Complexity



r norman <rsn_@_comcast.net> wrote in
news:[email protected]:

> On Sat, 24 Apr 2004 04:46:39 +0000 (UTC), Tim Tyler
> <[email protected]> wrote:

>>Because of global competion for nutrients, organisms do
>>not have to be in the same environment or physical
>>location to be in competition with one another.
>>
>>I.e. those resources that are tied up in the form of
>> forests should be subtracted from the pool of
>> resorces available for forming bacteria.
>>
>>It is true that - at the moment - complex life is doing
>>rather better on land than in the sea. However, that
>>situation is probaly not going to last for very long. We
>>can expect some serious reinvasions of the ocean as the
>>land continues to fill up with complex organisms.

> You persist in these strange ideas. Probably the most
> critical nutrient (in the sense that it is usually a
> limiting factor in growth) is nitrogen and the only source
> for usable nitrogen by complex multicellular organisms is
> nitrogen fixation by bacteria. All other limiting
> nutrients like phosphorus or iron or whatever other trace
> mineral are usable only when dissolved in water and then
> the bacteria really do get first crack at them. Only in a
> tropical rain forest do you find nutrients primarily tied
> up in multicellular organisms and there they are almost
> entirely in plants, certainly not animals. Again may I
> remind you that this habitat, impressive as it is, forms
> only a tiny fraction of the biotic world.

Actually the total contribution of nitrogen to the nutrient
cycle from anthropogenic sources (fertilizer production,
fossil fuel combustion, and legume cultivation) is currently
approximately equal to the amount of natural fixation.
Unlike carbon dioxide, the potential impacts of this has
received little attention in the popular press. The impact
of anthropogenic phosphate production (also significant in
comparison to natural phosphorus cycles) is probably better
recognized by the public, although phosphate is generally
the limiting nutrient only in fresh water environments. I
would also note that, in those environments, rooted aquatic
plants and floating macrophytes such as duckweed frequently
outcompete cyanobacteria and unicellular algae for the
available phosphorus.

Now as to the thrust of Tim's argument that we will soon
replace the nutrient cycling function of bacteria, I am
somewhat dubious - but partly because I think it will prove
cheaper to utilize existing natural cycles than to try to
take over all these functions with technology. This argument
reminds me of the dichotomy between Planet Managers and
Planet Fetishers described by Evan Eisenberg in "The Ecology
of Eden". Either technology will save us or the return to
nature will triumph. Eisenberg thinks we need to find a
middle way, and I tend to agree with him.

Yours,

Bill Morse
 
On Sun, 25 Apr 2004 19:59:18 +0000 (UTC), Tim Tyler <[email protected]>
wrote:

<snip all except the point about competition for resources>

>r norman <rsn_@_comcast.net> wrote or quoted:
>> On Sat, 24 Apr 2004 04:46:39 +0000 (UTC), Tim Tyler
>> <[email protected]> wrote:

>> >Because of global competion for nutrients, organisms do
>> >not have to be in the same environment or physical
>> >location to be in competition with one another.
>> >
>> >I.e. those resources that are tied up in the form of
>> > forests should be subtracted from the pool of
>> > resorces available for forming bacteria.
>> >

>> Only in a tropical rain forest do you find nutrients
>> primarily tied up in multicellular organisms

>there are *plenty* of other forests besides tropical
>rain forests.
>
>The world's largest forests are in Russia. If you want to
>see forests, it is not to tropical zones - but to Siberia -
>that you should head.

By "nutrients", ecologists refer to limiting items like
nitrogen and phosphorus, perhaps iron and other trace
minerals. These are the factors that limit productivity. We
already had a go-around where I agreed that eukaryotes had
the majority of carbon biomass, but that is not considered a
nutrient for which there is competition. In terms of
nitrogen and phosphorus, prokaryotes have by far more
biomass than eukaryotes.

Furthermore, in virtually all terrestrial habitats, soil
stores a tremendous amount of the limiting nutrients. That
is true of taiga, the spruce-fir coniferous forests in
Siberia you are referring to. Only in tropical rain forests
is the soil quite deficient in these factors -- most of the
nutrients are tied up in the eukaryotic biomass.
Furthermore, in every habitat on earth, it is the
prokaryotes that generally control the availability of
nutrients. So it there is to be simple competition for
nutrients that controls things, the prokaryotes would win
hands down in virtually every instance.

I have never denied that there are large quantities of very
large, very "complex" organisms in virtually all of the
habitats I live in. Virtually all of my friends and even
some of my relatives are large multicellular organisms. All
I am trying to convince you of is the simple fact that we
large, "complex", multicellular organisms are not "taking
over" from the "simple" prokaryotes. They are here in
enormous numbers. They have always been here, as long as
life has existed on earth. And every indication is that
they will continue to be here as a major and often
controlling factor in the biosphere for as long as life
persists on earth.
 
Hi Jim,

Thank you for your well-informed comments. I think you are
reading some excellent material related to complex systems
theory. (Nicolis, Prigogine, Bar Yam).

in article [email protected], Jim Menegay at
[email protected] wrote on 4/26/04 8:12 AM:

> IMO, while there may be some philosophical interest in
> explaining complexity, complexity is not part of the
> explanation for any phenomenon of interest to biology,
> chemistry, or any other natural science. Some systems of
> great structural complexity have simple behaviors, some
> have complex behaviors, some have chaotic behaviors. But
> the same can be said of systems that are quite simple
> structurally. The notion of emergence is useful, but it is
> an idea much older than the rest of "complexity theory"
> and it is not really conceptually connected to any of
> these newer ideas.

