A "junk DNA" discussion

[Roy]

At least you showed a little class.

<No more rhymes now, I mean it!>

Anybody want a peanut?

Roy

[jordanriver]

How does this relate to junk DNA at all.

If anything, junk DNA is analagous to the dumpsters full of garbage left on a construction site after the building is done.

yeah, well, that's what they said about functional ncDNA/ncRNA at first, OFTEN. I guess you forgot POST 29:
"...previously considered 'junk' DNA..."
"...just thought to be 'junk' DNA..."
"...This so called "junk" DNA was thought to be evolution debris with no function..."
"...Pseudogenes have long been labeled as "junk" DNA, failed copies of genes that arise during the evolution of genomes. However...."
...I boldened those parts in POST 29, so you couldn't miss 'em, but I guess I didn't resize the font big enough after all.

...saaay, so, if they thought they had proof of Darwin's theory (common descent) in those examples, but those examples proved to be functional, then are the ones that are still left (where they haven't found function yet, or they haven't become functional yet) by default, proof of Darwin's theory while the funcion IS STILL UNKNOWN
....kind of like a 'Darwin of the Gaps' ?

"...If you want to claim that this 90% has function then you need to explain why we see no evidence of negative selection in those stretches of DNA..."

maybe you need to look again. A few cases are classified as neutrally evolving pseudogenes even though they are evolving (that means subjected to purifying selection)

I think you are ignoring the evidence that they are looking at.

What we see is that about 90% of the human genome is accumulating mutations at a rate consistent with neutral drift. If you want to claim that this 90% has function then you need to explain why we see no evidence of negative selection in those stretches of DNA. Either no mutation can change or do away with the important function that junk DNA has, or no mutations can occur in these stretches. Which is it?

ok, look, in your POST 21 , when I said "I don't know if 100% is argued for, but there is negative selection/purifying selection/, outside of conserved noncoding sequences.
at least that's what I've read..."

YOU replied:

"Yes, and that conserved sequence is included in the 10% of the human genome that is thought to have function."
POST 21

fine, I get it, ...so the negative/purifying selection doesn't count, because its from the ten percent that is now thought to be functional.
Now wait a minute, if I go to the trouble of finding negative selection in any of the other ninety percent, how do I know you won't just say, "ah , no, thats part of the 10% thats functional.

OR, if scientists find too many new functions in DNA/RNA that was thought to be "junk" from that 90% junk portion, ...
HOW DO I KNOW, that you won't just adjust your number and say, "Yes, and that sequence is included in the 15% of the human genome that is thought to have function."

IT WON'T BE THE FIRST TIME THE NUMBER GOT CHANGED:

It used to be 2% (since 98% was non-coding)
and the scientists said that if the DNA was non-coding, then it was "pseudogene"/"junk"/"no known biological function...

...Jerry Coyne said it in 2009, that if non-coding, then its junk:

'WHY EVOLUTION IS TRUE' Jerry Coyne ISBN 9780670020539
p 67
"We expect to find, in the genomes of many species, silenced, of "dead," genes: genes that once were useful but are no longer intact or expressed. In other words, there should be vestigial genes. In contrast, the idea that all species were created from scratch predicts that no such genes would exist, since there would be no common ancestors in which those genes were active.
Thirty years ago we couldn't test this prediction because we had no way to read the DNA code. Now, however, it's quite easy to sequence the complete genome of species, and it's been done for many of them, including humans. This gives us a unique tool to study evolution when we realize that the normal function of a gene is to make a protein--a protein whose sequence of amino acids is determined by the sequence of nucleotide bases that make up the DNA. And once we have the DNA sequence of a given gene, we can usually tell if it is expressed normally--that is, whether it makes a functional protein--or whether it is silenced and makes nothing. We can see, for example, whether mutations have changed the gene so that a usable protein can no longer be made, or whether the "control" regions responsible for turning on a gene have been inactivated. A gene that doesn't function is called a pseudogene.
And the evolutionary prediction that we'll find pseudogenes has been fulfilled--amply. Virtually every species harbors dead genes, many of them still active in its relatives. This implies that those genes were also active in a common ancestor, and were killed off in some descendants but not in others. Out of about thirty thousand genes, for example, we humans carry more than two thousand pseudogenes. Our genome--and that of other species--are truly well populated graveyards of dead genes."

