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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."
Doesn't DNA itself do this? So isn't he basically patenting all human beings that will be born after his patent is granted? Royalty payments might be something new to think about in parenthood.
I have a patent for using computers to solve anything related to the body. I'll just wait till his company gets further along, and bam, I'll hit him with the suit
Removal of this "junk-DNA", however, has been proven to be lethal.
Does this scare the shit out of anyone else?
slashdot!=valid HTML
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
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.
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.
Buffalo buffalo Buffalo buffalo buffalo buffalo Buffalo buffalo! http://goo.gl/J9bkO
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!
but it's getting to be repetitive to the point of comedy
You mean the BS patents that the U.S. government has been issuing lately?
I pledge allegiance to the flag...
of the Corporate States of America...
He hopes his patent will help him launch his company and make it a key player in this field. ... and take over the world!
Sounds pretty interesting, I just hope there isn't something deeper seeded in this guy, like wanting to take over the world... *plays pinky and the brain music*
...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?
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!!!
Now this guy comes along and you can be sure that even before he proves anything he'll have signed up for the 97% of the genome he's talking about, "just in case". And what can anyone else do about it? Nothing.
There should be no price on scientific advance. People who do this sort of things are not scientists, they are nothing more than minions of Satan out to prevent us from evolving and taking our rightful place at God's side.
Jon Erikson, IT guru
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!
That with a pair of Levi's and my old Commodore 64 Mandelbrot generator, I can create life? *bwhahahahahahahaha* ;-)
-psy
A patent application covering attempts to count, measure and compare the fractal properties of introns for diagnostic and therapeutic purposes has been made
I don't mean to ruin Mr. Andras Pellionisz's patent party, but I think the exons probably already does that...
The introns, he claims, may have the "building construction blueprints" in the form of fractal patterns that the exons use to build living tissue
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!
Admitting up front an almost complete ignorance of the science involved here (since when has that stopped any of us on Slashdot?), I think it is absolutely amazing that one can patent a hypothesis now...
(Did I mention that I was also completely ignorant of the details of the patent application?)
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.
I'm a little confused here.. so his theory is that the extra genetic material is in the form of fractals, which are supposed to represent some sort of blueprint for DNA? How can a fractal be a representation of something else? Isn't a fractal just a non smooth geometric shape? Is he saying the blueprint is in the specific arrangement of the fractals?
Everyone is entitled to their own opinion. It's just that yours is stupid.
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.)
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.
I cant say I know the answer. Both the distribution of sub-units in human language- sounds and words- and the DNA signal are power-law fractal. These represent the tradeoff between novelty (the message) and redunacy (communicate through noise). EE people know better coding systems for puhing signal through noise, yet nature seems to have settled on fractal.
On the other hand fractals occur everywhere in nature, usually as result of simple processes. A very simple case is to sum the heads of coin tosses- the resulting curve is fractal. Nothing too profound about randomness.
Actually God holds the patent on that and all DNA, but he doesnt have any Lawyers available to back up the claim.
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.
Its been two years since Clinton & Venter & Collins announced the human genome had been "sequenced" yet they dont even have a firm gene count yet. Of course that was just the "first draft", with the final draft now about 94% completed. I know its a very complex problem. These MicroSoftian "vaporware" announcements make me very skeptical about bold claims by other researchers.
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 genetic material is called exons, shouldn't junk DNA, that which serves no purpose, be called Enrons?
The mechanisms by which genes code for structure
are reasonably well understood. There's no need
to invoke mysterious fractal magic to explain
it.
A good non-technical book on the subject
is:
"The Art of Genes: How Organisms Make Themselves"
by Enrico Coen
The fact that he wants to invoke fractals in
introns to explain structure suggests that
he dosen't know the molecular biology very
well.
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.
" 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."
It's Russian Roulette with a gun that has infinte chambers.
We don't allow biotech firms to relase their little Frankensteins into the wild. We let them research and learn.
