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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
We can now wait 17 years before anyone gets to freely reap the fruits of this basic scientific discovery.
Patenting the method, as long as its not the only method? Thats fine. Patenting the discovery? Thats absurd.
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Seems that every few years someone figures out that something in nature that was perviously though to have no function or a trivial function to particular process is actually critically important. "Junk genes" was another way of saying "I don't understand this so I'm going to pretend that it doesn't matter."
No surprise that the "junk genes" in one of the most complicated structures in nature - DNA - that has been fine tuning itself for billions of years, turn out to have a function and a critically important one. True insight will always come from people with enough courage to say, "I don't know."
Maybe a programming analogy for the introns (non-genic DNA) is that they are subroutines. The exons (genes) use different subroutine calls, resulting in different executables (people).
So I guess mankind is just self-evolving code. Cool!
...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?
I've always been fascinated by the fact that mammals have five major appendages... and five major digits on four of those appendages and five major sense organs (tounge, lips, ears, eyes, nose) on the fifth one. Of course, it's pure conjecture that this might be a reflection of a lower-level self-symmetry, but it's still interesting conjecture.
The next Slashdot story will be ready soon, but subscribers can beat the rush and slashdot the links early!
I have been assuming for the last ten? years (since I read James Gleik's "Chaos") that blood vessels, tree branches, fingerprints, etc. were following fractal patterns. I am surprised that no one had been looking for these patterns in the Genome Project. The introduction of this new research project on the internet and already patented is an interesting twist. I thought from the article that he had patented his computer analysis pattern, but there are certainly plenty of very scary biological patents out there. I can understand the need to look outside of the traditional biological circles for this research, but going straight to the internet instead of the math department is way out of the academic research paradigm.
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?
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.
Now I know in the Fantastic Land of Slashdot that making money is always a bad thing, but at some point one has to grow up and become an adult about things and approach them with some measure of maturity.
Furthermore, where the hell have you been for the past 50 years? You didn't think money and greed were factors in the field of science? Money and greed are a factor in EVERY industry. There is no "innocent" industry left. I'm also not fond of the idea that someone who brings us such a great discovery should only have it attributed to him, and not also make a fortune. If somone comes up with something that could cure thousands of ailments and help billions, then he desereves a very large fortune indeed.
Mac OS X and Windows XP working side by side to fight back the night.
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!
I love how all these geneticists keep referring to the bits of DNA code they don't understand as "Junk DNA." It reminds me of the ancient Egyptians who, when mummifying a body, would carefully remove and preserve the organs in jars . . . except for the brain. The brain, to them, was just a bunch of gooey junk in the skull to be thrown away because it didn't serve any purpose.
The same geneticists now have the ability to tinker with the code of life and release their monstrosities into the environment that we depend on for our very lives. "Here let's see what happens when I do this! Don't worry, I'm a geneticist and I understand DNA completely and all the ramifications of releasing this new creation into the wild." And we thought nuclear (or is that nuke-u-lar) weapons were how we were going to destroy ourselves.
- Hail to our fearless misleader! Fool speed ahead!
God, I won't acept any other patent regarding my DNA as well as my relatives DNA (going back to Adan and Eva or whatever you call them). If anyone has a patent on this issue, and certainly doesn't need us to recognize it is god (be it aliens or a more stylized one like in religion).
How can any asshole claim to have a patent restricting me what I can do with my DNA and how to process is? This is just intelectual violence. We should find a different way to reward these scientists when and if their contributions to society are proven to be worthy.
I'm kind of stating to get bored about raping of the humans by other humans. You can't fit everything under the free market schema with hacks like patent law or copyright. It can help in certain cases, but generalized like this, they turn into a pie divider of societies gains through time which happens to be unacceptable (to me).
unfinished: (adj.)
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
It shouldn't take anyone very long to realize that the scientific field of genetics is in such an infantile state, and all the biotech buzz going around so far (to me personally) seems to be rather much ado about nothing. Albeit, we can make insulin, clone sheep, and poke the human genome, but really, other than the recombinant DNA technology we've developed to use with bacteria and a few crop-altering techniques, I really don't find biotechnology to be a very applicable science, or even practical for that matter.
Now, I'm not going to claim the theory, because I come up with many hairball theories about stuff all the time, not really having proof behind any of it, however, I always did suspect that this "junk DNA" was good for something, and I found it rather peculiar that fractitions (made the term up myself ^^) have found correlations between certain morphological structures and fractals. I actually attributed the fractal behaivor to be the result of some abstract physical phenomenon resulting from the cells themselves, not DNA, but this guy's theory holds a lot of weight with me as he is much more highly educated and obviously knows what he's talking about. I advise everyone to pay heed to this theory, because it has great potential to change the face of the WORLD as we know it. ;)
While on the subject of biotechnology, I would like to defend the genetecists' position against religious fanatics. From my studies, I have concluded that genetics is a subject of absolutely no spiritual/religious/moral import whatsoever. The moral dilemas in biotechnology can be considered very minute in comparison to that of other situation that politicions engage in. Obviously, anyone can agree that risky human experimentation is immoral (which is the same for any field of science), but other than that, I don't see any other relevant issues that are practical at the same time.
Also, just to set the records straight, cloning is a science that is centuries old. It brought us the Irish Potatoe Famine, and yet it also saved the wild orchid. I always hope to believe the benefits outweigh the losses.
I'm still waiting for some argument that "not destroying ourselves" is a goal that we should have
Well, in the words of Ren Hoeck, "Stimpy, you've really lost it this time." Survival is a mechanism bred into all creatures through the process of evolution.
Man, if I would have realized I was arguing with a religious fanatic I would have stopped wasting my time about four posts back. Bye bye, Christian Taliban. Go stone a harlot or something.
- Hail to our fearless misleader! Fool speed ahead!