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Human Genome More Like a Functional Network
bshell writes "An article in science blog says we may have to rethink how genes work. So called "junk DNA" actually appears to be functional. What's more it works in a mysterious way involving multiple overlaps that seems to be connected in some sort of network." From the article:
"The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.
The new data indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Nature paper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered."
Its what we in the programming field would call the Data Segment.
The question remains to be answered, what routing protocol does it use?(RIPv2, IGRP, OSPF, EIGRP)
Venter you are too late.
They need to hire some Perl and 60's-style-COBOL programmers who know how to read tangled code ;-)
Table-ized A.I.
I don't think evolution would be very kind to unneeded material.
It's always been my hypothesis that the "junk DNA" has something to do with error correction.
After all DNA is most certainly a form of information, and resistance to corruption of that information should definitely provide an evolutionary advantage.
Absolute statements are never true
Imagine a Beowulf cluster of...wait a minute.
Ronald said nothing. He flung himself from the room, flung himself upon his horse, and rode madly off in all directions.
It's somewhat funny - I remember having this exact discussion with my genetics professor. I was a chem major who is now a developer.
... but perhaps I've just looked at too much dissassembler. I will feel a little vinticated if this is proven.
It seems to me that DNA/RNA is "machine code" and data which runs on the laws of nature. It's a layer removed from silicon design, more akin to a self-modifying FPGA.
In other words we're so far only looked at the boot code and associated data. The "program" is what we were calling junk.
And it makes sense - if you think of the program as a massive recursion network which builds common parts (stem cells) and then organizes and specializes.
I know that's a simple bastardization
I said no... but I missed and it came out yes.
After assembling something, if there are any parts left over I simply declare them to be extra junk. With scientists declaring the same thing about DNA they can't identify, I guess the old saw is true, great minds do think alike.
Sigs are too short to say anything truly profound so read the above post instead.
... how to turn off the smirk genes in Brad McGehee's face!
Apparently, genomes with large lengths of "Junk DNA", tend to replicate better than those without. These junk sequences, have a higher probability of duplication than other sequences. In fact, even with a very abstract (and very inaccurate) model, like the Genetic Algorithm, it has been experimentally verified that having "intron" regions in chromosomes increases the convergence rate of the algorithm. Although Nature is highly redundant, there is generally no such thing as a "vestigial" or wasted part of an organism. Sure, there's the human appendix, but it was there for a specific purpose. It just so happens we don't use it anymore. Another million years or so and we will probably have evolved to a state without it.
I thought a key point of the Data Segment was that you could alter it at runtime.
Don't know about your genes, but my personal preference is to keep mine read-only.
I lost my sig.
My patent for "a functional network of multiply overlapping genetic transcripts distributed in 'junk' DNA" is on its way to the PTO.
--
make install -not war
Once they find the link between conscious thought and cellular manipulation, we'll finally understand the placebo effect eh? Theres obviously a large number of layers between the concious GUI and the hardware/data/software manipulation.
Well that just proves it once and for all - it's not junk, hence it was designed properly.
Therefore, God exists!
FUCK!
But, it sounds like most things in nature. Spagehtti code. One thing lead to another, and there it goes. You simply cannot tell what is essential and what is not.
"Intelligent Design?" Yous are real fucking morons.
These scientists have probably been looking at cells running in the debugger...
http://science.slashdot.org/article.pl?sid=02/11/2 2/1347202&mode=thread&tid=134
I just want to let the record show that I TOTALLY called this in Biology 110 back in 1997. "What," said I to myself, "our genetic code, the code that cells go through the ultimate of pains to pass on in billions of generations across many years, is mostly junk? Bullshit!" Turns out I'm right. BOOYAH!
But does this help or hinder the argument for evolution? I thought junk DNA was supposed to be the byproduct of the evolutionary process. No junk DNA would seem to indicate more of an overall design to the system, no?
Note that I write without any real knowledge of the biology behind genes.
However, I could imagine that it could be beneficial for network effects to keep track of any dependencies for the different modules in an evolutionary algoriths. For example, let's make a wild guess that blond hair, blue eyes and pale skin also have some common "junk" elements. Since they are all related to the concept of "not much sunlight", it would be very useful to have some form of abstraction mechanic in the genes that could link them together.
Maybe it could be a way for nature to make groupings or "templates" of related attributes. Different environments may require different attributes, but for all environments there are some groups of attributes that are more efficient.
If genes have a mechanism to group related attributes, it would make it slightly faster to switch between such "templates". This could in turn cause a slighty higher chance to inherit a group of features that together has provided an advantage in the past, instead of just inheriting a random mix of the parents.
So maybe a way to keep track of previous successful combinations? Even if the "active" genes are highly successful in the current environment, a species might come in a situation where it would be beneficial to rapidly evolve to fit an environment their ancestors lived in.
I lost my sig.
This junk code is simply comments. It's too bad we don't know what language they're in. ;)
Here
It's the same article, really. The blog just copy and pasted the entire article from the government website.
Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages. So, 90% of genes aren't "junk" after all. To anyone who does know something about the aforementioned topics, duh!