While you and I come to different conclusions, or
speculations, on the prospects for a coherent theory of
complex systems, I agree with you that there are some key
conceptual links that must be hammered out before complexity
theory should become taken for granted. AFAIK nobody has yet
proven (or argued convincingly) that there is a consistent
set of necessary and sufficient conditions for the emergence
of complexity. Until we reach such a point, or the complex
systems paradigm falls apart under its own weight, it will
be important to have skeptics like you making reasoned
arguments to the contrary. I, for one, remain optimistic
that the few loose ends remaining in complexity theory will
be satisfactorily tied up before long.

Cheers,

Guy
 
Jim Menegay <[email protected]> wrote or quoted:

> IMO, while there may be some philosophical interest in
> explaining complexity, complexity is not part of the
> explanation for any phenomenon of interest to biology,
> chemistry, or any other natural science. Some systems of
> great structural complexity have simple behaviors, some
> have complex behaviors, some have chaotic behaviors. But
> the same can be said of systems that are quite simple
> structurally.

[...]

"Self-organising systems" are the ones with the biological
relevance.

These are practically all complex systems. However not all
complex systems exhibit self-organisation.

If biological relevance is your criterion, "self-
organising systems" are the main bit of "complexity
theory" of interest.

They present alternative explanations for the existence of
complex structures to natural selection.

E.g. these days we know the patterns on zebras have at least
as much to do with reaction-diffusion equations as they
do with natural selection.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
Tim Tyler <[email protected]> wrote in message news:<[email protected]>...
> Jim Menegay <[email protected]> wrote or quoted:
>
> > IMO, while there may be some philosophical interest in
> > explaining complexity, complexity is not part of the
> > explanation for any phenomenon of interest to biology,
> > chemistry, or any other natural science. Some systems of
> > great structural complexity have simple behaviors, some
> > have complex behaviors, some have chaotic behaviors. But
> > the same can be said of systems that are quite simple
> > structurally.
>
> [...]
>
> "Self-organising systems" are the ones with the biological
> relevance.
>
> These are practically all complex systems. However not all
> complex systems exhibit self-organisation.
>
> If biological relevance is your criterion, "self-
> organising systems" are the main bit of "complexity
> theory" of interest.
>
> They present alternative explanations for the existence of
> complex structures to natural selection.
>
> E.g. these days we know the patterns on zebras have at
> least as much to do with reaction-diffusion equations
> as they do with natural selection.

Under which definition of complex/complexity do you think
that zebra patterns are complex? Which definition did you
have in mind when you say that practically all self-
organizing systems are complex?
 
Tim,

in article [email protected], Tim Tyler at
[email protected] wrote on 4/27/04 2:32 PM:

> "Self-organising systems" are the ones with the biological
> relevance.
>
> These are practically all complex systems. However not all
> complex systems exhibit self-organisation.

Can you please provide an example of a system that you
consider to be complex, but which does not tend toward self-
organization? Perhaps you meant that the manifestation of
self-organization is not realized by some complex systems
due to external constraints. If so, I would describe these
as networks that don't quite manifest complexity.

> If biological relevance is your criterion, "self-
> organising systems" are the main bit of "complexity
> theory" of interest.
>
> They present alternative explanations for the existence of
> complex structures to natural selection.

No, no, no! This is a nasty misconception, which is causing
knee-jerk dismissal of complexity theory among many
evolutionary biologists. Natural selection IS a mechanism of
self-organization. I agree that there are other mechanisms
of self-organization that are important in biology, but it
is misleading to imply that natural selection somehow
represents an explanation that is mutually exclusive to self-
organization.

> E.g. these days we know the patterns on zebras have at
> least as much to do with reaction-diffusion equations
> as they do with natural selection.

OK.

Guy
 
r norman <rsn_@_comcast.net> wrote or quoted:
> Tim Tyler <[email protected]> wrote:
> >r norman <rsn_@_comcast.net> wrote or quoted:
> >> On Sat, 24 Apr 2004 04:46:39 +0000 (UTC), Tim Tyler
> >> <[email protected]> wrote:

> >> >Because of global competion for nutrients, organisms
> >> >do not have to be in the same environment or physical
> >> >location to be in competition with one another.
> >> >
> >> >I.e. those resources that are tied up in the form of
> >> > forests should be subtracted from the pool of
> >> > resorces available for forming bacteria.
>
> >> Only in a tropical rain forest do you find nutrients
> >> primarily tied up in multicellular organisms
>
> >there are *plenty* of other forests besides tropical rain
> >forests.
> >
> >The world's largest forests are in Russia. If you want to
> >see forests, it is not to tropical zones - but to Siberia
> >- that you should head.
>
> By "nutrients", ecologists refer to limiting items like
> nitrogen and phosphorus, perhaps iron and other trace
> minerals. These are the factors that limit
> productivity. [...]

"Nutrients" are sources of nutrition - of nourishment.

Are you *sure* people are restricting the term to things
that are in short supply? Is there any reference supporting
such a usage?

> We already had a go-around where I agreed that eukaryotes
> had the majority of carbon biomass, but that is not
> considered a nutrient for which there is competition.

I do not see why that is relevant. Biomass is a simple
enough concept. Only weighing certain nutrients seems like
an attempt at confusing the issue.

You seem to be arguing that - since prokaryotes fail to
take full advantage of the available carbon, carbon
should be ignored in biomass calculations. I don't see
much sense in that.

> I have never denied that there are large quantities of
> very large, very "complex" organisms in virtually all of
> the habitats I live in. Virtually all of my friends and
> even some of my relatives are large multicellular
> organisms. All I am trying to convince you of is the
> simple fact that we large, "complex", multicellular
> organisms are not "taking over" from the "simple"
> prokaryotes. They are here in enormous numbers. They have
> always been here, as long as life has existed on earth.
> And every indication is that they will continue to be here
> as a major and often controlling factor in the biosphere
> for as long as life persists on earth.

