> RNA has taken over from DNA as the number one interest in microbiology
> over the last few years.  Very small bits of RNA we couldn;t see in my
> day control all kinds of cellular shit, usually to do with proteins.
> I've been trying to put together something on genetics that remains
> readable, but it's remained impossible to come up with something that
> can get non-scientists to see the wide picture, a bit like the way
> 'The Cell As City' does.  Chaz's attitudes on this probably need
> unravelling in the same way he sometimes presents history.  

>Roger
> Penrose had a go at consciousness some time back, but ends up leaving
> me in the familiar territory of 'what the furk does that mean' too
> soon.  

>One the up side Chaz - I seem to remember you run to fat as I
> do - it looks like those nerks eating plant sterols in vomit-tasting
> psuedo-lards like Benecol are storing the plant sterols in their
> hearts and about to explode into death faster than those eating
> buttered bacon!

> On 22 Jul, 00:20, Pat <PatrickDHarring...@hotmail.com> wrote:

> > On Jul 21, 9:56 pm, chazwin <chazwy...@yahoo.com> wrote:

> > > Here's one for Ian. He is curious about Pat's ideas on the "purpose"
> > > and intentions of RNA.
> > > During a conversation about teleology, I was insisting that the
> > > universe is basically devoid of purpose, whilst Pat was pointing out
> > > his theory that everything is connected by a vast Quantum god, and
> > > affects the world with a string theory model, in which He is
> > > demonstrated to be Omniscient, omnipresent and omnipotent. It seems
> > > that RNA is the main areas in intervention.

> > > Some quotes to give you the fell of the discussion:

> > > >For all we know, RNA could be using their hosts for experimenting.
> > > > Whilst it may sound silly, we know that, at the root level, it's RNA
> > > >that's calling the shots.
> > > > LOL!!  RNA rules.  And you're living proof.  I couldn't care less
> > > > what you think, Chaz.  RNA runs our machinery.

> > > I excused myself from the discussion, thinking it to whacky, and
> > > wanting to avoid the inevitable insults that were queueing up in my
> > > language processor.

> >      Rather, to give you one side of it.  Later, of course, Chaz comes
> > out with this one:

> > "The raison d'etre of the gene is to make an organism that survives."

> >      If he wants to have his cake and eat it too, that's fine by me.

> >    Also, to set the record straight, in the above passages he's
> > cobbled together and removed the context.  I had also put a link in to
> > an article entitled: When RNA Rules.  Here's the TEXT of that article
> > (if you want to find it, Google "RNA rules" and look for 'Whitehead
> > Institute'.  It was the sixth link when I did it.):

> >  When RNA rules

> > A newly discovered class of molecules plays an astonishingly powerful
> > role in biology

> > What do newly discovered molecules called microRNAs and the Internet
> > have in common? Both reshaped entire fields in the past decade, says
> > Whitehead postdoctoral fellow Andrew Grimson.

> > “That’s a fairly grandiose claim for microRNAs,” acknowledges Grimson,
> > who studies them. “But the discovery of the widespread role of these
> > molecules changed the landscape of biology very quickly.”

> > “Labs across the world, working on a variety of biological questions,
> > are now integrating microRNAs into their research,” says David Bartel,
> > Whitehead Member and Howard Hughes Medical Institute investigator.

> > Bartel and his colleagues have helped to fuel the frenzy by
> > identifying hundreds of the small RNA molecules and providing
> > compelling evidence that they regulate the production of thousands of
> > proteins in plants and animals.

> > “Computational work has produced a very big picture of what microRNAs
> > are likely to be doing in a very short time,” says Nobel laureate and
> > MIT Institute Professor Phillip Sharp.

> > Until the early 1990s, no one had a clue about microRNAs, which flew
> > under the radar because of their tiny size. Each one contains only 21
> > to 24 nucleotides, or letters of the genetic alphabet, so scientists
> > simply missed them. Victor Ambros’s group found the first microRNA—
> > lin-4—in 1993 at Harvard Medical School while studying a mutation in
> > the worm Caenorhabditis elegans.

> > Another Harvard researcher detected a second microRNA in 2000. One
> > year later, the floodgates opened with the discovery of nearly a
> > hundred in worms, insects and humans. At this point researchers began
> > calling these tiny regulatory molecules “microRNAs.”

> > The discoveries changed conceptions of RNA. Scientists have known for
> > decades that RNA molecules serve as messengers and translators,
> > building proteins from DNA sequences. But microRNAs determine which
> > DNA sequences get translated in a given cell, a responsibility once
> > considered the purview of proteins known as transcription factors.
> > MicroRNAs essentially choreograph biological ballets, helping to
> > determine where and when proteins can appear to perform. Thus RNA can
> > add “regulator” to the roles listed on its résumé.

