Re: Nature magazine article- My own reaction

[Judith Rosen <***>]

Here's my analysis of that "Neutrality versus the Niche" article from Nature
magazine I posted the link for:

According to this article, both sets of ideas are only accurate within
certain narrow parameters. Outside of those parameters they produce such
flawed predictions that it is clear that much more work is needed. But the
astonishing similarity in results between the simulations of the Neutralists
and the Niche-based scientists is hard for all of them to understand. They
have such opposing views of the theoretical basis for modelling ecosystems
and yet both groups came up with models that create simulations that "look
very much like" the real thing. And-- even stranger: The results look like
each other, too. What a head scratcher!

My first reaction as I started reading this article was to mentally scoff at
the whole notion that models based on mechanistic simplicity could truly
mimic complex systems. "Neutralists" look like just more of the same old
reductionist thinkers going by a different name... So, my first impression
of Hubbell and Bell's theoretical work was based on skepticism. However, I
read through the article several times and there was something in there that
tripped a memory. I decided to look a couple things up-- I had many
discussions with my father about how biology can be "counter-intuitive" in
the lessons it teaches us.

I found it...  The example I remembered. In "Life, Itself," he wrote:

[Robert Rosen]: "Experience with this [morphogenetic ideas of cell-sorting,
used to explain protein folding] approach has been most interesting. As with
the physico-chemical approach, it proceeds by minimizing something: an
objective function. But it is not the free energy of physical chemistry.
Instead of the thousands of variables and parameters inherent in the latter
approach, it contains very few; less than ten. But the interesting point is
that among these ten or so control parameters, which manipulate the hundreds
of spatial degrees of freedom of the folding polypeptide chain, some must
incorporate "global" information, such as distance from a centroid. In turn,
this information comes from a "generic" folded protein. That is, we must use
the properties of such a "generic" folded protein as a model of protein to
be folded. This in turn may be regarded as creating an impredicativity, the
hallmark of complex systems, and precisely the sort of thing which syntax
alone cannot handle."

"On the other hand, approaching folding from this direction reveals it to be
a synergetic process; one in which very few controls can manipulate a much
larger number of configurational degrees of freedom. Such synergies are
everywhere in biology, as they also are in any inordinately constrained
mechanism. My suggestion is, of course, that in biology they are indicators
of complexity rather than of mechanisms under constraints."

Thus, my father's work gives a completely different explanation for WHY the
Neutralists' theories/models/simulations "seem" to work at all, and also why
they only work under certain artificial constraints (i.e.; for only one
level of the "food web" in an ecosystem of a size between 0.2 and 50 square
km.). It is because the theories their models are based on only address one
aspect of biological phenomena. But I think that one aspect is one which
they actually may have gotten PARTLY RIGHT. In a different way, the same is
true of the Niche-driven theories of ecosystems (which similarly only work
some of the time, also under artificial constraints and specialized
conditions). My impression is that the Niche group perceive something about
complexity, but their mindset is still reductionist/mechanistic.  They are
confusing intricacy with complexity. They instinctively have some feel for
what's really going on, which I tend to doubt in the Neutrality group, but
they aren't aware of what complexity means, so how can they improve their
models?

Both schools of thought are partly right, and both are mostly wrong. What
they are calling "complexity", of course, my father  labels
 "complicatedness". Rosennean Complexity illuminates why it is that when you
model complex systems from a mind-set of simplicity (characterized by
traditional reductionist/mechanistic approaches), you are bound to end up
with anomalies, paradoxes, and side-effects. "Streamlining" (a more accurate
word than "simplifying" in this context)the parameters of a model is not
automatically bad-- it just needs to reflect accurately the direction that
living systems do it.

Ultimately, I believe that if these two groups spent some time analyzing
where AND WHY they are each wrong (and compared notes), they would get a lot
farther than they will by arguing over where they are both right and each
proceeding alone. This article illustrates (in my opinion) a common
scientific truth: that experimental results, both positive and negative, can
be instructive, if studied with an open mind. Looking at unusual phenomena
without preconceptions to see where the problem itself leads you was some of
my Dad's best advice.

Judith