Small organisms may well persist on life's fringes - in
environments large organisms can't easily enter.

However I do think the /main/ trend among living organisms
will be towards a single planetary-scale organism. Most of
the roles played by bacteria today in terms of food
production and chemical processing will be taken over by
organisms which are sterile clones of organisms produced in
factories. As such, although they may superficially remain
microscopic chemical processing factories, their full
reproductive phenotype will consit of a large number of
clone organisms, the factory from which they came - and its
R+D department.

I.e. their fate will be the same as that of our other
symbiotes: we will take over their reproductive
processes - and eventually make them part of the
phenotype of the dominant organisms.

Such organisms will out-compete free-living ancestral forms
for most applications - due to their being preferentially
cultivated by the dominant living creatures.

In the case of the bacteria, the ancestral free-living types
will (literally) be driven underground.

IMO, the most likely candidates for successful future small
organisms are parasites and pathogens. These creatures may
be with us for quite some time - though they probably won't
come to outweigh us; and the larger and more complex the
dominant organisms become, the more effort they are likely
to invest in eliminating them.

Ultimately, creatures will become larger because small
creatures results in inefficiency and wastage in the form of
internal friction in the form of conflicts between non-
relatives. Bigger organisms will continue to out-compete
smaller ones by exploiting cooperation and harmony to reduce
internal friction and disharmony, and thus will utilise
their resources more effectively.

So far the limits on size have been imposed by phenomena
such as asteroid impacts - and communication and
authentication problems among spatially-distributed
organisms. However these are problems which have solutions.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
On Tue, 27 Apr 2004 21:32:33 +0000 (UTC), Tim Tyler <[email protected]>
wrote:

>r norman <rsn_@_comcast.net> wrote or quoted:
>> Tim Tyler <[email protected]> wrote:
>> >r norman <rsn_@_comcast.net> wrote or quoted:
>> >> On Sat, 24 Apr 2004 04:46:39 +0000 (UTC), Tim Tyler
>> >> <[email protected]> wrote:
>
>> >> >Because of global competion for nutrients, organisms
>> >> >do not have to be in the same environment or physical
>> >> >location to be in competition with one another.
>> >> >
>> >> >I.e. those resources that are tied up in the form of
>> >> > forests should be subtracted from the pool of
>> >> > resorces available for forming bacteria.
>>
>> >> Only in a tropical rain forest do you find nutrients
>> >> primarily tied up in multicellular organisms
>>
>> >there are *plenty* of other forests besides tropical
>> >rain forests.
>> >
>> >The world's largest forests are in Russia. If you want
>> >to see forests, it is not to tropical zones - but to
>> >Siberia - that you should head.
>>
>> By "nutrients", ecologists refer to limiting items like
>> nitrogen and phosphorus, perhaps iron and other trace
>> minerals. These are the factors that limit
>> productivity. [...]
>
>"Nutrients" are sources of nutrition - of nourishment.
>
>Are you *sure* people are restricting the term to things
>that are in short supply? Is there any reference supporting
>such a usage?
>
>> We already had a go-around where I agreed that eukaryotes
>> had the majority of carbon biomass, but that is not
>> considered a nutrient for which there is competition.
>
>I do not see why that is relevant. Biomass is a simple
>enough concept. Only weighing certain nutrients seems like
>an attempt at confusing the issue.
>
>You seem to be arguing that - since prokaryotes fail to
>take full advantage of the available carbon, carbon
>should be ignored in biomass calculations. I don't see
>much sense in that.
>
>> I have never denied that there are large quantities of
>> very large, very "complex" organisms in virtually all of
>> the habitats I live in. Virtually all of my friends and
>> even some of my relatives are large multicellular
>> organisms. All I am trying to convince you of is the
>> simple fact that we large, "complex", multicellular
>> organisms are not "taking over" from the "simple"
>> prokaryotes. They are here in enormous numbers. They have
>> always been here, as long as life has existed on earth.
>> And every indication is that they will continue to be
>> here as a major and often controlling factor in the
>> biosphere for as long as life persists on earth.
>
>Small organisms may well persist on life's fringes - in
>environments large organisms can't easily enter.
>

I don't know how worthwhile it is to keep rehashing the same
old differences of opinion. You are the one who brought up
the notion that large eukaryotes were outcompeting the
prokaryotes by tying up available nutrients. You said (Apr.
24) "Because of global competion for nutrients, organisms do
not have to be in the same environment or physical location
to be in competition with one another. I.e. those resources
that are tied up in the form of forests should be subtracted
from the pool of resorces available for forming bacteria."
The fact is that carbon is not at all a limiting nutrient
about which there is any real competition. All autotrophs
are capable of fixing inorganic carbon which is abundant.
The real issue of competition deals only with those
resources which are limited. That is why I insist on
focusing on nitrogen and phosphorus. And in terms of these
two limiting nutrients, virtually all of the organic form is
tied up by prokaryotes. The Whitman, Coleman and Wiebe paper
previously cited in this thread says that 90% of the N and P
is tied up in prokaryotes.

You are entitled to your opinion about the future of life on
earth. However I still claim you are really incorrect about
the past and current status and role of prokaryotes in the
total biosphere.
 
Guy Hoelzer <[email protected]> wrote in message news:<[email protected]>...
> While you and I come to different conclusions, or
> speculations, on the prospects for a coherent theory of
> complex systems, I agree with you that there are some key
> conceptual links that must be hammered out before
> complexity theory should become taken for granted. AFAIK
> nobody has yet proven (or argued convincingly) that there
> is a consistent set of necessary and sufficient conditions
> for the emergence of complexity.