We've been playing with DNA ever since we've been raising our own plants and animals. We're doing the same sort of thing now, just on a much more microscopic scale.
The only danger (from an ethical stand point at least) is when we make *learning* about what we're made from above what we are. Things like creating a human life for the sole purpose of understanding it. (Ie you don't raise a child as an experiement.) Anytime one places X Y or Z above humanity then we all have a problem.
Course, there's so much argument about the whole thing because it's kind of subjective as to wheter one is placing somthing over humanity.
Having space in genetic code not used by anything would not be a huge disadvantage. If life was formed by random chance and evolution, it just means that the circumstances that brought about man were made off of a large slate, with different parts that happened to connect well across that genetic slate. It also makes sense that removing or altering seemingly meaningless parts of that slate would mess up indexing methods (skip ahead X number of A's, start reading, etc.)
Having a very large set of non-referenced entries in a genetic set would also be an advantage in itself. You have a large set of potential mutiations that can be subtly linked to to find advantages, and plenty of room to sort things out genetically. You can also have things like children who are genetically designed to be born to die to save their siblings.
Large-scale life itself is built on the idea that gross inneficiency is acceptable if it allows food and access to mates to be found at the larger scale. So simple bacteria has tight genetic code, fruit flies have fast-mutating genetic code, and large animals have inneficient code with different portions that mutate at varying rates. It's life competing with itself to explore all corners of possibility. Semmingly inneficient aspects are just another legitimate part of the process.
Ryan Fenton
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).
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
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.
By the way, it seems as though Wolfram is most interested in the non-fractal systems the CA produces - the fractal-like systems (can't remember the rule numberes off the top of my head, but many look like Serpinski's (sp?) triangle) were repetitive, always continuing, even after many iterations - on the whole never evolving.
The more dynamic rules seem fundamentally random, almost chaotic - but all seem to point to an organization of some sort. I do agree that there is something interesting going on with DNA - I think in some manner, it is going to end up being a simple Turing-like machine, with a very limited and simple ruleset, acting like a simple CA, and after having run for such a very, very long time - gaining an extreme level of complexity based on Wolfram's ideas.
While I have seen a lot of criticism here on /. about Wolfram, CAs, Mathematica, lawsuits involving everything, references to this book as being a doorstop - I think he is on to something, and I hope he is vindicated - something tells me he didn't write such a large book and sell it so cheaply for nothing. The book would be cheap (book price wise, if nothing else) at three times what it cost - he spent $15.00 a copy, and it is only selling in bookstores for $40-50.00 a copy - so you know he isn't making much money on each copy - and no one spends that much time and money on writing that large of a book on such a topic for a mere "vanity press book" - not unless he is completely nuts, which I don't think he is...
Reason is the Path to God - Anon
"Early Anti-HIV Treatments
For several years, the only drugs available for treating HIV infection were nucleoside analogue reverse transcriptase (RT) inhibitors. These drugs interfere with the action of a specific HIV enzyme (RT) involved in the replication cycle of HIV. The first anti-HIV drug, zidovudine (AZT), was originally developed in 1964 as a possible cancer treatment but was found to be ineffective against tumor cells. However, collaboration between the National Cancer Institute and the pharmaceutical company Burroughs Wellcome led to the discovery in the early 1980s of AZT's ability to suppress HIV replication in the test tube and paved the way for clinical trials of AZT.
Burroughs Wellcome, with input from NIH and the Food and Drug Administration, successfully conducted testing of AZT in HIV-infected individuals. Subsequently, NIAID's AIDS Clinical Trials Group (ACTG) conducted several clinical trials in partnership with industry to test four other nucleoside RT inhibitors: zalcitabine (ddC), didanosine (ddI), stavudine (D4T), and lamivudine (3TC). All five drugs are now licensed in the United States. Additional ACTG studies demonstrated the benefits of AZT therapy for preventing mother-to-infant transmission of HIV and for lowering the risk for developing AIDS in persons with HIV infection.
