Olivier Perriquet Class Visit – RNA Discussion Notes

Perriquet – Science Talk- RNA

AUCG
Single word – alphabet of 4 letters (combinatorics)
Levels of description:
Primary structure – letters
Exact atomic position
Secondary Structure – topological description

Focus— Secondary structure prediction from the primary structure
Using computational means

What role does RNA have in thought? (Seaman)

Single molecule or set of molecules
Homologs – closed in sequence / same function
We can assume they fold in space into a shape that is similar
Strengthens the prediction of a common structure

Over simplified model – abstractly [Limitology of current science]
Not caring of kinetics of folding, time folding, complex of molecules help

How to address molecular explosion

Does the folding cause the shape
Or is it what it is made out of

When sequence in same position – will fold in the same shape

Molecule is always moving
May have alternative folding

All molecules are alive – biopolimers – linear — sequences
Fold into space and make 3D info
The shape is specific and it will help the other molecules to bind.

Cell is many many molecules

Genes are expressed into proteins – active agent of the cell.
Each cell is expressed in a different way.

Enhance or inhibit the expression, feedback loops – relationships

The identity of the molecules – binary code
3d Shape –

Do we need a genetic code? Bio-memetic same attribute and behavior

2D

Is this a 3D code? (Seaman)

Computation and the reality of facts. Limitology of the facts.

production of 3D structure

referring to a model not really happens
in CS – np hard problem [sometimes instaneously solved by nature]

use analogue computers for particular cases (See Gordon Pask — Maverick Machines)
nature solved this problem
synthetic biology – how to change the mechanism of cells / expression
to divert it to make computation with the cell.

Ethics of this – Multi-perspective to knowledge production…

If you think of human as computer – you have to redefine computation.

We have discussed codes in thought – Proteins, Oscillations, Synapse

+ quantum processes – See

Interesting to think of synthetic biology — unpack these 3D codes and how they contribute to Neosentience…

We also spoke about scientific revolutions:

See Thomas Kuhn – The Structure of Scientific Revolutions

for Outline:

http://des.emory.edu/mfp/Kuhn.html

also we mentioned the Otto Rössler text about measures…

http://www.achtphasen.net/index.php/plasmaether/2010/12/11/p1890

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