Guy Hoelzer  wrote in
news:ch0v4u$d4h$1{at}darwin.ediacara.org: 

> in article cgvefb$2sg5$1{at}darwin.ediacara.org, William Morse at
> wdmorse{at}twcny.rr.com wrote on 8/30/04 7:43 AM:
 
 
>> Yet I think it is the norm in science (if you want to call it a
>> mistake that is your business) to first observe and classify
>> phenomena, and then to attempt to create definitions that correspond
>> to the classifications. 
> 
> I would not call this a mistake, as you have described it.  There is a
> difference, however, between constructing categories we wish existed
> and letting the evidence show us the categories.  I think that doing
> the former is a "mistake" when the latter is a viable alternative.
> 
>> Anyone observing life will classify it as a different phenomenon than
>> a flame or a tornado (despite the many similarities).
> 
> That is fine as a proposition, as long as we remain open minded about
> the possibility that our intuition may have led us astray.

Good point.
 
>> The question (which is what started this thread) is what makes it
>> different. 
> 
> Well, that question assumes the validity of your proposition that they
> are different.  I would prefer to think about the qualities that are
> essential to our notion of life first, justify the importance of those
> qualities through model exploration, then examine your proposition
> that these phenomena are fundamentally different.  I am not contesting
> your proposition here; I am merely wary about proceeding as if we know
> it is correct. 
> 
>> Flames, tornados, viruses, and living creatures all are structures
>> that self- organize and utilize an energy gradient. My intuition
>> tells me that flames and tornados are short term energy minima - they
>> will automatically appear rather quickly under the right conditions.
> 
> Yes, although I think of them more as concentrations of energy, rather
> than "energy minima."
> 
>> Viruses are rather a special case, which is why I mentioned them
> 
> Yes.  They are an excellent phenomenon for addressing these issues.
> 
>> - they don't really self-organize in the sense that the other
>> phenomena do, but the difference is subtle. Life presumably started
>> out as a short term energy minimum, but are far from that now.
> 
> Right.  I coined the term "life storms" a few years ago to suggest a
> metaphor for the way life may have originally appeared on earth.
> 
>> Cut a flame off from its fuel source and it will die, cut some
>> bacteria off from their fuel source and they will form spores that
>> can last at least hundreds of years until a fuel source reappears.
>> There is a difference - the difficulty is to define it.
> 
> Great point.  Bacterial spores and viral particles are like the
> stagnant structures of crystals, because they have virtually no active
> metabolisms. Setting aside, for the moment, the issues of punctuated
> metabolism (phases in which it is turned on or off), I have come to
> think of the host's cellular machinery as part of the viral structure.
>  That is, it is part of both the cell system and, potentially, part of
> the viral system. Ontologically, I see no problem in claiming that at
> any particular moment it is acting as part of one, or the other, or
> both systems simultaneously (its performance would then likely be
> compromised for both functions). 

An interesting observation. In isolation I could argue that viruses are 
not alive. There is a sharply defined structural boundary available that 
will fit this view of viruses. But from a more long term standpoint, 
viruses are intimately involved in information transfer between 
organisms. The boundary is moved outward to include the host organism, 
and suddenly the virus is "alive". 

But doesn't this take on the question give considerable weight to the 
observer, undercutting your argument on another thread about the 
objectivity of information? 

  
>> Now I agree that the phenomenological details are likely to be red
>> herrings, which is probably why Tim didn't like including electron
>> transport and it set off your pet peeve alert. I also don't like it
>> for those reasons - but as I thought about it more the knee-jerk
>> reaction subsided and it seemed that electron transport might in fact
>> be a very basic component of self-organizing systems that could
>> create long-term structures utilizing energy gradients.
> 
> I would ask what is the fundamental process that electron transport is
> achieving in your phenomenological view of life.  Then I would use
> that function in my definition of life, allowing for the possibility
> that other kinds of mechanisms might achieve the same function in
> other living systems (e.g., those from other galaxies far far away).

And long long ago? :-)

Tim will hopefully forgive me for replying here to both his and your 
comments. I had started a reply to his follow until I read this one - and 
I wanted to respond to several different points.

You ask about the process that electron transport is achieving. Tim 
indicates that information storage is fundamental to life and thinks that 
electron transport is an irrelevant detail. I may not be the best judge 
of this, because my master's thesis was on denitrification - a phenomenon 
intricately dependent on electron transport. But if we are looking at 
life as a process involving both information and energy use, electron 
transport starts to look like a key process. Energy gradients other than 
the chemical gradients involved in electron transport certainly exist - 
gravitational, heat, and kinetic gradients are all used by other self-
organizing systems in addition to life. But none of these three are 
particularly suited to information storage and transfer - although the 
National Archive and Records Administration might disagree, given their 
stated preference for stone tablets as a storage medium :-) The types of 
processes that might in the future be used for ultra-efficient 
information storage, such as quantum computing and various holographic 
systems, are not particularly useful for energy transfer. Electron 
transport is useful for extracting energy from a gradient (such as 
sunlight), storing energy for later use in maintaining structure (via 
phosphate bonds in the case of life on earth) and transfering information 
(via nerve synapses, again for life on earth).  Electron transport may 
not prove to be necessary for life, but on the other hand you may have to 
search long and hard to find life that does not depend on it.


Yours,

Bill Morse
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