First, evolution would weed that sort of thing out in a hurry. Two organisms with genes that achieve the exact same thing, but one has a more efficient encoding? No contest! And, yes, such is possible. DNA isn't some mystical "super" language. It can't violate basic principles. There surely are many many ways to encode the same thing.
Second, ever tried compressing a DNA sequence? They don't compress very well! Meaning, they don't have much redundancy.
Third, why this obsession with zeroing in on a magic gene that causes X? Do they think the language of DNA is context free? Defects could indeed be expected to have no context, but for the rest-- which genes determine a person's blood type? Eye color? Skin color? Going about that task by trying to find the magic gene for something like that is like a person who never learned to read trying to figure out the plot of a book by trying to recognize patterns of letters.
They used to think the Romans were just "lucky" with their aqueducts. Found it hard to believe the Romans really could carefully and correctly engineer such massive projects.
Intellectual Property is a monopolistic, selfish, and defective concept. It is "tyranny over the mind of man"
I walk down the street and see 100s of people who appear to be predominantly junk DNA.
It's full of stars
Our DNA as a hologram.
Would probably explain even more than just a network.
So supposing this is on the money, i cant help but think about all those genetically modified crops, and any kind of DNA manipulation for that matter, if it is so interconnected what errors could we be injecting into this "program"? I mean i can only guess what happens to my program when i send a pointer somewhere it doesn't belong. . . . .until it crashes that is
Finding out that not all viruses cause "sickness," and that the RNA injection of "friendly" viruses is a source of evolutionary change.
I'm guessing a lot of the "human genome" is *airborne*.
--
Toro
1% of 30 million is still a lot of watch variables....
Why it was called junk before you'd ask? Because our definition of what is useful wasnt all that accurate.. just looking at so called open reading frames and declaring everything else to be junk does not work. There is also the problem with insertions in a gene sequence that are either not or alternatively used. There are plenty of sequences that are never translated (no proteins are made of it) BUT without them we would be missing a big chunk of regulators etc. 'Recent' findings like ribozymes, IRES elemtens, attenuation elements etc. are all not translated into a protein yet serve a very specific function. Some of this 'junk' also serves as a insulator / separator between various sequences. We may never be able to map every nucleotide to some function but declaring it junk from the get go was just looking to be proven wrong. Just look up NCBI and look for some good reviews on this topic ;)
Being one of the 0.1% of /.ers that believe God created mankind, (and that we have been in slow genetic decline ever since),
I thought when this 'Junk DNA' was mentioned many years ago that given time, that opinion will be reversed.
Thus there was an advantage to ID biologist who would have the opinion, 'cells are an incredible biological computer with beautiful design, this is great fun reverse engineering it all, and there won't be Junk DNA because that goes against God creating life, so lets keep looking for its purpose'
flame away
46137
Silly humans, can't you see that DNA is a very sophisticated piece of machinery! Well it is. And once you get a handle on DNA, you'll have a fairly good grasp of the universe and be able to leave your monkey brothers behind.
PLANET FULL OF IDIOTS..There, I said it, and it felt really good!
The human KDE is *way* better.
"junk DNA" reminds me of the mysterious "dark matter", or "god" or whatever words we use to name something we know nothing about and don't understand, to give them some sort of magical status. It would probably be better to call it "unknown DNA", or "DNA Incognita", or even why not "Here be Dragons", to better remind us of how ancient maps were conceived (answer : it took ages to "publicly" discover all continents and isles).
One thing I'm sure is that Nature doesn't waste resources, only Humans do, so each yet unknown thing has certainely a very good reason to be there.
Votez ecolo : Chiez dans l'urne !
How do these newly published papers differ from what I just learned last semester from a 3-year-old genetics textbook? A single gene can encode for multiple proteins through mRNA processing (exon excision) DNA encodes for many various RNA strands (mRNA, tRNA, rRNA, snRNA, snoRNA, gRNA, pRNA...) DNA is very repetitious What new concepts do these new publishings offer, or are they just reaffirming whatever source my textbook originally used?
...can it run Linux?
Can you dual boot DNA? Like, you can be a human and then go to sleep and wake up a penguin? Hmm, perhaps you'd have to die first since that's the human equivalent of shutting down. Though maybe a soft restart would do, just get kicked in the head hard enough that it turns off for a bit and then reboots. Like a coma.
Coma: Nature's fsck.
One genome's junk is another gene's treasure...
The junk sections among other things contain quaternary structure that acts sorta like a giant difference engine to regulate transcription. But first they actually have to get over their pedantic little egos and realize that the field of genomics is Pyhrric at best.
oh...
the joke...
"I guess mother nature won't be fired for failing to comment her code sufficiently."
I remember hearing way back when that the Human Genome people were doing their job more quickly by only mapping the active DNA and skipping the "junk"... if that "junk" is in fact active, does that mean they have a lot more mapping to do? Or is my info just hopelessly out of date?
So ...
They are saying that the DNA is Broadband !
