Are we folding the whole thing?

Just watched a PBS two-hour documentary on the Genome Project. At the end, it talked about where research since that project has been taken off to. We're part of that next step. However...

What I found surprising to learn is that only a small percentage of our DNA has anything to do with us. Most of the DNA simply self-replicates itself into the next DNA. They called that part of the DNA "freeloaders" and even sort of like parasites that do no harm.

First off, is what they said in that PBS special true about the majority of our DNA being worthless junk?

Second, saying it is true, what part of the DNA are we folding here? I assume (probably wrongly) that we're building proteins using a DNA model then folding them. True?

Lastly, what would happen if we decided to cut out this useless junk from our DNA? Say we don't want the useless stuff to be passed along to our descendents and we snip it out.

Can't really answer the first question (I assume PBS knows better than me) :) although of course there could be a lot of DNA with functionality we don't know about.
On the second question though, we aren't building proteins using any kind of DNA model, because what DNA specifies is the order of the Amino Acids (residues), which is what we start out with as given. The idea is that someone could take some DNA and translate that into a string of amino acids, and then use something like DF to figure out what the structure of the protein will be (ie how its shaped, how it's folded) given this ordering of amino acids. In other words we aren't "building" them in the sense that we already know what the DNA has told us - that is, which residues (AA's) are in which order. All we do is fold them.

As to the last question..... well I don't know, but genetically engineering ourselves is a big "what-if" question, as well as "can we" and "if so, should we". All these questions have been asked by a lot of people in journals, books, even movies (ever see GATTACA?) etc. That's probably the subject for another thread, or perhaps even another board :D

You might have a bit better luck asking that on a PBS message board dealing with that program, where many of those studying the DNA are actually hanging out. If you ask about folding here, you can receive enough information - that some of my teammates said things to the effect, "I don't understand that. I no longer care. Just let me fold and do some good."

With added time to study, positions by scientists get changed as the subject becomes more understood. We used to have scientists chanting about "lower your cholesterol" - and then they noticed that we have "good" cholesterol and "bad" cholesterol, and we now work at building up the good side, and lowering just the "bad" side..

nVidia made the silly statement in their TnT chipset days that they looked forward to the day that their gpus would be able to render something like Toy Story in real time. The folks at Pixar laughed at the idea. (not only did they have a million? times the processing power, but they were only able to produce a few scenes a night).
Along came a fellow that showed how to speed up the rendering by performing the same step on 100s or 1000s of little bits at the exact same time; and suddenly that goal seems reachable in the very near future.

If we can help Howard out with similar ideas that will speed up the creation of these structures, then the goals we're seeking will become much closer to reality.

1. Yes there is are repeated patterns of nonsense encoded in our DNA. This is clipped out when the DNA is being translated to RNA. I believe these sections are called exons, but I'm not going to dig up my bio text to check. :p

3. It might be interesting to find out what happens if we clipped out these exons. Some scientists feel that exons are important to our DNA even though they do not encode protein information.

hm... maybe it's kinda like ECC for memory :rotfl:

How about making a protein only using a clipped DNA? As that ever been done to test is any of the "freeloaders" actually contribute anything? I'm talking about a computer model and not actually making a real protein that way ... unless that's easier.

Quick review for the non-biologically inclined (if you don't understand something, get a book :p )

Your DNA can be represented as a string 3 billion characters long, made up of 4 letters: A,G,T,C (GATTACA - get it?). It is made up of two types or 'regions' - coding regions and non-coding regions. Coding regions do just that - they encode the sequence of a protein. More precisely, each triplet of DNA letters (nucleotides) corresponds to a specific amino acid (the building blocks of proteins). There are 20 different amino acids so if you do the math, there is some redundancy. Also, certain DNA triplets (called 'codons') mean special things, like ATG means "start a new protein" and others mean "stop".

Because codons are triplets, there's 3 'reading frames', or 3 ways of interpreting a given piece of DNA, depending if you start reading at letter 1, 2 or 3 (if you start at letter 4, you're back in the same 'frame' as if you start at 1). Further, remember DNA is double stranded, so you can read the 1st strand or the second when translating to Amino Acids, for a total of 6 possible reading frames.

Because of the physical way the DNA is translated into proteins, we are not guaranteed that just because we see a start codon ATG in one of the six possible frames, that a protein starts there. However, we can predict fairly reliably which regions of DNA are coding and which are non-coding using some of these principles and other things we know. Non-coding regions are used, among other things, to help align the translation machinery with the start of the protein, to help maintain the 3-D structure of DNA, and other unknown purposes. Some pieces are remnants of ancient viruses that have mutated away into random noise over the generations.

