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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."
I find it interesting that the first thing he did after theorizing a possibility is to patent that process. What has caused such a change in the scientific world? Since when have scientists become so entranced with being rich -- is that what is attracting people to science these days?
I used to think that science was the last field which blatant greed had not infested yet, and I am proven wrong yet again...
This is my digital signature. 10011011001
...for the lethality of removing introns is simply that this may mess up gene regulation. The amount of mRNA transcript produced by each gene has to be carefully regulated for all parts of the cell to function properly. Having junk of the appropriate length in a gene is one way of slowing down the production of a transcript that the cell may not need a lot of. But, hey, that explanation just isn't as sexy as something involving fractals, now is it?
every problem looks like a nail.
Why should DNA act anything like computer code?
Let's look at it objectively, and see what it has to teach us, instead of straight-jacketing it into familiar metaphors.
What were you expecting?
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, 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!
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.
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.
Seriously, this patenting nonsense is completely antagonistic to the spirit of scientific inquiry. There are so many extremely difficult problems to be solved in molecular biology. How can we predict protein folding? How does morphogenesis produce perfectly formed organs? How do neural networks store and retrieve memories? It's a fascinating challenge and to solve it we need to maintain an open scientific environment with the free flow of ideas.
As others have noted , the Open Source software movement has drawn upon the paradigm of scientific research for its extraordinary growth and success.
What Pellionisz is doing is just the opposite. He's promoting the 'Proprietary Corporate Control' paradigm for scientific research.
Newton stood upon the shoulders of giants to make his great discoveries. These days people like Pellionisz use the boots of greed to trample science into the mud.
mhack
Building a better ribosome since 1997
From the article, "It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue." This is a very wild claim with nothing to back it up. The concept of "gene" is a leaky abstraction in this case. There's DNA, and there are proteins. Their high level interaction is called a gene, but the work in the cell is done by proteins, not the abstraction.
Just what is this guy proposing the fractals do? What is the mechanism for reading these fractals?
Until this guy can propose a specific biochemical pathway using his fractals that can't be explained on the basis of protein and transcription regulation, I won't take him seriously.
One of the fundamental problems in genetics is deciding whether a particular streach of DNA is or is not part of a gene. There are a number of very effective statistical methods for identifying genes, but they are not 100% accurate. Part of the reason is "alternative splicing" wherein a particular sequence might be an intron sometimes and an exon at other times. The whole gene, introns and exons intact, is transcribed to mRNA, then proteins splice out the introns, but in many cases, different parts may be left in or taken out, so that a single gene produces a number of related proteins. If somone tried to remove all the introns from any sort of eukaryote, it's exceedingly likely that they'd cut out something important unintentionally.
As for prokaryotes, they don't have alternative splicing, but they have very few introns to begin with. The most time-consuming step in cell division is DNA replication, so prokaryotes whose survival strategy is exponential growth are under a lot of evolutionary pressure to minimize junk DNA. It seems they don't need it, anyway. Higher organisms, however, are full of so-called "transposable elements" - essentially proto-viruses. They are genes that encode proteins that then act on the original gene, spliciing it out of the chromosome and putting it back somewhere else. The genome is full of these, along with non-functional truncated or mutated versions of them. These are mostly just parasitic.
Finally, there are the "highly non-conserved" portions of DNA. These are areas with extremely high variablility between members of a species, meaning that there is no evolutionary pressure to conserve the function. The best explanation for this is that there is no function.
Non-coding sequences can however play structural roles, since the chemistry of the nucleotide bases can introduce "kinks" into the DNA strand. These form the basis of many protein recognition sites for regulation, duplication, splicing, error correcting, etc.
We have all these ways for accounting for a lot of the DNA, but it sounds to me like this guy said to himself "Wouldn't it be cool if all this DNA were like, a fractal or something!" This would be a tremendous discovery if it were true, but the article shows no evidence that he has any clue how it might work or what it might accomplish.
For great justice.
Your kneejerk reaction to his decision to patent his idea is a most unfortunate and immature one. First of all, a biotech company is not an IT company or an internet startup. You can't start them in your garage. You need lots of expensive equipment and expensive highly trained professionals to work with it in the labs. You must also run testing trials, many of them which are also expensive. All of this takes money. Not millions, but billions.
Your kneejerk reaction to defend the privatization and monopolization of human knowledge is unfortunate. Government entitlements in general are antithetical to free markets, government monopoly entitlements particularly so.
1) Biotech and pharma companies routinely exaggerate their R&D costs, often by orders of magnitude, rolling standard corporate costs of doing business into the sum total.
2) most bio and pharma research is done with a mixture of private and public capital, yet those donating money to (e.g.) AIDS research are not given a portion of the "ownership" once the patent is granted. Indeed, that same patent prohibits, by force of a government gun, the donator from persuing research along the very same lines his or her donation helped to initially fund.
3) Patents stifle research. This has been demonstrated historically time and time again. The Wright Brother's patent led to the United States falling a generation behind in aircraft technology, stifling improvements so much so that with the advent of World War I the US government, in an unprecedented move (and a tacit admission that patents do in fact stifle progress, no surprise since they are antithetical to competition which unlike patents actually does promote progress) seized their patent, opened it up to all comers to promote competition, and granted the Wright Brothers an arbitrary 1% royalty so that the technology would be improved and we'd have a fighting chance against the much more advanced German aircraft (whose builders had not been hamstrung by such patents).
More recently, several lines of research into potential cures for breast cancer and AIDS have been stopped, in response to Cease and Desist letters sent by patent holders very similiar to the person you so blindly laud.
Your anti-slashot ranting and raving aside, monopolies are antithetical to competition, antithetical to free markets, and antithetical to progress. Yes, they enrich the inventor (sometimes, often they do not, they enrich instead the inventor's employer), but even in the best case (such as the Wright Brother's invention of the airplane, or perhaps this case), all further improvements on the technology will only come from a very limited group: the patent holder themself, or those few they license to use the patent. Vast numbers of researchers are thus excluded, and a vast number of improvements essentially left unexplored for at least 20 years.
With fundamental science like this, that's a lot of research, a lot of unrealized cures or treatments, and a lot of dead people as a result. Not in Fantastic Land, in the real, hard world.
There are other methods to funding research besides granting government entitlements to 20-year monopolies, and almost all of them are vastly better than the patent system we are employing today.
The Future of Human Evolution: Autonomy
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