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."

Comments

No. Bad Conclusion. Bad.

[eldavojohn]

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.

Re:No. Bad Conclusion. Bad.

[gandhi_2]

Too bad you passed up the "my junk ejecting DNA" opportunity for a cheap insightful comment.

Yeah, I had a cousin who did that a lot too

[TWiTfan]

Even when we begged him not to in front of people.

Re:Yeah, I had a cousin who did that a lot too

[WillgasM]

Hands on the table, Andy.

junk dna

[bdabautcb]

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?

Re:junk dna

[Hatta]

Not all untranslated DNA has other properties. Some of it really does just exist because it's good at getting itself replicated. It's an open question how much non-coding DNA exerts regulatory effects and how much is actually junk. This paper indicates that in at least one eukaryote, 3% non-coding DNA is sufficient to regulate all the coding DNA.

If that holds in mammals (unlikely, but not out of the question), the vast majority of our non-coding DNA would still be "junk". Human DNA is 98% non-coding, or 2% coding. 3% of 2% is a rounding error here, so it would still be accurate to say the human genome is 98% "junk". If regulatory sequences outnumbered coding sequences 10:1 you're still looking at >75% of the human genome being "junk".

I don't think the concept of "junk" DNA is ever going to go away. Evolution would predict that sequences that are good at replicating themselves would accumulate in the genome, even if they don't do anything "useful". And random errors that accrue during copying will persist unless there's a mechanism to select against them. If we found that 100% of our DNA had a purpose, that would be a pretty strong argument against the theory of evolution.

The interesting question here is what selective forces drive this plant to excise unnecessary DNA, and what mechanism it uses to do this. Understanding that mechanism might lead to future gene therapies.

Re:junk dna

[presidenteloco]

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene? Is it actually handy to have these around to allow for rapid bigger changes of set of active genes than just a few small mutations in the active genes can do? It would seem that almost all such massive additions to what's active would be deleterious, but maybe they provide a safeguard against rapid change of environment. So how far off from "being coding" are these junk regions anyway, and does it ever happen that they get reactivated?

Re:junk dna

[Medievalist]

It's like this: If you have a big enough ego, everything you don't understand must be unimportant junk.

Putting this in perspective with the traditional slashdot car analogy: all parts of your car that are not also part of a bicycle are just junk. This bladderwort's a bicycle, a honey badger is a car, see?

I'm here to help.

Re:junk dna

[gr8_phk]

I don't think the concept of "junk" DNA is ever going to go away. Evolution would predict that sequences that are good at replicating themselves would accumulate in the genome, even if they don't do anything "useful".

No, no it wouldn't. I am a fan of taking simple logic like that and concluding "it must be in play", but there are other equally valid pieces of simple logic that it must compete (or be in equilibrium) with. One of those off the top of my head: Evolution would predict that an excess of junk DNA would be detrimental to the organism since the likelihood of a random mutation turning some of that junk into something harmful goes up with the amount of junk. Other mechanisms would be in play too like "too much replicating junk takes resources away from the necessary DNA". It's really hard to say how strong the influence of these factors is or how many more we haven't even thought of.

The only way to prove that the DNA is junk is to remove it and see if the organism still exhibits all the capabilities of the original. And even at that, you don't know if the junk happens to contain something useful only in rare circumstances. But I'd agree if said organism seemed normal and could produce several generations of offspring that seem normal, then we could say the removed DNA was mostly junk.

Re:junk dna

[the gnat]

If you have a big enough ego, everything you don't understand must be unimportant junk.

I think people read too much into the use of the word "junk", and attribute a pejorative meaning that wasn't necessarily intended. The best explanation I've seen (can't remember the source, sorry) was something along the lines of "junk is the stuff I keep in my attic; stuff I throw out is garbage." Biologists are in fact aware that non-coding parts of the genome can be essential, and there was never any presumption that anything we didn't understand was unimportant - however, how much of the non-coding DNA is genuinely necessary is an open question, and it's hard to find an obvious use for most of it. Clearly some complex organisms get along fine without it, so it's not unreasonable to view junk DNA primarily as a side effect of millions of years of evolution.

Re:junk dna

[Anachragnome]

"... Any biologists out there?"

Nope. They've all specialized.

Re:junk dna

[mattack2]

Evolution would predict that an excess of junk DNA would be detrimental to the organism since the likelihood of a random mutation turning some of that junk into something harmful goes up with the amount of junk.

But wouldn't evolution also predict that the junk DNA would stick around, because the multitude of random changes necessary to get rid of the junk DNA would have to confer other benefits, so as to give positive reinforcement for its survival?

Re:junk dna

[CrimsonAvenger]

But wouldn't evolution also predict that the junk DNA would stick around, because the multitude of random changes necessary to get rid of the junk DNA would have to confer other benefits, so as to give positive reinforcement for its survival?

Not necessarily. As long as the random changes are not contra-survival, there would be no particular impetus one way or the other.

Re:junk dna

[mattack2]

You're right, but what is the positive reinforcement for the removal of the junk DNA then? It seems to me like the "more junk DNA means more places for an error" effect would be dwarfed by the "general" positive/negative mutation process... Heck, isn't it possible for the junk DNA to mutate into being NON-junk? (Which I guess is what a mutation that causes cancer would be.)

Re:junk dna

[interkin3tic]

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene?

I have heard this suggestion before. One of my professors in fact mentioned that he's a bit nervous when getting vaccines because there's a chance some bit of retrovirus which incorporated into the genome millions of years ago might combine with the non-virulent vaccine to make a supervirus.

I'd estimate the chances of that happening are in the same ballpark as two seperate meteorites simultaneously smacking into your head from opposites sides, smooshing your brain out of your nose, so don't skip the vaccines...