...hmmm, ...I think Jerry's numbers are off, though...:

A GENOME-WIDE SURVEY OF HUMAN PSEUDOGENES Dec 2003
"We identified ~20,000 pseudogenes in the human genome. The strategy used in this study ensures that each pseudogenic region represents a single event of gene or exon duplication and that regions matching up to the same protein are fused. Therefore, the number of regions should correspond to the number of (pseudo)-genes in between annotated genes. Nearly all of the regions appear as neutrally evolving and therefore nonfunctional according to their associated Ka/Ks values...
.......Although the discovery of almost 20,000 human pseudogenes represents the largest collection so far in any genome, the real number of human pseudogenes must be considerably higher. Our approach identifies neither pseudogenes derived from the duplication of non-protein-coding genes nor copies of partially retrotransposed mRNAs that include only the 3'-UTR and no (or little) coding region. The latter seems abundant in the genome....." (*UTR, that means untranslated region)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403797/

PZ MYERS says one and a half percent codes (@ 18 minutes, PLUS maybe 3% regulatory (@ 25:50 minutes), SO a total of about 5% is functional.
...of course at the end he hedges his bet in case more function is found
https://www.youtube.com/watch?v=DRsN7w7iW08

and RICHARD DAWKINS as recently as 2009 says 95% of our genome might as well not be there (that means the number was 5% before Method used the adjusted number):

THE GREATEST SHOW ON EARTH Richard Dawkins ISBN 9781416594789
p 332-333
"What pseudogenes are useful for is embarrassing creationists. It stretches even their creative ingenuity to make up a convincing reason why an intelligent designer should have created a pseudogene--a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something--unless he was deliberately setting out to fool us.
Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes. The neutral theory applies even to many of the genes in the remaining 5 per cent--the genes that are read and used."

even an AronRa video (AT 1 hour, eighteen minutes 1:18:00) cites 95% junk DNA, in his "Aronra The Foundational Falsehoods of Creationism -- Complete Series" video.
https://www.youtube.com/watch?v=bmQZ4f9f_Yw

AND James D. Watson said it in 2003 , and his number was 2%

DNA THE SECRET OF LIFE James D. Watson ISBN 0375415467
p 197-198
"...And remember, only about 2% of the human genome actually codes for proteins; the rest, unflatteringly referred to as "junk," is made up of apparently functionless stretches of varying length, many of which occur repeatedly. And junk can even be found strewn within the genes themselves; studded with noncoding segments (introns), genes can sometimes straddle enormous expanses of DNA, the coding parts like so many towns isolated between barren stretches of molecular highway."

and KENNETH MILLER in 1994 is one of the biologists who said DNA is junk if it is non-coding:

"The cluster itself, or more specifically a sixth b -globin gene, provides the answer. This gene is easy to recognize as part of the globin family because it has a DNA sequence nearly identical to that of the other five genes. Oddly, however, this gene is never expressed, it never produces a protein, and it plays no role in producing hemoglobin. Biologists call such regions "pseudogenes," reflecting the fact that however much they may resemble working genes, in fact they are not.
How can we be sure the sixth gene really is a pseudogene? Molecular biologists know that the expression of a gene like b -globin is a two-step process. First, the DNA sequence has to be copied into an intermediate known as RNA. That RNA sequence is then used to direct the assembly of a polypeptide, in this case, a b -globin. There is no evidence that the first step ever takes place for the pseudogene. No RNA matching its sequence has ever been found. Why? Because it lacks the DNA control sequences that precede the other 5 genes and signal the cell where to start producing RNA This means that the pseudogene is "silent." Furthermore, even if it were comehow copied into RNA, it still could not direct the assembly of a polypeptide. The pseudogene contains 6 distinct defects, any one of which would prevent it from producing a functional polypeptide. In short, this sixth gene is a mess, a nonfunctional stretch of useless DNA.
From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants of the past history of the b -globin genes.
The b -globin story is not an isolated one. Hundreds of pseudogenes have been discovered in the 1 or 2% of human DNA that has been explored to date, and more are added every month. In fact, the human genome is littered with pseudogenes, gene fragments, "orphaned" genes, "junk" DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design"
http://www.millerandlevine.com/km/evol/lgd/