Coding regions themselves, in multi-celled organisms , are sometimes divided into introns and exons. basically Introns are 'noise' in the middle of the coding regions, and get spliced out eventually before making the final protein. Introns are generally though to have little use though I could be wrong on that.

So to summarize, it is well established how to go about finding which regions of DNA may code for proteins and which do not. Only about 1% or less (I think?) of the human genome consists of possible coding regions. Removing all the 'junk' would be an interesting experiment but not practically possible in the forseeable future. If nothing else, they help reduce our chances of getting cancer and other diseases. If you only had the most essential parts of your DNA present, and a single mutation would have a good chance of being fatal. With the current 'setup' though, 99% of the time mutations will occur amongst the garbage and so have little or no effect on our health. I hope this makes it clear why even garbage could be very useful in DNA...

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Originally posted by Brian the Fist
Removing all the 'junk' would be an interesting experiment but not practically possible in the forseeable future. If nothing else, they help reduce our chances of getting cancer and other diseases. If you only had the most essential parts of your DNA present, and a single mutation would have a good chance of being fatal. With the current 'setup' though, 99% of the time mutations will occur amongst the garbage and so have little or no effect on our health. I hope this makes it clear why even garbage could be very useful in DNA...

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Wouldn't having a smaller DNA size reduce the chance for mutation, or does DNA not work like that?

I'm not a biologist, but it seems clear to me that mutations are going to happen. From my college days, and from the texts I've picked up since starting on G@H and DF, mutations commonly occur due to damage of one sort or another. Viral, environmental (most common), etc.

I think it's a really good point that the 'design' is such that those damages are most often occuring in noise rather than in critical segment.

Kinda like fault-tolerance in our favorite field of endeavor...

Yes, that is a good phrase to use - the human body (and in fact many other evolved organisms) is very fault tolerant. It is filled with redundancy to avoid a single point of failure in any system in most cases. That's why we have two of everything for example.. (eyes, ears, hands, etc)

You know, it's interesting -

Star Trek really played that very thing up with their Klingon race. Clearly the evolution started in the same place, but they were absolutely and totally war-like.

Therefore evolution gave them double everything. Heart, lungs, kidneys, etc.

Obviously theoretical science needs to 'play' with the discoveries that have been made and are being made. That's how science advances.

But the odds that we're going to improve on a billion years of evolution anytime in the near future are, imho, slim to none. Medical science is overwhelmed by the number of new ickies that surface, so anything that helps us shoot them at a genetic level is obviously beneficial. But I doubt we'll see any grand induced changes to the genetic structure of man in our lives...

(Before anyone accuses me of dragging down a serious discussion - go read the contributor list to Star Trek sometime... Reads like a who's who in the Aerospace, Applied Materials Science, and University worlds. Lockheed, Douglas, Boeing, Lytton, AT&T/Bell Labs, Raytheon, Raychem, Cal., MIT, Cal Poly, etc etc etc., all well represented... An awful lot of science went into the pseudoscience.)

Some current-scientific critiques of sci-fi items/technologies isn't even solicited, and still gets to the author(s).
Larry Niven's Ringworld fascinated enough in the science fields at colleges, that they went on to prove that it couldn't stay in orbit without some kind of help.
I smile thinking of those folks holding up banners that read, "The Ringworld is unstable!" at Niven's presentation at a sci fi convention. ;)

And a whole new generation of scientists then starts building their dreams of how THEY'D go about putting a ringworld up if they were kingemperor for a day... I think one could argue that a project like DF's biggest benefit is in the imagination and grandiose dreams it sparks. In the publicity and penetration it achieves for theoretical sciences... [shrug] Or maybe I need to stop sniffing glue. :bang: :crazy: :|ot|:

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Originally posted by tpdooley
Some current-scientific critiques of sci-fi items/technologies isn't even solicited, and still gets to the author(s).
Larry Niven's Ringworld fascinated enough in the science fields at colleges, that they went on to prove that it couldn't stay in orbit without some kind of help.
I smile thinking of those folks holding up banners that read, "The Ringworld is unstable!" at Niven's presentation at a sci fi convention. ;)

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Right... the same folks who told us the speed of sound is unbreakable and scoffed at the idea of going to the moon...

Science is ultimately about educated guesses because truly they don't have ALL the facts...

RS½