Re:junk dna

[wierd_w]

You also have to balance in the safety that this offers, in regard to random gene insertions from virus infections.

In a "clean" genome, these random insertions can break biologically critical genes. With a large "junk" store, the injection and integration of the virus has a much lower chance of disrupting a vital cellular mechanism.

Re:junk dna

[Hatta]

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene?

Yes! Even if the junk DNA doesn't serve a functional purpose in an organism, keeping it around can increase genetic diversity and potentially increase the adaptability of the species as a whole. Many of our functional coding genes have incomplete copies known as pseudogenes stuck in random places in the genome. It is possible for these genes to get reactivated with the right mutations.

Re:junk dna

[camperdave]

You're right, but what is the positive reinforcement for the removal of the junk DNA then? It seems to me like the "more junk DNA means more places for an error" effect would be dwarfed by the "general" positive/negative mutation process... Heck, isn't it possible for the junk DNA to mutate into being NON-junk? (Which I guess is what a mutation that causes cancer would be.)

Yes, but consider, that if there is going to be an error, would you want it happening in essential DNA, or in junk DNA that doesn't do anything anyway? Sometimes hiding your tree in a forest is a good thing.

Re:junk dna

[climb_no_fear]

Thanks, I can't sleep now, thinking about those meteorites.

Re:junk dna

[Medievalist]

I dunno. When I was having this argument 20 years ago all the geneticists I was working with at the time were insisting that "junk DNA" was literally leftovers with no purpose.

As an information scientist, though, I knew this had to be incorrect. Absent a really strongly supported, well understood mechanism it's illogical to suppose that natural selection would overwhelmingly favor massive storage abuse. It's more reasonable to suppose that there's something going on that's completely off the radar. Remember the presence of any number of understood mechanisms - such as DNA coding proteins, for one - does not in any way prove there's no further function of DNA that you don't know about yet.

To once again resort to car analogies, motor oil serves as a lubricant, a corrosion preventative, and a means of heat transfer. All these functions are critically important, and discovering any one of them would not mean the others do not exist. If 98% of human DNA does not code for protein, that's a very strong indication that DNA serves additional unknown function(s). It's best to keep an open mind.

Re:junk dna

[turbidostato]

"Absent a really strongly supported, well understood mechanism it's illogical to suppose that natural selection would overwhelmingly favor massive storage abuse."

It's only evolution works just the other side around. Absent a really strongly unfitting characteristic of the junk DNA, it's not going to go anywhere. And, as an information scientist you already have the tools to discriminate one from the other: random wandering. You expect higher stability on pieces of DNA that do something useful than on those that are just junk left there... exactly as it seems to happen.

Re:junk dna

[infinitelink]

Your science is dated. That old thought about DNA having a ton of junk was based on an absence of evidence: there was on the one hand "the central dogma" (that actual term used in science and, as my genetics professor put it, still about the best had) that DNA-->RNA-->protein, and thus it was assumed we could cause transcription in a tube and if no protein resulted, it was assumed "it must be junk; evolution demands it!!!" But then animals started dying when experimental gene therapies targeted "junk" for insertions. Then incredibly powerful detection techniques started finding that pretty much every region tested would produce some kind of useful RNA (though the tricky part is that we can't really understand the epigentics and regulation well enough to be sure of results or that we are actually finding everything that would/could be produced in vivo). Then new principles were discovered, such that DNA transcripts aren't location-bound of a parallel RNA corresponding to the codons of DNA, but that transcribed RNAs are edited; then more were found that transcribed RNAs can actually be edited in multiple ways to produced very different products; then it was discovered that DNA itself can be read from different frames to produce altogether different transcriptions just by starting at different points...the genome as we now understand it is ULTRA efficient and polysemic along any given length or approximate area, and what people don't seem to get about "evolution" is that it would not predict "that sequences good at replicating themselves would accumulate...": that's an abuse of "evolution", which is misplaced: the mechanical processes known to act on DNA would predict that is possible. What is observed is that in a given organism the DNA extant is usually useful for something and that changes may/not break some useful in favor of another, which may/not be be an advantage/disadvantage for the individual in a given environment (under certain conditions). Disclosure: I actually had to leave my biology studies (got very sick and haven't had the opportunity to return). I studied these kind of things under Karoline Luger at CSU, an amazing genetics mind (https://en.wikipedia.org/wiki/Karolin_Luger), among others.

Re:junk dna

[Anonymous Coward]

If we found that 100% of our DNA had a purpose, that would be a pretty strong argument against the theory of evolution.

The interesting question here is what selective forces drive this plant to excise unnecessary DNA, and what mechanism it uses to do this.

So according to your statement the given plant is a strong argument against the theory of evolution?

Re:junk dna

[The_Noid]

In this specific case, my guess as a biotechnologist would be Nitrogen starvation. Carnivorous plants live in nitrogen poor areas, they only get nitrogen from the insects they catch. DNA replication requires quite a bit of nitrogen, so less DNA means the plant needs less nitrogen to copy a cell.

Re:junk dna

[Medievalist]

Your logic seems circular to me. You've stated the conclusion as a premise ("evolution works just the other side around") and you've used your definition of what you expect to happen as the means of evaluating what has happened ("do something useful" = "the only function of DNA we have so far discovered"). It's not possible to repeatably test your argument; so even if it's correct it's not really science, it's philosophy (or possibly religion).

Supposing there are additional functions of DNA other than coding proteins is a much simpler explanation, and furthermore it's never wise to create dogmas that blockade avenues for research. Bednorz and Muller (the guys who invented theoretically impossible high temperature superconductors) won the Nobel Prize and made a lot of money by keeping both their minds and their options open.

