Re: Species diversity through time

On Thu, 29 Nov 2007 16:40:30 -0800 (PST), Nic
<harrisondalen@xxxxxxxxxxx> wrote:

On 28 Nov, 02:41, Bill Morse <wdNOSPAmo...@xxxxxxxxxxxxxxxx> wrote:
Nic wrote:
On 27 Nov, 03:02, Bill Morse <wdNOSPAmo...@xxxxxxxxxxxxxxxx> wrote:
r norman wrote:
On Mon, 26 Nov 2007 01:21:29 GMT, Bill Morse
<wdNOSPAmo...@xxxxxxxxxxxxxxxx> wrote:

r norman wrote:

(snip)

The question is: how do you go from an aggregation of matter than
can't do it to an aggregation that is already a 'self' that is
capable
of producing more self. That doesn't organize spontaneously unless
you define self-organization as a universe in which abiogenesis and
evolution is possible. Since we who hold the received view accept
that natural processes produce agiogenesis and evolution, then I
guess in your terms we must accept that the universe of natural
processes is
inherently 'self organizing'. I prefer my view, old-fashioned as it
may be.

As you note, the two views are not contradictory, and there are times
when I think the concept of self-organization is a more useful view. In
particular, simple selection doesn't help to understand what kinds of
aggregations are likely to organize, nor does it help to understand the
dynamics of larger aggregations such as ecosystems.

And "growth in complexity" does not form spontaneously. Once you
have a self that is capable of organizing other matter to create more
self
(which most people simply call 'growth' and 'reproduction'), you get
variations (which most people simply call 'mutation') that sometimes
allows 'self' to organize in a different way that might by some
measure be more complex. If that complexity is useful, it persists.
You might call that 'the natural tendency of self-organization to
create complexity' but most people simple call it 'mutation and
selection' or, more simply, 'evolution'.

I suppose it is possible that a very sophisticated version of
self-organization could help explain why certain body plans are more
likely than others. I'm not holding my breath. I might be more willing
to believe that it could help explain why eukaryotes could be
considered as a likely result once prokaryotes evolved - but that may
be simply because I know little about that transition.
Why would anybody suspect that the concept of self-organization is
missing from the 'received view of biology'?

Perhaps because it isn't stated in any of the standard texts? (Actually
maybe it is - I can't say that I have read any of the recent standard
texts.)

There is the secondary
and tertiary structure of proteins that in many cases can
self-assemble given only the primary structure, the sequence of amino
acids.

The self-assembly of proteins to me has little to do with the concept of
self-organization, which involves feedback processes.

There is the quaternary structure in which multiple protein
molecules self-assemble into dimers or trimers or larger groups or
even into truly huge polymeric filaments and tubules. Life itself is
based on reproduction, the self-assembly of structures at all levels
from proteins through macromolecules and cell organelles to cells,
cell assemblies, tissues , organs, and on up. The whole business of
development is that of controlling the self-assembly of the organism.
Somehow seizing on the notion of self-assembly and declaring it to be
a significant and novel new way of viewing biology is simply silly.

Again, self-assembly is different from self-organization. A hurricane is
an example of self-organization, but is not so far as I can see an
example of self-assembly. There may well be some examples in life that
involve both
processes, but they are different processes.

The problem is not that biologists can't understand the importance of
self-organization as The Organizing Principle of Biology. It is that
self-assembly is so obvious that nobody bothers even to mention it.
Instead, biologists simply go about the business of figuring out just
how it works. What are the mechanisms the produce self-assembly?
These turn out to be the mechanisms of biochemistry and biophysics,
What are the mechanisms by which self-assembly arises? These turn out
to be the mechanisms of evolution -- mutation and selection.

Both self-assembly and self-organization are produced by the mechanisms
of biochemistry and biophysics. But self-assembly is a process of
minimizing the energy of a system, while self-organization is a process
of maximizing the energy throughput of a system.

I like distinction you make (and the way you put it), but I'm confused
about whether self-organization maximises or minimises energy
throughput.

I'm glad you like the distinction, but it really isn't mine. I am just
parroting Lotka (in my case as discussed by Odum). Almost a century ago,
Lotka equated natural selection with maximizing power output.

In the case of Rayleigh-Bernard convection cells, it is definitely the
former, but in other cases the tendency is to put the brakes on. The
bath empties more slowly if the water going down a plug hole manages
to get a vortex started.

