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Junk DNA Refuted

The existence of large amounts of non-coding DNA (up to 97% in humans) in the genomes of eukaryotes has been used as an argument against intelligent design (and the role of a Creator) and as an argument for the random process of evolution. However, a recent study13 has shown that eukaryotic non-coding DNA (also called "secondary DNA") is functional as a structural element in the nucleus. Previously, there were two evolutionary theories that attempted to describe the reason for the existence of non-coding DNA One theory stated that non-coding DNA was "junk" that consisted of randomly-produced sequences that had lost their coding ability or partially duplicated genes that were non-functional. The second theory stated that non-coding DNA was "selfish", in that it consisted of DNA that preferentially replicated more efficiently that coding DNA, even though it provided no selective advantage (in fact was somewhat detrimental in that it was parasitic).
The new study examined the genomes of the single-celled photosynthetic organisms know as Crytomonads. These organisms exist as vastly different cell sizes, with the nucleus being proportional in size to that of the cell. Researchers discovered that the amount of non-coding DNA was proportional to the size of the nucleus, suggesting that more non-coding DNA was required in larger nuclei. As an added proof, the nucleomorph, a small piece of DNA contained within the plastid that codes for itself and photosynthetic function, was not changed in size, despite changes in cell size and nuclear content.
The new study is a stunning rebuttal to the evolutionary theories that attempt to discredit design and promote concepts such as "junk" DNA and "selfish" DNA.

According to the authors:

"Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA"


Beaton, M.J. and T. Cavalier-Smith. 1999. Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonal genomes. Proc. R. Soc. Lond. B. 266:2053-2059.

http://www.evidence.info/design/designgonebad.html#junk
 

D. Scarlatti

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Full abstract:

Genic DNA functions are commonplace: coding for proteins and specifying non-messenger RNA structure. Yet most DNA in the biosphere is non-genic, existing in nuclei as non-coding or secondary DNA. Why so much secondary DNA exists and why its amount per genome varies over orders of magnitude (correlating positively with cell volume) are central biological problems. A novel perspective on secondary DNA function comes from natural eukaryote-eukaryote chimaeras (cryptomonads and chlorarachneans) where two phylogenetically distinct nuclei have coevolved within one cell for hundreds of millions of years. By comparing cryptomonad species differing 13-fold in cell volume, we show that nuclear and nucleomorph genome sizes obey fundamentally different scaling laws. Following a more than 125-fold reduction in DNA content, nucleomorph genomes exhibit little variation in size. Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA. Cryptomonad nuclear DNA content varied 12-fold: as in other eukaryotes, larger cells have extra DNA, which is almost certainly secondary DNA positively selected for a volume-related function. The skeletal DNA theory explains why nuclear genome size increases with cell volume and, using new evidence on nucleomorph gene functions, why nucleomorph genomes do not.

[Emphasis added]

So how does the presence of structural DNA, and in particular, the results of this study, support "design" and/or contradict evolution? Please explain.
 
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I'm going to grab a copy of that paper, but I want to share my first intuision. This papers appears to be saying that the 'amount' of junk DNA is sometimes important. That is well known possibility. However, it is also well known that there are selfish elements, pseudogenes, and other things that cannot be explained by any desiger that is supposed to be competant.
 
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Originally posted by npetreley


Apparently not. But let it sink in, and then be patient. It takes time to dig up dirt about the personal lives of people whose ideas you want to discredit.

LOL, too true.  At first I thought you were just comic relief Nick, but I am starting to see what you mean.
 
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D. Scarlatti

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Originally posted by s0uljah
Didn't you read my post?

Yes, I read "your" post (I'll charitably refer to it as "your" post, since you apparently wish to take credit for someone else's words - "you" didn't write any of it). Didn't you read "my" question?

Now, further to "your" post, I ask once again:

How does the presence of structural DNA, and in particular, the results of this study, support "design" and/or contradict evolution? Please explain.
 
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chickenman

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you do realise that if the primary role of the extra DNA is structural (to maintain the size of the nucleus) the sequence wouldn't need to be the same. It is however 98 percent homologous. You're going to have to find a role for the junk DNA which depends on its sequence, before you can say that intelligent design has solved this problem
 
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Okay I read the Beaton & Cavalier-Smith paper over lunch and here are some brief comments.