now, back to original challenge

anyway, just so you don't say I listed all those examples of how the percentage evolves and adjusts, in order to get out of finding non-functional DNA that is selective
(although, this is trick wild-goose chase, because if it is selective, you can say, well that proves it was from functional part)

ok -- who cares, here goes:

this next paper acknowledges that there is selection in the CNSs (conserved noncoding sequences) are FUNCTIONAL REGIONS , yes we already know that........

ok , but it ALSO cites purifying selection in human noncoding sequences occurs OUTSIDE OF CNSs :

Widely distributed noncoding purifying selection in the human genome
"A major unanswered question is whether CNSs in the human genome accurately capture the distribution of functionally significant noncoding nucleotides, or, conversely, to what extent noncoding sites outside of CNSs are functionally significant in modern humans. Comparison of sequence divergence between species with population polymorphism provides a powerful approach for analyzing selective forces acting on genomic sequences (8, 11, 12).

Here, we apply human polymorphism data and divergence data from multiple species toward analyses of conservation and selection at nucleotide resolution in noncoding regions. The results suggest that a substantial fraction of the human noncoding genome is under active negative selection in modern populations, with much of the effect arising outside of CNSs.
http://www.pnas.org/content/104/30/12410.long

and not just humans
non-coding DNA creating new genes, NEW FUNCTIONS (2014) that are UNDER SELECTION:

New genes spring, spread from non-coding DNA
"The new genes showed evidence of being under selection, meaning that they were spreading through the population as flies carrying them gained an edge in reproduction. They fell into two broad classes: genes found at high frequency tended to be larger and more complex, and therefore likely had more significant functions, than those found at low frequency.

The researchers studied testis because earlier work showed a relatively high rate of adaptive evolution for male reproductive function, Begun said. They plan to expand their studies to other tissues.

Zhao said that it's possible that these new genes form when a random mutation in the regulatory machinery causes a piece of non-coding DNA to be transcribed to RNA.

"If it has a beneficial effect, then it gets selected," she said. It's difficult to say at this point how important this phenomenon is for generating new genetic material, Zhao said.
http://www.sciencedaily.com/releases...0123142029.htm

That sciencedaily piece cited NATURE, and in their abstract specify that the new genes derived from "ancestral intergenic, unexpressed" frames;

"Comparative genomic analyses have revealed that genes may arise from ancestrally nongenic sequence. However, the origin and spread of these de novo genes within populations remain obscure. We identified 142 segregating and 106 fixed testis-expressed de novo genes in a population sample of Drosophila melanogaster. These genes appear to derive primarily from ancestral intergenic, unexpressed open reading frames, with natural selection playing a significant role in their spread. These results reveal a heretofore unappreciated dynamism of gene content."
http://www.sciencemag.org/content/343/6172/769

"intergenic" regions are of "unknown function" , "dark matter" that means they aren't in the 'current' percentage of known functional non-coding DNA

Most "Dark Matter" Transcripts Are Associated With Known Genes
"Estimates of the proportion of transcripts that map to locations separate from known exons range from 47% to 80% and are distributrd approximately equally between introns and intergenic regions. Dubbed transcriptional "dark matter", the "hidden" transcriptome, or transcripts of unknown function (TUFs), the exact nature of much of this additional transcription is unclear, but it has been presumed to comprise a combination of novel protein coding transcripts, extensions of existing transcripts, noncoding RNAs (ncRNAs), antisense transcripts, and biological or experimental background..."
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872640/

