Slashdot Mirror
RNA May 'Run' Genetic Coding
leonbrooks writes "First a Stanford Medicine Magazine article speaks about RNA 'produced by plants that turn genes on and off', and now a Science Magazine issue says 'For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA and of the proteins that supposedly took over RNA's functions in the transition from the 'RNA world' to the modern one. The shadow cast has been so deep that a whole universe [of RNA] has remained hidden from view, until recently' and speaks of 'an order of magnitude more transcripts than genes', suggesting that more actual coding is done through RNA than DNA. Is everything we know about genetics off-base? (no pun intended)"
Of course it's off base... I mean... first of all you've got that stuff about ribosomes... they're not even really called that... I was talking to God... and when He made them He actually called them, "those thingies" apparently we didn't realized that and started calling em something else... silly humans...
This is how science evolves. One theory revises another. At least they're willing to say they they were wrong, unlike hundreds of years ago.
No existe.
All your base are belong to RNA.
No, it's the new corporate buz-word.
"Who are in control, they are not in control of anything - they don't even control themselves!" - Glen Beck
Is everything we know about genetics off-base? (no pun intended)
I thought it was a great pun.
I 4 1 welcome our new ribo-nuclaic-acid overlords.
In some respects this seems kinda like a Duh.
There are obviously undiscovered genetic mechanisms that contribute to the "directedness" of evolution. I feel that random mutation really doesn't explain the the effectiveness of genetics that we observe. And NO i dont think it has anything to do with religion. It is some kind of smarty feedback loop mechanism built in on a low level, somewhat like how neurons learn, but for genes. I suspect there is a mechanism that somehow folds stress induced specialization of a living organism, back into the genetic blueprint. Once this mechanism is understood we will really start kicking ass in molecular biology instead of the flailing we are doing now with the incomplete data we have.
Then again.. I am completely insane. Someone care to set me straight?
Well, what you described was the normal job of RNA. According to the article, RNA also has the ability to block proteins, and also turn off specific genes.
They state that it has opened up many possibilities in finding out which gene does what. They mention that they have successfully used this technique to stop the spread of some diseases, like Hepatitis B and it could possibly lead them to discover more about cancer.
Read the HTML article, it is very interesting and informative for anybody who is interested in genetics.
Don't count your messages before they ACK.
Speaking just as a layman, mRNA is truly a fascinating subject
Using it, many, many parts of DNA can be turned off, and countless experiments can be done to find out exactly how we work. mRNA seems to be the scientific advancement we needed to spark the next revolution in the understanding of our most basic mechanisms. It is by turning things off that we can see most of what was hidden to us this far.
Already, it has some medical use, in reducing the further damage of macular degeneration caused by excessive production of blood vessels in the eye. And it's only just begun.
There's a lot of justified hype here. But so long as it can allow for real progress of science, I'll be happy - research in general needs some general PR on the public stage. Hopefully private and public interest in general research could at least be put in a positive trend for a while at least.
In the words of the fictional "MC Hawking", what we need more of is science.
RNA is the hardest to work with in the laboratory. It just fall to pieces. When I was working with DNA/RNA/protien it was just really hard to work with RNA.
so DNA->RNA->Protein
We could work with DNA we could work with most protiens. RNA? no way. well sortof but.. no way.
So DNA and Protein do play major rolls no doubt. but we could not get an angle on the RNA. 1990's tech.
It has been known for some time that transcription factors can help determine what other genes can be transcribed. For example, in maintaining circadian rhythms in fruitflies there is the PER and TIM (timeless genes). These bind to the gene promotors, creating a negative feedback system, such that both are inversely proportionate to each other, and are antiphase with CLK/CYC transcription factors:
P ages/C/Circadian.htmld ian
(first link I found on the subject)
http://users.rcn.com/jkimball.ma.ultranet/Biology
http://www.scienceden.com/mbiology/research/circa
ok as someone that works in this field let me say this:
RNAi is a very useful tool, but this is definitely several years behind the curve. RNA has been shown to regulate much more than previously thought. However talk about "the secret world of RNA" is pretty much like claiming that there is a "secret world of open source software." Neither one is very secret or very new.
