Re: [asa] Information and knowledge

On 4/12/07, David Opderbeck <dopderbeck@gmail.com> wrote:
>
> There was a relatively lossless transfer of some information over a
> series of communications channels.
>
>

And there is the nub of your misconception. Shannon deals with the transfer
of information in *lossy* environments. What you don't see because you don't
design storage semiconductors like I do is all the error correcting codes
such as the Reed Solomon coding on the disk drive. All of these are the
result of Shannon's ground-breaking work in 1948! The reason why it appears
to you as lossless is because we mitigate the loss using Shannon's
principles. In fact, if you look at the TCP/IP protocol stack resending
packets is part of said protocol because we assume that information gets
lost. Charles Bennet has a much harder task than Shannon did because he also
has to deal with dealing with entanglement, coherence, and as Einstein
coined "spooky action at a distance". I love physicists as they have a way
with language such as "brown muck" in QCD. :-)

As for the biology side of it it used to be believed that RNA was for the
most part messenger RNA (mRNA). This is where you get the information
transfer analogy, but the analogy breaks down rather quickly. Now we know
about so-called non-coding RNA. Information is not an ontic entity and as
Randy's friend alluded to in biology "the medium is the message". See the
following from the wikipedia article for more details
http://en.wikipedia.org/wiki/Non-coding_RNA:

Transfer RNA *Main article: Transfer
RNA<http://en.wikipedia.org/wiki/Transfer_RNA>
*

Transfer RNA (tRNA) is RNA that transfers the correct amino
acid<http://en.wikipedia.org/wiki/Amino_acid>to a growing polypeptide
chain at the ribosomal site of protein
biosynthesis <http://en.wikipedia.org/wiki/Protein_biosynthesis> during
translation.

Ribosomal RNA *Main article: Ribosomal
RNA<http://en.wikipedia.org/wiki/Ribosomal_RNA>
*

Ribosomal RNA (rRNA) is the primary constituent of
ribosomes<http://en.wikipedia.org/wiki/Ribosome>.
Ribosomes are the protein-manufacturing
organelles<http://en.wikipedia.org/wiki/Organelle>of cells and exist
in the
cytoplasm <http://en.wikipedia.org/wiki/Cytoplasm>. rRNA is transcribed from
DNA, like all RNA. Ribosomal proteins are transported into the nucleus and
assembled together with rRNA before being transported through the nuclear
membrane <http://en.wikipedia.org/wiki/Nuclear_membrane>. This type of RNA
makes up the vast majority of RNA found in a typical cell. While proteins
are also present in the ribosomes, solely rRNA is able to form peptides.
Therefore ribosomes, having a catalytic function, are a form of
ribozyme<http://en.wikipedia.org/wiki/Ribozyme>
.

Mammalian cells have 2 mitochondrial (23S and 16S) rRNA molecules
[1]<http://ribosome.fandm.edu/>and 4 types of cytoplasmic rRNA (28S,
5.8S, 5S (large ribosome subunit) and 18S (small subunit)). 28S, 5.8S and
18S rRNAs are encoded by a *single transcription unit* organized into 5
clusters (each has 30-40 repeats) on the 13,14,15, 21 and 22
chromosomes<http://en.wikipedia.org/wiki/Chromosome>.
These are transcribed by RNA polymerase
I<http://en.wikipedia.org/wiki/RNA_polymerase_I>.
5S occurs in tandem arrays (~200-300 true 5S genes and many dispersed
pseudogenes), the largest one on the chromosome 1q41-42. 5S rRNA is
transcribed by RNA polymerase
III<http://en.wikipedia.org/wiki/RNA_polymerase_III>
.

Cytoplasmic rRNA genes are highly repetitive because of huge demand of
ribosomes for protein synthesis ('gene dosage') in the cell.

Small nuclear RNA and small nucleolar RNA *Main article: Small
nuclear RNA<http://en.wikipedia.org/wiki/Small_nuclear_RNA>
*

Small nuclear RNA (snRNA) is a class of small RNA molecules that are found
within the nucleus of eukaryotic cells.