(emphasis mine)

and 'Genome Biology' page referring to this NATURE paper refers to the intergenic regions as "Much of the "junk" DNA in Drosophila..."
http://genomebiology.com/2004/5/10/s...ht-20051026-01

also wiki cites this PLOS paper, that intergenic regions are AKA dark matter

[jordanriver]

correction, not NATURE, but SCIENCE MAG in that last citations

[Roy]

...saaay, so, if they thought they had proof of Darwin's theory (common descent) in those examples, but those examples proved to be functional, then are the ones that are still left (where they haven't found function yet, or they haven't become functional yet) by default, proof of Darwin's theory while the funcion IS STILL UNKNOWN

Science doesn't deal in proof, only in supporting evidence and disproof. If anyone, anywhere, stated they had proof of Darwin's theory, they were wrong. By definition. Period.

Which suggests that either those people you are referring to weren't scientists, or they didn't make the claims you are ascribing to them. Either way, nothing you have said here is relevant to the actual scientific claims.

Roy

[klaus54]

Science doesn't deal in proof, only in supporting evidence and disproof. If anyone, anywhere, stated they had proof of Darwin's theory, they were wrong. By definition. Period.

Which suggests that either those people you are referring to weren't scientists, or they didn't make the claims you are ascribing to them. Either way, nothing you have said here is relevant to the actual scientific claims.

Roy

Roy,

You have to realize that JR is an exceedingly confusing person.

She/he admits there's no micro/macro boundary, yet believes that evolution is restricted to within-kinds (with no way of defining what a "kind" IS), uses scare quotes around "science" when he/she cites (the misused term) Darwinism, and now makes manifest that she/he misunderstands scientific method through his/her use of "proof".

The sheer beauty of Creationism is that it can explain ANYTHING and NOTHING simultaneously.

K54

[jordanriver]

Science doesn't deal in proof, only in supporting evidence and disproof. If anyone, anywhere, stated they had proof of Darwin's theory, they were wrong. By definition. Period.

Which suggests that either those people you are referring to weren't scientists, or they didn't make the claims you are ascribing to them. Either way, nothing you have said here is relevant to the actual scientific claims.

Roy

hello Roy. This reply is for Klause54

you are replying to the part where I said

".......saaay, so, if they thought they had proof of Darwin's theory (common descent) in those examples, but those examples proved to be functional, then are the ones that are still left (where they haven't found function yet, or they haven't become functional yet) by default, proof of Darwin's theory while the funcion IS STILL UNKNOWN
....kind of like a 'Darwin of the Gaps' ?.........."

that microscopic segment of that very big post was A WISECRACK

one can tell by how I ended that microscopic segment, with the WISECRACK PUNCHLINE "kind of like a 'Darwin of the Gaps'

any normal person should have been able to discern that that was A WISECRACK, not the serious part.


....I guess I had better search the emoticons for a "this is for the sarcasm impaired", if ever I crack wise again.

[jordanriver]

Roy,

You have to realize that JR is an exceedingly confusing person.

K54

I think the problem is you.

[klaus54]

Maybe you're just too smart for me, JR.

I am an "evolutionist" afterall.

K54

[jordanriver]

Maybe you're just too smart for me, JR.

I am an "evolutionist" afterall.

K54

ok that was good cracking wise.

[klaus54]

ok that was good cracking wise.

Sorry.

I meant Darwinist.

Only stupid ignoramuses could be one of those.

K54

[Method]

yeah, well, that's what they said about functional ncDNA/ncRNA at first, OFTEN. I guess you forgot POST 29:
"...previously considered 'junk' DNA..."
"...just thought to be 'junk' DNA..."
"...This so called "junk" DNA was thought to be evolution debris with no function..."
"...Pseudogenes have long been labeled as "junk" DNA, failed copies of genes that arise during the evolution of genomes. However...."
...I boldened those parts in POST 29, so you couldn't miss 'em, but I guess I didn't resize the font big enough after all.

Yes, we all know how creationists use out of context quotes. The problem is that you refuse to deal with the evidence.