Unfortunately, HIV rapidly develops resistance to these and other anti-HIV drugs. Researchers have attacked the problem of drug resistance-which is particularly harmful because of HIV's high rate of replication and mutation-by using regimens of multiple anti-HIV drugs. NIAID-supported researchers were among the first to show (in 1995) that treatment with combinations of AZT and other nucleoside analogue RT inhibitors was more effective than treatment with AZT alone. In addition, combining 3TC with AZT slowed the virus from developing resistance to AZT and, in some cases, restored AZT sensitivity in patients who carried virus that had become resistant to the drug. As a result of these NIAID-supported studies, combination therapy emerged as the preferred treatment modality for HIV infection."
note the sentence "However, collaboration between the National Cancer Institute and the pharmaceutical company Burroughs Wellcome". From experience I can assure you that "collaboration" means the industry bought patents from the research institute. They just want to milk aids patients as much as possible without doing any real research (theoretical, or at least research that actually analyses the virus, dissemintates it, not just searching for a drug that eliminates 1% more virii than their last "discovery")
Also you can see from the above paragraph that the research will only be effective in the short term. Research in this direction, no matter how far it goes, will not eliminate aids, it will merely slow it down.
btw. I agree there is a (very) small fraction of stuff coming from pharmaceutical industries. But it is minute
I too am reading Wolfram's book, and it is excellent (and very interesting). But Wolfram takes a great deal of credit which IMHO ought to go to Fredkin, who originally proposed and explored this idea.
No slight against Wolfram intended, but we ought to give some credit where it is due.
The Future of Human Evolution: Autonomy
Oh by the way, we have NEVER witnessed macro evolution. Only micro evolution. Prove me wrong on this one.
I witness it every Sunday. Homo sapiens go into a building with a tall steeple, and come out transformed into Pan troglodytes. Oh, sorry, I shouldn't be insulting chimpanzees like that.
Of course, micro- and macro- evolution are just concepts creationists came up with since they figured out that species undoubtably DO evolve. So, to make sure there's still a job for God to do, they've decided to amend their "theory" to say that any change greater than X amount in an animal's DNA must be the result of divine creation rather than evolution.
I still have not seen any creationist describe a mechanism by which macroevolution is prevented. I suppose God lets animals adapt to their surroundings, but at a certain point they get too close to becoming another "kind" so He wipes them out, or changes the environment so they adapt back the other way?
Besides, why should anyone have to prove you wrong? If you promote a theory that goes against almost all of mainstream biology, geology, biochemistry, paleontology, astronomy, and cosmology, and posits the existence of an omnipotent invisible friend, isn't the burden of proof on YOU?
Hey kids, there's only 5 days left 'til Yak Shaving Day!
Saying DNA sequences is a 'fractal' (really self-similar) is nice, but not that profound, yet.
In fact if it were a uniform fractal then it would have VERY LITTLE evolutionary mechanistic importance. Only if the law were sufficiently different that physical mechanisms translating DNA patterns into phenotypes (expression of organisms) could account for observed differences in organisms would something behind the fractal law matter.
Indeed, most of the thinking on the introns is involved in eludicating the mechanisms of the "fractal pattern" but this is all in the mechanisms of replication and crossover. There is little science showing mechanistic (and not just correlations) translations back.
As far as patenting "all methods of observing fractal patterns" I point out this prior art:
R Roman-Roldan, P Bernaola-Galvan, J. L. Olivier, "Sequence compositional complexity of DNA through an entropic segmentation method." Physical Review Letters, V80, p1344 (1998).
Here is its introductory paragraph:
"The analysis of sequence correlation structure, in both the spatial and the frequency domains, resulted in the finding of short range[1] and long-range[2] correlations in nucleotide sequences, thus uncovering a complex fractal structure of DNA."
Both[1] and [2] refer to a large number of references each.
The paper then goes on to discuss an information theory based statistical approach to derive an automated algorithm for hierarchical partition of DNA sequences in to succesively more homogeneous regions. The obsevations is that the breakups are self-similar and thus roughly fractal.
