[MD] Levels in electronic computers

[Magnus Berg]

Hi Ian

On 2010-07-20 07:52, Ian Glendinning wrote:
> So in fact Magnus,
>
> It's not 3D Fit , but 3D Fit "ONLY" ... arrangements created without
> ANY bonding a chemist would call chemical bonding .... not whether
> geometry is significant, since it is always of some significance.

That would be more like what I'm getting at, yes. And geometry is of 
course always significant since it was "invented" in the Big Bang. We 
can never escape that, but that's just usual lower level dependency.

> The fuzziness would be on the sliding scale of what counts as chemical
> bonding, but I guess you are free to define the condition of no
> bonding (no bonding of significance).

Fuzziness only appears if you examine classical objects. Then you see 
that those two molecules, or those two objects, bonded. And then you 
wonder, why did they bond? And since you think we're now in the 
borderline of the chemical and biological levels, it must either of 
those two, putting those two types of bonding on one scale. On such a 
scale, any bond well inside the chemical "level", should be chemical, 
and any bond well inside the biological level should be biological.

But that's wrong!

DNA molecules, a very long way into the biological level, are bonded 
using chemical bonds. And bang goes the one fuzzy scale theory. We can't 
just leave the lower level behind when we enter a new one. The new level 
just goes off in a new direction, orthogonal to all lower ones, into its 
own dimension.

> A little sceptical that there may in fact be are other fit-only /
> non-bonding cases - but we'd have to get into the depths of physical
> chemistry ... catalysts, surfactants, detergents, etc ... that we
> might not usefully consider as part of the "organic" layer.

Most people don't think computers contain organic patterns either. I'm 
more inclined to thinking, "they must contain organic patterns because 
they can obviously support intellectual patterns". So if we find the 
orthogonal dimension where biology starts, I'm open for including 
non-biologish stuff as well.

> I think we need to move on to the "significance" of the fit definition
> .... what is enabled by that definition. (See the general comments by
> Krim et al about the "value" in finely honed definitions of a given
> layer.) I'm still a process man at heart.

Ah, yes, I got a few ideas about that the other day, but it was a bit 
too early to post it then.

Imagine a large molecule floating around in the primordial soup, or in a 
lab for that matter. If it were to encounter a chemically compatible 
molecule that wants to bond chemically with it, then it would have no 
choice. It would snap into a hard chemical static bond with the other 
molecule and form a new larger molecule and it would never be able to 
revert that process, never be able to get out of that bond, (short of 
another stronger bond).

If it instead was able to form a much looser bond with another molecule, 
one that could block any future attempts from static chemical bonds 
because it simply sits in the way, it would in the future have much more 
choice over its own destiny. I'm not implying a concious choice by the 
molecule, but I'm very much implying a more dynamic future for it. And 
dynamic is good, we know that much.

The process involved could be that an intrusion in one molecule fits a 
protrusion in the other, and when the protrusion is inserted in the 
intrusion of the other, there might be some friction causing both to 
expand a little and thereby locking them into place, but only for as 
long as they're warm enough, then they might break loose again.

Or is that too sexy for you Ian? :)

	Magnus