1. Finding a function for a handful of transposable elements does not evidence function in the millions of other transposable elements. The same applies to the other categories of junk DNA.

2. You still can't explain why 90% of the human genome is accumulating mutations at a rate consistent with neutral drift.

maybe you need to look again. A few cases are classified as neutrally evolving pseudogenes even though they are evolving (that means subjected to purifying selection)

You need to look again. Look at that second sentence. You try to claim that a sequence is neutrally evolving while being subjected to purifying selection. Which is it? If it is subjected to purifying selection then it is not neutrally evolving.

You need to explain why 90% of the human genome is either,

1. functional but impervious to deleterious mutations, or . . .

2. protected from any and all mutations.

fine, I get it, ...so the negative/purifying selection doesn't count, because its from the ten percent that is now thought to be functional.
Now wait a minute, if I go to the trouble of finding negative selection in any of the other ninety percent, how do I know you won't just say, "ah , no, thats part of the 10% thats functional.

I will gladly accept any evidence you bring forward for function in the other 90% of the genome. No one is stopping you, or any ID/creationist for that matter. What is interesting is none of the so-called ID/creationism Iluminati are not doing these experiments. Why is that?

IT WON'T BE THE FIRST TIME THE NUMBER GOT CHANGED:

Then you have just proven that there is no dogma among geneticists where it concerns the percentage of junk DNA in genomes.

It used to be 2% (since 98% was non-coding)
and the scientists said that if the DNA was non-coding, then it was "pseudogene"/"junk"/"no known biological function...

...Jerry Coyne said it in 2009, that if non-coding, then its junk:

Except none of those things are actually said or claimed. As usual, creationists can't be relied on to honestly comment on the words of real scientists. Nowhere does Coyne claim that the amount of functional DNA is 2%. Nowhere does he claim that all non-coding DNA is junk.

this next paper acknowledges that there is selection in the CNSs (conserved noncoding sequences) are FUNCTIONAL REGIONS , yes we already know that........

No one is arguing that all non-coding DNA is without function. Finding function in some non-coding DNA does not evidence function in all non-coding DNA.

"intergenic" regions are of "unknown function" , "dark matter" that means they aren't in the 'current' percentage of known functional non-coding DNA

Can you explain why some intergenic regions are accumulating mutations at a rate consistent with neutral drift?

[Method]

Okay, so in this case that you've found in the bowels of history you could claim that my thesis is "wrong". Now show us where I said that EVERY Evolutionist believes the same (here that "junk" DNA represents "the remnants of an Evolutionary progression"). Another example would be that many Evolutionists accept the notion of Punctuated Equilibrium while many others do not. So?

The truth of the matter is that there is no dogmatic stance with respect to junk DNA. It just so happens that the evidence has stacked up on the side of junk DNA, so that is the conclusion that scientists have adopted until new evidence shows otherwise.

As sfs has shown, the theory of evolution is neutral as to the amount of DNA in any given genome. Different lineages will experience different selective pressures with respect to genome size.

The problem is that ID/creationists start with their conclusion that the majority of a genome should be functional, and no amount of evidence will budge them from that dogma. We show them that only 10% or less of the human genome is under purifying selection. Their response? Point to DNA in that 10% to make the outrageous claim that this function means that the other 90% is also functional . . . for no apparent reason.

Now, would you like to wager -- here in public and in writing -- that I could not find numerous articles/papers where (non-Creationist) PhD researchers explicitly state that "junk" DNA serves as evidence for an Evolutionary history?

Of course junk DNA can be used as a phylogenetic marker. So can functional DNA. A genome is a direct record of a species evolutionary history, be it functional or non-functional DNA. I really don't understand what your argument is in this case.

[jordanriver]

Yes, we all know how creationists use out of context quotes.

WRONG ANSWER.


I INCLUDED THE CONTEXT, PAL.


if anybody is interested, the post Method refers to was POST 29


Notice that the boldened parts are not alone in the citations, THE REST OF THE CONTEXT WAS THERE ALSO.


in the past I have had citations deleted for using too much context as far as that goes. But that is better than someone accusing me of quote mining.