Re:junk dna

[LienRag]

Part of the junk DNA being (still hypothetic but very likely) virus DNA that merged with its host's, there is very little chance that it plays any role at all...

Re:junk dna

[cellocgw]

"... Any biologists out there?"

Nope. They've all specialized.

Didn't you mean "speciated" ? :-)

Re:junk dna

[turbidostato]

"You've stated the conclusion as a premise ("evolution works just the other side around")"

Nope. I didn't set conclusion as premise, evolution *does* in fact works the other way around, it is a premise (under this conversation constrains): random mutations happen all the time, if they produce a better fit, they get selected by means of higher offspring, if they are deletereal they get off the pool and if they are neutral, they simply accumulate. It's believed -and supported by experimentation, that random mutations on functional DNA tends to be bad more often than good. So when a mutation happens in a non-functional section it usually won't be deletereal, so it's going to be accumulated above the average for functional DNA, hence a testable prediction: intra-species DNA variation within non-functional sections of DNA will be higher than within functional segments.

"so even if it's correct it's not really science"

It is: I sustain an hypothesis (evolution goes from genes to phenotypes, not the other way around) and offer a prediction deducted from it (junk DNA will show higher random wandering than functional DNA). What's your hypothesis that:
a) better explains why junk DNA wanders away more than known to be functional.
b) offers an experiment that will render different results under your hypothesis than mine.

"Supposing there are additional functions of DNA other than coding proteins is a much simpler explanation"

No, it isn't, since it requieres a magic wand. Here, the null hypothesis is that DNA that after roughly 60 years of scrutiny seems to do nothing, in a way that perfectly fits into current theory, does in fact nothing. You prefer to think that something that seemingly does nothing, does nevertheless do something, your turn.

"it's never wise to create dogmas that blockade avenues for research"

That *is* phylosophy, I also read Khun or Feyerabend. But one thing is being open to criticise a theory (of course we can bet, and we should, that there are some functionality hidden in at least part of the so known junk DNA, and in fact we already give epygenetic/regulatory value to quite a lot of what was thought as junk DNA just a decade ago) and another quite different is ignoring the value of any given current theory without proper instrumentation -what else do you offer to your argument which basically can be simplified to "nature is wise and that looks like an unwise waste of effort, so there must be something else going there" that looks better than current knowledge and can be falsified?

"Bednorz and Muller [...] won the Nobel Prize and made a lot of money by keeping both their minds and their options open."

Nope. They won Prize and money because they offered an alternate theory supported by experimental results, not just because their open mindness, or else The Office of the Nobel Laureates would be requiered to give the Prize to those that support Area 51 aliens or the Armstrong Never Reached the Moon too.

Re:junk dna

[Medievalist]

I guess we'll have to disagree since our arguments have conflicting premises.

1) You are still not giving up your definition of "functional" which I still contend is circular reasoning.

2) You've characterized my argument as an anthropomorphization of nature which is not my intent at all. I am merely refusing to accept a dubious categorization. The burden of proof is on those who would make this categorization, and I find their arguments very unconvincing.

3) You've discounted my point regarding the B&N Nobel Prize by saying they created a valid theory to explain their empirical results - this is not true. The prize was for "their important breakthrough in the discovery of superconductivity in ceramic materials" (direct quote) which was not adequately explained by any theory at that time. According to Wikipedia, there's still no scientific consensus on why it works.

My hypotheses is that "there is no such thing as nonfunctional DNA, every byte of it functions to some purpose" and mainstream science is already testing this idea (by continuing to find additional functions). The fact that we have not uncovered every purpose in the brief period we've even known about DNA is expected; humans do not normally exhaust the interesting characteristics of even simple elemental substances (like lead, for example, or carbon) when they've been known for centuries. You're aware of carbon nanotubules and buckyballs? Aerosolized lead influence on crime rates? These are new discoveries of properties of substances we've known of for a thousand years or more.

To believe we know enough about DNA to categorize any part as "nonfunctional" is hubris. As you mentioned, the concept of "junk DNA" has already been partially disproven over the last ten years, and I'm fairly confident that more remains to be discovered.

âoe...the scientific community will need to rethink some long-held views about what genes are and what they do, as well as how the genomeâ(TM)s functional elements have evolved." -- Francis S. Collins, 2007

Re:No. Bad Conclusion. Bad.

[ColdWetDog]

Go for it. Only 5 comments at present.

Think fast, though.

Re:No. Bad Conclusion. Bad.

[Cyberax]

Wrong! Most of junk DNA is... wait for it... JUNK!

We can tell the composition of the junk for approximately 66% of the human genome. There is a small amount of regulatory elements mixed with all this junk, but the junk itself is not necessary for anything.

Even without the extreme examples such as bladderwort we readily observe 10x variability in the amount of DNA between fairly recently separated species.

That's not junk DNA

[MobyDisk]

That's not junk: Those are comments!

Re:That's not junk DNA

[Bacon Bits]

Shit that means we're the product of summaries and articles? And God is the editor? I guess that actually explains a lot....

Re:That's not junk DNA

[Anonymous Coward]

Are you sure posting that here is a great argument for it not being junk?

Re:That's not junk DNA

[Anonymous Coward]

no dumbass, the code variety

Re:That's not junk DNA

[Briareos]

Nah, I'm pretty sure it's intrusive ads all the way down...

That plant just got it's leaves on a copy of DNAdBlock.

Re:That's not junk DNA

[Zeromous]

> That's not junk: Those are slashdot users!

FTFY

Re:That's not junk DNA

[steelfood]

I think everyone would really appreciate it if you didn't comment on anything else anymore.

Not really proven

[Animats]

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.

Re:Not really proven

[Anonymous Coward]

Welcome to pseudoskepticism, where lie is logic and confusion is clarity.

