Language found in Junk DNA

Seymour Cray touched on the junk dna issue in a speech in 1996

An Imaginary Tour Of A Biological Computer

Programming Code Needed by Living Cells

The next question is how much of it is program code. You know how embarrassed we are about our program code now. It gets bigger and bigger. For the DNA in a human cell, about 10 percent of the memory is program code. What's the other 90 percent? Biologists tell us it's mostly noise. But if you look close, it looks like old program code that doesn't run anymore. And that's probably what it is.

Let's look at the part that's program code. It's organized into a lot of subroutines -- 150,000 subroutines. Now, that's a lot of subroutines for any program. We call those genes. And we have this great big project worldwide now, the human genome project, to reverse-engineer this thing, and to identify how each subroutine works in the program. And more than that, the end result of this human genome project is to identify every bit in every sequence so we know exactly the code it needs subroutining. Now, that is a monster undertaking. We've been working on it as a human group for 10 years, and I think we can estimate about 20 years to finish. They are at somewhere between 15 and 20 percent through identifying function -- function, not bit sequences yet. So we have this big DRAM memory, 150,000 subroutines, and we are working on decoding it and figuring out what each one does.

The Operating System for Living Cells

How much of the program code is operating system? Well, that's another embarrassing thing we have with our computers. The operating system is always too big. So how big is it in the biological system. The answer is a little over 50 percent. That's kind of embarrassing. If we look at this and ask how did that get so big, well, you know, every system you add more extensions to the extension folder, and they keep piling up, and they never get smaller. When you think how long this biological system has been upgrading its operating system and how long it might take, then, to initialize, you know, the more extensions you have in the extension folder, the longer you have to wait while the screen goes through this long sequence. When you think about how big this is, you probably won't be surprised to hear it takes 13 years to initialize the operating system, but if all goes well, you get a smiley face, and it's just like a MacIntosh.

So his theory is that most of the DNA is basically unused, legacy stuff that has been superceded by more modern DNA code. An interesting theory, though being neither a computer scientist or a biologist, I can't really comment further..

Well worth a read though... fascinating article.

there's also the notion that the DNA strand is essentially the cosmic string/thread, uniting the higher order of conscious & sentient beings

Also That DNA is the cosmic string which weaves through the multi-universes, or call them dimensions, that exist side by side...
the junk areas are utilized in creating your other 'selves',
and only look 'blank' to this universes' illusion of reality

in earlier history, religion mis-stated that model & called the process/concept an 'Immortal Soul' instead.

read more of the eastern & existential materials available on creation cosmology philosophy and such...& have an epiphany

Originally posted by St Udio
there's also the notion that the DNA strand is essentially the cosmic string/thread, uniting the higher order of conscious & sentient beings

Also That DNA is the cosmic string which weaves through the multi-universes, or call them dimensions, that exist side by side...
the junk areas are utilized in creating your other 'selves',
and only look 'blank' to this universes' illusion of reality

This is sorta what i believe.

I think DNA is perfection. I know thats a bit out there, but i really do think science hasn't realised the full extent of DNA's purpose. Whether that is intentional or not is up to you..

How something on a molecular scale can code for something which allows consciousness to sit in the driving seat its created, and replicate, and repair itself....its just beyond chance or probability.

DNA..the chicken or the egg? Which came first, DNA, or the life it codes for?..

So, if this unused portion seems to be 'old code' that has been replaced by newer/better code......do 'footprints' of the 'missing link' exist there?? Could we see what was tried ( as a mutation, maybe) and then rejected?

I wouldn't dismiss it as junk so quickly. Just cuz you can't understand a chinese man's ching chung chang doesn't mean it doesn't have a meaning.

Originally posted by St Udio
there's also the notion that the DNA strand is essentially the cosmic string/thread, uniting the higher order of conscious & sentient beings

Also That DNA is the cosmic string which weaves through the multi-universes, or call them dimensions, that exist side by side...
the junk areas are utilized in creating your other 'selves',
and only look 'blank' to this universes' illusion of reality

in earlier history, religion mis-stated that model & called the process/concept an 'Immortal Soul' instead.

read more of the eastern & existential materials available on creation cosmology philosophy and such...& have an epiphany

And that notion is sort of odd, because you can look at the sequence of base pairs and tell what bits are coding for proteins and what that protein sequence is. At its lowest level it's just sugars, phosphates and nucleotides. How all those proteins fold and interact, that's the magic. But there's no extra dimensions/universes/fairies or what not in there.

I think people that have such notions haven't really studied what it is, they hear stuff on TV and let their imaginations fly instead of taking a few chemistry and microbiology courses.

How all those proteins interact to produce something as complex as a living cell, that's the true magic, and it's so wonderful that you don't need to conjure up fairies in the garden for extra spice.