We are Dead Stars looking back Up at the Sky
The last time something like this was announced the Intelligent Design wakos went crazy. E.g. if "junk DNA" contains meaning then Evolution is wrong because that whole theory is based on protein encoding genes. If there is some overall all control mechanisms outside of the genes then that can only be evidence of some intelligently designed mechanism.
What about Genetically Modified vegetables ?
is that modifying the broad DNA enough to affect the edibility of the food ?
We are Dead Stars looking back Up at the Sky
how predictably people label things they don't understand as "junk"? Well, gee willikers, we sure can't figure out what that there stretch of DNA is doing, it must be junk! Oh, you wanna know why, if it's useless, it's been preserved for a couple of billion years or so? Dunno, maybe my grad student has an idea. Gimme a beer.
It's the "Bible Code" in the DNA . . .
We are Dead Stars looking back Up at the Sky
Interesting. Not that I sort of expected something like it for a while.. though maybe not as a "functional network". There is so much going on or that could be going on in there, maybe we need to have simulations made like the ones that allowed circuits to program themselves wierdly/organically using induced currents, just so we can get a handle on the tricks that evolution may have drawn on. For example rereading a sequence with a byte offset. Incremental diffs (maybe some of this happens in polyploidal plants..), even something really hard to understand conceptually like using holographic information storage in some bits, or electromagnetic/quantum/local chemistry effects between different parts of dna. IANAbiologist but it stands to reason that valuable tricks which increase robustness or variation at little expense are bound to get taken up in an organism. It may be that much "junk" dna really is junk but that parts of it are laced with important data bits that do in fact get used. Hope we can find some relatively simple microorganism that demonstrates some of these same issues... Anyway it seems we have made another milestone if the report is true and now we get a slightly better handle on what is going on. Only thing... last time I checkd it was extremely hard for grads of a joint biology/cs program (students who wanted to go into this field) to get a paying job after graduation (except sometimes at a drug company) (in Japan). I don't know if this has changed but certainly we need a lot more people who know a hell of a lot about biology and computer science to crack this in our lifetimes.
"Dammit, Jim! I'm doing all I can. I'm a Doctor, not one of your shiny youngbuck Engineers!"
"This creature has no recognizable central nervous system - no heart, lungs, kidneys, liver or even a simple brain that I can find. Maybe if I WERE an Engineer I could make sense of all of.......this..."
If McCoy couldn't envision a connection between data networks and the human genome, what does that say about - Wait...he was an actor, right? Not a real doctor in the future...?
Roddenberry has some explaining to do!
FU classes, FU C++
C all the way!
Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages. So, 90% of genes aren't "junk" after all. To anyone who does know something about the aforementioned topics, duh!
If they hadn't suspected it, multiple groups around the world wouldn't have worked on this thing for such a long time. It's one thing to have a theory, another to prove it, despite what creationists may sayFirst, evolution would weed that sort of thing out in a hurry. Two organisms with genes that achieve the exact same thing, but one has a more efficient encoding? No contest!
Actually, generally no and genome sizes can very a lot. There are a great many things that can complicate this. But you do see effects like this in cases like viruses that have limited space to pack DNA in the virus capsid. Not only do these viruses not have junk DNA, but even use some compression like techniques.
Second, ever tried compressing a DNA sequence? They don't compress very well! Meaning, they don't have much redundancy.
I think you are thinking of the coding regions. Redundancy is a notable feature of many non-coding regions.Third, why this obsession with zeroing in on a magic gene that causes X? Do they think the language of DNA is context free? Defects could indeed be expected to have no context, but for the rest-- which genes determine a person's blood type? Eye color? Skin color? Going about that task by trying to find the magic gene for something like that is like a person who never learned to read trying to figure out the plot of a book by trying to recognize patterns of letters.
I think you've chosen very poor examples to illustrate you're point. Those are all features controlled by a very small number of genes or a single gene. In other context though, this could be an important way of thinking. For example, cell machinery matters too. Kinda like software vs hardware.To match your analogy, if you can't read you have no hope of understanding the plot. First you have to figure out how to read. You might be able to figure out words from patterns of letters though. You have to start somewhere.
The magic gene thing is a matter of hoping for a solution that is actually simple and viable. If it's one gene, a single drug has a good chance of working. There are many diseases that actually work this way, so why wouldn't you look for a simple answer first. Things that involve lots of genes, like cancers, haven't had much success.
Reduce, reuse, cycle
...I never believed in the idea of 'junk' DNA either. I have had several arguments with my sister, a post-doc biochemist teaching at a major university, about the stuff. I suspect part of the issue is that there are certain types of people who are so caught up in how much they know, that they really think they know everything, and so allow themselves to make idiotic conclusions like that which lead to labeling the 'junk' sections of DNA.
Now, for my other pet peeve: We only use 10% of our brain. Who is the knob that came up with that one !
The only thing that gives me huge pleasure in this (sorry) is that I find Richard Dawkins overbearing, overclaiming, and pompous. It's nice to know that his approach to genetics (believing the "gene" is a highly conserved element) is now so hugely out of date. When his book, the Selfish Gene, came out the title peed me off because it suggested, to the general public, that a gene could have intention. Now it's becoming clear that the genetic system is more like a general purpose filing system than a magnetic tape. And we're still at the level of trying to understand it by reading the pattern of 1s and 0s (well, 0-3s in fact) off the disc because we really don't understand how it's organised.