The biggest contention I have is this quote from the article: "This knack of completely eliminating a protein makes RNAi a valuable research tool." This is wrong, because RNAi does not work like this at all. This is actually one of the drawbacks to using RNAi to eliminate proteins. It does not eliminate, it reduces. To get rid of a certain protein, the classic method is to completely remove the DNA that codes that protein from the organism studied. This is referred to as a "knock out" because the organism has no ability to make that proteind from the removed DNA. RNAi however, provides only a "knock down" because the DNA is still there and no matter how much RNAi is used there is still some expression of the protein. Also, many RNAi protocols are transient supressors not permanent knock outs of protein.
So basically this is an exciting new field but don't necessarily believe all the hype because this is no miracle answer. The article is good, but oversimplified.
The article is referring to short interfering RNAs (aka micro RNAs), which exert their effect post-transcriptionally (i.e., they are not involved in 'coding' as the summary suggests, but rather in suppressing the expression of 'coding' mRNAs that have already been produced via transcription).
It is not that what was previously known was 'wrong'; RNAi is just an additional (and important) layer in the regulation of gene expression beyond what was previously recognized.
I hate when ppl say, "no pun intended" when they obviously intended to pun.
It's worth noting that the field of "genetics" precedes even the identification of DNA and RNA. It may be that what we now know about gene regulation is wildly incomplete (although even that is unlikely, although possible) but Mendelian genetics is completely agnostic as to whether "genes" are protein-coding or not.
What I'm listening to now on Pandora...
...DNA and RNA code *you*!
No, wait. That can't be right...
Paleotechnologist and connoisseur of pretty shiny things.
There may not be that many single genes, but apparently, genes also code in combination. So combinations of two genes would give you the square of the number of currently identified genes, being 30.000 ^ 2 = 900.000.000. Think what triple combinations would do.
NOVA's new, toned down, show recently did a piece on this. You can view it at http://www.pbs.org/wgbh/nova/sciencenow/3210/02.ht ml
For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA
What is this? Maybe during the OJ Simpson trial, but for anyone that's taken an intro bio course, that's bunk. RNA is a huge part of the entire thing...there are organisms that rely on RNA as their primary genetic material.
Once again, Slashdot, if you're going to post science news, have someone as an editor that knows some basic science!
"There is no time, sir, at which ties do not matter," Jeeves, (Jeeves and the Impending Doom)
http://www.sciencemag.org.nyud.net:8090/cgi/conten t/summary/309/5740/1507?rbfvrToken=bba41c737e9d32e 852952029f4e32998530ff0d1
http://www.sciencedaily.com/releases/2005/09/05090 6081607.htm
25% of HIV patients (according to Squire et al, 2003; see also Budka, 1991) develop HIVD, HIV-Dementia Complex.
Macrophages become distributed throughout deep grey and white matter structures (such as the Amygdala).
Theory 1: Retroviral envelope proteins are cytotoxic (and neurotoxic).
Theory 2: Neuronal degregation is caused by macrophage factors associated with AIDS and HIV.
I'm not sure it has anything to do with "facilitation of transmission". It may be a resultant of random processes caused by the virus.
until recently' and speaks of 'an order of magnitude more transcripts than genes', suggesting that more actual coding is done through RNA than DNA.
No, that's not what it suggests. The coding is still done (almost) exclusively through DNA; we know that because we can synthesize DNA (and DNA only) from scratch and have it work.
What they are talking about is that RNA isn't just a short-lived intermediate in the cell, but has many other functions. That's been known for several decades, although people are only now slowly waking up to how important and widespread those functions are.
As a rough analogy, you can think of DNA as the disk drive of a cell and RNA as its RAM. The disk drive contains all the information you need to boot, but RAM is where most of the action happens, and a lot of stuff on disk is copied into RAM, often several times.
