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Searching for Life's Blueprints
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."
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.
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.
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.....
We're like rats, in some experiment! -- George Costanza
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.
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!!!
Greg Bear's 85 novel, Blood Music 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.
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.
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.
So if we don't really understand what all this DNA stuff does, why do we allow biotech firms to tinker with it and then release their little Frankensteins into the wild. Seems like Russian Roulette to me.
Nature has been playing Russian Roulette with DNA for billions of years. DNA gets snipped, clipped, and chipped by nature all the time. Bacteria are natoriously promiscuous (sp?) with their DNA and the DNA of what they infect.
I doubt a few labs can out-pace the experiments of nature like those probably going on in your body right now.
But, you never know for sure. Although most nasty biological things come from nature, humans have accidentally bread things like the killer bees infesting the America's.
IMO, accidental lab results are not likely to be any more problematic than what nature gives us. But, it may still contribute to the *quantity* of "bugs" that cause problems. IOW, add to the pool of annoying pests like Aids, Malaria, shark attackes, etc.
Bigger problems will probably come from specific bio-weapons research. Osama's group would love to build a virus that only attacks those not (allegedly) descendended from Muhammed's ancient followers, for example. Or perhaps extreme Christian fanatics who target people with a "gay gene". "Genecide" will take on a whole new meaning.
Table-ized A.I.
After having read Stephen Wolfram's A New Kind of Science, 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).
Those who can, do. Those who can't, simulate.
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.
Eat at Joe's.
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).
My other sig is also a
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.
LRC, the best-read libertarian site on the web