Re:Not really proven

[Anonymous Coward]

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.

No need for Venter, nature has already done this experiment for us. Single Nucleotide Polymorphisms, or snips, occur in the human genome by the tens of millions. When a snip occurs inside a gene, it can have an effect such as increased incidence of a disease. Also snips in gene control regions can effect phenotype. But for the junk DNA, the tens of millions of random junk snips you and I have different, they just don't seem to have any effect whatsoever. If the code sequences in the junk matter, the effect on the individual seems to be very slight.

Re:Not really proven

[Daniel Dvorkin]

Also snips in gene control regions can effect phenotype. But for the junk DNA, the tens of millions of random junk snips you and I have different, they just don't seem to have any effect whatsoever. If the code sequences in the junk matter, the effect on the individual seems to be very slight.

Except for, you know, all the SNPs in noncoding regions which come up as significant in practically every GWAS ever.

Re:Not really proven

[Anonymous Coward]

I've always been skeptical of the junk DNA claim. Suppose you clone a creature, and play with the junk blocks. Suppose that block actually controls the finer locations of a few different hair/fur follicles. Would a researcher ever notice such a minor difference? Probably not.

Re:No. Bad Conclusion. Bad.

[the biologist]

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

[Savage-Rabbit]

The carnivorous humped bladderwort...

Sounds like something from an episose of red Red Dwarf.

Re:The carnivorous humped bladderwort

[Gavin Scott]

Actually it's prey will simply evolve tiny little towels to wrap around their heads.

G.

Re:The carnivorous humped bladderwort

[Daetrin]

Sounds like something from an episose of red Red Dwarf.

Personally i prefer blue Red Dwarf. (That way i don't need to change the bulb.)

Re:The carnivorous humped bladderwort

[adisakp]

The carnivorous humped bladderwort...

Sounds like something from an episose of red Red Dwarf.

Or Hyperdrive

Re:No. Bad Conclusion. Bad.

[gandhi_2]

He did at least mention "sperm" but I believe it only counts with word boundaries because it is scored with regular expressions.

Angiosperm does not count, because /\bsperm\b/

Re:No. Bad Conclusion. Bad.

[freeze128]

You are suspiciously well-versed in biology for a software developer....

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

I often eject junk DNA myself, and it is highly efficient compared to courting a female.

PNA anyone?

[stanlyb]

It was thought the the PNA is just a junk "addition", but recently, SURPRISE, it was found out that it is even more important than DNA, in some aspects of course...
Or with other words, NO, i will not give up my junk DNA, it is mine. Period.

Junk DNA Research

[raftpeople]

Recent research showing how junk DNA is involved in brain development:
http://machineslikeus.com/news/brain-development-guided-junk-dna-isnt-really-junk-0

Re:Junk DNA Research

[hughbar]

That would explain a great deal about the modern world.

Re:No. Bad Conclusion. Bad.

[iluvcapra]

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.

Re:No. Bad Conclusion. Bad.

[Mitchell314]

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.

How the fuck did you miss EPIGENETICS??

[Anonymous Coward]

This "junk" DNA concept was never more that a popular "science" sensationalism term.
Fact of the matter was, that *we simply didn't know what it was for*. Which is something *entirely* different than "it is useless junk".*

But for many years we now know that the unknown areas are actually there to control how and how much the known areas are read. Yes, they are essential, and yes, they are a *feature* of higher organisms than that plant.

Because we now also know that our DNA is *compressed* (yes, if you though "like ZIP?" you thought right), allowing multiple genes to be stored at the same place, depending on how you read it. Which is why our DNA is so much shorter than that of many primitive animals and hence there’s less risk mutation overall.

Fuck, it's like OP lived under a rock for the last 10-20 years... and of course everybody here is clueless enough to not notice it.

___
* But it's so extremely typical of arrogant morons in the medical society, who think if they don't know something, it can't exist, because are clearly a "God" and know everything! The same thing happened to the spleen, the tonsils and the foreskin. All three fulfill an important job. All three got (and in primitive countries still get) removed for trivial invalid non-reasons. Only recently did they find out that the spleen is the "barracks" of the "standing army" of the immune system, and it's not that long ago that we found out the tonsils are its "main entrance guards".

Re:How the fuck did you miss EPIGENETICS??

[Anonymous Coward]

and yes, they are a *feature* of higher organisms than that plant.

Onions have 8 times the DNA of humans, so does that make them a "higher organism"?

Re:How the fuck did you miss EPIGENETICS??

[Anonymous Coward]

This "junk" DNA concept was never more that a popular "science" sensationalism term.

Wrong. That you think so is actually the result of popular sensationalism which has hilariously oversold the death of the junk DNA concept, convinced people like you that THERE CAN BE ONLY ONE winner between theories of epigenetics and junk DNA, and so on.

But for many years we now know that the unknown areas are actually there to control how and how much the known areas are read.

We also know there really is junk. It's a mixture, not just one or the other. There are plenty of organisms with no-known-function sequences which freely accumulate mutations from generation to generation. Genes which actually do important things should be better conserved by natural selection, even when we don't know what they do.

Scientific theories about junk DNA do hypothesize that it may function as a reserve of fragments which could be reactivated in future descendants after mutating into something useful. I.e., it may be more of a junk parts box than a landfill, which is why it's "junk" rather than "garbage". Lots of junk is partial or corrupted duplications of known-to-be-functional sequences, after all. But that doesn't mean that today, right now, it's anything other than junk.

Because we now also know that our DNA is *compressed* (yes, if you though "like ZIP?" you thought right), allowing multiple genes to be stored at the same place, depending on how you read it. Which is why our DNA is so much shorter than that of many primitive animals and hence there’s less risk mutation overall.

