Rethinking junk DNA

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Mefiante (July 17, 2009, 17:22:10 PM):
Mmm, where did you get this hypothesis? Who's idea is it? Could you perhaps point to any scientifically peer-reviewed articles stating this hypothesis. I am interested.
No, I’m afraid can’t cite you any papers off the top of my head. Nor should it be necessary to do so because it is plainly implicit in the concept and definition of “Junk DNA” (or here and here and here).

These facts are also NOT indicative of no intentional design or NO directed purpose either. Such claims are outside the scope of science.
I’m puzzled and intrigued. Not by the assertion itself (which is in any case wrong), but by your actually making it to begin with. If you really think that it is so, what on earth possessed you to initiate this topic here in the “Science and Technology” subforum!?

'Luthon64
rwenzori (July 17, 2009, 17:52:11 PM):
I’m puzzled and intrigued. Not by the assertion itself (which is in any case wrong), but by your actually making it to begin with. If you really think that it is so, what on earth possessed you to initiate this topic here in the “Science and Technology” subforum!?

Brilliant! LOL! ;D ;D

Remind me never to cross verbal swords with you!
Teleological (July 19, 2009, 19:47:01 PM):
Which facts have rendered which hypothesis useless?

The absence of facts. Please pay attention!

Ugh... which facts (or lack thereof) have made which hypothesis useless? Do elaborate on this hypothesis.

It is gratifying that you know this. What you do not seem to realise that if there were indications of design or directed purposes, science would have picked it up. Absence of evidence *is* evidence of absence. Not proof, perhaps not very strong evidence either, but evidence nonetheless.

Quote
Hold on, are you actually proposing that science can scientifically prove the presence of other minds? That is new. How do you think science can do that? Which methods would you put forward? Do elaborate on this wild idea of yours.
And what evidence in nature will yield evidence of other minds (other than human that is) for you? You do believe humans have minds don't you?

lol. I'm not sure you have one! I was not speaking about minds at all. re-read?

Indications of design or directed purposes implies the presence of a mind or minds that intentionally directed something. Like this :P:
You say science would have picked it up.
I will ask you again how you would propose science can scientifically prove the presence of other minds (other than human)? How do you think science can do that? Which methods would you put forward?

EDIT: it suddenly struck me that I know you and there is something that you hate. "I don't know"

How does this apply? Quite easily. By analogy if you will. We found an object. Is this object designed or not? The default position is "We don't know". To change this position we need evidence either way. Or, and I know this will kill you, it stays "We don't know"!

The onus of evidence resides on your shoulders, you claim design.

So... how about you apply your "I don't know" hypothesis to "junk DNA"?
How does this "I don't know" attitude hold with the hypothesis that:
"More or less neutral genetic junk that has accumulated through evolutionary processes over the history of the genotype because DNA rarely “trims the fat” so to speak."

While no peer-reviewed literature has been provided for this hypothesis, and no clear definition has been given for "neutral genetic junk", do you think this kind of attitude should be applied to genetic regions we do not fully understand yet?

Mmm, where did you get this hypothesis? Who's idea is it? Could you perhaps point to any scientifically peer-reviewed articles stating this hypothesis. I am interested.
No, I’m afraid can’t cite you any papers off the top of my head. Nor should it be necessary to do so because it is plainly implicit in the concept and definition of “Junk DNA” (or here and here and here).

Still no peer-reviewed literature about that hypothesis of yours? Come on, you can do better than wiki links.

These facts are also NOT indicative of no intentional design or NO directed purpose either. Such claims are outside the scope of science.
I’m puzzled and intrigued. Not by the assertion itself (which is in any case wrong), but by your actually making it to begin with. If you really think that it is so, what on earth possessed you to initiate this topic here in the “Science and Technology” subforum!?

Yes, it must be wrong because you said so right? But, let's not get too far off topic here.

More functions of "neutral genetic junk"...


'Junk' DNA Has Important Role, Researchers Find
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ScienceDaily (May 21, 2009) — Scientists have called it "junk DNA." They have long been perplexed by these extensive strands of genetic material that dominate the genome but seem to lack specific functions. Why would nature force the genome to carry so much excess baggage?
Mefiante (July 19, 2009, 21:08:15 PM):
Still no peer-reviewed literature about that hypothesis of yours? Come on, you can do better than wiki links.



Yes, it must be wrong because you said so right? But, let's not get too far off topic here.
No, thank you. You win. I’ll pass on all counts – in keeping with this thread’s ruling spirit of not answering questions, not reading supplied material, evasion, deflection and having next to nothing to offer.

'Luthon64
Teleological (July 20, 2009, 08:13:50 AM):
Still no peer-reviewed literature about that hypothesis of yours? Come on, you can do better than wiki links.



Yes, it must be wrong because you said so right? But, let's not get too far off topic here.
No, thank you. You win. I’ll pass on all counts – in keeping with this thread’s ruling spirit of not answering questions, not reading supplied material, evasion, deflection and having next to nothing to offer.

'Luthon64

That is a pity really. But.... more about "neutral genetic junk" ;D.

'Junk' DNA Proves To Be Highly Valuable
Quote
ScienceDaily (June 6, 2009) — What was once thought of as DNA with zero value in plants--dubbed "junk" DNA--may turn out to be key in helping scientists improve the control of gene expression in transgenic crops.


Quote
That's according to Agricultural Research Service (ARS) plant pathologist Bret Cooper at the agency's Soybean Genomics and Improvement Laboratory in Beltsville, Md., and collaborators at Johns Hopkins University in Baltimore, Md.

For more than 30 years, scientists have been perplexed by the workings of intergenic DNA, which is located between genes. Scientists have since found that, among other functions, some intergenic DNA plays a physical role in protecting and linking chromosomes. But after subtracting intergenic DNA, there was still leftover or "junk" DNA which seemed to have no purpose.

Cooper and collaborators investigated "junk" DNA in the model plant Arabidopsis thaliana, using a computer program to find short segments of DNA that appeared as molecular patterns. When comparing these patterns to genes, Cooper's team found that 50 percent of the genes had the exact same sequences as the molecular patterns. This discovery showed a sequence pattern link between "junk" and coding DNA. These linked patterns are called pyknons, which Cooper and his team believe might be evidence of something important that drives genome expansion in plants.

The researchers found that pyknons are also the same in sequence and size as small segments of RNA that regulate gene expression through a method known as gene silencing. This evidence suggests that these RNA segments are converted back into DNA and are integrated into the intergenic space. Over time, these sequences repeatedly accumulate. Prior to this discovery, pyknons were only known to exist in the human genome. Thus, this discovery in plants illustrates that the link between coding DNA and junk DNA crosses higher orders of biology and suggests a universal genetic mechanism at play that is not yet fully understood.

The data suggest that scientists might be able to use this information to determine which genes are regulated by gene silencing, and that there may be some application for the improvement of transgenic plants by using the pyknon information.

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