Review II:

Although the author has taken into account most of my comments on his
misinterpretations of the non-equilibrium thermodynamic theory. I am
not convinced of the technical correctness of the results. The main
result of the paper is based on eqs. (32-34). As I have mentioned in
my previous comments, the author needs to explain why it is not
appearing a second time derivative in equation (33). As I can see in
eq. (33) a second time derivative of p_\gamma need to be
included. This modifies the main result on the stability of
ecosystems.

Review V:

The revised version of JTB1852 "Thermodynamic stability of Ecosystems"
goes a long way toward addressing my concern that the article was
essentially uninteresting and uninformative to empirical ecologists.

In particular, the Introduction of the revised article makes the
author's motivation and reasons for beleiving that ecologists should
be interested in what he has to say quite clear, in contrast to the
original version. I have a couple of suggestions that I think will
enhance the acceptability and readability of the manuscript and these
are listed below.

1. The first paragraph of the Intro can be toned down. I can think of
   very many evolutionary biologists who will get aggravated by a
   statement like "Stasis...now forms a major focus of evolutionary
   study at all levels of the hierarchy of life on earth" Stasis has
   received some attention, but punctuated equilibrium is hardly as
   important in mainstream evolution as this paragraph suggests. For
   example, The work of Elena and Lenski cited in the begining of
   paragraph 2 of the Introduction is on asexually reproducing
   bacteria where the stasis is due to the population having to "wait"
   for de novo beneficial mutations to arise (a mechanism very
   different from the Gould and Eldredge formulation of punctuated
   equilibrium in speciation, which involves long periods of
   evolutionary fine tuning, punctuated by major shifts in selection
   pressures due to range expansions etc.). The Lenski & Elena model
   breaks down, for example, in sexual organisms where the meiotic
   shuffling of the genome keeps generating ample genetic variants
   each generation and allows for long periods of consistent responses
   to selection (e.g. see Joshi et al. 2003 Journal of Genetics 82(3):
   147-162; or Teotonio and Rose 2001 Evolution 55: 653-660 and
   references therein, or even Lenski's earlier work on bacteria
   e.g. Travisano et al. 1995 Science 267:87-90. I suggest not making
   such a sweeping statement about the importance of punctuated
   equilibrium as a phenomenon, and mentioning also that the
   underlying mechanisms/causes of a punctuated equilibrium pattern at
   different levels (e.g. micro and macroevolutionary) can be very
   different.

2. On a similar note as the comment above, the discussion of
   succession in ecosystems (citing Odum & Odum, and Margalef) on page
   2 top is likely to provoke controversy. Succession is a somewhat
   outdated view in community ecology and in the 1970s and especially
   1980s, community ecologists have focussed on finer dynamics, like
   species turnovers etc. within what at a gross scale would probably
   be stasis. Again, we come to the problem of what is stasis: Stasis
   in the Gould and Eldredge sense of macroevolution is actually a
   period wherein fairly intense changes may be occuring in the
   genetic composition of the population as it is fine-tuned to its
   environment by selection. Once again, it will help if the
   statements of succession are not made so strongly, but in a
   somewhat more guarded manner.

Review VI:

Unfortunately in addition to making some of the changes that to me
were important to this paper, the author has added some new
embellishment which detract from the paper's merits. There is also a
major problem area for me which has not been corrected and in my view,
still needs to be so to recommend this paper for publication. My
conclusion will be that I still think the paper has a significant
enough contribution to make for all concerned to stay with it but I'm
afraid it would take at least one more round, at least for me, to
recommend it for publication.

The details are as follows:

Author has now added James Lovelock and the so-called 'Gaia
Hypothesis' to the second paragraph of the paper. There is merit in
much of Lovelock's writing (like that the Earth functions as a single
system at its highest level and that O2 has been put into the
atmosphere and maintained at PAL levels by life itself, an idea of
course not originating with Lovelock) but the hypothesis itself to the
extent that there is one (there are actually about 6 conflicting ones
in fact), what is sometimes called 'homeostatic Gaia' is simply false
("heterostatic" might be a more appropriate term for a system that
progressively moves away from equilibrium a fact which is not without
significance with respect to a thermodynamic understanding of
planetary evolution). What's more the author even uses some of
Lovelock's illegitimate teleological language to describe it. There is
not the time or space here to go through this in detail but it is
logically incoherent and empirically wrong. Author, from the beginning
has cited Swenson's 'problem of the population of one' which deals
with planetary evolution, or evolution of the planet as a whole but
it's not clear to what extent he's read these papers.  I will make the
same point with respect to what I think is the major substantive
problem with the paper which is found at the end. It was a point I
brought up in my first critique and spent some time with but which the
author has not seemed to grasp.