You're really, really dumb. No, human DNA is not ultra special "compressed" DNA. There are no mechanisms akin to Zip compression. I don't think you have the slightest fucking clue how that kind of compression works. If you did, you'd never say something as stupid as claiming compression helps increase resistance to mutation.

Zip and other common lossless compression algorithms work by building dictionaries of repeated bit sequences found in the original file. The output file contains both dictionary updates and commands to copy strings from the dictionary. E.g. if I write a document which uses the word "ambidextrous" a lot, the compressor might choose to first embed a command making "ambidextrous" dictionary entry 53, then every time it's used in the source file it just encodes a reference to entry 53 instead.

This implies greatly increased sensitivity to errors. If a bit flip corrupts a dictionary entry, all subsequent uses of that dictionary entry are corrupted too. Even if a bit flip merely corrupts one reference to a dictionary entry (i.e. it selects the wrong entry), it's likely to produce much more than one bit flip in the output. Compression greatly magnifies sensitivity to errors.

In biology, we know plenty of instances where the genetic code is tolerant of mutations by permitting sloppiness. For example, there's often two or more ways to encode any given amino acid in a protein-coding DNA sequence, so a single base pair mutation is much less likely to screw that protein up. Put that same sequence through the equivalent of Zip compression, and point mutations are almost guaranteed to create many errors, meaning it's way less likely that the protein (or regulatory function, or whatever) will still work the same way.

So even though fewer base pairs implies fewer mutation events, each mutation would have a dramatically increased chance of doing something bad. The huge increase in side effects also implies it would be far less likely for even tiny mutations to improve survival chances, which pretty much knocks the stuffing out of evolution. An organism with a compressed genome might well be doomed to never adapt.

But it's worse than that for your dumbshit loony theory -- if you actually bothered to think, you'd realize that if junk DNA is real, mutations in the junk are almost neve

Re:No. Bad Conclusion. Bad.

[Cyberax]

Oh no. Not ENCODE junk again.

ENCODE detected that at some point in the life of cell about 80% of DNA was translated into RNA. That doesn't mean it's functional in any way - it's just transcribed. Also, I'd like to see your source for the 50% evolutionary conservation of junk DNA - the top estimate is about 15% of the whole genome ( http://www.sciencenews.org/view/generic/id/349505/description/Reports_of_junk_DNAs_demise_were_based_on_junky_logic_and_dubious_definitions ).

Not necessarily relevant to, say, mammals...

[Gavin Scott]

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.

Unfortunate name

[saveferrousoxide]

So, this is offtopic but I thought humped bladderwort was a pretty unfortunate name. However a Google search and a couple of clicks later I land on the broom-rape cancer-root, of which there is an alpine, a Mexican, and an American variety.

Re:Unfortunate name

[MoonRabbit]

Orobanche uniflora -the official flower of the NYPD.

Re:Unfortunate name

[Anonymous Coward]

Orobanche uniflora -the official flower of the NYPD.

You're serious? 'Cause the symbolism would be baffling indeed:
It is native to much of North America, where it is a parasitic plant, tapping nutrients from many other species of plants

Re:No. Bad Conclusion. Bad.

[chromas]

It's only art if it's documented.

Re:No. Bad Conclusion. Bad.

[Cyberax]

I'm extremely familiar with genetic algorithms. Pure junk is generally useless because you're no better off than starting from scratch. You need at least something that is _almost_ junk or a way to create imperfect copies of existing functional elements within a genome.

Unsurprisingly, there are mechanism for both of these. And they don't need junk DNA - bacteria can evolve just fine and they have virtually no junk DNA.

Then the question: "why junk DNA?" and the answer so far is that it has negligible fitness penalty, any observable effects become noticeable only when DNA grows to humongous size (20-30Gb) because it takes very long to replicate it.

Next question: "Then why does this plant has so little junk?". That's probably because it has some rogue transposable element that chews portions of DNA randomly.

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

WRONG! IT IS NOT JUNK! IT IS EPIGENETICS!

Fuck, did I fall through time and come out in 1980 or what? How does nobody fucking know this here?? THERE IS NO SUCH THING AS "JUNK DNA"! It's just as much sensational bullshit as "We only use 10% of our brains" (AT THE SAME TIME! WE STILL USE 100% IN TOTAL!!). Just that it's much more arrogant, since it assumes that because we didn't know something it MUST be "junk". A notion which has looong been rejected and replaced by the concept of epigenetics.

Shit, it's like you're all from the past!

junk DNA not trash DNA

[nosh]

Can junk DNA be seen as "potentially useful junkyard parts" that some random mutation might re-activate into a gene or part of a gene? Is it actually handy to have these around to allow for rapid bigger changes of set of active genes than just a few small mutations in the active genes can do?

That why they are called junk DNA and not trash DNA, because at least part of it is ready to be reused later.

Some parts will be to control which genes are actually activated, some might even only be necessary to determine how the DNA is folded to determine what genes get more exposure, but the thousends of broken and useless copies of genes around in the junk DNA surely also have the function of collecting mutations until they might get by chance to something useful one day.

While even proteins coded by genes many parts are just filler, the important parts do not allow much changes to still get a surviving organism. You do not want too much mutations on the active genome, or you waste too much with sterile mutants. But to get something truly different, you often need to do many changes at once, and the chances to get there with only active genome are practically not there.

Why?

[queazocotal]

A quick google reveals that phosphorus is about 1/10th of the total mass of DNA.
Or, for an 80Mbase pair genome, about 160M atoms of phosphorus per cell.
Randomly assuming the cells are 10um in size, and cubic leads to a volume of 10^-15m^3, or a mass of 10^-15 tons ish.
10^-9 grams.
Working out the mass of potassium in DNA comes out to 10^-15 grams.

