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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.
Is everything we know about genetics off-base? (no pun intended)
I thought it was a great pun.
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.
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.
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.
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
Of course RNA can code for more than DNA does: RNA editing, where the RNA sequence itself is modified after transcription; differential intron splicing, where different bits are cut out of the pre-mRNA to form different forms of mRNA. Then there's post-translational modifications to the proteins themselves... A single gene can produce dozens of different proteins (there's one expression in brain tissue which produces around 900 different proteins, but I don;t recall its name) many of which can be completely different from each other. Not to mention functional RNAs themselves. The human proteome probably contains hundreds of thousands of proteins. So yes, it all comes from DNA, but RNA is more than just an intermediary.
of course, biting monkeys is not to everyone's taste - Konrad Lorenz
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"
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.
Wow, and I thought my background in circadian research would never be useful!
A proposed schematic of the Drosophila's circadian system is illustrated here. In the associated paper, we basically created a mathematical model of the schematic using standard biochemical equations and harnessed the power of computers to test the model against results from actual "wet-lab" experiments.
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."
Its interesting that you mention HCV because that is exactly what my lab is working on. The problem with RNAi is that there no effective delivery method for humans.
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.
As someone who has thought about this seriously, I basically agree with much of what you said, but it needs clarification. A basic reference is "Darwin's Dangerous Idea", by Daniel Dennett, and his basic slogan is "Cranes but no skyhooks".
One basic idea is that hereditary variation occurs on many different time scales simultaneously, e.g. cutlural (mimetic), epigenetic (DNA methylation), as well as regular DNA mutations which themselves fall into several classes each with a different frequency of occurrence ( simple sequence DNA, duplications, point mutations). My own thinking is that this non-uniformity of time scales of hereditary variation, when viewed in retrospect, can appear pseudo-Lamarkian, i.e. locally goal directed.
This multiple time scale search is a known strategy of search in certain genetic algorithms, and in some circumstances speeds up the search considerably. So in some sense one could regard Darwinian evolution itself as a process of distributed design (Dennett), with the pseudo-Lamarkian "goals" and different time scales of search partially giving the retrospective appearance of intelligence.
Whence we reconcile the major apparent discrepancy between darwinian evolution and "intelligent design" (as it would be understood by a rational person).
Not so many realize this, so I'm glad to meet you.
Or maybe they are not usefully described in the computer program metaphor.
DNA is not a program. For one, "program" implies that there is a fixed temporal order to the instructions. But organism development is initiated by cues from the environment, the order of execution is not stored anywhere. And its not even like subroutines, since what the DNA does is producing proteins. They are little machines that help to produce material substances when epigenetic mechanisms ask for them. The epigenome is more like a factory that produces according to information from the environment combined with its genetic capabilities than any sort of computer running a program. If you must view it as some turing machine, you need to include the whole environment, since much of the controlling information is "stored" there.
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