> > MicroRNAs bind to messenger RNAs that code for proteins involved in
> > activities ranging from development to cancer, and disrupt the
> > production of these proteins. In humans, microRNAs regulate roughly
> > one-third of protein-coding genes, and that’s a conservative estimate.

> > Going through the genome
> > “This is the first discovery of a broad biological mechanism that’s
> > been made since genomics,” says Nobel laureate Phillip Sharp, who is
> > investigating how microRNAs work at MIT, where he is an Institute
> > Professor.

> > Scientists determined the scope of microRNA activity in a matter of
> > years by mining recently published DNA sequences. Bartel, an RNA
> > biochemist, and computational biologist Christopher Burge of MIT
> > played a leading role. They collaborated to develop computer programs
> > that scanned genomes to identify microRNAs and their messenger RNA
> > targets. Their work helped to ignite interest in microRNAs as
> > biologists in labs around the world realized the tiny molecules
> > regulate a large portion of the protein-coding genes in plant and
> > animal cells.

> > “Computational work has produced a very big picture of what microRNAs
> > are likely to be doing in a very short time,” says Sharp. “ “It feels
> > like the field is moving at warp speed,” agrees Burge, a Whitehead
> > Career Development Associate Professor of Biology. “Genomic approaches
> > have provided a number of important insights, and there has been nice
> > synergy with molecular and biochemical studies.”

> > Finding the first microRNAs
> > Rosalind Lee and Rhonda Feinbaum, researchers in the Ambros lab, were
> > conducting painstaking experiments on C. elegans when they bumped into
> > the first microRNA.

> > They knew that early development of worm larvae required proper levels
> > of the novel protein lin-14. They also knew that something was
> > regulating those levels and assumed it was another protein, so they
> > set out to isolate the gene for that protein. The result amazed them.

> > The gene fell on a stretch of DNA once termed “junk” by some, a
> > stretch outside the protein-coding region of the chromosome. It
> > appeared to code for a small RNA molecule— lin-4—that somehow
> > regulated lin-14 levels.

> > The researchers wondered if lin-4 was an esoteric molecule or a
> > harbinger of a new class of RNAs. “We had no basis for saying that
> > lin-4 was part of something much broader,” says Ambros, who now works
> > at Dartmouth Medical School.

> > His lab had no luck searching for additional RNAs in the next few
> > years. He was thrilled when researchers in the lab of Harvard Medical
> > School’s Gary Ruvkun discovered another gene in C. elegans that coded
> > for a small RNA called let-7 in 2000. In addition to cloning let-7,
> > Ruvkun’s group examined the genomes of a number of other animals and
> > found the gene for let-7 in most of them. The study foreshadowed the
> > role of genomics in later research.

> > In 2001, Rockefeller University associate professor Thomas Tuschl
> > (formerly a postdoctoral fellow in the Bartel lab), Ambros and Bartel
> > independently found dozens of additional small RNA genes in worms,
> > flies and humans and decided to call them microRNAs.

> > Leveraging genomics
> > Bartel realized he needed to look outside the toolbox of classical
> > biology. In 2001, he approached Burge—who had previously developed
> > algorithms to identify protein-coding genes in the human genome—and
> > Lee Lim, who had just completed his PhD training with Burge. The
> > researchers jumped at the chance to explore a new class of genes. Lim
> > worked jointly with the two labs to write a computer program that
> > could scan DNA sequences and predict microRNA genes.

> > He started by examining known microRNAs. Each microRNA is generated
> > from a piece of RNA that folds back on itself to form a structure that
> > resembles a hairpin. Lim scanned the genome of C. elegans for DNA
> > sequences that would give rise to hairpins after being transcribed
> > into RNA. He then looked for ways to further refine the search.

> > The double-stranded RNA of a hairpin is chopped and processed into a
> > single-stranded microRNA by proteins called Drosha and Dicer. But
> > apparently these proteins don’t recognize every hairpin. Lim whittled
> > down the list of potential microRNAs by eliminating DNA templates for
> > hairpins that lacked Dicer-friendly characteristics.

> > Lim then screened the remaining microRNA candidates by comparing the
> > genomic sequence of C. elegans with that of the related worm C.
> > briggsae. He reasoned that most of the genuine microRNAs, those
> > performing critical biological functions, would be conserved across
> > species.- Hide quoted text -

> - Show quoted text -...

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