Or around one ppm, perhaps 20 if considering only dry matter.

This would seem to indicate my initial thought it might be due to elemental phosphorous deficiency making DNA manufacture unreasonably expensive in a potassium constrained environment unlikely.
Nitrogen?

Obvious, isn't it? It's carnivorous.

[K. S. Kyosuke]

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?

Re:No. Bad Conclusion. Bad.

[Cyberax]

There is junk DNA. Read about SINEs and LINEs for a start.

Thats sad

[Anonymous Coward]

I assumed this article was about Carnivora, that weird "super drug" they advertise all the time on Coast to Coast AM.

It's for religious-politic reasons.

[Requiem18th]

As Hatta explained, some parts of gnomes really are useless, others code for genes and others provide structure. And indeed this chaos displays the lack of foresight evident in organically evolved systems. The word "junk" not a problem unless you want to argue that every gene in all genomes is there according to some intelligent design, which of course, it's what members of the Abrahamic religions are so desperate to pass for science.

Re:It's for religious-politic reasons.

[Anonymous Coward]

Only a minority of the Abrahamic religions believe in Intelligent Design, and those members that do seem to be somehow concentrated between the left and right coasts of half of a continent.

Attack of the Killer Tomatoes!

[jeffy210]

"The bladderwort, named for its water-filled bladders that suck in unsuspecting prey, is a relative of the tomato"

Anyone else think of this movie?
http://www.imdb.com/title/tt0080391

Re:Attack of the Killer Tomatoes!

[Anonymous Coward]

Thing is, it's not a meaningfully close relative of the tomato, the summary is misleading at best.

Good eatin'?

[sinebubble]

I wonder what this carnivorous humped bladderwort tastes like.

Re:Good eatin'?

[camperdave]

I wonder what this carnivorous humped bladderwort tastes like.

Probably just like the carnivorous smooth backed bladderwort.

Re:No. Bad Conclusion. Bad.

[Lumpy]

Clouding a perfectly good FoxNews level Slashdot article with real facts...

What is this place coming to? Facts! Reading the Article! SHAME ON YOU!

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

As a geneticist and a neurobiologist, I would still make the argument that perhaps non-coding regions are functional in terms of transcriptional regulation, especially in more complex organisms, and provide a buffering layer of control which is responsive to external stimuli - with implications for neural development and neural repair throughout life.

Re:No. Bad Conclusion. Bad.

[interkin3tic]

Indeed, repetitive heterochromatin (that which is called junk DNA) is found at centromeres which are where sister chromatids are held together. Centromeres are essential for mitosis and meiosis in most macroscopic species, certainly plants and humans. And I think the consensus is that if you don't have "junk DNA" sequences for the centromere, the centromere will pick a place on the chromosome to form, and that area will become junk DNA even if it's not meant to be. So you will always have "junk DNA" if you have mitosis the way we do it.

Re:No. Bad Conclusion. Bad.

[Sulphur]

Unsurprisingly, there are mechanism for both of these. And they don't need junk DNA - bacteria can evolve just fine and they have virtually no junk DNA .

No junk, then no junk DNA

Sorry, but junk DNA is not junk

[WillAffleckUW]

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.

Re:Sorry, but junk DNA is not junk

[WillAffleckUW]

(dang - sorry, meant bootstrap not boostrap)

Re:Sorry, but junk DNA is not junk

[Anonymous Coward]

I thought boostrap was a new kind of rap, where people on speed try to make lyrics really really fast.

Re:Sorry, but junk DNA is not junk

[WillAffleckUW]

"usually evolutionarily conserved fallback from when you were a fish or ratlike creature - kicks in."

There is no reason to believe that natural selection will preserve unused gens so long. Random mutation would have likely destroyed the genes a long time ago without any selective pressure to preserve them. There is absolutely no evidence to suggest that we all share a common ancestor. I know these views are unpopular around here but it doesn't make them any less valid.

Oh, silly silly anti-evolutionist. Tell that to your fuel-producing mitochondrial DNA that we stole millions of years ago and inherit from our mothers.

Oh, wait. If that fails, your brain won't have the energy to talk.

bioinfo guy here

[Anonymous Coward]

There's no dogma or notion in molecular biology that repetitive non-coding sequences are necessary for life. For one, two of the three domains of life lack them almost entirely.

Re:bioinfo guy here

[Flere Imsaho]

But that's not the same as saying it's junk for eukaryotes.

Re:bioinfo guy here

[Anonymous Coward]

Ummm single celled bacteria and archaea lack junk because they are SINGLE CELLS. Eukaryotes have complex cell, tissue, and developmental structures. Obviously they need to regulate/coordinate these structures

Re:bioinfo guy here

[Anonymous Coward]

What about the pufferfish, then? Much, much less non-coding DNA than the rest of the family, but no obvious side effects.

Re:No. Bad Conclusion. Bad.

[Mitchell314]

Technically speaking, my line of work was with linear genetic programming as opposed to vanilla GAs, but disallowing or penalizing fitness scores based on having non-functional code can easily slow convergence. I'm focused more on the math/statistics side than coding side, but for our cases our calculated expected value of beneficial point mutations was higher when non-functional operands were permitted. Negative, but still better than for equivalent individuals with removed junk.

Re:No. Bad Conclusion. Bad.

[RoknrolZombie]

Don't worry - it is - the drones fly so high up in the air that you can't see them, but they can see YOU.

Relative of the tomato???

[Hans Adler]

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)."

Re:Relative of the tomato???

[Anonymous Coward]

No kidding, that was my first thought too. It's like saying humans are a relative of the lemur.

Re:Relative of the tomato???

