Searching for Life's Blueprints 310
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."
so he can patent some of me (Score:3, Funny)
i've got him beat (Score:3, Funny)
Re:i've got him beat (Score:5, Insightful)
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 [tuxedo.org], 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
Re:i've got him beat (Score:2)
Precisely the reason patents on such things can be a good thing. There is a lot of very hard work that needs to be done, and one really good way to get them done is to let people make money off of the work they do.
However, I'd like to consider the option of requiring any entity which uses patent protection for inventions to release all details of the production of patent protected products when the patent expires.
I don't like the idea of discoveries being locked away as secrets for much longer than it takes for a company to turn a good profit on them. I'd just hate to see useful technology lost because the few people who know how to do it got hit by a low flying airliner.
Heh (Score:4, Funny)
Does this scare the shit out of anyone else?
nature scares vs. lab scares (Score:2, Interesting)
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.
Re:nature scares vs. lab scares (Score:2)
Re:nature scares vs. lab scares (Score:2)
Think of it this way: what is your purpose, and how do you derive your purpose from a reality that is entirely accidental?
Re:nature scares vs. lab scares (Score:2)
I'm making arguments based on reason and observable phenomena. You're countering with petty insults. "Tiresome" doesn't even begin to describe it.
Re:nature scares vs. lab scares (Score:2)
Anyway, I don't think it's a question of risk at all. Aren't there high-risk endeavors that most people would agree should be attempted anyway? And aren't there low-risk endeavors that should not be attempted?
For example, if "fishberries" are wrong, they're wrong whether they're risky or not.
Re:nature scares vs. lab scares (Score:2, Insightful)
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.
Re:nature scares vs. lab scares (Score:2)
You, meanwhile, have this built-in survival instinct that is a by-product of accidental natural processes. You can't account for it. You can't justify it. There's no point to it. All you can really do is mindlessly obey it.
You're the one whose argument against fishberries is that they're bad because nature accidentally made you feel threatened by them. But somehow I'm the one who's not thinking?
Russian Roulette (Score:2)
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.
Re:Russian Roulette (Score:2)
And where, exactly, is it written that fish should not mate with strawberries? Isn't it entirely possible that--as natural outcomes of natural processes--we ourselves are the natural mechanism by which these genetic materials get transferred?
Re:Russian Roulette (Score:2)
In much the same way that nature is the authority on heavier-than-air flight? And in the same way that nature is the authority on information transmission, storage, and retrieval? On the face of it, creating "fishberries" is no more egomaniacal than creating the "Internet", or the "Apollo Project".
Do you use an automobile? Modern medicine? Plastics? Don't accuse me of hubris--you're just as unnatural as I am.
Whatever authority you claim nature has, it obviously does not have the authority to prohibit genetic shenanigans. So who--or what--are we offending, exactly?
Re:Russian Roulette (Score:2)
Nature leads to man, which leads to fishberries, which leads to man-eating fishberries. Nowhere have we deviated from the natural course of events. Unless you're allowing that man can do unnatural things--which I think you are. But that takes you into the metaphysical space, where we must allow for a higher authority than Nature itself, that can judge what is natural and what is unnatural.
Are you prepared to admit such an authority? I doubt it, but I could be wrong.
Patent First: (Score:5, Insightful)
I used to think that science was the last field which blatant greed had not infested yet, and I am proven wrong yet again...
Re:Patent First: (Score:3, Insightful)
Maybe that guy went a bit quickly to the patent office, but still... scientists don't have hats made of money [penny-arcade.com]
Damn right (Score:4, Insightful)
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.
Re:Damn right (Score:4, Insightful)
get your lazy bum out of your chair and check WHO actually discovered things.
ALL (not some, ALL) medicines currently known against aids were first researched at a university
same for virtually any other disease.
You seem to think that competition (= not cooperating, but working to kill off, or at least bancrupt, your collegues) works, it doesn't.
Even the simplest of molecules used in the human body has thousands and thousands of possible incarnations. WAY to much for even multinationals to research.
In universities, where researchers are given a free hand in research, they occasionally stumble upon new medicines. Eg. someone is researching some ancient plant and discovers a poison the plant uses to kill of insects that helps against a disease.