Originally posted by frayed1
So, if this unused portion seems to be 'old code' that has been replaced by newer/better code......do 'footprints' of the 'missing link' exist there?? Could we see what was tried ( as a mutation, maybe) and then rejected?

To some extent I think you can, I remember reading about them finding old point deletion mutations that were selected against by having their promoter regions deleted. The old code was still there, but it had deteriorated over time, if it's not being 'used' then there's no evolutionary selection against mutations in it.

Originally posted by rrahim1
I wouldn't dismiss it as junk so quickly. Just cuz you can't understand a chinese man's ching chung chang doesn't mean it doesn't have a meaning.

True, but.

A fast overview...when you make a protein, there's a transcription step that happens. Leaving a lot of steps out, a reader enzyme comes in and copies off a protein coding sequence from your DNA into messenger RNA. That coding sequence usually has a lot of 'introns' or junk in the middle of it. An editing enzyme will sweep the RNA and cleave out all the intron bits and toss them in the garbage. Then the mRNA leaves the nucleus and is translated into a protein by a ribosome.

So, if your analogy is that the DNA is someone talking, and a gene is a sentence, then the first pass might be:

Four ss ss ss ss ss ss score and adolfkjasd;lfkjadj seven years 234234jllll2kkkkkkkkkkk ago our fjfjfjfjfjfjfjffjfj fathers br br br br br br stop stop stop stop stop brought forth upon 0000000000000000000000000000 this continent 989898989898989898989898989898989898 stop stop stop stop a new nation we the pe-ple in or-d-r to biiiiiid a m conceived in liberty 242424242424 stop stop stop stop stop adddcated to th333333333 and dedicated to the proposition ohsycnyu see by the daaa ealy l---t that all men stop stop stop stop stop stop are created equal.

Now, all the crud in between the words is stripped out to make the first line of the Gettysburg address. You can look at the mess and tell that bits of it resemble other similar 'proteins' like the Star Spangled Banner or the preamble to the constitution, only with errors. Other bits are just repetitious junk. It all gets tossed on the floor of the nucleus, so to speak, before the mRNA carrying the Gettysburg address line leaves the nucleus for translation into a protein, because the mRNA editing enzymes know what's protein code and what ain't.

From the anonymous board, in reponse to this thread:

www.abovetopsecret.com...
with so much of our dna "unused" and like only 19% of our brains in use, what would we humans be capable of if eg the brain used 50% of its power????????

This is interesting, because it invovles two misconceptions.

1. Humans DO NOT use only 19% of their brains (usually the urban myth is that they use 10% of their brains, this is also untrue). Humans use all of their brains.

2. "Junk" DNA isn't junk, it is not unused. DNA is usually said to be arranged into genes within the whole genome. Genes are small units that are translated into proteins. Every protein has a corresponding gene or genes.
So called "junk" DNA is peices of DNA that don't code for any proteins. So when researchers first found out that there was segments of dna in the genome that don't make any proteins, they called it 'junk', because the focus of DNA research at the time was on the creation of proteins. Its not that it had no function, its that the function simpy wasn't to create proteins. THe functions were unknown.

Lots of researchers now think that lots of the so called '"junk dna" is actually instructions on when to translate the protein coding dna into protein, iow, that "junk dna" is really 'non-coding regulating dna".

If the coding protein is a blueprint, then the junk dna is like the foreman.

Originally posted by Nygdan

If the coding protein is a blueprint, then the junk dna is like the foreman.

And that's probably true, because stretches of it are strongly conserved. But some of it IS just trash. What's interesting is that there are a lot of chunks that look like near perfect copies of old retroviruses, but altered so that they can't express anymore.

If you were Dr Evil, you might have some fun transcribing some of the simplest ones off and seeing what those old viruses did.

Originally posted by Tom Bedlam

Originally posted by rrahim1
I wouldn't dismiss it as junk so quickly. Just cuz you can't understand a chinese man's ching chung chang doesn't mean it doesn't have a meaning.

True, but.

A fast overview...when you make a protein, there's a transcription step that happens. Leaving a lot of steps out, a reader enzyme comes in and copies off a protein coding sequence from your DNA into messenger RNA. That coding sequence usually has a lot of 'introns' or junk in the middle of it. An editing enzyme will sweep the RNA and cleave out all the intron bits and toss them in the garbage. Then the mRNA leaves the nucleus and is translated into a protein by a ribosome.