IMO, no one has given a sufficiently clear definition of
either "emergence" or "complexity" so that it even makes
sense to talk about necessary and sufficient conditions.

For example, you are now using "emergence" in a sense which
is totally different from the sense in which I had
paraphrased Bar-Lev as using it as the distinguishing
characteristic of a complex system. You seem to be using
"emergence" to mean a process of change occuring in time.
But I was using it to describe a relationship between the
descriptive properties of a system and the descriptive
properties of its subsystems. Time does not appear at all in
my sense of the word "emergence", which is, I think, the
standard one in this context.

If one wishes to study the "emergence" (your sense) of
"complex systems" (Bar-Lev's sense), then one is looking at
the emergence of emergence! And, to add to the confusion,
one must recognize that there are two different ways that
this can happen. The obvious way is that the emergent
property of the system is a novelty - that property simply
didn't exist before. The less obvious way is that the
property itself is not new - the novelty is that this
property becomes classifiable as emergent. This might happen
because the system evolves so as to become sufficiently
differentiated that subsystems can be recognized.

My main point here is that sloppy use of terminology leads
to misleading intuitions. And, I think that the whole field
of "complexity" is plagued by bad choices of terminology and
some very, very bad intuitions. Furthermore, I don't see the
situation as likely to improve when books can be sold by
coining meaningless, but evocatative, phrases such as "the
edge of chaos". IMO.
 
Guy Hoelzer <[email protected]> wrote or quoted:
> Tim Tyler at [email protected] wrote on 4/27/04 2:32 PM:

> > "Self-organising systems" are the ones with the
> > biological relevance.
> >
> > These are practically all complex systems. However not
> > all complex systems exhibit self-organisation.
>
> Can you please provide an example of a system that you
> consider to be complex, but which does not tend toward self-
> organization?

TV-screen static has very large Kolmogorov complexity - but
shows not the slighest hint of self-organising processes.

> > If biological relevance is your criterion, "self-
> > organising systems" are the main bit of "complexity
> > theory" of interest.
> >
> > They present alternative explanations for the existence
> > of complex structures to natural selection.
>
> No, no, no! This is a nasty misconception, which is
> causing knee-jerk dismissal of complexity theory among
> many evolutionary biologists. Natural selection IS a
> mechanism of self-organization. I agree that there are
> other mechanisms of self-organization that are important
> in biology, but it is misleading to imply that natural
> selection somehow represents an explanation that is
> mutually exclusive to self-organization.

I don't think I said what you seem to think I did.

I agree that natural selection IS a mechanism of self-
organization.

I agree that there are other mechanisms of self-organization
that may be significant in biology.

I fail to see much sign of any disagreement that might have
prompted the "No, no, no!"

*If* I had claimed that natural selection and self-
organization were mutually exclusive you would have a point
- but I never said any such thing.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
Jim Menegay <[email protected]> wrote or quoted:
> Tim Tyler <[email protected]> wrote in message
> news:<[email protected]>...

> > "Self-organising systems" are the ones with the
> > biological relevance.
> >
> > These are practically all complex systems. However not
> > all complex systems exhibit self-organisation.
> >
> > If biological relevance is your criterion, "self-
> > organising systems" are the main bit of "complexity
> > theory" of interest.
> >
> > They present alternative explanations for the existence
> > of complex structures to natural selection.
> >
> > E.g. these days we know the patterns on zebras have at
> > least as much to do with reaction-diffusion
> > equations as they do with natural selection.
>
> Under which definition of complex/complexity do you think
> that zebra patterns are complex? Which definition did you
> have in mind when you say that practically all self-
> organizing systems are complex?

Now you're trying to get me to give a binary definition of
complexity ;-)

In this case, I'm happy to go with the plain
dictionary entry:

"complex": consisting of interconnected or interwoven parts.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
in article [email protected], Jim Menegay at
[email protected] wrote on 4/28/04 2:44 PM:

> Guy Hoelzer <[email protected]> wrote in message
> news:<[email protected]>...
>> While you and I come to different conclusions, or
>> speculations, on the prospects for a coherent theory of
>> complex systems, I agree with you that there are some key
>> conceptual links that must be hammered out before
>> complexity theory should become taken for granted. AFAIK
>> nobody has yet proven (or argued convincingly) that there
>> is a consistent set of necessary and sufficient
>> conditions for the emergence of complexity.
>
> IMO, no one has given a sufficiently clear definition of
> either "emergence" or "complexity" so that it even makes
> sense to talk about necessary and sufficient conditions.

I disagree. I suspect that the confusion resides more in
your mind than in scientific communication within the
complexity community. I don't mean this as an insult. It is
our responsibility to make these terms clear to those who
see there meanings as vague.

> For example, you are now using "emergence" in a sense
> which is totally different from the sense in which I had
> paraphrased Bar-Lev as using it as the distinguishing
> characteristic of a complex system.

I presume you meant "Yaneer Bar-Yam", rather than Bar-Lev. I
have know Yaneer for years, and our views and semantics are
very closely aligned on these issues. Again, your suspicion
that we are at odds seems to result from a combination of
our lack of precision in describing our views and the way
you perceive our descriptions.

> You seem to be using "emergence" to mean a process of
> change occuring in time.

Yes. Emergence is a process and all processes fundamentally
depend on the temporal dimension.

> But I was using it to describe a relationship between the
> descriptive properties of a system and the descriptive
> properties of its subsystems.

This is closer to the meaning of complexity, although it
lacks the critical aspect of interaction structure among the
parts defining the topology of the network.

> Time does not appear at all in my sense of the word
> "emergence", which is, I think, the standard one in this
> context.

I am certain that the standard use of emergence in this
context requires a temporal dimension. I don't think that I
have ever seen it used to represent a static pattern.