Understand that we don't understand even the energy production in a cell, transport systems haven't even all been identified.
The processes we're talking about are not only VERY sensitive, but also play on a very small scale (transport systems in a cell for example, work by merging, melting, mixing, breaking, etc molecules that contain thousands of atoms, and each and every one of those atoms has a function. Determining the composition of a single of the molecules is a work that takes years with the most advanced tools available.
Keep in mind that the biggest thing that happened last year in biotech was the succesful analysis of ONE enzym involved in energy production in the cell (out of more than 10.000 different enzyms).
That analysis took 5 years of intensive communication between a lot of different universities. With competition (that means without communication) you don't stand a chance.
Most, if not all biotech startups fail, promise great things, but deliver none. And these are the things you want to stimulate ?
Re:Damn right (Score:2, Insightful)
Before you go all holier-than-thou with academia, I would suggest to you that with out the finanical support of the biotech firms much of that research would not be funded or possible. Lets not forget that those biotech students often have the desire to graduate and take home a paycheck. You can't have one without the other.
You need to foster that learning environment and you need the application of the technology to keep the cycle going.
What needs to happen is a balance to keep everyone on track and honest, having that patent keeps the control with the idea maker. I can see where it would be in the best interest of the professor to patent his ideas, lest you have biotech firms run with his idea, make billions, and never return the favor back to the university with grants, scholarships, etc.
Don't think though that the university system can be solely creditted with all the great achievements. In order to have the luxury of time devoted entirely to research, somebody has the pay the bills, buy the equipment, pay the profs, fund the grants.
Re:Flat out wrong. (Score:2)
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
Re:You have no idea what you're talking about (Score:2)
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)
Re:Damn right (Score:3, Insightful)
mhack
Pot. Kettle. Black. (Score:5, Insightful)
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.
Re:Pot. Kettle. Black. (Score:3, Interesting)
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.
Re:Pot. Kettle. Black. (Score:2)
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.
you can do biotech in your garage (Score:2)
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
Re:Patent First: (Score:2)
It's not like the medical field that has come to a point where more and more doctors see a patient and think of a yacht (not all! I do have 5 doctors in my family and about half are still pretty humble people). Most scientists still see something strange and thing of a big lab and more strange things!
Re:Patent First: (Score:2, Insightful)
Don't assume all patents are established entirely with profit in mind.
There are concepts of protecting intellectual property and the value of research in terms of both time and money.
-Alex
Re:Patent First: (Score:3, Informative)
Not necessarilly, and even if it were true, if the scientist publishes first, that is prior art and the corporate patent won't hold up in court. Indeed, if the USPTO were not being criminally negligent in its fudiciary duties under the constitution, it wouldn't even grant the patent in such a case.
Re:Patent First: (Score:4, Informative)
Yeah...academics used to do their thing for the massive ego gratification, now they do it for profit. Don't know that it's necessarily worse this way.
It's not like scientists were ever this pure group of unbiased, purely objective people who are solely out to benefit the world and increase the knowledge of all. That's the publicity answer. Fact is, we fall to the same weaknesses as everyone else, including the great god Profit, and this shouldn't be surprising.
For what it's worth, the worst example was of a couple of guys, Ziegler and Natta, who invented a class of catalysts while working at a university. They worked really well, so they left the university (who paid for the research) and started a company, without giving the university a dime. They made millions, I believe. It happened in the 50's. So this isn't really new...though more widespread as universities have realized they can make a lot of money that way (patents) without much effort.
A good way to look at it. (Score:4, Interesting)
Re:A good way to look at it. (Score:5, Informative)
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.
Re:A good way to look at it. (Score:4, Informative)
Of course, the idea of the virtual machine isn't necessary, since the machine is real.
DNA is less like a C header file than it is like a C program.
The basic mechanisms by which DNA is used create proteins is well understood on one level. What isn't well understood is all the regulatory mechanisms that interact with that process.
Why is a given stretch of DNA transcribed into mRNA? Why is it that only particular pieces of a stretch of DNA end up in the mRNA. What determines how long that mRNA transcript exists in a cell, and how many times it is translated into a protein?