Now, how do we boot an organism and then switch to Runlevel 5 so we get the graphical interface?
Pining for the fjords
Ugh. Creationists have long argued that there is no junk DNA, just DNA that we don't understand yet. This is just another nail in the tomb of evolution as far as all those inbred, illiterate, creationist hillbillies are concerned. Just wait to hear the chorus of "told you so's" from those trailer-dwelling, pick-up truck owning douche bags.
In the words of MC Hawking: "Fuck the creationists. FUCK THEM."
Oh yes? So what was EXACTLY the function predicted by intelligent design for "junk DNA"?
Singularity: a belief in the "God" idea with the "demiurge" relation inverted.
Nature is NOT an idiot. Of course she doesn't carry massive amounts of "junk DNA" along on every cell devision. Apparently ego-fueled "scientists" who see nature as an idiot who has to be corrected have come around a little. Now, if we can just get them to respect nature and the evolutionary process enough not to cross every moral line there is before they find out that stem cells are not a panacea for all man's ills. Nature did NOT overlook stem cells as a repair mechanism. It is for egocentric scientists to explore WHY she doesn't use them to repair things like Parkinson's disease before they go off promising things they will never deliver. A little respect for the complex process of evolution equals common sense in science. And it will save the taxpayer billions of dollars in bogus research funding.
E Proelio Veritas.
Haha
but... but... but... (head explodes)
After all of the evidence of the wondrous complexity of life, people still believe in evolution? Ok, so now, who's operating on blind faith in the religion of evolution, whose high priests are the scientists who hand down accepted dogma and ridicule those who disagree? The shoe's on the other foot now.
Does this imply that while certain characteristics depend very strongly on individual groups of molecules in a particular chromosome, in general our genetic information might be better thought of as somehow a property of the entire chromosome, analogously to thinking of the same chromosome's (relativistic) mass being a property of the entire chromosome rather than the algebraic sum of the parts?
Every time someone, who has a "because-I-said-so" belief system, sees the real life working out of the scientific method, with its "theory/evidence/new theory" cycle, they feel it provides an opportunity to disparage the method that provided the evidence they site as proof that the scientific method is wrong.
"My parents, and the people they gave authority for thinking over to, believe this (insert any mythology), you use the scientific method, one of us is wrong."
It isn't a choice between your particular set of "because i said so" mythologies and the scientific method. Its a choice between the entire set of "I insist this is true in spite of evidence" mythologies not limited to yours, on the one hand, and the scientific method, on the other.
The great thinkers of our history, including social justice, philosophical, religious and spiritual, thinkers, agreed on many things; kindness, generosity and justice come to mind, but where they differ is caused by the level of science and evidence of the universe we live in, or their willingness to study it.
Be kind and test your assumptions. Today's findings are another proof of that premise.
Oh great, that just killed my idea for a weight loss program using a pair of scissors and a guide to junk DNA.
Carbon based humanoid in training.
The press release this story is based on is absolutely terrible, in that it's using a definition of "functional" that i can only describe as bizarre. The discovery in question is that much more of the genome is copied into RNA than we'd realized. According to the story, that makes it "functional."
In reality, it only shifts the issue: we now have tons of RNA with no apparent function. That RNA is in the exact same situation that junk DNA was - in essence, we now have a junk RNA question. If that RNA turns out to be nothing more than a byproduct of the RNA copying mechanism, then it truly will be junk. If it is junk, what does that mean for the underlying DNA? Is it magically not junk, despite producing nothing of use?
Until we know whether these RNAs perform some function, the talk of "no junk DNA" is little more than overinterpretation and hype.
______ This mind intentionally left blank.
I believe in God, but I don't want to assert that things have to be a certain way for God to exist. I would say there are two extremes one could take on the issue. First is the idea that everything should be found to be exactly optimal because it was engineered by an infinite mind. You've basically stated that position, but qualified it with a the genetic decline. The second is that life is here because a machine was engineered that would produce us via a purely natural process. This position doesn't point to the being as perfect, but rather the substance and laws of our reality from which life arose. Alternately, those who do not believe in any divine influence will see everything as self-extant.
:)
Anyhoo... I don't know exactly where I stand.
You found your belief in God on what is known as the Teleological Argument. There are a number of formal reasons why this argument is a poor one. The wiki link I've given you is a good place to start learning why it's not good, and Richard Dawkins' The Blind Watchmaker" has a fairly exhaustive treatment.
They once removed a part of the brain that was obviously useless, and getting in the way of their operation to a vital part... the patient could never again acquire new knowledge after the operation (as in Memento).
So I never believed them when they were saying "junk DNA".
As usual, that was just hubris.
You can't take the sky from me...