In addition it should be pointed out that the author's attempt to push
the significance of his own paper (which deals with a narrow region of
thermodynamic developmental space) and has led him to adopt the the
discredited 'homeostatic' hypothesis of Lovelock then finds its way
into footnote 1 where he says it is contentious whether or not human
domination of the biosphere is leading to greater biosophere
homeostasis. Contentious is a remarkable understatement. This footnote
has got to come out along with the whole planetary homeostasis notion
itself.

Perhaps more important than the particular insertion of 'homeostatic
Gaia" into this paper (a big problem in and of itself) is that the
author in so doing goes in the opposite direction of what at least
this reviewer was trying to suggest should be the spirit of this
paper, and the only one in which it is legitimate from my point of
view (important though nevertheless). It deals with a particular
NARROW range of evolutionary or ecological dynamics that sits and fits
within a broader and much more already developed framework. Author
seems to keep wanting to extend it out of this narrow range, or
characterize the full range of developmental evolutionary or
ecological dynamics in this way.

On page 2 author has now included references to both Odums as well as
Margalef as I suggested and makes good use of them so this is a
plus. BUT with the use of Raup and Sepkoski to again attempt to
bolster the 'homeostatic' notion he stumbles again into the same
problem as above. These data do not generalize to planetary ecosystems
in general today whatsoever. The conclusion is based on an idealized
notion which denies the radical transformation of the Earth going on
right in front of our eyes. Please tell it to the rain forests
or...that ecosystem stability is increasing.

In the next paragraph he, as he did originally an correctly cites
Swenson for the "problem of the population of one". In his original
paper he cited a paper by Swenson (1989) where this does not
appear. And here's what I said in the first comments:

On page 6 the author refers to the "problem of the population of one"
and cites Swenson, 1989. This is an extremely important idea and it is
right to attribute it to Swenson, but the paper he cites, to the best
of my knowledge does not contain this idea. I've included a number of
references below from Swenson that do and the author should use one or
more of these to make this point rather than the one he uses (several
are online and I've put the URLs).

Author has now picked one, but whereas this has the issue as the title
so it's a good choice from that point of view, from my experience with
students it is hard paper to locate so suggest using it but also (or
instead) one of the other more accessible papers. There are lots to
choose from and many of them contain points that the author should be
noting and citing so any of them could do double duty.

Author now also has cited Lotka as was recommended but leaves in the
citation " Kay (1991) and Schneider and Kay (1994) have argued in a
convincing way..for the description of ecosystem characteristics and
evolution in terms of thermodynamic theory."cita In my comments I
pointed out that the Schneifder and Kay papers where they are right
(and there is much error in these papers) simply restates in
impoverished terms what has been said by the actual pioneers who I
then recommended author cite. He has cited them but left these
in. What he says they've showed was showed by others. To make this
reviewer happy these should come out.

Serious problem: Author now says "It is further suggested..change..in
constraints...greater..entropy production.  He is suggesting something
that has already been shown. This is just the major problem set up in
Swenson's paper and the most general characteristic of evolutionary
dynamics that had been left unexplained until a decade an a half ago
(e.g., see Swenson 2000). Author does not seem to have read his own
remarks at the end about entropy production increasing and Swenson's
work in Discussion and Conclusions. Swenson has to be cited here.

THE REAL SUBSTANTIVE PROBLEM: In Discussions and Conclusions author
mentions Swenson's law of maximum entropy production after noting his
paper a particular narrow region (namely close or near to stasis
conditions). In his original paper author says

"One question we have not addressed here...is why ecosystems have
tendency to grow and increase in complexity. A possible explanation
not in conflict with the proposed framework has been proposed by
Swenson..."

I suggested that this limitation be put in the paper clearly at the
outset so as not to overclaim and confuse the reader. Instead what the
author has now done in his intro is to claim this in some sense as
something this paper is now 'proposing' yet there is nothing really
about it in the paper at all. So author has gone in the opposite
direction from what this reviewer in any case suggested. Now instead
he says

"Although most of this paper addressess...we have also ventured into
the speculation on a wider scope of the application of thermodynamic
principle..."

BUT as pointed out few paragraphs above this "speculation" of the
author's has already been widely addressed and written about. It is
the central problem that Swenson's work which he cites addressed and
solved.

"It is interesting that this apparent duality of ecosystems, to move
toward stable stationary states of minimal entropy production over
relatively short time scales where the external....towards systems of
higher internal entropy production over longer evolutionary time
scales under changing external constraints, is mirrored within
individuals.  It appears that an individual advances towards a state
of minimal entropy production over development from birth to death
(Prigogine, 1967) while there is empirical evidence that there is a
long term evolutionary trend...(cites Zotin, 2001)."

