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Carnivorous Plant Ejects Junk DNA
sciencehabit writes "The carnivorous humped bladderwort, found on all continents except Antarctica, is a model of ruthless genetic efficiency. Only 3% of this aquatic plant's DNA is not part of a known gene, new research shows. In contrast, only 2% of human DNA is part of a gene. The bladderwort, named for its water-filled bladders that suck in unsuspecting prey, is a relative of the tomato. The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life."
The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life.
False. Unsurprisingly, nowhere in the paper was this dubious claim even approached. Instead you can find this even in the summary:
However, extreme genome size reductions have been reported in the angiosperm family tree.
Emphasis mine. And then further into the actual paper:
Relaxed selection pressure for unnecessary functions probably led to gene losses, whereas in other cases, gene family expansions may have been promoted by selection. Evidence for localized selection on the U. gibba gene complement, however, does not provide support for the existence of genome-wide selective forces that might favour reduction of nonessential, non-coding DNA.
There would likely be no bladderwort had there been no junk DNA in its ancestral line and other findings point to such noncoded DNA as necessary for evolution.
I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations.
My work here is dung.
Too bad you passed up the "my junk ejecting DNA" opportunity for a cheap insightful comment.
THL phish sticks
Even when we begged him not to in front of people.
The cow says "Moo." The dog says "Woof." The Timothy says "Thanks, valued customer. We appreciate your input."
My understanding is that junk DNA is no longer a useful term because the DNA that isn't translated has been found to have structural and other epigenetic properties. I wonder if the complexity of mamallian vs. plant development plays a role here. Any biologists out there?
Koalas. They're telepathic. Plus, they control the weather. -Margaret
That's not junk: Those are comments!
This demonstrates only that organisms with little junk DNA can exist. To really demonstrate that "junk DNA" does nothing, someone needs to take an organism that has lots of junk DNA, sequence it, replace all the junk with the DNA equivalent of nulls, synthesize the new DNA, grow a new organism, and produce a few generations of it. Good project for Craig Venter.
There's a suspicion that "junk DNA", while currently turned off, sometimes gets turned on when mutation flips a bit, and this helps evolution along. An organism with little or no junk DNA may not evolve further, but can exist and reproduce just fine.
I believe a more prudent falsifiable hypothesis would run along the lines of (and I'm sorry, I'm only a software developer): Due to relaxed external selective pressures the bladderwort's RNA polymerase has become adept at writing coding errors to the 3% noncoded DNA during replication and this actually still serves a vital function -- especially if the bladderwort is to survive in a much larger window than a few generations.
As a biologist and software developer, I have a hard time understanding what you are trying to say here.
The carnivorous humped bladderwort...
Sounds like something from an episose of red Red Dwarf.
Only to idiots, are orders laws.
-- Henning von Tresckow
Um, where do you get those numbers? At least 76% of the non-coding human genome is transcribed -- to what end we cannot be certain in all cases, but the RNA transcripts from these often are fed back into gene expression and regulation. It's estimated that well over 50% of non-coding DNA is heavily conserved by evolutionary processes and contributes significantly to fitness.
Don't blame me, I voted for Baltar.
Junk for an individual. Not necessarily junk for the evolution of a species. This issue comes up in computer science too with genetic algorithms, pushing pressure to keep the encoding as compact as possible 'may' lead to the side effect of increasing the probability of being stuck on a local optima. There's a lot of math 'n stuff involved that can better be explained by experts, but here's the short version: let's say that a genetic algorithm engine has an individual settled for a local optimum with all the bits just right. But there's a possible mutation that could lead to finding a slope leading to a better optimum. Obviously there's the issue that the mutation is going to compromise something important, and you end up with a mutant with good potential but a weaker fitness score, so the mutation is more likely to be discarded. However, if there's non-functional bits in the individual, there's a higher chance that the mutant can score better by compromising something that wasn't in use to being with, hence non-functional coding genes having some use in the long run. Now this is a huge simplification on a complex matter, but this does come up.
I read TFA and all I got was this lousy cookie
I note that the little digital clock on my desk does not need a 1TB disk drive full of software in order to operate either.
Constructing a large mammalian brain complete with things like "instincts" might well make use of non-protein-coding information of some sort.
One thing about biology and the functioning of cells that you learn pretty quick is that "if it can happen then it probably does", and this is a very strong argument against writing off anything that appears to be conserved as "useless".
Simply finding an organism that itself has no need of other information simply says that it's not a universal requirement, and doesn't really tell you anything about whether other organisms might have found a use for it.
G.
Only 3% of this aquatic plant's DNA is not part of a known gene, new research shows. In contrast, only 2% of human DNA is part of a gene. ... The finding overturns the notion that this repetitive, non-coding DNA, popularly called 'junk' DNA, is necessary for life.
What's so difficult to understand? Obviously, when it actually finds itself in need of some junk DNA, it just eats up a few people. Isn't this called Just-in-Time in business management?
Ezekiel 23:20
I beg to differ with the "conclusion" that most DNA is "junk" DNA.
As we learn how DNA is used to create RNA, mRNA, siRNA, miRNA, circRNA, microRNA, etc - by folding, spindling, adapting to environmental messages and signals, we find that a lot of what you think is "junk" DNA is in fact ... NOT.
Some is, of course, but the conclusion is ... WRONG. Most of the actual junk is actually viral rewrites (true junk), but a lot of the other stuff is boostrap shifted code designed to handle various conditions that may or may not be present.
For example, if you take a drug that shuts down a primary biochemical pathway, the cells turn on a second biochemical pathway - which may or may not be optimized. If the secondary biochemical pathway is shut down by drugs or damage, a tertiary - conserved, usually evolutionarily conserved fallback from when you were a fish or ratlike creature - kicks in.
You think it's junk. It's just code that turns on when you mess with the program or force certain conditions to occur.
-- Tigger warning: This post may contain tiggers! --
That claim is seriously misleading. According to Wikipedia, the closest connection between the bladderwort and the tomato seems to be that both are asterids of clade euasterids I. As are all other solanaceae besides tomatos (e.g. potatos, tobacco, petunias), all other lamiales besides bladderwort (e.g. acanthus, olives, plantains - the little green plants not the bananas, verbena) and many other plants such as forget-me-nots or gentiana. Initially they even got the time of the evolutionary split wrong by a factor of 1000!
I guess the truth is that the tomato genome is exceptionally well known and the two species are close enough to make a comparison reasonable. And to quote from the actual original article's abstract: "Unexpectedly, we identified at least three rounds of WGD [whole genome duplication] in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis)."