[elyons]

Second author on the paper here and the person who did the analyses that lead the the conclusion of three WGDs since divergence with tomato. We had to phrase the claim like that because tomato was the closest relative with a published genome. These analyses would have been a lot easier if there were genome sequences of plants more closely related to Utricularia, especially if some had more shared WGDs.

Re:Relative of the tomato???

[Hans Adler]

Obviously you (the authors) are not to blame for this. In the original article everything was in the proper context. But the author of the report in Science should have explained what bladderworts are like and instead ran away with a misunderstood bit of information ripped out of context. *This* is what provoked comments such as "Where pray tell then are the GM tomatoes that eat aphids?" and references to killer tomatos. (Of course, otherwise we might have been speculating instead on how many of you gave their lives for science during this research. Carnivorous plants are still a man-bits-dog topic, after all.)

I can't say I'd be that surprised if it was really

[NotSoHeavyD3]

junk. I mean I look at it like this. When I upgrade to a new computer I copy the entire contents of my hard drive to the new bigger one.(Since that's the easiest thing to do. I don't have to figure out what's my data and what's not. Just plug it in and tell my new computer to copy everything and come back hours later.) Admittedly a lot of the stuff I'm copying over are OS files and installed programs. I always tell myself to go back and clean that stuff out but I never do since that'd take time and effort and the new hard drive isn't that much so it isn't worth the effort. After 3 or 4 upgrade and numerous reinstalls I've accumulated quite a bit of junk code myself on my current computer. (It might even be 50% of the data is just junk.) I still have plenty of free space on my drive so in the end I don't really care.

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

YOU ARE WRONG! WITH EXCLAMATION POINTS!

You've committed the fallacy of the excluded middle. Junk DNA has not been absolutely rejected and overturned by epigenetics. The two concepts are in fact compatible -- not all junk has to have an unknown function just because epigenetic functions of non-protein-coding DNA are being discovered.

In fact, there's plenty of evidence that junk DNA truly is a thing that exists. Evolution is primarily conservative: most mutations do something bad, and are therefore selected against. The default assumption is that functional genes (epigenetic or not) should be conserved across generations, and when they aren't, it should be clear why (e.g. because mutations in one particular base pair code the same protein in the end). So you can look at drift rate and get a very good idea of whether a given region is functional, even if you don't know what the function is.

And guess what? Many species have tons of poorly conserved DNA, long sequences where all mutations seem to be neutral. It's not very likely that these sequences have a hidden function. Often there's something else obviously junky about them too. For example, many junk sequences are known retroviral insertions.

Re:No. Bad Conclusion. Bad.

[joocemann]

QFT 1000000X!

This doesn't say crap about 'junk DNA'.

About a thousand LNC-RNA papers and miRNA papers, and others, in the last decade would say this plant paper doesn't say much at all about other species' DNA.

Re:No. Bad Conclusion. Bad.

[iluvcapra]

My reading of those critiques was that because someone could not describe the purpose of this DNA, it was "junk," despite the fact that the DNA was getting transcribed and was having biochemical interaction in the cell. I think the "conservatives," or the ones how think there's a lot of junk, are thinking teleologically about the "purpose" of DNA and are simply excluding these other sequences because the cannot give a complete account of their purpose or whatever advantage they may confer to the phenotype.

As such I think the whole idea of "junk" DNA is teleological because it assigns arbitrary purpose (and confers subjective judgment) to the non-"junk."

Re:No. Bad Conclusion. Bad.

[infinitelink]

What's with the "junk" theorizing about "junk" being "not necessarily junk" for evolution? And the "junk" assumption that the "junk" need be explained in terms of evolutionary dependence on "junk"? The "junk" in the human genome has been mentioned, http://science.slashdot.org/comments.pl?sid=3745175&cid=43712851, to contain segments with products for transcription etc., e.g. the ribosome is a ton of RNA (plus proteins), (and the other molecular factory machinery/parts aren't all proteins, but include a bunch of RNA), but RNAs are also products in and of themselves for purposes beyond protein synthesis. RNAs are known, for instance, to be produced and refined, self-assemble into structures with enzymatic, then be transported to locations where they can be put to such work. Heresy as it may be for a biology guy to say so, I am much opposed to "tie everything amphorously to evolution and use some correlational research to show how this or that contributes/detracts from fitness during selection then profit!!!" (grant money) when the much harder, i.e. real, science of finding what actual mechanisms and material functions this crap is involved it of far more interest, practicality, is more revealing, and more honest science. In a word, it's testable with results leading to reproducible, testable experimentation and knowledge that humanity can then put to good use for other ends. "Evolution" becomes this useful catch-all word/concept/thing for lazy science and scientists looking for money, an explain-all rather than the philosophical concept that it is which seeks to describe things in rather...metaphysical terms. Avoiding that laziness requires, I don't know, actually discovering real functions and processes rather than all the statistical-correlational crap that we're inundated with today, which used to be a means not for inferring material to concoct historical science, but to pour over large sets of data to find indications as to where we should research next to discover the next new mind-blowing/understanding-shifting/world-altering thing. The theorizing is nice, but it's still not hard science, even though by piggy-backing on hard things known it may be presented as such.

Re:No. Bad Conclusion. Bad.

[Cyberax]

Again, we CAN describe the function of about 70% of junk - it simply wants to replicate itself as much as possible. Google for "retrotransposons". Non-junk actually _has_ a purpose - it's used to encode the cell functions.

Re:No. Bad Conclusion. Bad.

[Mitchell314]

First off, I am a math guy, not a science guy. I have never pursued a grant for anything evolution related, so don't complain at me about it. Don't whine at a fireman for making a mediocre cop. And pay bloody attention to what you reply to, my post was about the issue (whether or not junk DNA being useless) also appearing in computer science.