Here is what I said in my last comments and author has ignored it
altogether:

There is also as far as I can tell a confusion or conflation between
gross entropy production and (e.g., mass) specific entropy
production. If the author is erroneously conflating these it is
important that he not. Many have done this before him including
Prigogine himself in one particular paper but clarified in later
work. In living things in general as they grow and develop the
specific entropy production decreases (think of it as generalized
specific metabolism), but the gross entropy production (viz., the
total amount of food or energy gradient required to maintain it in its
growth) increases as required by the balance equation of the second
law. Swenson has a good discussion of this although I cannot find the
citation showing that even if there were no other factors operating to
cause it this is the expected (and necessary) result simply for
example as the result of allometric surface/volume relations. That is
since transport of matter/energy into a thing is some function of the
surface while what must be internally 'fed' is some function of the
volume then allometric relations predict that the efficiency of
transport ceteris parabus will decrease (why things divide etc. or why
there are many things rather than one, or why lungs etc. see the
generalized discussion on the extension of space-time 'diffusive'
surfaces in Swenson's paper the author cites and also in broader terms
in the "Development of Space-Time..." paper in the Annals New York
Academy of Sciences below ). In any case, the specific entropy
production goes down while the gross entropy production goes up.

When the author talks about a 'duality'...and cites Prigogine to say
that over development from birth to death an individual advances
towards a state of minimum entropy production he is making an error
that Prigogine himself made and others copied for a while nearly four
decades ago. But it is entirely false. As a thing grows from birth to
adulthood and its size increases its entropy production (as required
by the balance equation of the second law) necessarily INCREASES, that
is its total or gross entropy production. Typically, on the other hand
it's (mass) specific entropy production goes down. I have looked
briefly at the Swenson papers and this discussion can be found in
almost any number of them (e.g, below) including I believe the one
from 1989 that the author cites (but e.g, see "Thermodynamic Reasons
for Perception Action Cycles" or any of the others). The author is
conflating entropy production in general with specific entropy
production. In general to restate what I stated last time (see above)
due to general allometric relations, e.g, surface-volume as an
example, as any thing grows while the the gross entropy production
increases (and following Swenson it is exactly due to this that we see
the dimensions of space-time filling up or out, the general trend in
planetary evolution) but the specific entropy production shows a
negative sign. That is why crudely put things then divide, replicate
etc. and why there is not one big thing but space-time highly and
progressively differentiates itself.

SO THERE IS NO DUALITY; IT IS PART OF THE SAME DYNAMICS. FURTHER this
is not equivalent to the simple case described by near equilibrium
thermodynamics which is the source for the authors formalism and where
some number of forces or 'sources' are allowed to disappear and one or
more are not. The total entropy production as well as the specific
entropy production of such a system necessarily monotonically
declines. This is the entire content of what's given sometimes as
Prigogine's theorem of minimum entropy production. It is entirely
derivable from the second law and Onsager's relations. Namely, if the
second law most generally says potentials or forces are spontaneous
dissipated then given Onsager's relations a system with n number of
forces where some subset of them are allowed to be 'used up' or
dissipated will show a monotonic decline in entropy production.

None of these facts contradicts Swenson's principle it should be
underscored. In both cases the system will pick the path or assembly
of paths that minimize available potentials at the fastest rate given
the constraints. In fact the simplest and most easy case used by
Swenson (the "Guass-in-a-box" experiment) used to demonstrate the
principle of maximum entropy production is the case where the gross
entropy production monotonically declines.

Author needs to go and study, as well as cite the relevant papers on
this matter. More particularly he must not conflate specific entropy
production with gross or total entropy production. To do so not only
misses one of the keenest insights of the literature of the last
decade and a half but fails to understand the dynamics as
well. Author's formalism and contribution is still important in this
context but the author must get it right if the contribution is to be
valid.

In conclusion, I am on the author's side, but I will not be if the
next time the author ignores in particular this very important part of
my critique.  Here are the citations I provided last time for the
population of one. The bottom paper on the general thermodynamic
understanding advanced by Swenson of the "law of entropy production
maximization" should be cited in author's paper.

Population of One:

SWENSON R. 1991. End-directed physics and evolutionary ordering:
obviating the problem of the population of one. In The Cybernetics of
Complex Systems: Self Organization, Evolution, and Social
Change. F. Geyer, Ed. :41-60. Intersystems Publications. Salinas, CA.

SWENSON, R. 1997. Autocatakinetics, evolution, and the law of maximum
entropy production: a principled foundation toward the study of human
ecology. Adv. Hum. Ecol. 6: 1-46.  http://www.spontaneousorder.net/

SWENSON, R. & M.T. TURVEY. 1991. Thermodynamic reasons for
perception-action cycles. Ecol. Psych. 4: 317-348
http://www.ecologicalpsychology.com

Swenson, R. 1996. "Thermodynamics and Evolution." In G. Greenberg and
M. Haraway, eds., The Encyclopedia of Comparative Psychology. New
York: Garland Publishers, Inc.
http://www.entropylaw.com/thermoevolution2.html

General Review Swenson's principle:

Swenson, R. (2000). Spontaneous Order, Autocatakinetic Closure, and
the Development of Space-Time. Annals New York Academy of Sciences,
vol. 901, pp. 311-319, 2000.
http://evolution.philosophyofscience.net/