Small nucleolar <http://en.wikipedia.org/wiki/Nucleolus> RNAs (snoRNAs) are
a class of small RNA molecules that guide chemical modifications (
methylation <http://en.wikipedia.org/wiki/Methylation> or pseudouridylation)
of ribosomal RNAs (rRNAs) and other RNA genes.

Small Cajal body-specific RNA

Small Cajal body <http://en.wikipedia.org/wiki/Cajal_body>-specific RNAs
(scaRNAs) are a class of small RNA molecules similar to snoRNAs which
specifically localize in the Cajal
body<http://en.wikipedia.org/wiki/Cajal_body>,
a nuclear organelle involved in the biogenesis of
snRNPs<http://en.wikipedia.org/wiki/SnRNP>.
U85 is the first scaRNA ever described. Unlike typical snoRNAs, U85 scaRNA
can guide both pseudouridylation and 2'-O-methylation.

microRNA *Main article: miRNA <http://en.wikipedia.org/wiki/MiRNA>*

microRNA (also miRNA) are RNA genes that are the reverse complement of
portions of another gene's mRNA transcript and inhibit the expression of the
target gene.

gRNAs *Main article: Guide RNA <http://en.wikipedia.org/wiki/Guide_RNA>*

gRNAs (for guide RNA) are RNA genes that function in RNA
editing<http://en.wikipedia.org/wiki/RNA_editing>.
Thus far, gRNA mediated RNA editing has been found only in the mitochondria
of kinetoplastids <http://en.wikipedia.org/wiki/Kinetoplastid>, in which
mRNAs are edited by inserting or deleting stretches of
uridylates<http://en.wikipedia.org/wiki/Uracil>(Us). The gRNA forms
part of the
*editosome* and contains sequences that hybridize to matching sequences in
the mRNA, to guide the mRNA modifications. Other types of RNA editing are
found in many eukaryotes, including humans.

The term "guide RNA" is also sometimes used generically to mean any RNA gene
that guides an RNA/protein complex via hybridization of matching sequences.

Efference RNA

Efference RNA (eRNA<http://en.wikipedia.org/w/index.php?title=ERNA&action=edit>)
is derived from intron <http://en.wikipedia.org/wiki/Intron> sequences of
genes or from non-coding DNA. The function is assumed to be regulation of
translational activity by interference with the transcription apparatus or
target proteins of the translated peptide in question, or by providing a
concentration-based measure of protein expression, basically introducing a
fine-tuned analog <http://en.wikipedia.org/wiki/Analog_%28signal%29> element
in gene regulation as opposed to the
digital<http://en.wikipedia.org/wiki/Digital_%28signal%29>on-or-off
regulation by
promoters <http://en.wikipedia.org/wiki/Promoter>. Research into the role of
eRNAs is in its infancy.

Signal recognition particle RNA

The signal recognition
particle<http://en.wikipedia.org/wiki/Signal_recognition_particle>(SRP)
is an RNA-protein complex present in the cytoplasm of cells that binds
to the mRNA of proteins that are destined for secretion from the cell. The
RNA component of the SRP in eukaryotes is called 4.5S RNA.

pRNA

Promoter RNAs (pRNA) are RNAs that correspond to promoter regions and act as
a scaffolding to bind the antisense strand of promoter directed siRNAs
resulting in epigenetic remodeling and siRNA directed transcriptional gene
silencing in human cells.

tmRNA

tmRNA has a complex structure with tRNA-like and mRNA-like regions. It has
currently only been found in bacteria<http://en.wikipedia.org/wiki/Bacteria>,
but is ubiquitous in all bacteria. tmRNA recognizes ribosomes that have
trouble translating or reading an mRNA and stall, leaving an unfinished
protein that may be detrimental to the cell. tmRNA acts like a
tRNA<http://en.wikipedia.org/wiki/TRNA>first, and then an
mRNA <http://en.wikipedia.org/wiki/MRNA> that encodes a peptide tag. The
ribosome translates this mRNA region of tmRNA and attaches the encoded
peptide tag to the C-terminus of the unfinished protein. This attached tag
targets the protein for destruction or
proteolysis<http://en.wikipedia.org/wiki/Proteolysis>.
How tmRNA works<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10881189&query_hl=5>

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Received on Thu Apr 12 13:17:02 2007