Junk DNA

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Re: Junk DNA

Postby Calrid » Sat Dec 24, 2011 1:11 am

anon wrote:
Wikipedia wrote:...the lack of function and sequence conservation in a majority of noncoding DNA indicates that much of it may indeed be without function.

For the life of me, I can't figure out what this sentence is supposed to imply. "Function" how? To do what? Nothing exists in a vaccuum; therefore anything that exists, functions - and unless I'm wrong about the existence of God, DNA wasn't invented to serve some specific purpose. I don't think it's just sloppy language though (though it is Wikipedia) - I think, on the other hand, that people in general have a very hard time abandoning a view of their own place in the world as an inherently privileged one - that the world I can know, is the world.


Come on guys read a magazine pop science or not, the information is there:

http://www.newscientist.com/search?doSe ... y=junk+DNA

Junk DNA is not junk.

Wikipedia is fine, but if no one updates it it grows stale and surely you read the fact that it wasn't junk?
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Re: Junk DNA

Postby Tab » Sat Dec 24, 2011 1:11 pm

anon wrote:
Tab wrote:Recursive enough = independent of externalities.

No such thing though...


:lol: Absolutist.
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Re: Junk DNA

Postby anon » Sat Dec 24, 2011 1:50 pm

Tab wrote:
anon wrote:
Tab wrote:Recursive enough = independent of externalities.

No such thing though...


:lol: Absolutist.

O:)
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Re: Junk DNA

Postby turtle » Sat Dec 24, 2011 2:27 pm

anon---where do you want this thread to go?
there are some good posts and some junk posts..
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Re: Junk DNA

Postby lizbethrose » Mon Dec 26, 2011 8:46 am

"Junk DNA" is a misnomer. It's, more accurately, non-coding DNA, but that doesn't mean it's just sitting around doing nothing. It isn't. It has function and purpose; it's just that, back when the term was coined, no one know what that function and purpose involved. (One thing it apparently does, is absorb mutations)

I think what the 'argument' boils down to is, "What's a more valid theory--evolution or 'creationism?" In creationism, there is a cause--God, the Creator-- this God creates 'things' that have function and purpose, so, if there's function and purpose in non-coding DNA, it could only have come from the Creator God.

But is that necessarily true? Isn't it possible that evolution is also following a much longer path (in time) that also has function and purpose? What is that purpose and what caused it? We don't know anymore that the biologist who coined 'Junk DNA' knew. And we may never know, totally. But we're starting to learn that there's no such thing as totally useless--junk, in other words--DNA.

And I'm still confused by your OP, particularly when you said this:

I think, on the other hand, that people in general have a very hard time abandoning a view of their own place in the world as an inherently privileged one - that the world I can know, is the world.


I still don't understand the correlation between that and non-coding DNA.
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Re: Junk DNA

Postby anon » Mon Dec 26, 2011 10:09 pm

lizbethrose wrote:And I'm still confused by your OP, particularly when you said this:

I think, on the other hand, that people in general have a very hard time abandoning a view of their own place in the world as an inherently privileged one - that the world I can know, is the world.


I still don't understand the correlation between that and non-coding DNA.

Well, Liz, since you insist on calling it "non-coding DNA" rather than "junk DNA", you seem to be leveling the same criticism as I am. The world doesn't revolve around me - I am not the center of the universe. I'm trying to take this criticism slightly farther than that, but it's no big deal.
"Distraction is the only thing that consoles us for our miseries, and yet it is itself the greatest of our miseries." - Blaise Pascal

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Re: Junk DNA

Postby tentative » Mon Dec 26, 2011 11:08 pm

anon wrote:
lizbethrose wrote:And I'm still confused by your OP, particularly when you said this:

I think, on the other hand, that people in general have a very hard time abandoning a view of their own place in the world as an inherently privileged one - that the world I can know, is the world.


I still don't understand the correlation between that and non-coding DNA.

Well, Liz, since you insist on calling it "non-coding DNA" rather than "junk DNA", you seem to be leveling the same criticism as I am. The world doesn't revolve around me - I am not the center of the universe. I'm trying to take this criticism slightly farther than that, but it's no big deal.