> If one wishes to study the "emergence" (your sense) of
> "complex systems" (Bar-Lev's sense), then one is looking
> at the emergence of emergence!

You have misunderstood Bar-Yam's use of the term. He uses
the phrase "emergence of complexity" in the same way I do.

> And, to add to the confusion, one must recognize that
> there are two different ways that this can happen. The
> obvious way is that the emergent property of the system is
> a novelty - that property simply didn't exist before.

Yes; the property might never have existed for any other
system before, but it is much more likely to be a newly
manifested example of the property. Every tornado emerges
as a newly manifested vortex, but vortices have been
manifested before.

> The less obvious way is that the property itself is not
> new - the novelty is that this property becomes
> classifiable as emergent.

This implies a view that is strongly at odds with my
understanding of complex systems. All properties of
everything in the universe emerged. Can you give me an
example of a property that you think did not come into
existence in an emergent way? You might want to take a look
at the recent book by Harold Morowitz (a physicist) called
"The emergence of everything". This book should make much
more concrete for you the meaning of emergence.

> This might happen because the system evolves so as to
> become sufficiently differentiated that subsystems can be
> recognized.
>
> My main point here is that sloppy use of terminology leads
> to misleading intuitions.

As does "sloppy" listening.

> And, I think that the whole field of "complexity" is
> plagued by bad choices of terminology and some very, very
> bad intuitions. Furthermore, I don't see the situation as
> likely to improve when books can be sold by coining
> meaningless, but evocatative, phrases such as "the edge of
> chaos". IMO.

"Edge of chaos" is much more than a catchy phrase. Do you
know what it means in this context?

Guy
 
r norman <rsn_@_comcast.net> wrote or quoted:
> On Tue, 27 Apr 2004 21:32:33 +0000 (UTC), Tim Tyler
> <[email protected]> wrote:
> >r norman <rsn_@_comcast.net> wrote or quoted:

> >> I have never denied that there are large quantities of
> >> very large, very "complex" organisms in virtually all
> >> of the habitats I live in. Virtually all of my friends
> >> and even some of my relatives are large multicellular
> >> organisms. All I am trying to convince you of is the
> >> simple fact that we large, "complex", multicellular
> >> organisms are not "taking over" from the "simple"
> >> prokaryotes. They are here in enormous numbers. They
> >> have always been here, as long as life has existed on
> >> earth. And every indication is that they will continue
> >> to be here as a major and often controlling factor in
> >> the biosphere for as long as life persists on earth.
> >
> >Small organisms may well persist on life's fringes - in
> >environments large organisms can't easily enter.
>
> I don't know how worthwhile it is to keep rehashing the
> same old differences of opinion. You are the one who
> brought up the notion that large eukaryotes were
> outcompeting the prokaryotes by tying up available
> nutrients. You said (Apr. 24) "Because of global competion
> for nutrients, organisms do not have to be in the same
> environment or physical location to be in competition with
> one another. I.e. those resources that are tied up in the
> form of forests should be subtracted from the pool of
> resorces available for forming bacteria."

A point I stand by - you don't have to occupy the same niche
to be able to compete with something - using the same
nutrients is enough.

I did say that bacteria were "in the middle of a period of
decline" and that "their decline seems likely to continue".

As the roles for complex organisms continue to grow, they
will continue to compete for resources with simpler
creatures.

Such processes can be seen to be at work at the moment, and
have been going on for billions of years.

I don't think is is reasonably possible to dispute that the
complex organisms are getting a larger share of the resource
pie as time passes - since it's plain enough that they
started off with no resources at all.

I suppose it could be argued that they haven't made /that/
much progress since trees were invented - but I don't buy
this - I think the rise of complex organisms has a
continuous character - and that there's still significant
potential for future development.

Absolute numbers of bacteria may actually increase - but
their proportion of life's total has fallen historically.

I think it will continue to fall for some time to come - as
they are systematically outwitted by the complex organisms
which they must either compete with or crawl away from.

Existing symbiotic relationships with bacteria are likely to
be terminated - now that we can simply steal most of the
chemical secrets of the bacteria and make them our own.

As an example of the sorts of things that will happen, we
will come of evict our gut bacteria. Our insides will be
sterilised and we will absorb predigested food -
dispensing with farts and innumerable intestinal pathogens
in the process.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
in article [email protected], Tim Tyler at [email protected]
wrote on 4/29/04 4:25 PM:

> Guy Hoelzer <[email protected]> wrote or quoted:
>> Tim Tyler at [email protected] wrote on 4/27/04 2:32 PM:
>
>>> "Self-organising systems" are the ones with the
>>> biological relevance.
>>>
>>> These are practically all complex systems. However not
>>> all complex systems exhibit self-organisation.
>>
>> Can you please provide an example of a system that you
>> consider to be complex, but which does not tend toward
>> self-organization?
>
> TV-screen static has very large Kolmogorov complexity -
> but shows not the slighest hint of self-organising
> processes.

OK. While I find Kolmogorov complexity (KC) to be a valuable
measure, it's isolated value does not inform us of whether
or not you have a complex system in the emergent, physical
sense. Despite my ignorance of TV-screen static, I have two
hypotheses that could account for your observation that
would be consistent with my understanding of complex
systems. First, it might be merely complicated, which could
still result in a large KC value. Second, self-organization
of systems manifested in space generically exhibit a
threshold spatial scale at which self-organization
manifests. This is why I used the phrase "tend toward self-
organization", as opposed to "self-organize." If the scale
of the system is too small, it will tend toward self-
organization without actually self-organizing. I know that
this logic can appear slippery, but it is not. A similar
phenomenon would be the movement of a fleck of dust floating
in the air. The dust particle is within the reach of the
earth's gravity, yet it does not fall. Suspended particles
are always tending to fall (the "feel" the pull of gravity),
but they don't actually fall unless their mass and density
surpass a threshold, just like you and I feel the pull of
gravity without falling through the floor.