If the /. editor is trying to claim that RNA codes for things in and of itself, then that opens an interesting possibility: Mainly that RNA, in addition to DNA, must be transferred to produce a clone (for example) because some of the RNA is unique and not coded for by DNA.
And no, I didn't RTFA because I was afraid I might barf after reading the Slashdot leader.
It's not Kerry Mullis. It's Kary Mullis
--
Error 500: Internal sig error
You misspelled "fuck."
Just thought I'd help you out.
+++ATH0
Can they use this information to get the goddamn HSV1 virus out of my trigeminal nerves? (And the nerves of, what, something like 80% of the population of the planet?)
Fucking cold sores.
+++ATH0
We got to know about DNA, no harm in that. Now we can get to know about RNA too. Isn't science marvelous.
Are the conclusions that you've drawn here actually made in any significant peer-reviewed journals?
+++ATH0
Science, Vol 309, Issue 5740, 1507 , 2 September 2005
[DOI: 10.1126/science.309.5740.1507]
Introduction to special issue
In the Forests of RNA Dark Matter
Guy Riddihough
For a long time, RNA has lived in the shadow of its more famous chemical cousin DNA and of the proteins that supposedly took over RNA's functions in the transition from the "RNA world" to the modern one. The shadow cast has been so deep that a whole universe (or so it seems) of RNA--predominantly of the noncoding variety--has remained hidden from view, until recently.
Nor is RNA quite so inert or structurally constrained as its cousin; its conformational versatility and catalytic abilities have been implicated at the very core of protein synthesis and possibly of RNA splicing. Noller (p. 1508) discusses how the basic building block of RNA--the double helix--has been fashioned into the intricate "protein-like" three-dimensional surfaces of the ribosome. A further parallel between RNA and protein is revealed in the structure of an RNA group I self-splicing intron, which uses an arrangement of two metal ions for phosphoryl transfer much like that seen in many protein enzymes (p. 1587). Another group I-like intron catalyzes the formation of a tiny RNA lariat, a reaction strikingly similar to one seen in group II introns and spliceosomal introns (pp. 1584 and 1530). This unusual lariat, at the very 5' end of the resultant mRNA, is suggested to help protect the mRNA from degradation. The dynamics of the RNA messages passed between nucleus and cytoplasm provide a complex and sophisticated layer of regulation to gene expression, covered by Moore (p. 1514), who describes the teams of proteins that escort and regulate mRNA throughout the various stages of its life (and death). Death for many mRNAs occurs in cytoplasmic foci called P-bodies, which can also act as temporary storage depots for nontranslating mRNAs (see the Science Express Report by M. Brengues et al.).
Figure 1
CREDIT: A. Baucom and H. Noller
Small noncoding microRNAs (miRNAs) have been found in such abundance that they have been christened the "dark matter" of the cell, a view reinforced by an analysis of the small RNAs found in Arabidopsis (pp. 1567 and 1525). The role of miRNAs and of their close cousins small interfering RNAs (siRNAs) in RNA silencing is discussed by Zamore and Haley (p. 1519), and illustrated in the poster pullout in this issue and in research showing that miRNAs can repress the initiation of translation (p. 1573) and, intriguingly, can also increase mRNA abundance (p. 1577). [See also this week's online Science of Aging Knowledge Environment (SAGE KE) and Signal Transduction Knowledge Environment (STKE)]. The phrase "dark matter" could well be ascribed to noncoding RNA in general. The discovery that much of the mammalian genome is transcribed, in some places without gaps (so-called transcriptional "forests"), shines a bright light on this embarrassing plentitude: an order of magnitude more transcripts than genes (pp. 1559, 1564, and 1529). Many of these noncoding RNAs (p. 1527) are conserved across species, yet their functions (if any) are largely unknown: A cell-based screen shows one, NRON, to be a regulator of the transcription factor NFAT (p. 1570). Of course, in some cases it is the act of transcription that is the regulatory event, as in the case of the transcriptional regulation of recombination (p. 1581). Finally, even the coding and base-paring capacity of RNA can be altered--by RNA editing, in which bases in the RNA are changed on the fly. Analysis of editing enzymes (p. 1534) reveals that the cell-signaling molecule IP6 is required for their editing activity.
