Re: [asa] Information and knowledge

That's why I said "*relatively* lossless." I'm well aware the Shannon deals
with compression and lossy environments. The transfer from laptop hard
drive to flash memory stick is "relatively" lossless exactly because
engineers have gotten pretty good at data compression. If only my transfer
of it into my student's brains could be so efficient!

As to RNA, that isn't the point I was trying to make. The point is that you
can take information from a genome out of the biological realm entirely and
process it in a mechanical realm, a computer. It is not inconceivable that
in the relatively near future engineers will be able to then take that
information out of the mechanical realm and return it to the biological.

Indeed, this is *already* being done in the area of gene synthesis (see, e.g.,
here: http://www.blueheronbio.com/genemaker/technology.html). I don't have
time to research the specific point just now, but I've no doubt that the
process described here involves algorithms that make use of Shannon's
information theory.

Given all this, I can't see how computational biology is an example of
"teleportation" if ordinary computing is not. If communications theory
shows that "information" has some ontological status with respect to
computer networks, the same seems to hold for "information" with respect to
biological networks. In both instances, information theory can be used to
limit the lossiness of the transmission.

The real question, IMHO, is a philosophical one -- whether Shannon's
theories really imply that information has ontological status apart from the
media in which it resides. I'm not convinced that the ability to
communicate across media with limited lossiness must carry such big
implications.

On 4/12/07, Rich Blinne <rich.blinne@gmail.com> wrote:
>
>
>
> 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 14:12:02 2007