Re: [Phys-l] Bonds, energy; formerly: More Stupidity in state exams

[John Denker <jsd@av8n.com>]

At 10:26 PM +0100 8/9/11, Dr. Keith S. Taber wrote:
> > The terminology 'energy-rich phosphate bonds'is not helpful in this
> > regard, but perhaps 'easily-disrupted-by-energy phosphate bonds' does
> > not have quite the same ring? Of course, energy does tend to be given
> > out when these bonds break (in the context of the whole reaction
> > going on), and I think some biologists feel it is therefore being
> > pedantic to point out that like any bond energy is required to break
> > them.

On 08/09/2011 03:52 PM, chuck britton wrote:
> hmmm, and I thought that the 'Energy' was released when the fragments 
> RE-bonded with oxygen or whatever.


Let's be careful here.  There are two ideas on the table, one of
which is completely OK, while the other is completely wrong.  When
somebody says one thing, we should not accuse them of saying the
other.

Specifically:  
 -- Suppose I say ATP is a high-energy molecule or an energy-storage 
  molecule.  That is IMHO a perfectly reasonable thing to say, as
  explained below.
 -- I did not say that you can get the energy out by breaking bonds. 
  That's just silly.  That's not what I said, and not what I meant.

As I see it, it's like a book on a high shelf in the sub-basement.
It's got a higher energy than any of the other books.  There are two
ways of looking at it:
  a) You can liberate energy by moving the book to a lower shelf.  
  b) The fact that it's still in the sub-basement -- far below "ground" 
   level -- is sometimes relevant but sometimes not.

In particular, fact (b) does not change fact (a).

1) This is not a language problem.  I am allowed to talk about one thing
without mentioning all the other things that could have been mentioned.  
I am allowed to say that 1+1 equals 2 without mentioning the fact that
2+2 is not equal to 17.  I am allowed to say that the reactants have 
greater energy than the products without saying anything about "breaking" 
bonds.

2) Language allows you explain an idea and give it a name, and then use 
the name again and again.  This is what language does for a living.  On 
the rare occasions when you are talking to someone who doesn't understand 
the meaning, you ought to explain, but this is an exceptional case.  The
fact remains that in the general case, you do not need to re-explain
the meaning every time you use a word.

In particular, potential energy is gauge-invariant.  If you are talking
to someone who doesn't understand this profound, fundamental fact, you
ought to explain ... but you should not demand that biochemists re-explain
this fact to each other every time they use the word "energy".

This is key to the present discussion, because when I say the ATP molecule
has a high energy, gauge invariance requires the listener to ask "high
relative to what?"  
 -- Anybody who has the slightest clue will know that I mean the reactants
  have a high energy relative to the products.
 -- If somebody overhears our conversation and is too clueless to ask 
  "relative to what", please don't blame the language.  An eavesdropper
  who doesn't grasp the fundamental principles of energy shouldn't be
  part of the ATP conversation, in any language.  You can't participate
  in our conversation if you don't know what we're talking about.

3) There is a third way in which this is not a language problem:  Sometimes
you just have to draw the picture.

        ------------------------------------------------------
       |                                       "zero level"
       |  binding
       |  energy
       |
       |
       |             ------------
       |             intermediate
       V                state
       ----------
        initial
         state

                                    ------------
                                       final
                                       state


   Tangential remark:  It is slightly troublesome that binding energy is 
   always measured downward, so that more binding energy means less actual 
   energy, but there are very good reasons for this.  The advantages 
   outweigh the disadvantages, and this usage is not going to change 
   anytime soon.  If anybody has a specific, constructive suggestion for 
   a better way to handle this, that would be great, but I haven't heard 
   any viable suggestions yet.  This is only very tangentially related to
   the issues heretofore mentioned in this thread.

Again I invoke the principle that I am allowed to talk about one thing a
without being required to mention all the other things that could have
been mentioned.  I am allowed to say that the initial state has a higher
energy than the final state, without mentioning the intermediate state
at all ... and double-especially without mentioning the "zero level",
which we know (by gauge invariance) is completely arbitrary and irrelevant
to the actual physics that is going on.

I am not required to mention the intermediate state, and indeed we often
don't know about or care about the intermediate state.  Catalysis can 
change the intermediate state ... whereas (by conservation of energy) 
nothing can change the energy-difference between the initial state and 
the final state.

Again I say this is not a language problem.  The language police should
please go find another windmill to tilt at.  If somebody mentions the 
energy of a reaction, and the listener does not immediately bring to 
mind the relevant picture (see above), then they ought not be having the 
conversation at all, in any language, and changing the terminology is
not going to help.