Not only that but the trend towards greater 'complexity' with organism complexity is also observed here.
Note that traditionally fractals are defined on a continuous geometrical space, and since there is a minimum breakpoint size (one base pair) in sequence analysis this is not a true fractal---there will only be self-similarity in some "scaling range".
Note I am a physicist in nonlinear dynamics and happen to know a little bit about information theory. I am not a biology or genetics expert.
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
Example #1: The guys who manufactured the polio virus from scratch earlier this year said everything was "off the shelf".
:-), but usually dont have industrial resources.
Examples #2: There are now several gene manipulation projects being submitted to the Intel National Science Fair. I know 15-year old geniuses are smarter than me
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
This is the first chapter of greg egan's book, diaspora, which describes a simulated neurogenesis in software, the technique of which was reverse engineered from the fractal patterns of human DNA.
Although this is science fiction, and art in only the literary sense, would it not qualify as prior art?
---
the pen is mightier than the sword, the sword is mightier than the court, the court is mightier than the pen.
I've shown your first example to be flat out wrong, yet you continue giving them, you might have an incredible stroke of luck and give one example but those examples are vastly outnumbered.
Even if (I do not agree to your point) the industry did indeed discover that particular substance, they could not even start to look without the university doing the hard part (figuring out how reverse transcriptase works). The industry simply did the easy work (finding the stick to put in the proverbial wheel).
If I were to accept your assumption you'd get to this
-> the institute analysed the enzyme, figured out it's function, a way to identify it, to check if a given molecule functions and it's molecular structure (this is VERY VERY VERY VERY hard, it's been done for only a small number of enzymes ( the industry let a number of random generated (I'm not kidding about the random part) substances loose on the enzyme, until one proved to inhibit it, this, you can do in your kitchen (provided the university gives you access to a sample of reverse transcriptase). For some reason this is called research.
* imagine a 3 dimensional space containing atoms (size of the structure : about 3/1000000000000 meter). You need to find the 3 dimensional layout given measurements of the radiation they put out when heated (measurement size about 1 mm, and you get one single value). 30% of the measurements you get are flat out wrong, and every now and then the structure changes for no apparent reason (because that's what enzymes do, they change their molecular structure to facilitate changes in another molecule)
The DNA coil doesn't curl exactly the same way everywhere; it curves more sharply in some places and less sharply in other places.
Mostly this averages out, and in many places it doesn't matter, but like every other imaginable property, sometimes evolution has taken advantage of this.
Professional Wild-Eyed Visionary
See for instance the 8 year old research in:
CA Chatzidimitriou-Dreismann, RMF Streffer, D Larhammar (1994), "Are there any fractals in DNA of living organisms"
RF Voss (1994), "Long-range fractal correlations in DNA introns and exons", Fractals, 2(1):1-6.
Professional Wild-Eyed Visionary
What part of the word Primer eludes your understanding. A primer is an entre into a subject to a definitive discourse. I challenge you to write an essay that short that 1) is coherent and an gives introductory analogies, 2) addresses the question asked 3) is as comprehensive. 4) is not just jargon
furthermore the discussin I gave does offerto long range interaction possibilies, for example the mention of histones and the mention of cross-over oligeriazation (I avoided the jargon).
I do however apologize for the bad spelling. The whole thing was written very quickly to aid the discussion. perhaps I can be excused if I omitted a few points.
Some drink at the fountain of knowledge. Others just gargle.
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 once took a crack at that. I colaborated with David Wolpert on "self dissimilarity", which is a concept Wolpert cooked up as a way of measuring organizations inicative of life. Lots of people study self similarity (like sand piles that mainitaina constant shape more sand is added). Wolper realized that Life was not organization. For example a diamond lattice has very low entropy but is dead. At theother end of the scale Air (gas) is disorganized as possible, but its dead too. So life is not a matter of organization or even dynamic self organization (growing sand piles are dead too).
the concept of self dissimilarity is also the opposite of fractals. As You change scales (a microscope zooming out for example) what you should see is that at some scale and scales near it, things have a particular organizational structure (say liver cells making up some smallsection of the liver) then at some scale the organization shifts radically (many organs, then skelton, then skin, then outside the body, then many bodies, then a planet, etc...)