Second, major logic fallacy and incorrect use of basic terms right off the bat

What's with the "junk" theorizing about "junk" being "not necessarily junk" for evolution

That is not a theory, not even close. Burden of proof by default lies on a positive claim (the post I replied to), and what I wrote is a negation of that, and an acceptable statement.

And the "junk" assumption that the "junk" need be explained in terms of evolutionary dependence on "junk"

Again, why complain at me about this? I neither wrote nor implied any such thing.

Put up or shut up!

[Anonymous Coward]

I'll believe it when the scientist remove their junk DNA.

Re:No. Bad Conclusion. Bad.

[slick7]

Wrong! Most of junk DNA is... wait for it... JUNK!

Or is it a place holder until non-junk DNA becomes available?

Useful vs necessary

[Anonymous Coward]

There is a difference between useful and necessary. Backups, for example, can be useful when you need them but they aren't necessary for your computer to function. Lots of genes maybe dormant and only activated when needed or they may perform useful functions but that's not to say what they do is absolutely necessary in all conditions. The cost of duplicating a gene must be weighed with the degree it benefits the organism in a particular environment.

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

I think you missed the point. Right now, we think that "non-coding" DNA is essential to all forms of complex life (such as animals and plants - but not bacteria). This "non-coding" DNA is thought to control complex regulatory functions that are not traditionally found in "coding" DNA (i.e. protein coding genes). Why do scientists think all this non-coding DNA is necessary? Because these organisms are really complex. For example, the human body has over 200 different cell types, and the human genome needs to know *when* and *where* to turn on each type of cell. It is very difficult to fit all of this regulatory information in a protein-coding gene. So basically, it's incredibly surprising to find a complex organism that DOESN'T have this DNA. It makes you wonder why humans have so much - and how does bladderwort get everything done? Even though bladderwort's ancestors may have had a ton of "non-coding" DNA, it's still surprising that bladderwort itself can exist without it.

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

Unsurprisingly, there are mechanism for both of these. And they don't need junk DNA - bacteria can evolve just fine and they have virtually no junk DNA.

Bacteria have a deletional bias - thus, very little junk dna. It's unclear how much selection acts on genome size in bacteria.

Then the question: "why junk DNA?" and the answer so far is that it has negligible fitness penalty, any observable effects become noticeable only when DNA grows to humongous size (20-30Gb) because it takes very long to replicate it.

This can't possibly be true.

Next question: "Then why does this plant has so little junk?". That's probably because it has some rogue transposable element that chews portions of DNA randomly.

??? This is generally NOT the mechanism behind massive genome reductions

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

SINEs and LINEs may be selectively beneficial! Just because nobody has ascribed a fitness benefit to them doesn't mean none exists. SINEs and LINEs likely underlie many genome rearrangements. We know almost nothing about how genome rearrangements work - whether they are programmed, selected on, etc. If you compete two plants - one with SINEs and LINEs, the other without - over evolutionary timescales, I'd be willing to bet that the plants with SINEs and LINEs win. I'd hardly say they are examples of "junk" DNA

Re:No. Bad Conclusion. Bad.

[hyperfl0w]

This pissed me off so much I just registered FactCheckScience.org Currently finishing PhD thesis writing (bioinformatics) so I dont have time to invest in a domain. If anyone has a stellar idea, I'm an Open Source supporter and happy to share the domain. This has to stop.

Re:No. Bad Conclusion. Bad.

[Anonymous Coward]

Take a deep breath, and say to yourself less than one percent of junk DNA has biological activity in the cell. Unless, of course, you use ENCODE's physical chemistry definition of biological activity. One of the definitions of biological activity ENCODE used was "is transcribed", even when the transcribed RNA is then immediately discarded. Note that junk DNA tends to be copied in one copy number, but the mRNA it is supposed to control by binding tends to have copy numbers in the thousands (the small amount of junk mRNA that binds other RNA's is more properly thought of as noise). It has been shown in animal models that large amounts of this junk DNA can be excised with no discernible effect. It has also been shown that our cells have specific mechanisms to suppress sections of this junk DNA, as they are potentially harmful transposons. More of it is degraded viral DNA. You really don't want that active either.

Note that this stuff is junk DNA, not garbage DNA. It clutters the place up, and at this stage has no biological function. It could provide material for mutation and future adaptation. But I wouldn't hold my breath while waiting.

It was pointed out to the ENCODE team as early as 2007 that their definition was useless. It is also kinda cyclic. It also hinges on the odd assumption that 70% of the Human genome is impervious to deleterious mutation in the absence of selection pressure. But rather than correct their error they decided to piss $288M up against the wall. But then, I'm just an angry biochemist, pissed off at such a stupidly wasted opportunity. What would I know about it?

A gentle critique of ENCODE

Re:No. Bad Conclusion. Bad.

[Warma]

Next question: "Then why does this plant has so little junk?". That's probably because it has some rogue transposable element that chews portions of DNA randomly.

??? This is generally NOT the mechanism behind massive genome reductions

I'm not the one you're responding to, but as a curiosity, what is the mechanism behind genome reductions?
What kind of copying errors decrease the size of the DNA chain and how probable they are compared to block copies etc., which increase it.

Re:No. Bad Conclusion. Bad.

[ockegheim]

There’s an interesting discussion of all this here:

http://www.abc.net.au/radionational/programs/ockhamsrazor/the-junk-dna-controversy/4635168

One thing it talks about is the difference between trash, which you throw away, and junk, which keep in the garage in case you ever need it again (or aren’t motivated enough to throw away).

MOD PARENT UP!

[steelfood]

One of the authors of the paper. Hello mods?