It's Kary Mullis, and he made an absolute fortune from PCR. The patent on Taq-pol is one of the most valuable patents ever.
Secondly, you should be modded down for copy-and-pasting that diatribe against HIV/AIDS which is quite off topic.
And while Kary Mullis made a brilliant discovery (PCR) he came up with it while he was stoned (no joke). This explains a lot of his unconventional theories...
"A week in the lab saves an hour in the library"
Get yourself some Valtrex .
9/11 Eyewitnesses to Explosive WTC Demolition 1 of 2
Do read it, it is a good book.
but natural selection. I don't recall the source, but a physicist once said that chance does not exist but "uncaused effects" do. In other words, nothing happens without a series of events before it.
Science is really about distilling the inumerable naturalistic forces at work in the universe into coherent theories. At the macroscopic level, many of these forces appear random but so many forces come into play that is impossible to account for all of them in one observation.
I think it's the lack of certainty in the world that people object to more than anything else. The constant changes, alterations, and arguments to knowledge that science brings in attempting to answer some essential human questions disturbs a great many. The truth is science will never be able to answer with utter certainty these questions and will most often answer with a realm of probability rather than a black or white answer. Filling the gaps in human knowledge with "intelligent design" is just lazy thinking.
Imagine if intelligent design was applied to math, we'd end up with Pi to the value of 3 because 3.14.... ad infinitum is messy and reveals a level of unsettling uncertainty in the universe. Let's stop all scientific investigation and just apply a deus ex machina answer to all those niggling little science questions where the answer is never a round number, yes or no, true or false.
I am sure I don't need to tell you that you are welcome to the comfort of whatever designer you feel is necessary in your world. Just don't teach it as science and I won't ridicule and belittle your beliefs, because that's what those that believe intelligent design is science are doing to science.
Then again, I could be completely wrong about intelligent design since I am completely smashed and can barely find the backspace key...but that's another level of uncertainty in the universe for another time.
Commentators in this thread seem to have missed one of the main implications of the quoted article (this implication is not a new one anyway): Early organisms were functionally organised, and genetically coded for, by RNAs. DNA and proteins, including the catalytic functions of enzymes, came later. See the following, for example: "1: Nature. 2002 Jul 11;418(6894):214-21. Related Articles, Links The antiquity of RNA-based evolution. Joyce GF. Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. gjoyce@scripps.edu All life that is known to exist on Earth today and all life for which there is evidence in the geological record seems to be of the same form--one based on DNA genomes and protein enzymes. Yet there are strong reasons to conclude that DNA- and protein-based life was preceded by a simpler life form based primarily on RNA. This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA."
Um, no, you are not off base. ISTR my 9th grade bio teacher speaking of this back in 1983 or thereabouts.
C|N>K
The machinery which is doing the splicing and dicing is effectively a form of coding, too, even if it doesn't have its official coding license from an appropriate scientific authority.
DNA isn't the only thing inherited; in the case of mitosis, you get half a cell packed with stuff, and in the case of sexual reproduction the egg constitutes a whole cell packed with stuff. Complicated stuff, including RNA.
In the words of the fictional "MC Hawking", what we need more of is science.
MC Hawking is my homie, you insensitive clod!
"The newly born animals are then whisked off for a quick run through a giant baking oven." --heard on Food Network
Fine, but please don't call it Science.
The information in Natural Selection comes from just that: Natural Selection. Form A is better adapted than Form B. Form A survives.