>>> If biological relevance is your criterion, "self-
>>> organising systems" are the main bit of "complexity
>>> theory" of interest.
>>>
>>> They present alternative explanations for the existence
>>> of complex structures to natural selection.
>>
>> No, no, no! This is a nasty misconception, which is
>> causing knee-jerk dismissal of complexity theory among
>> many evolutionary biologists. Natural selection IS a
>> mechanism of self-organization. I agree that there are
>> other mechanisms of self-organization that are important
>> in biology, but it is misleading to imply that natural
>> selection somehow represents an explanation that is
>> mutually exclusive to self-organization.
>
> I don't think I said what you seem to think I did.
>
> I agree that natural selection IS a mechanism of self-
> organization.
>
> I agree that there are other mechanisms of self-
> organization that may be significant in biology.
>
> I fail to see much sign of any disagreement that might
> have prompted the "No, no, no!"
>
> *If* I had claimed that natural selection and self-
> organization were mutually exclusive you would have a
> point - but I never said any such thing.

Thanks for clearing this up. I'm sorry for my over-reaction.

I have found that most evolutionary biologists that I talk
to have the kind of misconception I described above. While I
am glad that we actually share a common understanding on
these issues, I am pretty sure that most evolutionary
biologists would interpret the statement "They [self-
organizing systems] present alternative explanations for the
existence of complex structures to natural selection" as a
confrontation to Darwinism. I think we should strive for
clarity that avoids this kind of misinterpretation.

Regards,

Guy
 
"Tim Tyler" <[email protected]> wrote in message
news:[email protected]...

> If biological relevance is your criterion, "self-
> organising systems" are the main bit of "complexity
> theory" of interest.
>
> They present alternative explanations for the existence of
> complex structures to natural selection.
> E.g. these days we know the patterns on zebras have at
> least as much to do with reaction-diffusion equations
> as they do with natural selection.

Apropos which, an Evolutionary Philosophical Thought: One
might shoose a fairly encompassing way of looking at it
through a zooming lense; such as that self-organization is
What Is in_ self-knotting _ and complexity increasing
formation; and that this can be seen to occur at different
levels; AS DO our efforts to explain this multifaceted
phenomenon.

(BTW, the simulatnaeously highest an lowest, simplest, and
most general, of all evolution-relevant explanations, would
have to be: "What Is self-patterns").

P
 
Tim Tyler <[email protected]> wrote in message news:<[email protected]>...
> TV-screen static has very large Kolmogorov complexity -
> but shows not the slighest hint of self-organising
> processes.

I'm not disagreeing, exactly, but I can't resist pointing
out that your example suggests yet another ambiguity in the
concept of complexity. Wolfram's book contains many pictures
of something that looks a lot like TV static that were
generated by very simple algorithms. That is very low
Kolmogorov complexity.

I understand that your point was that a particular instance
of TV static probably cannot be generated by a simple
algorithm. But then, who is interested in the complexity of
a particular instance?

Second (hopably amusing) point: Ever wonder what happens if
you point a video camera at a TV screen which is being fed
from the camera? I have seen it claimed that (depending on
the zoom) this is an example of self organization.
 
"Tim Tyler" <[email protected]> wrote in message
news:[email protected]...
> Guy Hoelzer <[email protected]> wrote or quoted:
> > Tim Tyler at [email protected] wrote on 4/27/04 2:32 PM:
>
> > > "Self-organising systems" are the ones with the
> > > biological relevance.
> > >
> > > These are practically all complex systems. However not
> > > all complex systems exhibit self-organisation.
> >
> > Can you please provide an example of a system that you
> > consider to be complex, but which does not tend toward
> > self-organization?
>
> TV-screen static has very large Kolmogorov complexity -
> but shows not the slighest hint of self-organising
> processes.
[snip]

Certainly this TV static example is true, and another
outstanding example of why Kolmogorov complexity isn't
suited to biology. Kolmogorov complexity (KC) is really a
measure of regularity, which isn't particularly interesting
in discussing biological complexity.

KC is also particularly ill-suited to your dictionary
definition of complex as "consisting of interconnected...
parts" in another part of this thread. You can certainly
have networks that are simple -- being highly regular -- or
networks that are complex -- connections are highly random
(low to high Kolmogorov complexity, respectively). You can
also have networks within an "intermediate" regime, akin to
Watts' & Strogatz's small world network, that are not only
complex in an algorithmic sense but are also highly
analogous to real world systems, many of which display both
self-assembling and emergent properties.

So to beat my dead horse, many of the nitpicks in this
thread seem to come down to a frustratingly plastic
definition of complexity and how to measure
it.
 
Guy Hoelzer <[email protected]> wrote in message news:<[email protected]>...
> in article [email protected], Jim Menegay
> at [email protected] wrote on 4/28/04 2:44 PM:
>
> > Guy Hoelzer <[email protected]> wrote in message
> > news:<[email protected]>...
> >> While you and I come to different conclusions, or
> >> speculations, on the prospects for a coherent theory of
> >> complex systems, I agree with you that there are some
> >> key conceptual links that must be hammered out before
> >> complexity theory should become taken for granted.
> >> AFAIK nobody has yet proven (or argued convincingly)
> >> that there is a consistent set of necessary and
> >> sufficient conditions for the emergence of complexity.
> >
> > IMO, no one has given a sufficiently clear definition of
> > either "emergence" or "complexity" so that it even makes
> > sense to talk about necessary and sufficient conditions.
>
> I disagree. I suspect that the confusion resides more in
> your mind than in scientific communication within the
> complexity community. I don't mean this as an insult. It
> is our responsibility to make these terms clear to those
> who see their meanings as vague.