To cook up a reasonable single valued measure of self-dissimiarity you ask the question how much additional information is need to predict the probabilty distribution of some quantity (say cell density) at the next higher scale given knowledge of what it is at this scale. this function if plotted as a function of scall will have plateaus then abrupt jumps in a living system.
Note by this defintion, the the work performed in a say a large corporation is a sign the corporation is alive. If you think about it you might even agree that an alien entity from another planet who did not even know what humans were or looked like, might by studying the activity inside a building come to conclusion it was alive.
many dyanmical systems (sand piles, waterfalls, streams,) dont qualify as life under this definition. But the distribution of fish in the ocean does (single fish, then school, then large distances between schools, then schools confinded to costal regions, then deep water open ocean schools...) so maybe the ocean is alive.
Oviously a single parameter defintion of life is not going to satisfy anyone. but it is an interesting start to trying to quanitify life in a mathematical sense.
fractals are of course not a sign of life by this defintion. I once tried to look at the pattern of predictibitily of dna sequences using this definition. But was unable to find clear discontinuities. On the otherhand shakespears collected works showed some signs of life and well that is dead but was composed by a living person.
Some drink at the fountain of knowledge. Others just gargle.
For example the IT industry in the near past (not 100% but to an important degree)). They say that it was more important than patents the secrecy and time2market.
... MOST OF THE TIME. And when they do offer it for a resonable price is because economically that makes sense to them, specially in applications where it is not hard to use an alternative techology - read: there are competing technologies. If there are no competing technologies because the PO granted them with a monopoly on the ONLY way to do something, then....).
After that was gone, most of the game is getting patents so that you can have a nice deck of cards (patent portfolio) so you can "play" with your competitors. If you don't have patents, you can't play (can't play without cards).
Patents are a way to divide the pie, not to promote technological advance. YES, the promote "this particular advance" and thus delay all related advances 20 years. They "kill a line" or way of doing something, so more research is needed to find an alternative way of doing the same (this is usually common when the monopoly patenty doesnt want to license the patent for a logical price, which is
There should be some other way to reward research, for example, with beign the first to market, or with having a good brand and a good image, or a grant up to certain limited amount of profit from the research, or maybe....that you can keep the invention in secrecy for your own use untill somebody else finds about it be it by coincidence or whatever.
Also, let's not forget that 99% of the usefull inventions are ever patented, and the people patenting stuff never pay a dime for them, and usually use that knowledge to lock people that truly contributed to society and facilitated this very research that is being patented.
unfinished: (adj.)
I posted a related response to your BIG SPECULATION issue here that I think will interest you. It may at least amuse you if not answer the issue and point to simmilar past specualtions by David Wolpert (per review published) about how life should scale in organization.
Some drink at the fountain of knowledge. Others just gargle.
---Again, what's life?---
The question, especially as it is formed here, is largely meaningless. I understand how it would be nice for the layman if certain things could be boiled down into simple essentialisms, but essentialism stands on dubious ground to begin with. You're going to have to do better than asking "what is life?" you're now going to have to explain what sort of answer you're looking for, and give "life" an operational definition instead of a nigh mystical one.
---I think he is on to something, and I hope he is vindicated---
I think you're mistaken as to the nature of the criticism the book has taken. It's not a matter of him being wrong, it's a matter of him doing an exceedinly sloppy and wordy job of describing theories that plenty of other people have already been discussing for some time. That he makes grand, unqualified conclusions where others were much more careful doesn't set him up for "vindication" even if he is right.
skill these days. I've always wanted to study
the subject.
You may never see this comment. Pity that
people don't have email on slashdot.
Professional Wild-Eyed Visionary