NASA flew F15 fighters with neural net control, based on Pellionisz' NASA Senior National Research Council advisorship. Having done his "Academic Homework" and "Government Duty" Pellionisz now laughs off those lecturing him on Academic Publications (or Government Accomplishments) - and feels free to pursue his inventions using the most effective strategies, especially if they not only have the potential of billions of dollars in revenue but also helping human kind with new kinds of genetic diagnosis, gene dicovery, drug discovery and therapy.
Pellionisz has dubbed his new company Helixometry Inc. The name ("helix" refers to the unique spiral folded-over shape of the DNA molecule) alludes to what he says is the fractal math at work inside DNA.
His theory is highly speculative. But there is at least one other important piece of anecdotal evidence that he might be on the right track: As organisms become more complex, they seem to have more intron DNA.
"It's not a perfect correlation," says UCSF's C. Anthony Hunt, "but it is a trend. It's as if the more advanced organisms had made a larger number of steps to get to where they are now."
In other words, although people are made up of the same basic stuff as other organisms, the instructions for making a person should in theory be more complex, which could account for the large amount of intron DNA found in humans.
Junk (not likely)
by Red Rocket on Friday November 22
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.
Re:Junk (not likely)
by Richiemann on Friday November 22
Actually the gooey junk in the skull has a purpose: "cooling down the blood". It is mostly water, isn't it? ;)
This does not surprise me
by vga_init on Friday November 22
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.
... 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. ;)
by fain0v on Friday November 22
Are there any developmental disorders that have been tracked to a mutation in an intron in any animal models?
by Anonymous Coward on Friday November 22
YES. There are already a good number of dreaded hereditary diseases where there is a "run" on introns, meaning that some basepair sequence gets repeated a huge number of times (compared to healthy people). There are many cancerous cases, as if "growth" would go out of control. A particularly interesting case is the so-called Huntingtons' disease, see
by Anonymous Coward on Friday November 22
No worry, God can claim prior art.
Re:is there something profound about "fractal"?
by RealityProphet on Friday November 22
I'm not really sure what your question is, but if its, "why did nature choose fractals?" then I think you answered your own question. a fractal pattern is created by building on simpler processes. This seems to be the exact way nature evolves: take a known good solution to a problem (a life-form) and add to it a little something to make it better. It seems a match made in heaven (hmmm...)
Re:I'm quite skeptical about this...
by girl_geek_antinomy on Friday November 22
From what I understand of fractals-in-nature, aren't fractal patterns pretty ubiquitous in non-random non-identical data? If so, this isn't a great surprise - we know intron material is non-random non-identical. Should it really surprise us that much that if we throw sufficient computing resources at it it yields fractal-like information?
What worries me more is that if this patent is granted, a lot of effects which are a feature of things we already know about intron DNA, and relate to its interaction with histone protein, particularly, will end up being swallowed up by the patent, when in fact it's just to do with the physical and chemical properties of the DNA.
by wiggys on Friday November 22
I'm convinced that we possess 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.
Re:A primer on DNA structure
by gacp on Friday November 22
This guy has a point. There are fractal patterns. And you forget the cytoskeleton, and that DNA-binding protein complexes could ride on it to put to close contact regions in the DNA that are linearly far appart. `Junk' DNA can compute this perhaps, and many other things, like non-random crossing-over. Indeed, many `random' mutations and reorganizations, and gene duplications may very well be decidedly not random.
Besides, there is more control needed for complex organism that just the Central Dogma provides for. But after all, the Central Dogma is a DOGMA---you disagree, you are left out of the game of Science, Inc. I spell it out for you: NO FUNDING.
And if you ever dare to think about putting the reality of Natural Selection to the test... well, you better start running for your life (no need to worry about your career, you no longer have one). No, evidence won't help you.
But it's nice to see that the Great Wall Of Silence is cracking after all these years. At least the laymen will know that something is being hidden by Science Inc.
by Anonymous Coward on Friday November 22
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."