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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."
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.
Cantankerous old coot since 1957.
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.
Some drink at the fountain of knowledge. Others just gargle.
If you're really interested in this sort of thing, you might want to check out something called OOOP , which is a intriguing combination of biology and OOP.
mhack
Building a better ribosome since 1997