Anon, it isn't the words, it's the attitude that bristled your hair. I have no problem poking holes in the arrogance balloon, but the words don't bother me. There has to be a middle ground somewhere. The word junk doesn't have to be arrogant dismissal. It simply means I can see no apparent use for it right now. Like my pile of "good stuff" that I refer to as junk, maybe some day, some place... On a rare day in a rare state of mind, it is more than possible to find reverence for all that is. But in the day-to-days we make judgements, and those judgements are about our tiny little place in the universe. If I have heartburn, it isn't about the necessity of making judgements, it is making thoughtless judgements and projecting them onto the rest of the world.
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Re: Junk DNA

Postby lizbethrose » Tue Dec 27, 2011 7:50 am

My husband believes there's no such thing as 'junk.' "No 'thing' is junk." So he saves things--they may have a 'use' sometime in the future--and he's often been correct. On the other hand, he calls me a 'pack rat' because of what I save, because I save memories.

I think both points of view apply to DNA.
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Re: Junk DNA

Postby anon » Tue Dec 27, 2011 1:50 pm

tentative wrote:Anon, it isn't the words, it's the attitude that bristled your hair. I have no problem poking holes in the arrogance balloon, but the words don't bother me. There has to be a middle ground somewhere. The word junk doesn't have to be arrogant dismissal. It simply means I can see no apparent use for it right now. Like my pile of "good stuff" that I refer to as junk, maybe some day, some place... On a rare day in a rare state of mind, it is more than possible to find reverence for all that is. But in the day-to-days we make judgements, and those judgements are about our tiny little place in the universe. If I have heartburn, it isn't about the necessity of making judgements, it is making thoughtless judgements and projecting them onto the rest of the world.

To be honest, I never thought of people who use the term "junk DNA" as being either arrogant or dismissive. I'm not after people with bad attitudes. My own attitude is bad enough. I'm after something else.

What is the purpose of your heart? What is its function? And for whatever answer you provide... is it possible to undergo something like a paradigm shift (not necessarily in Kuhn's sense) and see that answer as utterly irrelevant? Perhaps some particular heart pumps blood to some particular brain. Does that necessarily imply that the function of the heart is to pump blood to the brain? The heart functions, and that is one thing that happens when it for a while when it functions in a particular way (we call it "alive" when it functions in that particular way).

Are "your" DNA really yours? Perhaps they have some function that has nothing to do with you. Is a parasite in your body yours? What is the difference? Is the difference that the parasite has a level of independence from your body? But, then, so does your heart. It can be transplanted. Is it that the parasite supposedly doesn't contribute to the health of your body? But, then, the bacteria in the yogurt you eat does contribute to the health of your body.

So some theist may come along all excited and say yes, yes, it's true! Everything has its purpose, nothing is junk! We just haven't discovered what the true function of some thing is yet! But nothing has a fixed function, that it was meant to work at. Everything that exists simply functions. Because everything that exists functions, but not in just one set way, the world is completely open and filled with possibility. Hearts can be transplanted, genes can be modified, habits can be changed. Theories can be modified. Walls can be seen as permeable, universes can be discovered. "Killer whales" can be seen as gentle, loving parents. Your own children can be seen as the vicious killers that they sometimes are.

This thread is about teleological thinking in science. It's about the tendency of people to think teleologically, even when there is no conscious mind posited as the reason for natural events. I think this kind of thinking is so ingrained in people that they are blind to the fact that they are doing it, and say things like "it's just words". When the Wikipedia article says of "junk DNA", "much of it may indeed be without function", I detect really, really, bad science.

Unless... somebody makes a good argument for such a view. I kind of wish somebody would, so I don't have to. I think Tab is capable, with his recursiveness argument. For instance...

[Gödel, Escher, Bach] is a very personal attempt to say how it is that animate beings can come out of inanimate matter. What is a self, and how can a self come out of stuff that is as selfless as a stone or a puddle?"

Hofstadter seeks to remedy this problem in I Am a Strange Loop by focusing and expounding on the central message of Gödel, Escher, Bach. He demonstrates how the properties of self-referential systems, demonstrated most famously in Gödel's Incompleteness Theorem, can be used to describe the unique properties of minds.

Would human hearts exist without their function as a support for human "selves"? Things don't just develop in vaccuums. They develop, grow, and change in support of something that doesn't seem to exist at all - i.e. a "self". Could "junk DNA" exist at all, in the absence of "things" that exist on a higher order?
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Re: Junk DNA

Postby anon » Tue Dec 27, 2011 1:53 pm

turtle wrote:anon---where do you want this thread to go?
there are some good posts and some junk posts..