These are all open questions before you even get to the question of protein folding and catalysis, and you have to assume that all the proteins in a cell have some involvement in gene regulation. How does a muscle cell know that it is time to stop producing myosin. Somehow, there is a feedback loop.
The analogy works if you change it a bit (Score:5, Informative)
If you're really interested in this sort of thing, you might want to check out something called OOOP [ooop.org], which is a intriguing combination of biology and OOP.
mhack
Re:A good way to look at it. (Score:2)
Now, a protein has a LOT more than three particles in it. Even if we take the vastly oversimplified approach of modeling it as a strand of amino-acid "pearls", then there are hundreds of bodies. Each amino acid is actually made up of a dozen or more atoms, and each atom consists of many electrons, protons, and neutrons. The interactions are complex: to a reasonable approximation, the large-scale forces look like classical electrostatic interactions, but there are definitely quantum contributions that, again, can only be approximated, not solved exactly.
Note that computations like what Folding@Home does are only approximations. The protein folding problem can't be solved exactly -- you can only model it, and your model is only as good as your scientific knowledge.
Re:A good way to look at it. (Score:2, Informative)
Because genes are so neatly digital, people tend to think of them as being all the information in a cell. Actually a cell is like a computer - some information is stored explicitly as software, and the rest is hardware, but it is really hard to tell where software ends and hardware begins. After all, floating point coprocessors work with big internal tables - so are those tables hardware or software? And think of the IBM keyboard BIOS. It started out life as hardware and ended up as software that emulate the hardware. Similarly, some proteins are taken from the same gene, but with a different set of exons.
Another thing is that biological systems love hacks, so the borders are constantly shifting. I think there's a good chance of finding introns doing unexpected stuff.
Re:A good way to look at it. (Score:2, Interesting)
The analogy of "bytecode" and "virtual machine" is flawed anyway: it gives the impression that the cell's transcriptional apparatus is just an interpreter (highly parallelized, sure) that chugs down the DNA, reads the "code", and produces the appropriate proteins to do the cell's business. But that's misleading... for the most part, the cell's transcriptional activity is in some steady state, until outside stimuli signal it (in a complex way) to change one part of the humming machine, and then that change cascades to other portions of the cell's transcriptional activity, until the cell has reconfigured itself to handle the stimulus. There's a lot of feedback between the proteins and the dna (the transcriptional apparatus _is_ protein), etc.
A better analogy might be... well, I'm not sure there's a decent analogy at all. Maybe the "cell is a virtual machine," and outside stimuli are a form of programming language... Bleh, that's no good at all either.
At any rate, your post makes it seem like bioinformatics researchers have made a universal choice to put their research priorities in the wrong order... but that's certainly not the case. Working to decode the cell's apparatus in different ways simultaneously makes everyone's research more productive and useful.
Oh Joy, another patent on genetics. (Score:3, Insightful)
Patenting the method, as long as its not the only method? Thats fine. Patenting the discovery? Thats absurd.
No Big Surprise (Score:3, Insightful)
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."
In programming terms... (Score:3, Insightful)
So I guess mankind is just self-evolving code. Cool!
He hopes his patent will help him ... (Score:2, Funny)
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*
Of course a simpler explanation... (Score:5, Insightful)
Junk DNA (Score:2, Interesting)
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.
Re:Junk DNA (Score:2, Interesting)
Oh, by the way, if it was useless, how could errors in it affect our health?
Re:Junk DNA (Score:2)
like this img src=. there. a blank image tag.it's useless. now if I make an error in it, like give it an incorrect URL, it'll sit there for awhile trying to execute the code and eventually fail. same thing with your DNA. coded in a certain way, it might not do anything, but once there's an error that changes it from "useless" to "harmful" we've got a problem.
programming? (Score:2, Interesting)
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.....
When you have a hammer (Score:5, Insightful)
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.
Re:When you have a hammer (Score:2)
introns affect DNA folding (Score:3, Interesting)
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.
Affect the folding how? (Score:2, Interesting)
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.
By varying the stiffness of the coil (Score:2)
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.
Math in Nature (Score:3, Interesting)
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!!!