The paper does not find a function in junk DNA. It is refered to as functional because the amount of DNA (primary plus secondary) has selectable effects on the phenotype of the cell. It isn’t some found function of secondary DNA, but rather a function for DNA period. Beaton & Cavlier-Smith (1999) is attempting to identify the selection pressures that lead to genome expansion. Thus anyone attempting to use this paper as evidence against evolution has a flawed argument. Basically, they are ignoring, either by deception or ignorance, the conclusions of the authors, which deal with the evolutionary aspects of genome size. This is readily apparent to just about anyone reading this paper. If anyone here, (s0uljah, npetreley, etc.) wants to contest my understanding of this paper, I invite you to get a copy and read it yourself. The paper is available free from the following link.

Beaton & Simth (1999)

This paper uses a class of related organisms that have two sets of DNA: one in the nucleus and the other in the “nucleomorph.” This is because these organisms are the result of a symbiotic fusion of a red alga with a biflagellate host, several hundred million years ago. The nucleus of the biflagellate host has been maintained, whereas the red alga has lost most of its DNA and nucleus. The nucleomorph is all that remains of the red alga’s nucleus. The morphology of these organism is a good argument against intelligent/common design, since the chloroplasts are inefficiently placed inside an extra membrane. Plants and algae don’t have this odd organelle-within-an-organelle configuration. If these creatures are the result of scient design, then it is not a very good one with respect to organization. Furthermore, the differences in chloroplast placement imply that the same scient designer is not responsible for plants/algae and cryptomonads, since there isn’t a common design there.

More info on cryptomonads:
http://www.wikipedia.com/wiki/Cryptomonads
http://www.talkorigins.org/faqs/evolution-research.html#endosymbiosis

Now back to the paper. Here is a section of the paper with discusses various attributes of secondary DNA. It is good background information for those who don’t want to read the paper.

Although it us widely assumed that mutational explanations, specifically the selfish DNA hypothesis, can explain the existence of so much non-Coding DNA (Maynard Smith & Szathmary 1997), comparative evidence strongly indicates that only a small fraction of secondary DNA in nuclei (e.g. most transposons) is simply genetically parasitic. A significant fraction of non-coding DNA, notably introns (Cavalier-Smith 1978, 1985d) and dispersed repetitive sequences (e.g. Alu repeats, L1 elements), is likely to be ‘selfish’ in origin (Cavalier-Smith 1985e), but is today predominantly not actively spreading genetic parasites. As ex-selfish DNA, their maintenance and persistence in the genome must be explain in the same way as other non-coding DNA. Most secondary DNA must be either neutral junk or functional.

Let’s look at the interpretation offered by the website in s0uljah’s post:

The new study is a stunning rebuttal to the evolutionary theories that attempt to discredit design and promote concepts such as "junk" DNA and "selfish" DNA.

What is interesting after I read this paper is that the above interpretation is found no where in the paper and is not supported by it. It takes a rather far stretch to justify the above interpretation using the actual study. In fact the paper has nothing to do with design, pro or con. It is only testing between three evolutionary theories, finding two insufficient to explain the observations. It confirmed that the third evolutionary explanation is the only one that explains the data. Since it shows that there is an explanation from evolutionary theory that stands up with all the data, it is amazing how the webpage can even claim that evolution has been discredited here. In no way has this paper supported any concept of design or anti-evolution beliefs.

The quote that the website offers up to support its claims is from the abstract of Beaton & Cavalier-Smith (1999).

Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA.

To a person who hasn’t read the paper carefully or even at all, the quote looks like it is saying that the authors have shown that there is no such thing as selfish or junk DNA. However, this is not this case, and the above quote is actually referring to the two hypotheses of why secondary DNA accumulates, not hypotheses of whether it does something or not.

Here are the three hypotheses:
  1. Secondary DNA accumulates because it is junk and there is no strong selection pressure against it: the ‘junk’ hypothesis.
  2. Secondary DNA accumulates because it is parasitic: the ‘selfish’ hypothesis.
  3. Secondary DNA accumulates because the mass of DNA directly determines nuclear volume and the nuclear volume is under selection: the ‘skeletal’ hypothesis.

Using cryptomonads, the authors looked at ratios of cell volume to the size of the nuclear genome and the nucleomorph genome. What they found is that the size of the nuclear genome scaled up with the volume of the cell, but the size of the nuclemorph genome stayed relatively constant. If in these organisms DNA accumulated because of the first or second hypotheses, then the nucleomorph’s genome should be affected just like the nucleus’s genome. Because this doesn’t happen, the authors argue (probably correctly) that the first and second hypotheses cannot account for the observations. The authors then showed how the third hypothesis accounted for both the scaling of the nuclear genome and the non-scaling of the nucleomorph genome. (Read the paper for more information.)

