Re: Nature magazine article- On niches and neutralities

[Judith Rosen <***>]

Regarding John K.'s feedback on my assessment of the Nature article content:

> John Kineman wrote: I wouldn't imply that it is such a black and white
>  matter of mechanism vs complexity - they do have to be related as
>  Howard has been arguing (maybe I was too shy on supporting this
> aspect of Howard's points).

Where did I say mechanism vs complexity? I was saying mechanism without
complexity is the reason for the extremely limited range of usefulness in
both these models' results. In other words, I was saying that both the
Neutrality people and the Niche-based people are proceding from a
mechanistic direction, which is the problem. We have all agreed (haven't
we?) that models are by nature reductionist and yet still both necessary in
science as well as useful despite their limitations. We have also discussed
my father's belief that even reductionistic models will perform better if
they are constructed with a better understanding of the fundamental
situation (ie from a perspective of complexity).

> John Kineman wrote: Also, I would add that ecologists are
> already thinking functionally out of necessity and have been for some
> time.

If that's true, it's a new development or else it's something that has been
tacit without directly addressing the fact. In that case, I'm sure the very
same ecologists may well deny till their dying breath that they are doing
that. I would be interested in Dan Fiscus' perspective on that-- Dan, if you
read this one, could you comment, please?

 > John K. wrote: But there hasn't been a fundamental theory of  > functions
that they could refer to and say "we're doing that" as the
 > mechanists can by pointing to physics. You will find quite a lot
> of Rosennean thinking in ecology, I've concluded, but it tends to go
> unjustified on theoretical grounds, or there are very confused
> attempts to justify it mechanistically. Hence it is why I think landscape
> and ecosystems ecology are good domains to adavance Rosennean
> theory I am familiar with.

Agreed. The "Rosennean thinking" is mostly unconscious and unintended, as
far as I can see. Which was my point with both the Neutralists and the
Niche-based philosophies. They both have certain aspects of my father's view
but they are not integrated and non-integrable unless both groups let go of
the theoretical basis from which they are operating. That basis is the same
one: Newtonian mechanics and Cartesian reductionism. So they wind up
contradicting each other's results which they think contradicts each other's
theoretical basis, not getting the fact that they're both operating from the
SAME theoretical basis underneath-- and they have indeed contradicted it.

> John K. wrote: Some attempts at that are being made at using agent->
based models to simulate dispersion through a suitability (niche)
> landscape, and adding complex factor by allowing the organism to
> modify its own suitability factors as it goes. This puts in the
> "impredicative loops" that RR spoke of -- like the 3-body problem.   >
While such impredicativities cannot
>  be represented in explicit dynamic (time differential)
>  equations (functions of time), they can be approximated by
> iterative loops. The result becomes unpredictable by any other means
> than running the iteration - very much like fractal images generated
> from the Mandelbrot set. There is no deep mystery in this - they are
> simple calculations just done iteratively where outputs modify inputs,
> thus approximating the simultaneouls causalities that confound
> prediction. I would classify this as computational compexity - but the
> key is that it becomes a better approximation of real life as one
> reduces the interation interval toward zero and include more and more
> inter-related factors. One cannot reduce that interval to zero nor can
> one include all the factors, so it is still a generalization, but its
> organization is much more in line with functional complexity.

As far as I am able to follow this, I see no statements that concern me in
terms of "RR's" ideas. By what definition do they use the word
"suitability"????? Isn't the concept of function creeping in there? How do
they explain the process by which a plant, say, "modifies its own
suitability factors as it goes"? How do they explain the method by which a
plant sets its suitability factors? And how do they justify the inclusion of
a concept of function here and the exclusion of the same concept elsewhere
in biology?


>
> When two or more similar species (tropical forest trees) have
> essentially the same environmental limits, as is the case in this study
> area that is small and homogenious with respect to presumed niche
> factors, their distributions can then be dominated by other dynamics
> (how they utilize a niche in real time), which can include biotic
> interactions (others who are doing the same thing), disturbance, and
> more. Niche optimization theory, taken as an extreme, was that organisms
> will segregate their requirements over evolutionary time (like Darwin's
> finches) and essentially adapt to micro-niches. This was generally shown
> to be true, but only for the case where micro-niches are stable long
> enough for species to adapt to them. What if they are changing faster
> than evolutionary adaptation?

