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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.
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.
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.
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.
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