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Author Topic:   The Bladderwort Test
Mac_townie
Junior Member (Idle past 3843 days)
Posts: 1
From: Greenbelt, MD
Joined: 04-09-2013


Message 16 of 25 (699301)
05-17-2013 8:05 AM
Reply to: Message 1 by Taq
05-15-2013 6:21 PM


Virus infections?
Taq writes:
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.
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.
Obviously, I am not a biologist. So, I don't know how a bladderwort reproduces or if that method of reproduction is more or less susceptible to being affected by viral infections than vertebrates or onions.

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 Message 1 by Taq, posted 05-15-2013 6:21 PM Taq has replied

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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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 Message 18 by Dr Adequate, posted 05-18-2013 10:29 AM Taq has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 18 of 25 (699384)
05-18-2013 10:29 AM
Reply to: Message 17 by Taq
05-17-2013 9:27 AM


Re: Virus infections?
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.
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?

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 Message 17 by Taq, posted 05-17-2013 9:27 AM Taq has replied

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 Message 20 by Taq, posted 05-20-2013 10:52 AM Dr Adequate has not replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


Message 19 of 25 (699392)
05-18-2013 12:50 PM
Reply to: Message 18 by Dr Adequate
05-18-2013 10:29 AM


Re: Virus infections?
Am I missing something?
Yes. You're missing the possibility that Taq may have momentarilly slipped a cog and relayed a picture to us that was not same one in his mind.

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Taq
Member
Posts: 9972
Joined: 03-06-2009
Member Rating: 5.5


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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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 21 of 25 (699469)
05-20-2013 11:43 AM
Reply to: Message 20 by Taq
05-20-2013 10:52 AM


The Odds
Of course, I could be completely wrong about this.
I think you are. If you add "junk" to reduce the 75 % to 3 % you've made the target for a cosmic ray about 100 times bigger. The chances that one will hit the coding regions doesn't change -- they are just as big (or small) a target. Now the chances are much greater the ray will hit somewhere though are much higher. It's just that if the cosmic ray hits at all it is much more likely to hit a non coding region.
Sort of like if you are trying to avoid being hit by random street gunfire. You aren't a big target but you do have a chance of being hit. So you carry around a great huge barn door strapped to your back. Your chances of being hit in the body don't change but your (you and your door) chances of being hit change by a lot-- it's just that most of the hits will be to the barn door.

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NoNukes
Inactive Member


Message 22 of 25 (699471)
05-20-2013 12:15 PM
Reply to: Message 21 by NosyNed
05-20-2013 11:43 AM


Re: The Odds
If you add "junk" to reduce the 75 % to 3 % you've made the target for a cosmic ray about 100 times bigger.
That's true, but some agents don't act like cosmic rays. If you have an infectious agent that is going to attach to something, maybe having some 'blubber' does provide protection.

Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)
I would say here something that was heard from an ecclesiastic of the most eminent degree; ‘That the intention of the Holy Ghost is to teach us how one goes to heaven, not how the heaven goes.’ Galileo Galilei 1615.
If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass

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kalimero
Member (Idle past 2444 days)
Posts: 251
From: Israel
Joined: 04-08-2006


Message 23 of 25 (703262)
07-17-2013 10:41 AM


A clarification about transposable elements
Transposable elements are found in every living organism, usually represent a large fraction of the genome and
are correlated with genome size.
They are classified into many groups and contribute to genetic and epigenetic variability in the genome (also this and this and this), which is important for evolution, as it drives speciation.
They are thought not to contribute to fitness (or to contribute negatively), but that is not to say that they don't take part in the evolution of a species. Thus, I think that whether or not they are functional (and some are, constituting the promoter regions or fine-tuning certain genes through RNAi) they still contribute to the diversification of life, which makes them "important" (I guess).

  
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 24 of 25 (703311)
07-18-2013 3:51 AM


Cell size
Seeing this thread pop up again reminded me of something I read the other week, in a discussion of genome size in birds. Birds, apparently, have smaller genomes on average than mammals, and I read posited somewhere that this was about weight reduction for flight. Whilst this idea was dismissed as silly, since the total weight of all an organism's DNA doesn't amount to much, it was pointed out in response that birds have smaller cells than mammals, and that cell size correlates very well with genome size.
Is it this simple? Is the size of a genome just a matter of how much space there is in the cell? Are there mechanical reasons to do with DNA function why a bigger cell would need the coding regions more spread out?

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kalimero
Member (Idle past 2444 days)
Posts: 251
From: Israel
Joined: 04-08-2006


Message 25 of 25 (703375)
07-20-2013 9:03 AM
Reply to: Message 24 by caffeine
07-18-2013 3:51 AM


Re: Cell size
From Sarah P. Otto (2007):
"Although cell size typically is larger in polyploids, adult size may or may not be altered; as a rough generalization, polyploidization is more likely to increase adult body size in plants and invertebrates than in vertebrates (Gregory and Mable, 2005; Otto and Whitton, 2000).
The poor correlation between cell size and organismal size was even remarked upon by Albert Einstein, who wrote Most peculiar for me is the fact that in spite of the enlarged single cell the size of the animal is not correspondingly increased (Fankhauser, 1972). The key to accurately predicting the effects of ploidy on body size must come from developmental biology. In cases where
morphogen gradients guide development, ploidy need not affect adult body size (Day and Lawrence, 2000) because ploidy need not alter the overall density of cellular material, only how it is packaged (i.e., into cells that are twice as large and carry twice as much DNA). By contrast, where growth is determined by cell-cell interactions or where there is a fixed number of cells in the adult, ploidy, by altering cell size, should directly influence adult size (Gregory et al., 2000)."

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