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Author Topic:   The Bladderwort Test
Taq
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Joined: 03-06-2009
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Message 1 of 25 (699211)
05-15-2013 6:21 PM


In the evolution v. creationism/ID debate there have been many claims dealing with the importance of non-coding, non-regulatory DNA (aka "junk" DNA). Most recently, the ENCODE project has made the bold claim that 80% of the human genome has a function, if you define function so that it is nearly meaningless.
T. Ryan Gregory took another approach to this debate in what he called the "Onion Test". As it turns out, the onion genome is made up of 15 billion bases, about 5 times as many DNA bases as the human genome. So why does the comparatively simpler onion need 5 times more DNA than a human?
Well, now there is the Bladderwort test. As it turns out, the bladderwort genome is made up of a paltry 82 million bases which is just ~3% the size of the human genome. Coding genes make up a whopping 75% of the total bladderwort genome compared to just 1.5% in the human genome. The evolution of the bladderwort removed massive amounts of junk DNA, and the plant is doing just fine. You can read more here:
Flesh-Eating Plant Cleaned Junk From Its Minimalist Genome
So the real test for those who argue that junk DNA has important function is to explain why the bladderwort genome can work so well with almost all of the junk DNA removed.
Anyone?

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 Message 4 by caffeine, posted 05-16-2013 4:40 AM Taq has replied
 Message 16 by Mac_townie, posted 05-17-2013 8:05 AM Taq has replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 8 of 25 (699246)
05-16-2013 10:46 AM
Reply to: Message 7 by Dr Adequate
05-16-2013 9:52 AM


As I recall, this has been done with mice. They were fine.
Only ~2 million bases were removed from the mouse genome, and it also happened to be non-coding DNA that did have some conservation which could have indicated function. Like you say, there were unaffected.
Megabase deletions of gene deserts result in viable mice - PubMed

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 9 of 25 (699247)
05-16-2013 10:51 AM
Reply to: Message 4 by caffeine
05-16-2013 4:40 AM


There seems to be a bit of a leap of assumptions here. The claim is that, since this organism is doing just fine without all that non-coding DNA, it must not, therefore, serve any purpose in that organism. The conclusion doesn't really seem justified.
I would agree that we can not jump to the conclusion that the lost DNA served no function. What we can conclude is that whatever function it may have had it had very little impact on fitness when it was removed. Also, the complexity of the bladderwort is on par with plants that have thousands of times more DNA than it does, so we can also conclude that junk DNA is not required for morphological complexity.
I highly doubt that the evolutionary pathway leading to such a small genome in the bladderwort was a long one. From every indication, junk DNA was pared away from the genome in great swaths. What is more interesting is that the gene count is actually higher in the bladderwort than other species with larger genomes which could indicate that the extra genes are compensating for the function found in the lost junk DNA. That's about the only hope I see for those who want to argue for non-disposable function in junk DNA.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 10 of 25 (699248)
05-16-2013 10:54 AM
Reply to: Message 6 by AZPaul3
05-16-2013 8:30 AM


Given the new stem cell announcement yesterday we do have a way to resolve this issue.
Clone a chimp that has had its genome stripped of, let's say, half the identified junk DNA and see what kind of "thing" develops.
There are major bioethical problems with these types of experiments. Chimps and other great apes are given nearly the same considerations as humans where it concerns experimentation.
A much better candidate would be the zebrafish, or the mouse.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 13 of 25 (699254)
05-16-2013 11:54 AM
Reply to: Message 11 by AZPaul3
05-16-2013 11:35 AM


And a serious question: How do geneticists determine between coding and non-coding areas of the genome? Base pair repeats for 1000s of pairs? What else?
I am much more familiar with prokaryotes, but I would assume that gene detections is based on an upstream ribosome binding site, a recognizable promoter region, and intact reading frames. Eukaryotic genes will also have exon excision sites.
From what I understand, repetitive DNA is usually associated with non-coding DNA and is a common feature in transposons and retroviral sequence.
Edited by Taq, : No reason given.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 17 of 25 (699303)
05-17-2013 9:27 AM
Reply to: Message 16 by Mac_townie
05-17-2013 8:05 AM


Re: Virus infections?
Just a guess...perhaps the junk DNA helps minimize the effect on the next generation from viral infections of the reproductive cells.
More places for the virus to intrude on the DNA without corrupting coding genes could be an advantage for a species.
Not only retrovirus and transposon activity, but base substitutions and indels as well. One of the potential functions of "junk" DNA is to act as a sponge to soak up mutations.
Another interesting function is the use of junk DNA in immunity, but not in the way you may be thinking. Cells can actually expel their DNA and use it to trap pathogens:
"ETs consist of nuclear or mitochondrial DNA as a backbone with embedded antimicrobial peptides, histones, and cell-specific proteases and thereby provide a matrix to entrap and kill microbes and to induce the contact system."
Innate immunity turned inside-out: antimicrobial defense by phagocyte extracellular traps - PMC
But as you can see, none of these functions has a sequence specific function. Pretty much any sequence of DNA will do.
Edited by Taq, : No reason given.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 20 of 25 (699465)
05-20-2013 10:52 AM
Reply to: Message 18 by Dr Adequate
05-18-2013 10:29 AM


Re: Virus infections?
I don't see how that's meant to work. The mutation rate is usually given per base pair, and given the way in which copying errors occur, we might expect this choice of units to reflect the nature of that process. The "junk" would only "soak up" such errors if there were a fixed number of them per organism instead.
Am I missing something?
There are also environmental sources of mutagenesis, such as UV and chemical mutagens. If 75% of your genome is coding regions what are the chances that a stray cosmic ray will strike a coding region compared to a genome that is only 3% coding regions?
Of course, I could be completely wrong about this.

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