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Author Topic:   The Bladderwort Test
Taq
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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:

http://phenomena.nationalgeographic.com/...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 2 of 25 (699213)
05-15-2013 7:17 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the The Bladderwort Test thread in the Proposed New Topics forum.
    
Coyote
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Posts: 6117
Joined: 01-12-2008


Message 3 of 25 (699216)
05-15-2013 7:40 PM


'Junk' DNA Mystery Solved: It's Not Needed
'Junk' DNA Mystery Solved: It's Not Needed
Tia Ghose, LiveScience Staff Writer
Date: 12 May 2013 Time: 01:00 PM ET

One person's trash may be another person's treasure, but sometimes, trash is just trash.

So-called junk DNA, the vast majority of the genome that doesn't code for proteins, really isn't needed for a healthy organism, according to new research.

"At least for a plant, junk DNA really is just junk it's not required," said study co-author Victor Albert, a molecular evolutionary biologist at the University of Buffalo in New York.

While the findings, published Sunday (May 12) in the journal Nature, concern a carnivorous plant, they could have implications for the human genome as well. Genes make up only 2 percent of the human genome, and researchers have argued in recent years that the remaining 98 percent may play some hidden, useful role.

More...

http://www.livescience.com/...9-junk-dna-mystery-solved.html


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

Belief gets in the way of learning--Robert A. Heinlein

How can I possibly put a new idea into your heads, if I do not first remove your delusions?--Robert A. Heinlein

It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers


  
caffeine
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(1)
Message 4 of 25 (699229)
05-16-2013 4:40 AM
Reply to: Message 1 by Taq
05-15-2013 6:21 PM


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've heard to argued that a lot of 'Junk DNA' may serve a function in the sense that it keeps particular parts of coding DNA distant from each other. The DNA of the bladderwort may have evolved a particular formation that meant most of this DNA could be safely removed without harm, but this doesn't mean you could do the same thing to another organism's DNA - since it may require a different formation to function effectively.

By analogy, we could point to the fact that the tail has shrunk to a vestigial remnant of its former self in ape evolution. We would not be justified in concluding from this that tails are an irrelevance with no function in the animals that still possess them.


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Percy
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Message 5 of 25 (699237)
05-16-2013 7:43 AM
Reply to: Message 4 by caffeine
05-16-2013 4:40 AM


caffeine writes:

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.

What might help test the theory that "junk" DNA doesn't do anything is to see if it usually corresponds to regions of rapid evolution, indicating an area not subject to selection. By "rapid evolution" I mean that the rate of change is roughly equal to the rate of copying errors. What they call the molecular clock should run at a much faster rate in non-functional regions.

Of course, if its function is to act as spacers this won't help, but at least theoretically this, too, is possible to study, say, by somehow excising "junk" DNA regions and studying the effects.

--Percy


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AZPaul3
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(2)
Message 6 of 25 (699239)
05-16-2013 8:30 AM
Reply to: Message 4 by caffeine
05-16-2013 4:40 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.

Better yet we could do this with a human genome. A republican one would help keep the horror to a minimum since it could be argued that republicans show no signs of being sentient beings.

Mengele would be so proud of me.

Edited by AZPaul3, : cuz


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Dr Adequate
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Message 7 of 25 (699240)
05-16-2013 9:52 AM
Reply to: Message 6 by AZPaul3
05-16-2013 8:30 AM


As I recall, this has been done with mice. They were fine.
This message is a reply to:
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Taq
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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.

http://www.ncbi.nlm.nih.gov/pubmed/15496924


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Taq
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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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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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AZPaul3
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From: Phoenix
Joined: 11-06-2006
Member Rating: 3.6


Message 11 of 25 (699250)
05-16-2013 11:35 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.

Mus musculus zombisus (frankenmouse)

But seriously, excising 0.1% is not much of a test when the present view is that more than half the genome is non-coding.

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?


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AZPaul3
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From: Phoenix
Joined: 11-06-2006
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(1)
Message 12 of 25 (699251)
05-16-2013 11:40 AM
Reply to: Message 10 by Taq
05-16-2013 10:54 AM



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.

I let the humor get the better of me. That was not a serious suggestion.


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Taq
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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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AZPaul3
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Posts: 4088
From: Phoenix
Joined: 11-06-2006
Member Rating: 3.6


(1)
Message 14 of 25 (699276)
05-16-2013 4:44 PM
Reply to: Message 13 by Taq
05-16-2013 11:54 AM


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

Your are quite correct.

I keep forgetting that you do not have to look at the gene itself through mixing it in a bunch of chemicals to see what falls out the bottom anymore. These things are transcripted in data files in raw ATCG format. Computer programs then are used to search the files for specific sequences (known sequences from other genomes) or using AIs to identify likely novel sequences.

It gets quite complex.

Gene finding Strategies

And then this popped up:

quote:
Even the concept of a 'gene' is under revision. Genes have long been regarded as discrete entities located linearly along chromosomes, but recent investigations have demonstrated extensive transcriptional overlap between different genes. Specifically, genomic regions from otherwise distinct and apparently well characterized protein-coding loci (which may be very far apart in linear genomic space) often appear to combine to produce transcripts with the potential for encoding novel protein species.

source

Now even a gene may not be just its own gene but part of several different genes using this specific sequence.

Cool.

Edited by AZPaul3, : cuz


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sfs
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Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 15 of 25 (699292)
05-16-2013 10:11 PM
Reply to: Message 6 by AZPaul3
05-16-2013 8:30 AM


quote:

Clone a chimp that has had its genome stripped of, let's say, half the identified junk DNA

A problem with this kind of thought experiment is that there really isn't such a thing as "identified junk DNA". What is identified is functional DNA, along with a rough estimate of how much of the total is functional.
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