We've known for a while that DNA isn't just genes. For example, there are certain sequences associated with histones, and this has been known for a while (though I don't have the papers to site on me). Histones aren't functional in the same way most proteins are. They're more like DNA "spools" (thanks to wikipedia for this analogy). A human DNA strand is about 1cm long, which obviously is a lot bigger than the nucleus of a cell. So DNA coils up into a very tight structure in multiple layers of coiling. First it coils in spirals, then these spiraled segments bend around histones and then there's an even higher layer of folding that takes place. All of this managed to shrink the actual DNA to a size small enough to fit in the nucleus.
Most parts of DNA are inaccessible in this coiled state. To create proteins form the genes, small segments are either exposed or can be exposed, in such a way that transcription factors can get to the necessary segments.
What's important about this is that the parts of the DNA that code for histone placement don't follow a simple pattern, and it's not a repetitive pattern. That is, it's very hard to go looking through a segment of DNA and identify the sequences associated with histones, though a good deal of light has been shed recently on how this is done. Off of the top of my head, I have no idea how much DNA is involved in this, but it's a significant chunk. About 150 base pairs associated with a histone wrapping and these base pairs wouldn't be used for creating proteins. But the placement of the histone markers is important because it has some effect on what genes can be available for transcription (and thus being used to create proteins).
This kind of functionality is clearly important, but the key research in genes has been in determining the causes of disease because this is clearly one of the more important aspects of having access to genetic information. Genes encode for proteins and creation of malformed proteins or the inability to create certain proteins is the cause of genetic diseases. Many cancers are related to a malformed TP53 gene. This gene encode for a protein call p53. p53 is generally responsible for fixing certain mutations in DNA, if it can, or causing apoptosis (cellular suicide) if it's unable to fix the DNA. So if the TP53 becomes mutated in such a way that it can't produce function p53, cells are unable to repair genetic damage and unable to undergo apoptosis when the repair is unfixable, thus the cells become "immortal."
This is really the more important kind of stuff we need from genetics right now. That's not to say this work isn't important. It is. But the stuff that's going to result in disease cures is the stuff associated with proteins we use and proteins we need to function properly. That's why the research has been so heavily leaning in the direction of identifying genes associated with known proteins.
I'm sure it wasn't a responsible scientist who popularized the term, it was probably a science writer. But it's just a variation on the pointy-haired boss credo "Anything I don't understand is therefore easy" morphed into "Anything I don't understand is therefore unimportant or unnecessary." It's like that other popular fact, "we only use 10% of our brains!" No, we only know what 10% of it is doing.
I guess this bugs me so much because I see the problems caused by an ignorance of the facts every day. "Hey, quit standing around! Let's git'r'done!" Yeah, charge into a situation like a bull in a china shop. Hey, asshole! There's a reason why we didn't want you to go through that wall, the cat-5 was back there! Wow, a new hire that I just found out about this morning? Why yes, we have no computer for him, we told you there's a reason why we have to be informed of hires once a position is announced.
Kwisatz Haderach
Sell the spice to CHOAM
This Mahdi took Shaddam's Throne
Machine simulation of genetic/evolutionary algorithms often produces so-called "junk" which when analysed further, this frequently proves to be tied to the function of the overall organism in mysterious ways. I'm sure that leading GA researcher John Koza made this observation in early papers, but it's something that anyone playing with genetic algorithms will encounter sooner or later.
I couldn't find the quote I was looking for, but only this broad statement from Genetic Programming: Biologically Inspired Computation that Creatively Solves Non-Trivial Problems, Koza (1998):
you had me at #!
Not data. This assumes it is compiled already and this is the object code.
...
/* comment */ // comment
:-)
...
I think DNA is more like an interpreted language and this is just comments between the actual lines of code
Like PHP, there are so many ways you comment:
# comment
So, it appears as junk, or can be mistaken for data.
Yes, still having my morning tea
2bits.com, Inc: Drupal, WordPress, and LAMP performance tuning.
I might be more interested (and look at it more carefully) if the fractogene site didn't look like half of the crank science web sites around. Using nice buzz words like "self similarity" and "fractal". And "reverberates" just makes me think of someone talking about "good vibrations".
The science may be good - I am not a biologist and really didn't read much past the first page, but the presentation is enough to drive away anyone who has ever visited timecube or similar sites.
http://www.wired.com/science/discoveries/news/2007 /06/junk_dnap hp/id/1155
http://www.ideacenter.org/contentmgr/showdetails.
After reading what some actual scientists have to say about this, I think its worth noting that the way this article phrases and "explains" things is seriously confused and confusing, and most of our discussion here is a complete mess because of it. Understanding biology's position on JunkDNA is a LOT more complicated than just thinking you know what the word "junk" implies.
- encode-from-scientific.htmle ts-wired.htmlk -dna.htmln k_get_over_it.php
Here's some posts relevant to this issue:
http://genomicron.blogspot.com/2007/06/more-about
http://genomicron.blogspot.com/2007/06/junk-dna-g
http://sandwalk.blogspot.com/2007/06/wired-on-jun
http://scienceblogs.com/pharyngula/2007/06/its_ju
That made it difficult study its amounts and behavior until newer techniques were invented. DNA is practically eternal compared to RNA.