Here is a resource regarding some of the meanings of
"complexity" as used within the scientific community. http:-
//www.santafe.edu/projects/CompMech/tutorials/ComplexityMea-
sures.pdf I think that each of these meanings has been
adequately made clear. What has not been made clear on this
thread is which of these meanings the poster is using.

> > For example, you are now using "emergence" in a sense
> > which is totally different from the sense in which I had
> > paraphrased Bar-Lev as using it as the distinguishing
> > characteristic of a complex system.
>
> I presume you meant "Yaneer Bar-Yam", rather than Bar-Lev.
You are right, of course. My mistake.
> I have know Yaneer for years, and our views and semantics
> are very closely aligned on these issues. Again, your
> suspicion that we are at odds seems to result from a
> combination of our lack of precision in describing our
> views and the way you perceive our descriptions.

No, it was my lack of precision that caused you to suspect
that I suspect... I was not accusing you of using
"emergence" incorrectly. I was just pointing out that there
are two meanings to the word.

> > You seem to be using "emergence" to mean a process of
> > change occuring in time.
>
> Yes. Emergence is a process and all processes
> fundamentally depend on the temporal dimension.
>
> > But I was using it to describe a relationship between
> > the descriptive properties of a system and the
> > descriptive properties of its subsystems.
>
> This is closer to the meaning of complexity, although it
> lacks the critical aspect of interaction structure among
> the parts defining the topology of the network.

Yes. Bar Yam defines a "complex system" as one which has
"emergent properties". And, if you check the Wilkipedia
article on "emergence" you will discover that you are
directed to "emergent properties", but "emergence" is
defined as a process - as you would prefer.
>
> > Time does not appear at all in my sense of the word
> > "emergence", which is, I think, the standard one in this
> > context.
>
> I am certain that the standard use of emergence in this
> context requires a temporal dimension. I don't think that
> I have ever seen it used to represent a static pattern.

Check this (another example appears below):
http://llk.media.mit.edu/projects/emergence/

> > If one wishes to study the "emergence" (your sense) of
> > "complex systems" (Bar-Lev's sense), then one is looking
> > at the emergence of emergence!
> [snip]
> > And, to add to the confusion, one must recognize that
> > there are two different ways that this can happen. The
> > obvious way is that the emergent property of the system
> > is a novelty - that property simply didn't exist before.
> [snip]
> > The less obvious way is that the property itself is not
> > new - the novelty is that this property becomes
> > classifiable as emergent.
>
> This implies a view that is strongly at odds with my
> understanding of complex systems. All properties of
> everything in the universe emerged. Can you give me an
> example of a property that you think did not come into
> existence in an emergent way? [snip]

Sure. Have you perhaps noticed that some of the paragraphs
that I have written in this thread are "skeptical",
"sarcastic", or even "obnoxious"? You may have even noticed
that some of the sentences had these properties. But I'll
bet that you won't find any words with those properties, and
I'm sure I didn't type any letters or punctuation marks with
those properties. These are emergent properties at the
sentence level.

But note! I had the idea of being skeptical, sarcastic, or
obnoxious even before I broke my thought into sentences and
my sentences into words.

If that example doesn't satisfy you, how about a biological
example. Imagine a species of prairie rodents inhabiting the
American Great Plains from Mexico to Canada. Imagine that
the average size varies with latitude. In fact, a regression
coefficient tieing the latitude to the size of the rodent is
a property of the species. Now, imagine that the species
breaks up into a collection of distinct subspecies, perhaps
due to the construction of East-West highways. But within
each subspecies, there is not any correlation of latitude
with size. The regression of size against latitude has
become an emergent property. As I said:
>
> > This might happen because the system evolves so as to
> > become sufficiently differentiated that subsystems can
> > be recognized.
> >
> > My main point here is that sloppy use of terminology
> > leads to misleading intuitions.
>
> As does "sloppy" listening.
Well, sloppy listening leads to misleading intuitions only
if one believes what one hears. I rarely do that ;-)
>
> > And, I think that the whole field of "complexity" is
> > plagued by bad choices of terminology and some very,
> > very bad intuitions. Furthermore, I don't see the
> > situation as likely to improve when books can be sold by
> > coining meaningless, but evocatative, phrases such as
> > "the edge of chaos". IMO.
>
> "Edge of chaos" is much more than a catchy phrase. Do you
> know what it means in this context?

Yep! I know several things that it means. See my reply to
Wirt. Incidentally, I'm curious as to whether Wirt's
proposed meaning is the one you had in mind. When I
described this phrase as "meaningless", I had in mind the
fact that (like "complexity") it means different things to
different people. A word or phrase with too many meanings is
just as useless for scientific communication as a word with
no meanings. On the other hand, it IS useful in poetry.

Incidentally, while preparing this post, I browsed the
website of the Santa Fe Institute and discovered some quotes
from a couple of biologists that I really respect. I believe
that I endorse their viewpoints regarding "complexity" in
general and the Santa Fe version of it in particular.

The first is from a review of a debate between Maynard Smith
and Kauffman: http://www.santafe.edu/sfi/publications/Bulletins/bulletin-
spr95/12debate.html

Towards the end of question time, Maynard Smith suggested
that his real problem with a lot of complexity theory is
that it fails to ground itself in reality. Maynard Smith:
"My problem with Santa Fe, is that I can spend a whole
week there... and not hear a single fact." Kauffman: "Now
that's a fact!"

