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To: Frank Schuurmans <fps@xs4all.nl>
Hi Frank,
>I intent to use the web as a place to put all kind of
>information and ideas, since you already put the email
>messages on the web.
Can we link sites?
>I've studied biology and specialised in microbiology
>(more specific microbial physiology and environmental
>microbiology). A large part of microbial physiology
>deals with metabolic pathways. Metabolism is a term
>used for all chemical transformations taking place in
>a cell. As an example of a metabolic pathway I'll put
>information on the citric acid cycle on the web.
I have actually studied one year to be a doctor. Don't
ask what went wrong. So I know a little about metabolic
pathways, ATP, that sort of thing.
>It might be interesting to note that metabolic pathways
>are often draw as a map. Since the maps are drawn by
>biochemicists the often lay the emphasis on the chemicals
>that are chaged instead of the enzymes (so they can draw
>the chemical structure in the map :),
>it would be
>quite difficult to draw enzymes since they are very
>complex).
This is an interesting challenge. It may be possible
to model an enzyme directly with a weblet. Each webneuron
would take the place of a small piece of the enzyme maybe
a single amino acid. I presume an enzyme is a long folded
string of amino acids? i.e. a protein, but with a special
purpose.
The three dimensional folding is indeed a difficult thing
to model. Links and webneurons don't appear to be enough
for this. You need to bring real space co-ordinates in
somewhere. Maybe we need to make webneurons even smaller
down to the fabric of space itself?
>So a metabolic pathway is a collection of
>'linked chemical reactions':
>
> chemical 1 -> chemical 2 -> chemical 3
>
>Those reactions are catalysed by enzymes. Enzymes are
>one or more polypetides and a polypetide is 'a chain of
>amino acids'.
>
>All polypetides are made using a set of 20 amino acids.
>
This is good stuff. It is going beyond any limits I had previously set,
and to much smaller structures than the brain neurons.
>The sequence of the polypetides is coded in the DNA using
>4 different 'chemicals'. One gene = One polypeptide.
>
>This is in short the biological system I based my ideas on.
I see a similarity between the way DNA replicates and the
standard model of a computer - the Turing machine.
>The metaphor:
>
>Data are the chemicals and hups are the enzymes coded
>by maps (DNA) using the basic operator hups (amino acids).
>a collection of hups is a set of chemical reactions is
>a cell. A specialised cell is a neuron. a group of cells
>forms an organ (for example a 'database program'). A group
>of organs forms an organism (a computer) a group of
>organisms forms a ecosystem (the internet or a intranet).
>
>Or an organ is a computer and a set of computers forms
>an organism.
>
>Just names, I don't care how they are called as long as I can
>use my computer this way.
This all sounds brilliant, how does it relate to
my original ideas?
>Great reaction of Tim Murphy, it is exactly as I would like
>to develop this (I mentioned this before to you didn't I?)
Yes, right from the start.
>Could we setup a 'chemical reaction' ? :)
Maybe using CGI scripts between computers?
]]>
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