The only thing worse than these poorly-written articles are the inane comments they generate.
The biologists who actually study DNA have known the following for a long damn time. Any "science" writer who gets them wrong should be sent back to writing obituaries and wedding announcements.
Most DNA in multicellular organisms does not code for proteins. Some non-coding DNA performs other functions. Lots and lots of non-coding DNA has no function at all. None. It's not "data", it's not "metadata", it's not structural or anything. There are very long stretches of DNA that you can alter radically or even delete and it makes no difference to the organism at all.
I'm just a layman and my technical knowledge on this subject is just about nil, so don't take my word for it. Go read what a Biochemistry Professor at UToronto (Larry Moran) says here or here or what another biologist (T. Ryan Gregory) says here.
Biology is insanely complex and messy, especially compared to computer science. Here's a hint for all the programmers, database admins, sysadmins, and other bright and talented professionals who feel moved to speculate about DNA and similar subjects: If the viability of your idea depends on the assumption that the actual researchers are too dim or ill-informed to make the connection, it's either a bad idea or it was done years ago.
What it is simply control machinery. Much of biology is the combination of essentially different cellular functionality. Requiring it to be either, or, simplifies the process beyond recognition. What if to conserve cellular space, the sequence controlled the assembly of material? It is neither simply data, nor simply machinery, but both.
The beuaty of nature is its ability to create and vary in a controlled and impossibly complex manner. My bet is that the sequence is like the CNC controls on a milling machine, or the layering controls in a rapid prototyping machine, and the cellular building blocks are like the cutting or layering of material.
Examples of codependent cellular systems abound creating a seemingly single life form but combining into life, like us.
But most importantly, the post says nothing interesting, new or insightful whatsoever:
Is this a new idea? Absolutely not. People were discussing this idea as soon as (if not before) Watson & Crick published.
Similarly the idea of self-modifying RNA/DNA code/data has been around since Watson & Crick.
This is just wrong, wrong, wrong. We don't know where the boot code is, so we haven't "looked at it".
Does it? Show us the recursion, please. Oh, you don't know that it's even _there_, do you?
"organizes and specializes" -WTF!??
Bastardization? You said nothing that was either clear or new! "Vinticated(sic)"? You can hardly be vindicated for writing crap.
Editors, you're failing. Please don't mod posts up if you know nothing about the subject area. Here you've given a 5 to a post devoid of content.
The major leap people seem to be making here is that these transcripts actually do something. Just because something is transcribed into RNA does not make it functional. The transcriptional machinery is surprisingly sloppy and often produces a distribution of transcripts rather than 1 particular type of a precise length. Often many of the aberrant transcripts are later recognized through a process known as non-sense mediated decay, whose role is to identify and break down abnormal RNA transcripts. So if you take a snapshot of all the transcripts in a cell at any given moment, then it's likely that you'll see a variety of these weird transcripts. The real question is do that actually do something? If you're going to look at very rare transcripts at the extreme tail of the distribution (in terms of how common they are in the entire pool of transcripts made from a single gene), then you're going to need to show some kind of function. Otherwise you could just be studying artifacts that get rapidly degraded or are just too rare to have any effect. I saw someone present something similar at a conference last fall and the guy got ripped a new a**hole.
As this was one of the very few predictions of intelligent design, glad someone remembered to point it out when it was found.
(The only other predictions of intelligent design that I recall were the absolute failure of SETI and the finding of primitive bacterial or fungal life on Mars w/o any sign of more advanced life).
Given the current state of science, one cannot tell in the case of a GM organism whether deleted generic code had a function even though it appears as "junk", or whether the newly added code hasn't unpredictable side effects because it interferes with other "junk" or "active" code. I think everybody can see the analogy with computers, ie data versus code. In many architectures both can be deeply intertwined and are sometimes indistinguishable from each other (e.g LISP, Tcl). It's like blindly hand-patching running executables, or buffer overflow exploits.
is a dangerous thing.
The fundamental misunderstandings of how the genome actually works that have been demonstrated by the unveiling of the original HGP results (22,000 genes found rather than 100,000) and now this realisation that junk DNA might actually not be junk, really make me think that perhaps biotechnology should be slowed right down. It is hardly at the stage where it really is a technology as opposed to rather speculative experimentation.
I believe that ID didn't predict what, exactly, the function would be, only the existence of such a function.
It takes a lot of hubris to label the part of the genome you don't understand as "junk DNA." This was painfully obvious right from the start, and yet the term propagated throughout papers and textbooks as law.
dah
"Having the human genome sequence is similar to having all the pages of an instruction manual needed to make the human body".
We are expecting to obtain from the genes some information that is simply not there. Having the human genome is more like having the USPTO patent repository. So we might know how and why products could be made. However, that knowledge does not tell when thoses products are made, how they interact in the marketplace and why deficiencies might come to exist. Throughout history, we have been jumping to conclusions as soon as we uncover a little bit of information, but the fact is that we don't know much and should try to be less arrogant.
yeah, I'm sure all those Alu fragments are doing something important and this isn't hyped at all.