The second quotes Robert May about SFI: http://www.santaf-
e.edu/sfi/publications/Bulletins/bulletinSummer01/feature-
s/may.html

"The Institute was created as a better understanding of the
relation between simplicity and complexity in nonlinear
systems emerged," he says. "It saw itself as maybe the place
that could help articulate what replaces the simplistic
Newtonian dream. That was a pretty large thing to take on:
the boldness with which that vision has been articulated has
contributed to all the attention SFI received." This
attention tended to become polarized, he says, between
uncritical admiration on the one hand and disparagement on
the other, "neither of which reflects the much more
interesting and richly textured reality of the place."

So where does May stand? "I'm an enthusiast for the idea,"
he says, "but a rather analytic critic for what is an
accomplishment and what is charismatic blather."
 
Guy Hoelzer <[email protected]> wrote or quoted:
> Jim Menegay at [email protected] wrote on 4/28/04
> 2:44 PM:
> > Guy Hoelzer <[email protected]> wrote in message

> > And, I think that the whole field of "complexity" is
> > plagued by bad choices of terminology and some very,
> > very bad intuitions. Furthermore, I don't see the
> > situation as likely to improve when books can be sold by
> > coining meaningless, but evocatative, phrases such as
> > "the edge of chaos". IMO.
>
> "Edge of chaos" is much more than a catchy phrase. Do you
> know what it means in this context?

"Edge of chaos" *is* an evocative phrase.

However... subsequent researchers generally failed to
confirm Langton's suggestion that the location might be of
interest in terms of being a particulary attractive spot for
performing computations - and his Lambda parameter hasn't
actually proved to be of much use :-(

Cosma Shalizi offers some criticism of the whole idea - and
winds up offering a purely memetic explanation for the
existence of the phrase:

``Given that that the opinion of specialists was never
unanimous behind ?life at the edge of chaos,? and there is
every possibility it?s wrong, why was this idea picked up by
some segments of educated opinion and adopted? ? even
adopted pretty widely; I seem to recall Al Gore making some
hay with the notion, and hearing that it was being touted by
management witch-doctors. The obvious answer is that it fits
nicely with some wide-spread prejudices: basically,
antinomianism, a dislike of rules and rigidity and
formality, a positive relish for rule-breaking.''

- http://cscs.umich.edu/~crshalizi/notebooks/edge-of-
chaos.html

However... I have to number myself as among those who
thinks that there really /is/ something to Langton's
intuitive idea ;-)

"Self-organised criticality" (e.g. the pile-of-
sand/landslide effect) is the simplest way I know to clearly
illustrate to sceptics that there really /is/ something to
the notion that complex systems can tend to migrate towards
the "edge" of zones where chaotic behaviour arises.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
lock to reply.
 
Guy Hoelzer <[email protected]> wrote or quoted:
> in article [email protected], Tim Tyler at
> [email protected]
> > Guy Hoelzer <[email protected]> wrote or quoted:
> >> Tim Tyler at [email protected] wrote on 4/27/04 2:32 PM:

> >>> If biological relevance is your criterion, "self-
> >>> organising systems" are the main bit of "complexity
> >>> theory" of interest.
> >>>
> >>> They present alternative explanations for the
> >>> existence of complex structures to natural selection.
> >>
> >> No, no, no! This is a nasty misconception, which is
> >> causing knee-jerk dismissal of complexity theory among
> >> many evolutionary biologists. Natural selection IS a
> >> mechanism of self-organization. I agree that there are
> >> other mechanisms of self-organization that are
> >> important in biology, but it is misleading to imply
> >> that natural selection somehow represents an
> >> explanation that is mutually exclusive to self-
> >> organization.
> >
> > I don't think I said what you seem to think I did.
> >
> > I agree that natural selection IS a mechanism of self-
> > organization.
> >
> > I agree that there are other mechanisms of self-
> > organization that may be significant in biology.
> >
> > I fail to see much sign of any disagreement that might
> > have prompted the "No, no, no!"
> >
> > *If* I had claimed that natural selection and self-
> > organization were mutually exclusive you would have a
> > point - but I never said any such thing.
>
> Thanks for clearing this up. I'm sorry for my over-
> reaction.
>
> I have found that most evolutionary biologists that I talk
> to have the kind of misconception I described above. While
> I am glad that we actually share a common understanding on
> these issues, I am pretty sure that most evolutionary
> biologists would interpret the statement "They [self-
> organizing systems] present alternative explanations for
> the existence of complex structures to natural selection"
> as a confrontation to Darwinism. I think we should strive
> for clarity that avoids this kind of misinterpretation.

"Self-organisation" /is/ in conflict with what is
characatured as "panadaptionism" - the idea that most
prominent features of organisms exist because they are
favoured by selection.

There are other self-organising forces *besides* natural
selection. They are responsible for things like animal
patterning, tree-shaped structures, drainage patterns and
the development of the brain.

Natural selection may get the final say - but the generation
of variation /often/ involves alternatives that can be
easily produced.

It may be quite reasonable to say that a branching tree was
one of the early variations formed - because there was a
short sequence of developmental instructions that led to it
and the sequence could easily be reached by mutation.

The idea that simple instruction sequences produce apparently-
complex, patterened and purposeful-looking results is well
known to those interested in fractals and cellular automata.

It may be that processes like those play significant roles
in development - and that those are the processes we should
invoke as primary explanations for the observed phenomena
(rather than saying natural selection is responsible).

Wolfram probably takes this "anti-selectionism" the
furthest:

``For while natural selection is often touted as a force of
almost arbitrary power, I have increasingly come to believe
that in fact its power is remarkably limited.''

- S.W. A.N.K.O.S., p.392.
--
__________
|im |yler http://timtyler.org/ [email protected] Remove
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