I'm looking for some good back and forth on the subject.
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"The bombs we plant in each other are ticking away." - Edward Yang

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Re: Junk DNA

Postby Tab » Tue Dec 27, 2011 7:35 pm

Things don't just develop in vaccuums.


One word: Spandrel.
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Re: Junk DNA

Postby anon » Tue Dec 27, 2011 8:03 pm

Tab wrote:
Things don't just develop in vaccuums.


One word: Spandrel.

I know, I know... but are you agreeing with me that things that exist function, but don't have an inherent function or purpose? Or are you disagreeing with me and saying that something that exists "may indeed be without function" - or that the true purpose of any natural thing is of a mysterious nature (i.e. known only by God)? Exaptation doesn't happen in a vacuum. It also refutes the idea that natural things have a purpose. That is, unless God changes his mind.
"Distraction is the only thing that consoles us for our miseries, and yet it is itself the greatest of our miseries." - Blaise Pascal

"The bombs we plant in each other are ticking away." - Edward Yang

"To a fly that likes the smell of putrid / Meat the fragrance of sandalwood is foul. / Beings who discard Nirvana / Covet coarse Samsara's realm." - Saraha
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Re: Junk DNA

Postby Tab » Tue Dec 27, 2011 8:35 pm

There's also neutrality. If something - like junk DNA - costs nothing in particular to maintain in the genome, then its "purposeless" existence is not selected against - unlike microbal cases, where genome size forms a bottleneck during division.

I dunno Anon. It's cold, splitting logs in the backyard might serve you better than these hairs. I do not see the purpose in what you're doing at the moment, and yet, it exists. :-"
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Re: Junk DNA

Postby anon » Tue Dec 27, 2011 10:37 pm

Ok, dammit, I'm switching sides.

Nick Lane wrote:In his celebrated book Chance and Necessity, the committed atheist and Nobel Prize-winning molecular biologist Jacques Monod tackled the theme of purpose. Plainly, he said, it is pointless to discuss the heart without mentioning that it is a pump, whose function is to pump blood around the body. But that is to ascribe purpose. Worse, if we were to say that the heart evolved to pump blood, we would be committing the ultimate sin of teleology – the assignment of a forward-looking purpose, a predetermined end-point to an evolutionary trajectory. But the heart could hardly have evolved ‘for’ anything else; if it didn’t evolve to pump blood, then it is truly a miracle that it happened to become so fine a pump. Monod’s point was that biology is full of purpose and apparent trajectories, and it is perverse to pretend they don’t exist; rather, we must explain them. The question we must answer is this: how does the operation of blind chance, a random mechanism without foresight, bring about the exquisitely refined and purposeful biological machines that we see all around us?


source
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Re: Junk DNA

Postby Tab » Tue Dec 27, 2011 10:43 pm

Lol. There were plenty of proto-hearts that didn't pump blood. None of them stuck around long enough be observed though.

Evolution's like ice-sculpture, you only see the bits that stay.
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Re: Junk DNA

Postby anon » Tue Dec 27, 2011 10:47 pm

anon wrote:Ok, dammit, I'm switching sides.

Nick Lane wrote:In his celebrated book Chance and Necessity, the committed atheist and Nobel Prize-winning molecular biologist Jacques Monod tackled the theme of purpose. Plainly, he said, it is pointless to discuss the heart without mentioning that it is a pump, whose function is to pump blood around the body. But that is to ascribe purpose. Worse, if we were to say that the heart evolved to pump blood, we would be committing the ultimate sin of teleology – the assignment of a forward-looking purpose, a predetermined end-point to an evolutionary trajectory. But the heart could hardly have evolved ‘for’ anything else; if it didn’t evolve to pump blood, then it is truly a miracle that it happened to become so fine a pump. Monod’s point was that biology is full of purpose and apparent trajectories, and it is perverse to pretend they don’t exist; rather, we must explain them. The question we must answer is this: how does the operation of blind chance, a random mechanism without foresight, bring about the exquisitely refined and purposeful biological machines that we see all around us?


source

Sure, anon, but let's take this one step further...