This is one of the landmark-quotes on the "Junk DNA Portal" http://www.junkdna.com/ . The collection of articles since Dr. Ohno coined the term "Junk DNA" in 1972 features, of course, the "NIH Blessing" that "Junk DNA" is anything, but... Will there be life after the "death of Junk DNA"? Of course. Those who are searching for a name of "Genomics beyond Genes" will find that International PostGenetics Society (http://www.postgenetics.org) established in 2005 defined "PostGenetics" as going beyond genes, and in its European Inaugural became the first international organization to formally abandon this catchy misnomer. "PostGenetics" is the postmodern era of "Genetics" (1905-2005). Techies (the readership of slashdot) will not rest until the algorithm of genomic coding ("beyond genes") will be available, since algorithms are "software enabling", while loose talk on "wet biology only" is generally "software unfriendly". http://www.fractogene.com/ provides an algorithmic approach - and also provides insights to the myriads of "junkdna diseases" where the genes are pristine but glitches in the "junk" might doom you at any time; http://www.junkdna.com/junkdna_diseases.html . "PostGenetics" has been an "uphill battle" from 2002 (FractoGene) till yesterday. Now it is expected that (1) the press will look beyond the "life and death of junk dna" and will "discover" PostGenetics (the wonderful opportunity is the 35th Anniversary on 30th of June of Dr. Ohno's coining the term "junk DNA"), (2) a similar "cut-throat race" will emerge between slow but huge and rich government programs for a "DECADE OF DECODE" (after ENCODE) on one hand, and focused and streamlined private domain industry, going directly for tangible results in Bioenergy, Synthetic Genomics (etc). While they are already well underway, it is clear that "regulation" is a key factor, and both in Bioenergy and Synthetic Genomics (let alone bio-based Nano- and Information Technology) a software-enabling understanding of Genome Regulation will be vital. pellionisz_at_junkdna.com
"The beauty of nature is its ability to create and vary in a controlled and impossibly complex manner."
:)
You can thank God for that.
The "Information Theory" of Shannon kicked off von Neumann' "Computer Science". "Genomic Information", however, is even less clearly defined than (loose) "Biological Information". With Fig.30. from "Supplementary material", featured on http://www.junkdna.com/ it is downing to all that "all A,C,T,G letters are equal - but some are more equal than others" (to paraphrase in PostGenetic Genome Farm George Orwell). Someone pointed out that DNA sequences compress very poorly - another reminder that "genomic information" (*all* information there is to define organelles, organs and organisms) is already compressed; to the extreme. Since living systems are "built" from the "bricks and mortar" of proteins, the genome must specify the "raw materials" (protein-coding sequences, formerly called "genes" do that for a living). However, as already pointed out in 2002 by FractoGene, the "architecture" of *what kind of a building* a genome erects is compressed into the "blueprint of life" - and the sets of auxiliary information of how to put together the "bricks and mortar", since the "compression" is fractal, looked like a self-similar repetitive jumble; termed by non-algorithmic thinkers like the late Dr. Ohno "Junk". Readers of this column (techies) be happy - there is a colossal "boom" in the offing for "information technology of Genomics" (beyond Genes). It will be incomparably bigger than the "Internet boom" - since it *includes* the Internet itself - but goes much further by establishing an entirely new (transdisciplinary) discipline. Pls. look at the presently 53 Founders of International PostGenetics Society (http://www.postgenetics.org) and you will be amazed of the kinds of "leading edge" mathematicians, computer scientists, neural network experts - and of course bioinformaticians - in addition to "wet" genomists. Please join IPGS if you care, and be part of it as much or as little as you can. pellionisz_at_junkdna.com
Those wishing to look beyond "websites" for FractoGene can look up the refereed science paper (in full) at http://www.junkdna.com/fractogene/05_simons_pellio nisz.pdf
If we find a gene that translates to GOTO or GOSUB...so help me....
Ice Cream has no bones.
Of course it's spaghetti code. It is the marinara fingerprint of our Pasta Lord and Creator in the skies.
In other news:
"A study (abstract, pdf) says we may have to rethink how genitals work. So called "junk skin" (often surgically removed from children) actually appears to be functional. What's more it, the sensitive tissue involving multiple overlaps seems to send touch and pleasure sensations to the brain."
It's a fact. I work at that company.
Don't worry though, most of us here aren't evil.
And by the way, the mechanisms for DNA replication and gene expression/regulation are very different between bacteria and eukaryota; you're better off not mixing the two things together in your mind.
Wanted to point out this article that is seemingly related, although goes unmentioned within the Story blurb or the linked article:
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Russian Human Genome Project discovers Extraterrestrial abilities to modify DNA through a "biological internet" http://www.agoracosmopolitan.com/home/Frontpage/2
I also wanted to comment that I've spoken to this whole "junk DNA" thing before, so I get to say "I told you so!": http://slashdot.org/comments.pl?sid=45367&cid=469
Cum catapultae proscriptae erunt tum soli proscript catapultas habebunt. (When catapults are outlawed, only outlaws will
First, evolution would weed that sort of thing out in a hurry. Two organisms with genes that achieve the exact same thing, but one has a more efficient encoding? No contest!