But this may be one of the reasons it's getting a lot of attention. Drug companies are rarely excited about a cure, but pay close attention to long-term treatments. One suggested use for this is reducing the viral load of hepatitis C. While some have suggested that the immune system may be able to knock it out if the viral load is reduced by a factor of ten, the likely outcome is that people take this RNAi treatment for life in order to avoid liver damage.
Viruses are really just lumps of DNA/RNA wrapped in proteins that happen to cause certain cells to produce more copies.
Anything new thing a virus does is random, but after it has been filtered by natural selection it isn't technically random.
If a new effect of a virus were to facilitate transmission, it would be selected for.
Genetics is confusing because it's backwards: the effect preceeds the cause. Nothing is done for a purpose, but some changes are kept or dropped for a purpose. (It's like a really weak bandpass filter, put a signal that is initially white-noise through it enough times and you will get a signal that perfectly fits in the pass-band --although in genetics the filter is changing, and noise is continuously added)
That's your deck, and we find it to be marked.
"Everything seems to depend on the kind of god people worship."
Really? Name for me one religion (of any import) that has not had members that were killers.
"Natural selection cannot create information, it can only select between existing sets of information."
This only shows how little you understand about the subject of information.
ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz
You cannot create information from the above, you can only select from the existing set of letters.
"I don't happen to be an IDer..."
Baloney. Elsewise, you'd know that even if a genetically fabricated organism existed, its creator would have to have evolved. You cannot proceed backwards infinitely.
The implications of this are profound: Genetic evolution may be driven less by the germ-line replicators of our own cells (DNA nucleus) than by RNA virus aka retrovirus symbionts in the environment. In other words a lot of what our DNA is designed to do may be to work with the RNA viruses in our environment to create us. That would mean that if we alter the RNA viruses in our environment we are essentially causing mutations in our genetic code.
Seastead this.
Random mutations, and other mechanisms, provide potentially successful combinations (though, more often than not, less successful combinations).
Natural selection 'decides' which is the more successful.
This DNA/RNA combination sounds familiar if you're in Canada and caught the first couple of episodes of ReGenesis.
One of the plotlines of the show deals with a genetically engineered combination of Camel Pox (bacteria/DNA) and Ebola (virus/RNA). Trust the brilliant researchers to claim it as their own "new" idea instead of crediting science fiction...
I do not fail; I succeed at finding out what does not work.
Yes you are OBVIOUSLY right, Natural Selection can only operate on existing forms. That's why the introduction of variation, upon which natural selection operates, is an essential ingredient of the process of Evolution.
Also, the creation of organic molecules happens in the absence of 'Life'. You're not suggesting an intelligent designer worked on Hydrogen, Oxygen Nitrogen and Carbon (and the rest) to create the organics we can observed astronomically, on Titan and in the lab, are you?
Scientists are still working on theories of the origins of life as we know it. It is a difficult subject but still no reason yet to give up and say 'God dunnit'.
I believe the Quakers and Amish are both pacifist, yet both are obviously religious. There are lots of pacifist religions in Asia.
Jehovah's Witnesses have got in trouble around the world for refusing to join or even support the military (won't even work in military hospitals) and are wholly politically neutral.
Religion isn't necessary for war (see radical godless Communism), its just that both are seemingly ubiquitous forces in human nature, and its difficult to unravel connections between the two.
America's war in Iraq is hardly motivated by religiousness, even if the right wing is fermenting support for war to gain political power for itself. Bush is there for money, political power and control of resources.
The mega-suburban churches are whipping up support for the war so they can get in with the administration and start demanding favors: invoke an American state religion that banishes freedom of belief, freedom of expression (particularly if boobs are involved), and civil rights for anybody who falls outside the state moral code.
Religion? Do you think these people really even believe in a god, or is it just more politics as usual?
Yes.
It's pretty clear that there is a lot more to the story of biological regulation and inheritance than "DNA encodes proteins".
Two facts:
1) Far more proteins than genes
2) Conserved "non-coding" DNA
Biologists have known the first fact for a long time now--getting on for a decade. When the human genome was sequenced it was obvious that the 32,000 genes weren't sufficient account for the hundreds of thousands of proteins we know exist (I'm personally betting it's into the millions, depending on precisely how you count minor structural variants.)
