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
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
But if biophysicist Andras Pellionisz is correct, genetic science
may be on the verge of yielding its third -- and by far biggest --
In addition to possessing a 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:
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
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
"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."
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.
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. 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
But Pellionisz' credentials and prior accomplishments make him
much harder to dismiss than the average cyberspace sci-fi wacko.
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.
The Hidden Fractal Language of Intron DNA
To fully understand Pellionisz' idea, one must first know what a
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
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
Thinking about whether junk DNA has a purpose "is a rather
obvious question for scientists to ask," says UC Berkeley
mathematics Professor Jenny Harrison, a world-renowned expert on
When Harrison examined the strings of amino acids involved, the
idea that had also dawned on the mathematically inclined Pellionisz,
in addition to several other theorists, immediately jumped out at
her: If junk DNA really is junk, some of it is certainly organized
in a pretty peculiar pattern, one that looks amazingly like a
"This is a fractal form of nature that must stop at some stage,"
Harrison says simply, adding that the fractal pattern looks exactly
like others that appear in nature. She's been batting the topic
around with Pellionisz recently, and is continuing to think about
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."
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
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
"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.
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. 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
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.
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.
"All I know is that I'm in a race," Pellionisz said last week.
"And the clock is already ticking."
[Comment by Dr. Pellionisz on March 21, 2010] The above article appeared in the electronic version (SF Gate) of the San Francisco Chronicle on Nov 21, 2002. Today, over 7 years after introducing the concept that "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" requires some explanation why it was filed to a US patent application, rather than the usual "peer reviewed science publication". It was certainly not because Dr. Pellionisz was not familiar with science publications, having written well over 100 by that time. The reason was that Dr. Pellionisz' "FractoGene" concept had its origins with his 1989 paper "Neural Geometry; Towards a Fractal Model of Neurons"; invoking a recursion from proteins to DNA. At that time not only Crick's (false) "Central Dogma of Molecular Biology" (that mistakenly claimed since 1956 that such recursion of information "never happens", but also the "Junk DNA" erroneous theory by Ohno since 1972 still ruled. Moreover, both leading scientists still lived and dominated genomics, and never in their life recalled their mistaken axioms. Thus, the 1989 publication could only appear in the Proceedings of the Coppenhagen meeting of the Neural Net community (just breaking through with another paradigm-shift from AI to Neural Nets), and peer-review was done by Neural Net pioneer colleagues to whom such recursion was "taken for granted". Moreover, published by Cambridge University Press in the UK, the occasionally overbearing US scientists could not prevent publication. Nonetheless, the existing NIH grant to Dr. Pellionisz was discontinued, and a new NIH proposal (acknowledged in the publication) was flatly denied for the double lucid heresy of violating both cardinal axioms of genomics. Though Ohno passed away in 2000, Crick still lived in 2002 when Dr. Pellionisz conceived FractoGene (and at odds with Crick also on the turf of Neural Nets, where Dr. Pellionisz brought out his highly mathematical "Tensor Network Theory" explaining the space-time coordination of existing cerebellar neural networks, while Crick attempted to explain consciousness by theoretical biology without the benefit of any mathematics at all) Dr. Pellionisz saw zero chance that FractoGene would pass peer review of the establishment. Thus, filing FractoGene to USPTO served not for undue financial gains, but to establish Dr. Pellionisz' priority - and perhaps to help sustaining his efforts and that of his like-minded colleagues. While it is unfortunate that the two obsolete axioms set back genome informatics by half a Century (1956-2006 when Dr. Pellionisz' "International PostGenetics Society" officially abandoned the misnomer "Junk DNA"), still one more year was needed when the ENCODE results concluded similarly. Answering Dr. Collins' call that "the scientific community will have to re-think long-held beliefs", Dr. Pellionisz could publish his peer-reviewed paper "The Principle of Recursive Genome Function"; specifying that the protein-to-DNA action sets off a "fractal iterative recursion".