Why, exactly? This is a huge, simplified assumption. Without physical proof that this is true, you're just asserting--and potentially displaying the same ignorance of subject matter you decry.
Second, ever tried compressing a DNA sequence? They don't compress very well! Meaning, they don't have much redundancy.
Ever try compressing a random sequence of numbers? Clearly there's little redundancy. But, that does not prove that there is information or structure in there.
Going about that task by trying to find the magic gene for something like that is like a person who never learned to read trying to figure out the plot of a book by trying to recognize patterns of letters.
Let's just put it this way--how would such a person figure out the plot without first learning to recognize the patterns of letters (aka the words and sentences)? To make a bad evolutionary pun, we need to crawl before we can fly. That's why research to this point has focused on the low hanging fruit simple traits.
Build a man a fire, he's warm for one night. Set him on fire, and he's warm for the rest of his life.
I think a good analogy to our genetic information is a large, complex work of literature. We've only just figured out the alphabet, and we're beginning to figure out what the words are, though we don't know what most of them mean or how their meaning is affected by context. We don't understand how to parse the sentences, or identify paragraphs or chapters, much less interpret the full meaning with emotional content and nuances, such as irony. Yet we're already trying to rewrite the book. It's going to take a very, very long time (measure in decades or centuries) before we become sufficiently "literate" that we can write a better book, much less avoid really botching up a decent one. It is the certainty of botched-up works that makes me so pessimistic about genetic engineering.
There are two factual errors in the argument that leaving "junk" in the Genome is cheap and safe. First, recombination requires energy - and mind you, the DNA *IN EACH AND EVERY CELL* when it replicates consumes a lot of energy with recombination. Second, while you can "comment out" useless "junk" in the sw code, we know that tons of "junk DNA diseases" (see http://www.junkdna.com/junkdna_diseases.html) are caused by glitches "in the Junk". Therefore, Nature not only has an incentive of getting rid of unneded code for reasons of energy, but also to save itself from "junk DNA diseases" - if the "junk" is truly trash. However, it is now clear not only to pioneers (http://www.postgenetics.org see tab "Founders") - but is also "blessed by NIH" that there is "no more Junk". The challenge is no longer "why is it there", but "how does it work"? pellionisz_at_junkdna.com
The first junk DNA evolved in the primeval oceans; random bits of snapped-off pseudopods and discarded mucus. This "proto-junk DNA" coalesced into the primal "toe jam" that clung between the webbed toes of the first amphibious creatures to emerge onto the land.
Gradually, these separate strands of junk DNA gathered together in "junk tribes," trashing whole neighborhoods and giving rise to the theory that it was not a huge meteor that killed the dinosaurs but suffocation in their own junk DNA.
As time went by, various races of junk DNA came to dominate the evolutionary tree, giving rise to the hot dog, Windows© and Fox News.
Of course, this theory is called into question by proponents of the Intelligent Design theory, who argue that, contrary to observation, junk DNA was actually created by Bog The Almighty 4001 years ago and merely disguised to look much older.
Really.
The entire genome is like a program you are working on. DNA is like the raw code (.c, and .include) files stored on a FAT32 formatted harddrive (the cell).
RNA and proteins are the the compiling and compiled program, respectively. Polymerase would be the compiler, HIV would be a debugger program, etc.
Anyway, the point to all this is that junk DNA is deleted files on the file system. They are still there, and you may need them because you are working on a harddrive with sectors which frequently go bad (mutations). Deleted files are gone unless you can specify the first letter: that's the equivalent of lacking an intron, so they don't get included when you compile the program.
As a side note, you can make RNA which self-replicates on agar if you just add ATP. It's note the same thing as DNA, nor the same thing as traditional RNA, (it may have been the basis of life, though).
I'm a biology major primarily and computers are just a hobby, so this may not be perfect, and I'm probably posting this too late for anyone to read it, but here goes anyway.
Obligatory Soundbite Catchphrase
My experience with Perl developers is that writing tangled code isn't a problem for them. It's reading, even their own, tangled code that they find difficult. I sat down with a Perl guru where I worked some years ago trying to debug a particularly nasty piece of Perl code. The whole time he kept going on about "Who writes code like this!?!" until we looked it up in the CVS repository and it turned out it was he himself who wrote that particular block a few years earlier. Syntactic flexibility is nice but it has a downside.
In other words, he's an idiot.
My God, it's Full of Source!
OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
So, when such a prediction comes confirmed by observation, evolution models are changed to reflect it (that's science as usual). What changes will make ID models so as to reflect all of its predictions that are proven wrong by observation?
(BTW, that's how my question is relevant. A model is not 'true' or 'false', but 'better' or 'worse' depending on the number and accuracy of events it predicts. A vague 'all DNA has a function, but we don't know anything about it' is not of great value.)
(And Darwinism has nothing to do with god-hating - science doesn't pronounce about religion!)
Singularity: a belief in the "God" idea with the "demiurge" relation inverted.