Re:Math in Nature (Score:2, Funny)
Possibly. But if we ever come up with a mathematical theory explaining female behavior, it will make heavy use of imaginary numbers.
Re:Math in Nature (Score:2, Funny)
See what you want to see (Score:3, Interesting)
Re:Math in Nature (Score:3)
Wolfram's statements may show that scientists don't need to look any deaper that the 'formulas' to get an understanding of everything in nature.
That may be good for a while, but scientists will get bored quickly. Anybody who got as far as understanding the formulas without going any further may be nothing more than 'wannabe' scientists. The true scientist will still look for the formulas.
It's kind of like someone saying they are a programmer because they got a Word macro to format their text a certain way.
Another scientist who thinks he knows the answers (Score:3, Flamebait)
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.
Humans as fractal creatures? (Score:2, Insightful)
Re:Humans as fractal creatures? (Score:2)
'Course it
Re:Humans as fractal creatures? (Score:4, Insightful)
Basically, if you force something like this, then you can make a connection. Doesn't mean the connection is real.
Re:Humans as fractal creatures? (Score:2)
The skin is an organ -- in fact, it's recognized as the largest organ of the human body. (Insert dirty joke here.)
Fractals in biology (Score:3, Interesting)
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).
What took so long? (Score:2, Insightful)
It HAS been looked at before!!! (Score:3, Informative)
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.
psuedo-science (Score:5, Insightful)
So you're saying? (Score:2)
-psy
Prior Art (Score:2)
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
Junk (not likely) (Score:3, Insightful)
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.
Great! Patent anything! (Score:2)
(Did I mention that I was also completely ignorant of the details of the patent application?)
A primer on DNA structure (Score:5, Informative)
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.
Re:A primer on DNA structure (Score:2)
Re:A primer on DNA structure - far too simplistic (Score:2)
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.
Re:What life has to do with it? (Score:2)
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.
Re:Nice primer on DNA structure, but... (Score:2)
In Theory.. (Score:2)
Patents should go to ... (Score:3, Insightful)
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).
Re:Patents should go to ... (Score:2)
In this case it just gets worst, because what's basically beign patented is the underling "programming language" (for lack of a better word) the DNA uses and the actual data that is encoded.
What if an alien race came and claimed they patented DNA and forced to pay whatever royalties or inmediately terminate our grant to use the technology (to live).
This issue we are talking about are not Mickey Mouse movies or a technique to write to CD with more reliability or to produce scented beer. We are talking about what makes us human and "how we work".
I understand granting monopolies on this will help people try to reap the rewards from such a grant, turning knowing how humans are done into a profit & loss equation.
Also, we are talking about something that ALREADY has been invented (DNA and how it works) and the methods to extract usefull data from it though a 'kind of' reverse engineering are not inventions. It's like einstein patenting E=mc^2
I mean, patent stuff and inventions, not methods or things whos logic belongs to nature / phisics itself.
Just Read Blood Music (Score:3, Interesting)
Re:Just Read Blood Music (Score:2, Funny)
I'm quite skeptical about this... (Score:5, Interesting)
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 there something profound about "fractal"? (Score:2)
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.
Hey! (Score:2)
Extraordinary claims require extraordinary proof (Score:5, Insightful)
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.
"fractal" introns in DNA is published already. (Score:3, Informative)
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.
disappointment about DNA signal analysis (Score:2)
Re:disappointment about DNA signal analysis (Score:2)
Junk DNA (Score:2)
Structural Genes (Score:3, Informative)
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.
'Junk ' isn't impossible or useless. (Score:2)
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
This was predicted by Wolfram's Cellular Automata (Score:4, Interesting)
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).
Re:This was predicted by Wolfram's Cellular Automa (Score:3)
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...
Credit Where Credit is Due: Fredkin (Score:2)
No slight against Wolfram intended, but we ought to give some credit where it is due.
Fractal magic and patents (Score:2, Interesting)
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.
In Other News... (Score:2)
Prior "art"? (Score:2)
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?
This does not surprise me (Score:3, Insightful)
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.
Re:Getting to be a bit old hat (Score:2)
You mean the BS patents that the U.S. government has been issuing lately?
Re:just questions (Score:2)
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?