I have a theory (I'm channeling Monty Python's Flying Circus: Anne Elk's
theory of the structure of a Brontasaurus-- ?? "A theory, which is mine,
which belongs to me..."??? Trivia question for the day: Anyone remember what
her theory was?) on this subject, which as a "regular
person"/civilian/non-scientist I am either more or less qualified to develop
and expound, depending on one's point of view...   "What if the niches are
changing faster than evolutionary adaptation?" I think the organisms that,
under those circumstances, have behavioral adaptiveness options in addition
to their evolutionary model are likely to survive much better than ones that
are stuck  with only their evolutionary model. In other words, the organisms
that could adapt their behavior to compensate for their model being
"sub-optimal" for the new conditions were the ones that survived to evolve
into the organisms of our current planetary ecosystem. I believe that's
exactly what happened with the last mass extinction. Some climatalogical
insult (be it an asteroid or volcanic or whatever, in origin) caused an
immediate period of extreme climate fluctuation/change before equilibrium
set in again. Organisms that could move around, or send their seeds around
could avoid certain dangers. Organisms that could go into "stasis"
(hibernation) could wait it out. Organisms that could utilize alternate food
sources without negative consequences or that could utilize alternate modes
of reproduction (asexual or parthenogenetic forms) would keep their species'
populations up and,thus, out-compete other less-gifted organisms for limited
resources, etc. So those organisms would have an edge in such adverse
environmental conditions. The same will be true if/when it happens again. In
fact, I think it is already happening. What was that number Dan quoted for
how many species are going extinct yearly now? The organisms with the most
rigid requirements and the fewest options are the ones that can't survive
change.


> John Kineman wrote: This is a perfect case where the
> mechanistic view should be taken only as a past constraint on an
> otherwise functionally driven complex entity that can invent exceptions
> - hence as Howard said, the need to develop both perspectives as
> complements of each other.

I think there is no argument in any of my father's work with Howard's view
on this issue. Do you agree with that, Howard?

>John K. wrote: a living functional entity could establish patterns that
> are functionally driven, even when environmental constraints are        >
chaotic. That would be the place to look for Rosennean complexity
>  at work. Neither neutral nor environmental/niche models test this,
>  and it is hard to do because there are, in niche theory, an unspecified
> number of dimensions that are important. Any discernable pattern
> is assumed to be the result of one of these factors, so it is explained
> as a missing axes in the niche model. I am working on a method where
> we could include functional specs as niche axes in addition to
>  environmental constraints. That will extend niche modeling into the
> functional domain and allow testing of functional determination
> hypotheses.

Bravo! This is exactly what using a sound theoretical basis to build models
from is supposed to offer.

> Otherwise, none of the debate about niche models says very much
> about complexity.

My thoughts, exactly. The rest of your post ought to be the basis for a
book, John. I was still reading at the point where you thought nobody but
Dan would be.

Judith

In fact, the dynamics which neither niche models nor
> neutrality models can get at is where most of the complexity resides.
> The neutrality model's equal failure in this area (which is all that is
> demonstrated when "randomness" is shown to be as good as other
> approaches) tells us not to apply niche theory where there isn't a true
> functional difference (duh), and that neither approach tells us what
> happens then, except that things seem to mix unpredictably. That itself
> is misleading, because the random mixing of species is not itself a
> random process except when viewed in the aggregate. The colonization and
> growth of trees is still constrained by suitable conditions on a
> micro-scale, but what we're seeing is the random occurrence of those
> conditions. In other words, it may be shifting habitat availabilities
> that are involved, in which case the niche theory would indeed hold some
> promise over neutrality models, which have no potential for improvement
> and were invented to test if other hypotheses are confirmed or not (like
> comparing a road accident statistic to random probability - it isn't to
> say that random explanations are better, it is to test if the other one
> means anything). For example, in the lower columbia river we are trying
> to model the availability of suitable river factors (salinity,
> temperature, flow, depth) for outmigrating salmon. The location of
> suitable conditions change dynamically as the river changes. Maybe there
> are some persistent locations, or perhaps it all mixes randomly, but
> either way the salmon still track the location of suitable conditions
> (just as we know we would, as a general matter). Hence it is the niche
> that is changing randomly, not the response to the niche (which can have
> some plasticity too, particulary if we consider R-complex functions). So
> it is a matter of scale. Neutrality models don't test this. Niche models
> are rarely tight enough to test it either, as they presume very general
> niche dimensions - i.e., a general averaged niche within which an awful
> lot of dynamics and true complexity may be going on. Furthermore, if one
> is looking for micro-climate variations and modeling the niche space of
> a whole species, this is highly iinappropraite as well. At some scale of
> micro-response we have to look at individuals, not species. The bottom
> line is that this "news" suggests very little except that the dynamics
> are ultimately going to be intractable below a certain level of
> environmental constraint - sort of an uncertainty principle in niche
> theory (which was already there). Its like quantum mechanics
> approximation of quantum phenomenon - just a statistical view of the
> mechanical uncertainties and regularities.
> A functional view may provide better predictors than separate physical
> factors and may be able to say more than a random model. For example,
> you may perhaps segregate various strategies in a forest. The old R and
> K selection theory (generalists and specialists) was a functional
> specification, for example, and it is useful where detailed dynamics
> would be too difficult to track. Strategies related to patterns of
> disturbance have a lot to do with how distributions unfold in real time.
> That's introducing functional modeling and could be seen from a
> Rosennean perspective. The other place it applies, of course, is in the
> evolution and execution of life strategies. Solving functional problems
> could be a much more efficient process/theory than adapting to separate
> environmental selective factors.
>
> Enough - I'm probably well beyond the interest of all but perhaps Dan at
> this point.
>