In the checking I have done, it appears that the bath empties faster with a
vortex - and the vortex is often given as an example of self-organization.

Not in my bath. Wouldn't it be unfortunate for history if
Archimedes's bath had been anomalous?

Also evolution has produced many examples of
energy thriftiness and time killing. Lasting longer is sometimes
better than living faster.

While Lotka may well have been right in general, there are plenty of
articles indicating that his principle is often wrong in the particulars.
And there is the conundrum that if a particular self-organizing system
maximizes its power output, it creates a waste stream that another
self-organizing system can take advantage of. This would seem to mean that
a system with different species will make better use of an energy source
than a system with just one species. Does this have anything to do with the
increase in species diversity through time?

This is noticable in cities where the aphids on lime trees are
drenching parked cars with sugar. Probably not a typical case.
Typically things won't evolve to be wasteful - I think, but I don't
know. Maybe evolution is neutral about waste. I suspect not. It is
more likely a matter of what is evolutionarily reachable - the trees
can't for the time being, find something advantageous to do about it,
nor can the aphids, but micro-organisms sure can. Contrast this with
ecosytems in which macroscropic species clean up. After the lions
come the vultures, and after them there's nothing much left for the
micro-organisms but shit.

So it may have something to do with the enhanced evolvability of the
newer clades.

Evolution doesn't care (more appropriately 'doesn't give shit') about
waste or efficiency. If there is an abundance of nutrients, waste
means nothing. I have seen bears swooping migrating salmon out of a
river in Alaska -- it takes me longer to get the counter person at the
fish store to pick out a piece of salmon, weight it out, and wrap it
up than it did for the bears to walk away with a salmon in its mouth.
Then they would eat one or two bites out of the prime portion and
leave the rest. A variety of birds, mostly bald eagles, but there
was a distinct pecking order in which species gets it first, would
start to pick over the remains. Even then there were dozens of
partially eaten fish scattered along the riverbank. Why eat a fish
two hours old when you can get ample food only one hour, or fifteen
minutes old? So much for the macroscopic species cleaning up
efficiently! It doesn't happen that way.

Then there is the fact that much smaller ecosystems feed far more
efficiently: filter feeders eat everything and most of the smallest
heterotrophs in the aquatic ecosystem eat their food whole, again
leaving no waste. So it is not that macrosopic=efficient,
microscopic=sloppy and it certainly is not that "enhanced evolvability
of newer clades" (whatever that means) relates to the efficiency of
gobbling down nutrients.

Then you have to understand that digestion is not a terribly efficient
process in and of itself, so the feces of many animals turns out to be
quite nutritious. So what is the difference between not eating most
of your food, leaving it for others, and eating it all but not
digesting most of it, leaving your feces to be picked over by others?
In both cases, your efficiency is very low. In other words, you
can't argue about maximizing efficiency by armchair hypothesizing --
you must go out and make actual measurements of energy consumption and
actual energy utilization; measurements which are enormously
difficult. The one clear fact is that tropical rain forests seem to
be very 'efficient' in that most of the nutrients are in the active
biomass; the soil is very deficient. Peat bogs are incredibly
inefficient because there is an enormous amount of nutrient outside
active biomass. There are really good reasons for that difference but
it has nothing to do with size or complexity or newer clades.

.

Relevant Pages

  • Re: Species diversity through time
    ... when I think the concept of self-organization is a more useful view. ... self-assemble given only the primary structure, ... than a system with just one species. ... maximizing energy throughput or efficiency or whatever? ...
    (talk.origins)
  • Re: Species diversity through time
    ... when I think the concept of self-organization is a more useful view. ... self-assemble given only the primary structure, ... than a system with just one species. ... waste or efficiency. ...
    (talk.origins)
  • Re: Species diversity through time
    ... that natural processes produce agiogenesis and evolution, ... when I think the concept of self-organization is a more useful view. ... self-assemble given only the primary structure, ... of maximizing the energy throughput of a system. ...
    (talk.origins)
  • Re: Species diversity through time
    ... when I think the concept of self-organization is a more useful view. ... self-assemble given only the primary structure, ... These turn out to be the mechanisms of biochemistry and biophysics, ... of maximizing the energy throughput of a system. ...
    (talk.origins)
  • Re: Understanding MinEP and MaxEP
    ... > can process energy faster than the disorganized states. ... available without the self-organization. ... always result in increased dissipation in the system as a whole. ... are not capable of spontaneous generation. ...
    (sci.bio.evolution)