Ernst Mayr wrote:"The Wood Thrush migrates in the fall in order to escape the inclemency of the weather and the food shortages of the northern climates."

"The Wood Thrush migrates in the fall and thereby escapes the inclemency of the weather and the food shortages of the northern climates."

If we replace the words ‘in order to escape’ by ‘and thereby escapes’, we leave the important question unanswered as to why the Wood Thrush migrates. The teleonomic form of the statement implies that the goal-directed migratory activity is governed by a program. By omitting this important message the second sentence is greatly impoverished as far as information content is concerned, without gaining in causal strength.

Mayr is most definitely mistaken in his assessment of the situation - he makes the mistake of turning the world as he understands it, into the world. His fear of impoverished science ironically prevents him from wanting to investigate the complexity of the real situation any further. This is an example of science as the search for solid ground, to the detriment of exploration and advancement.

Teleology in scientific explanations is a bad business.
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"The bombs we plant in each other are ticking away." - Edward Yang

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Re: Junk DNA

Postby hooper » Wed Dec 28, 2011 4:42 am

My daughter's doing her 4th year in Biology
and playing with genes.

One thing I hear is- only a few of the genes are
being expressed (proteins are being made from them).
The rest are tangled up like in a big knot and
not available for use. Like the other ninety-some percent.

But, even then, there are sequences where
there is just a sort sequence that repeats
hundreds of times. This is junk.

But there's other junk; portions and even
entire genes of old viruses make up a large
percentage of our genome. Some peoples carry much
more of that than others, apparently!

Interesting stuff.

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Re: Junk DNA

Postby marmite » Tue Jan 10, 2012 3:05 pm

hooper wrote:My daughter's doing her 4th year in Biology
and playing with genes.

One thing I hear is- only a few of the genes are
being expressed (proteins are being made from them).
The rest are tangled up like in a big knot and
not available for use. Like the other ninety-some percent.

But, even then, there are sequences where
there is just a sort sequence that repeats
hundreds of times. This is junk.

But there's other junk; portions and even
entire genes of old viruses make up a large
percentage of our genome. Some peoples carry much
more of that than others, apparently!

Interesting stuff.

john


Was thinking this topic would be along those lines too, that only about 4% of your DNA is functioning and the rest is made up of ancient retroviruses, dead formally functioning DNA (such as the DNA that made your tail grow) and possible your dead twins ovaries as well as abit of Neanderthal (if your eurasian) a whole host of possible internal mutations capable of making you crazy or paralyzed at any moment. Your non-junk DNA is functioning now in the sense of a drunk trying to do a rubiks cube in the dark. Its not really purpose driven, there are mathmatical sequences found all over nature, common designs that function most effectly in this earth bound environment. Just like sand flowing downwards in a timer. Infact, i don't even know what im trying to say here.
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Re: Junk DNA

Postby Calrid » Tue Jan 10, 2012 9:24 pm

marmite wrote:
hooper wrote:My daughter's doing her 4th year in Biology
and playing with genes.

One thing I hear is- only a few of the genes are
being expressed (proteins are being made from them).
The rest are tangled up like in a big knot and
not available for use. Like the other ninety-some percent.

But, even then, there are sequences where
there is just a sort sequence that repeats
hundreds of times. This is junk.

But there's other junk; portions and even
entire genes of old viruses make up a large
percentage of our genome. Some peoples carry much
more of that than others, apparently!

Interesting stuff.

john


Was thinking this topic would be along those lines too, that only about 4% of your DNA is functioning and the rest is made up of ancient retroviruses, dead formally functioning DNA (such as the DNA that made your tail grow) and possible your dead twins ovaries as well as abit of Neanderthal (if your eurasian) a whole host of possible internal mutations capable of making you crazy or paralyzed at any moment. Your non-junk DNA is functioning now in the sense of a drunk trying to do a rubiks cube in the dark. Its not really purpose driven, there are mathmatical sequences found all over nature, common designs that function most effectly in this earth bound environment. Just like sand flowing downwards in a timer. Infact, i don't even know what im trying to say here.


Read those links I gave previously. There is evidence that non coding DNA can act to preserve important sections of DNA that are coding. In that case they need not code to have a function. It exists because if it is lost, then certain important coding genes become less likely to survive, providing a less "fit" genome overall.
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Oscar Wilde - probably.
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