So, if your analogy is that the DNA is someone talking, and a gene is a sentence, then the first pass might be:

Four ss ss ss ss ss ss score and adolfkjasd;lfkjadj seven years 234234jllll2kkkkkkkkkkk ago our fjfjfjfjfjfjfjffjfj fathers br br br br br br stop stop stop stop stop brought forth upon 0000000000000000000000000000 this continent 989898989898989898989898989898989898 stop stop stop stop a new nation we the pe-ple in or-d-r to biiiiiid a m conceived in liberty 242424242424 stop stop stop stop stop adddcated to th333333333 and dedicated to the proposition ohsycnyu see by the daaa ealy l---t that all men stop stop stop stop stop stop are created equal.

Now, all the crud in between the words is stripped out to make the first line of the Gettysburg address. You can look at the mess and tell that bits of it resemble other similar 'proteins' like the Star Spangled Banner or the preamble to the constitution, only with errors. Other bits are just repetitious junk. It all gets tossed on the floor of the nucleus, so to speak, before the mRNA carrying the Gettysburg address line leaves the nucleus for translation into a protein, because the mRNA editing enzymes know what's protein code and what ain't.

Yeah - but you may think the parts you are stripping away is not meaningful, and you may end up stripping too much. Let's go back to the Gettysburg Address, with more "seemingly meaningless stuff" stripped away...

"Seven years ago a nation conceived all men."

This sentence may make sense grammatically, but the original meaning is altered. In you're analogy to DNA, you think you're stripping away meaningless stuff, because what is left makes sense to the present understanding of science. But the stuff being stripped away may also be very meaningful, but not yet understood.

However, even the junk DNA seems to serve some purpose. I can't find a source for this, but I remember reading that experiments were done where some of this "junk" genetic material was removed from a gene of some oranism, but that organism failed to funtion propperly, even though the material removed was just "Junk".

Here's the wiki article on junk DNA. There are some theories as to what purpose the "junk" serves.

en.wikipedia.org...

Also, regarding this talk about a "hidden language" in the junk: nature is full of patterns, even in the most random of systems. This is Chaos Theory.

Article: en.wikipedia.org...

Chaos Theory finds that there are patterns everywhere in nature, so it's no surprise that the junk DNA behaves in the manner of a language with respects to patterns. And don't be surprised that all language's behave similarly...they are all created by man, who in turn was created by nature.

Originally posted by Soylent Green Is People

Yeah - but you may think the parts you are stripping away is not meaningful, and you may end up stripping too much. Let's go back to the Gettysburg Address, with more "seemingly meaningless stuff" stripped away...

If you read what I was saying, you'll see that my statement was that your cells do this on nearly every protein they make. You constantly discard introns, nearly every protein code you have is full of them. If your cells didn't have a pretty amazing editing system, you'd be dead.

Talaro probably says it better, maybe it will make more sense:

We have given the simplified definition of a gene that works well fpr prokaryotes, but most eukaryotic genes are not co-linear - meaning that they do NOT exist as an uninterrupted series of triplets coding for a protein. A eukaryotic gene contains the code for a protein, but located along the gene are one to several intervening sequences of bases, called introns, that do not code for protein. Introns are interspersed between coding regions, called exons, that will be translated into protein. We can use words as examples. A short section of co-linear prokaryotic gene might read TOM SAW OUR DOG DIG OUT; a eucaryotic gene that codes for the same portion would read TOM SAW XZKP FPL OUR DOG QZWVP DIG OUT. The recognizable words are the exons, and the nonsense letters represent the introns.

This unusual genetic architecture, sometimes called a split gene, requires further processing before translation. Transcription of the entire gene with both exons and introns occurs first, producing a pre-mRNA. Next, a type of RNA and protein called a spliceosome recognizes the exon-intron junctions and enzymatically cuts through them. The action of this splicer enzyme loops the introns into lariat-shaped pieces, excises them, and joins the exons end to end. By this means, a strand of mRNA with no intron material is produced. This completed mRNA strand can then proceed to the cytoplasm to be translated.

At first glance, this system seems to be a cumbersome way to make a transcript, and the value of this extra genetic baggage is still the subject of much debate. Several different types of introns have been discovered, some of which do code for cell substances. One particular intron discovered in yeast gives the code for a reverse transcriptase, and other introns can be translated into endonucleases. Some experts hypothesize that introns represent a "sink" for extra bits of genetic material that could be available for splicing into existing genes, thus promoting genetic change and evolution. There is also evidence that introns serve as genetic regulators and in ribosomal assembly."

Foundations in Microbiology, Kathleen Talaro

The little ones buried up in the middle of coding genes are probably noise, the reverse transcriptases are most likely remains of old retroviral infections, and of the rest some is apparently necessary for some functions we don't understand. Other bits don't appear to have any function since your cells don't bother copying it correctly from one generation to the next.

I'm sure that some of it fulfills some wonderful functions we haven't discovered yet. What I don't think is that you'll find a nice text message up in there, nor the magic genes to turn you into Superman.