What the authors didn’t do is show that there is no such thing as selfish or junk DNA, only that selfish or junk attributes of secondary DNA aren’t enough to explain why it accumulates. Because the webpage posted by s0uljah is claiming that they did the former, it is fundamentally flawed by depending on an erroneous interpretation.

But you don’t have to take my word for it; the paper is freely available online for you to read. If you have problems understanding the more technical aspects of the paper, I’ll be glad to discuss it. Please read the primary literature for yourself and post your comments in this thread.
 
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It now appears that my link to the paper is dead. The Catchword site is still saying that it is free to access, but the access page for the paper itself does not. :confused:

Okay, here is the link to the paper on Pubmed. If Catchword gets its act in order, clicking on the "Catchword" picture at the link should take you to the paper.
 
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D. Scarlatti

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Thanks Rufus, but I was hoping sOuljah would respond. Too bad he won't.

Sadly, it's typical of creationist apologists to misrepresent the conclusions of individual papers to suit their agendas, sticking some ridiculous headline on top, such as "Junk DNA Refuted," which doesn't even make sense, let alone summarize the contents of the paper.

The "Fellows" at the Discovery Institute, who include the leading creationist luminaries William Dembski, Michael Behe, and Jonathan Wells, do it all the time.

Then of course the lay creationists post these bogus "interpretations" on discussion boards, as if they've just single-handedly toppled the evolutionary edifice, and then subsequently refuse to answer questions about it and ultimately abandon the thread they started.

I thought there was a proscription against "bearing false witness" in the Bible, but sometimes you'd never know it. The only defense against charges of "bearing false witness" is ignorance, I suppose. Whatever it is, it's a pretty sad state of affairs.
 
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D. Scarlatti

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Originally posted by s0uljah
I suggest you, along with your cohorts, give me some time to get to all of your petty dribble.

You started this thread, by appropriating someone else's specious claim. You were asked a simple question, twice, once yesterday at 05:17 PM, and once today at 12:36 AM. This makes three times. If you've had enough time to evade it, you've had enough time to answer it. Now Rufus has generously given you a headstart with his estimable summary of the entire paper's contents.

So where is the "petty dribble"?

I can only wade through so much manure in a day...I *do* have a life and other work to do...

Yes, I see you've been incredibly busy:

Thread: Analysing crazy eights for seebs

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Thread: Junk DNA Refuted

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Thread: Theory anyone?

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Hopefully sometime in the midst of the overwhelming demands of your schedule you can find a moment to quit whining and answer a simple question.
 
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Originally posted by s0uljah
I suggest you, along with your cohorts, give me some time to get to all of your petty dribble. I can only wade through so much manure in a day...I *do* have a life and other work to do...

S0uljah, such comments are uncalled for. I request that you follow the guidelines of ChristianForums when responding. The first rule is a good place to start.

"1. Be kind to your fellow poster. No name calling. No flame-inciting language."
 
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Originally posted by RufusAtticus


S0uljah, such comments are uncalled for. I request that you follow the guidelines of ChristianForums when responding. The first rule is a good place to start.

"1. Be kind to your fellow poster. No name calling. No flame-inciting language."

Shouldnt you say the same to Scarletti?
 
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Originally posted by s0uljah


Shouldnt you say the same to Scarletti?

I don't know. He didn't use fighting words instead of simply addressing the points raised, like you did.

Do you wish to respond to the points I have raised? The paper is available online.
 
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Originally posted by RufusAtticus


I don't know. He didn't use fighting words instead of simply addressing the points raised, like you did.

Do you wish to respond to the points I have raised? The paper is available online.

He didnt?  Lets look...

Then of course the lay creationists post these bogus "interpretations" on discussion boards, as if they've just single-handedly toppled the evolutionary edifice, and then subsequently refuse to answer questions about it and ultimately abandon the thread they started.

Not exactly being "kind" or non-inflamatory, is it?

I thought there was a proscription against "bearing false witness" in the Bible, but sometimes you'd never know it. The only defense against charges of "bearing false witness" is ignorance, I suppose. Whatever it is, it's a pretty sad state of affairs.

Oh, accusations of lying give me warm fuzzies too.
 
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D. Scarlatti

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Still too busy to answer, s0uljah? I think I'm beginning to understand why:

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to be continued ...
 
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D. Scarlatti

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Thread: Attn: Muslims

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Looks like you're going to have to come up with a better excuse for not addressing the question, s0uljah.

Remind me to bump this thread up next time you tell us you're "too busy" to answer a simple question.
 
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