Why then do we still fixate on the "It's all DNA, one-gene, one-protein" model? Because it's easy, and we don't have anything to replace it with. But it's a blind alley, it's known to be a blind alley, and the next generation of biologists is going to have some fun getting us out of it, if they don't waste all their time trying to find the next miracle drug based on a model that is known to be false.
Some form of RNA-based regulation is entirely plausible as a means of increasing the expressive power of the limited coding regions. Who knows--maybe non-coding regions actually contain encrypted codons, and the RNA is doing decryption during transcription. That could plausibly have evolved as a defense against some kinds of viral attack.
Elaboration on the encoding during transcription is also a virtual certainty--where else are we getting those other 200,000 proteins from? And if it isn't RNA regulating the elaborative process, what is?
Blasphemy is a human right. Blasphemophobia kills.
So they're saying RNA is like a config file?
Excellent... I see a new O'Reilly book:
Bash Scripting For Your Genes!!!
A computer once beat me at chess, but it was no match for me at kick boxing. Emo Philips
And there's no evidence that this would affect any sort of selection, as widespread deep-structure damage to the brain is likely to hurt transmission probably more likely than it helps.
Is DNA the programming language and RNA the compiler? Or is it the other way around? Or is RNA more the operating system sending a set of 'priority interupt' flags to the currently running DNA process? Or perhaps RNA is the #includes and #defines to be preprocessed before the body of the code DNA gets run?
At least they're willing to say they they were wrong, unlike hundreds of years ago.
They are... as long as profits are not at stake.
While the scientific research community is willing to acknowledge the limits of their understanding, the corporations developing genetically engineered foodcrops maintain that their products are proven perfectly safe (implying that they have a perfect understanding of the effects of the changes they have made). This claim flies in the face of significant research. And they have no compunctions about applying political and economic pressure to independent university researchers who claim otherwise.
The grand irony in the whole mess is that, as far as Monsanto etc are concerned, it's really not about genetic engineering and whatever dubious advantages it might provide. It's really an intellectual property maneuver to establish ownership of the seed supply.
"Research is what I am doing when I don't know what I am doing." -- Wernher von Braun
Your quite right, but this confusion comes up a lot, perhaps because-
"the word gene... is shared by many disciplines, including classical genetics, molecular genetics, evolutionary biology and population genetics. Because each discipline models the biology of life differently, the usage of the word gene varies between disciplines. It may refer to either material or conceptual entities."
Surely this is what Douglas Hofstadter argued already 25 years ago in his Pulitzer winning "Gödel, Escher, Bach", when exploring the possibilities and limits of artificial intelligence?
Not at all a well-designed, efficient and elegant system, it looks instead like the genetics is the most convoluted Rube Goldberg style mess you could imagine. To make a gene work you first express the DNA as mRNA, then edit the mRNA to remove to bits you didn't want in the first place, then reassmeble the parts you did. Except that some of that "non-coding" mRNA is used for spacing the "coding" mRNA.
To turn a gene off, you don't just turn it off... you turn another gene on that makes a piece of interfering RNA that binds to some of the mRNA from the first gene. The second gene is controlled in the same way, maybe as a positive feedback from the first gene maybe as a negative feedback, maybe under the control of some other gene, which may or may not have the same promoter region. Layers on top of layers on top of layers of interlocking control systems.....
Little bits and pieces of RNA, recycled and reused, adapted from their former functions to serve some new function, forming a hugely complex interlocking mess that somehow functions. This is like a typewriter constructed from a couple of staplers, a telephone and a box of paperclips.
So, since inefficient, cumbersome and inelegant spaghetti code-type machinery is at the heart of every mammalian cell, that pretty much drives a stake in the heart of any thought that this was a product of rational design, right?
The man who does not read good books has no advantage over the man who cannot read them. - Mark Twain