On 07/01/2011 04:51 PM, scott wrote:
> For someone with no chemistry or biology education past basic
> school-level, that was really interesting, thanks. It answered some of
> the questions I had, and made me hungry to find out more...

The mark of a well-written piece. ;-)

Yes, I too have little chemistry knowledge, beyond what I could get from 
The Osborne Introduction to Chemistry. In particular, the idea of 
catalysis seems bizarre and inexplicable.

If you read a typical encyclopaedia entry, at best you'll discover that 
DNA makes proteins, and proteins do chemical reactions, and that's how 
cells work. It might even mention that there's an RNA step in between, 
tell you which organelles do all this work, and perhaps even show you 
the table of amino acids and which codons code for them.

The reality of the situation, as I wrote, is far, far more complex (and 
interesting).

If a human being had designed the cellular machinery, they would 
redoubtably have designed it as a set of independent little compartments 
that all do their own thing in an orthogonal way, signalling to each 
other as appropriate. But when you read about how /actual/ living cells 
work, you find a tangled mess of haphazard interactions and fortuitous 
reuses of molecules and structures for multiple simultaneous purposes - 
/exactly/ as evolution would predict. It's really a very striking 
demonstration, to me.

If you read a brick-thick tome like The Molecular Biology of the Gene, 
it talks about Daltons and thermodynamic equilibria and van der Waals 
forces and so forth as if you have any idea what the hell it's talking 
about. Only Behe describes proteins as "the motors, gears, pulleys and 
scaffolding of the cell". This explains what it's all about far more 
vividly than any discussion of activation energy levels.

Still, not being an expert chemist, I find myself lacking an intuition 
for how individual molecules of a substance behave. You can sort of 
imagine an amino acid chains as being like a string of beads on a 
necklace. The books tell us that some of these beads are watery, some 
are oily, some electrically changed negative or positive, some are 
acidic or basic, the beads are all different sizes... but it's difficult 
to really visualise exactly how that makes them move. Or, for that 
matter, how some RNA molecules can fold up and edit themselves, chopping 
out introns automatically.

Basically, I lack an intuition for how these molecules float around in 
their environment.

Then again, protein folding is one of the great problems of this decade. 
(Remember folding@home, anyone?) So maybe the chemists don't yet 
understand it either...

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