[Method]

WRONG ANSWER.


I INCLUDED THE CONTEXT, PAL.

Show me the context where Kenneth Miller (1994) said that all non-coding DNA was junk as you claim in post 107.

[jordanriver]

Show me the context where Kenneth Miller (1994) said that all non-coding DNA was junk as you claim in post 107.

referring to POST 107

Referring to Ken Miller's page
http://www.millerandlevine.com/km/evol/lgd/

and KENNETH MILLER in 1994 is one of the biologists who said DNA is junk if it is non-coding:

"The cluster itself, or more specifically a sixth b -globin gene, provides the answer. This gene is easy to recognize as part of the globin family because it has a DNA sequence nearly identical to that of the other five genes. Oddly, however, this gene is never expressed, it never produces a protein, and it plays no role in producing hemoglobin. Biologists call such regions "pseudogenes," reflecting the fact that however much they may resemble working genes, in fact they are not.
How can we be sure the sixth gene really is a pseudogene? Molecular biologists know that the expression of a gene like b -globin is a two-step process. First, the DNA sequence has to be copied into an intermediate known as RNA. That RNA sequence is then used to direct the assembly of a polypeptide, in this case, a b -globin. There is no evidence that the first step ever takes place for the pseudogene. No RNA matching its sequence has ever been found. Why? Because it lacks the DNA control sequences that precede the other 5 genes and signal the cell where to start producing RNA This means that the pseudogene is "silent." Furthermore, even if it were comehow copied into RNA, it still could not direct the assembly of a polypeptide. The pseudogene contains 6 distinct defects, any one of which would prevent it from producing a functional polypeptide. In short, this sixth gene is a mess, a nonfunctional stretch of useless DNA.
From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants of the past history of the b -globin genes.
The b -globin story is not an isolated one. Hundreds of pseudogenes have been discovered in the 1 or 2% of human DNA that has been explored to date, and more are added every month. In fact, the human genome is littered with pseudogenes, gene fragments, "orphaned" genes, "junk" DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design"
http://www.millerandlevine.com/km/evol/lgd/

and I believe you earlier said I took Jerry Coyne out of context and that he never claimed a 2% number,
EXCEPT I NEVER CLAIMED JERRY COYNE CLAIMED A PERCENTAGE,
...ONLY THAT IF NON-CODING, THEN ITS JUNK/PSEUDOGENE

from POST 107
...Jerry Coyne said it in 2009, that if non-coding, then its junk:

'WHY EVOLUTION IS TRUE' Jerry Coyne ISBN 9780670020539
p 67
"We expect to find, in the genomes of many species, silenced, of "dead," genes: genes that once were useful but are no longer intact or expressed. In other words, there should be vestigial genes. In contrast, the idea that all species were created from scratch predicts that no such genes would exist, since there would be no common ancestors in which those genes were active.
Thirty years ago we couldn't test this prediction because we had no way to read the DNA code. Now, however, it's quite easy to sequence the complete genome of species, and it's been done for many of them, including humans. This gives us a unique tool to study evolution when we realize that the normal function of a gene is to make a protein--a protein whose sequence of amino acids is determined by the sequence of nucleotide bases that make up the DNA. And once we have the DNA sequence of a given gene, we can usually tell if it is expressed normally--that is, whether it makes a functional protein--or whether it is silenced and makes nothing. We can see, for example, whether mutations have changed the gene so that a usable protein can no longer be made, or whether the "control" regions responsible for turning on a gene have been inactivated. A gene that doesn't function is called a pseudogene.
And the evolutionary prediction that we'll find pseudogenes has been fulfilled--amply. Virtually every species harbors dead genes, many of them still active in its relatives. This implies that those genes were also active in a common ancestor, and were killed off in some descendants but not in others. Out of about thirty thousand genes, for example, we humans carry more than two thousand pseudogenes. Our genome--and that of other species--are truly well populated graveyards of dead genes."

looks PRETTY PLAIN to me.