Complexity

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

Quoted message said:

irr <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

IRR <[email hidden]> wrote or quoted:

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Quoted message said:

The best-established way of measuring complexity is to
use Kolmogorov complexity.

This:

* Confines discussion to digital phenomena;
* Is difficult to measure;
* Has a subjective element - since it depends on a
choice of descriptive language.

The first is no problem, if we are content to confine
ourselves to the complexity of genomes.

The second is a problem in theory:

* Except in a few trivial cases, you can only put
bounds on the

metric -

Quoted message said:

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rather than measure it exactly (and even then the
lower bound is

rarely

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much use). I would suggest ignoring this problem -
and measuring the value using a conventional high-
quality compressor of a type that is capable of
dealing well with repeated sequences.

...and in practice...

* You need to sequence the genome in question before
you can measure its complexity;

The third makes the metric less asethetically
attractive. My approach would probably be to say
something along the lines of:

"Always use FORTRAN-77 as your language".

....]

IMO this third problem -- choosing a language with which
to quantify complexity -- is still *the* showstopper
when it comes to biology.

I like the answer I gave.

I almost always give this answer.

So far - IMO - I have had no serious complaints ;-)

Better check your audience ;-).

Quoted message said:

There may be a few even more "unbiased" languages out
there - but FORTRAN-77 is convenient enough.

Quoted message said:

While we might all agree that the primate brain is an
incredibly complex organ, it's not at all agreed upon
what it is we mean by this. For example, a Kolmogorov
measure fails miserably in classifying the brain as
complex, after all you're really only talking about two
dozen or so different recognized cell types stamped out
in enormous repetition with iterated connections between
them -- in other words, a digital representation of the
brain is incredibly compressible.

IMO - this makes no sense at all :-|

An acceptable digital version of the brain would handle
the same I/O - and produce similar inputs from similar
outputs. This sounds like a job for a huge computer with
an *extremely* lengthy description to me - and of course a
correspondingly enormous Kolmogorov complexity.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Certainly a huge computer, but really an extremely lengthy
description? Check out the top 500 list (top500.org) -- the
fastest computers in the world are and will continue to be
iterations of the single processor system you're likely
reading this reply on right now. While such massively
parallel systems -- including the human brain -- are
increadibly impressive to look at, they are remarkably
regular. Kolmogorov essentially a measure of regularity; low
in highly parallel architectures and high in random ones.

"John Wilkins" <[email hidden]> wrote in message
"]news:[email hidden]...

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irr said:

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

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IRR <[email hidden]> wrote or quoted:

> So for example (and in loose reference to one of
> your other posts),

there

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> are many, many groups of bacteria that cooperate,
> differentiate into

a

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> multitude of morphologically distinct cell types,
> and build

elaborate,

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> macroscopic (differentiated though monoclonal)
> structures. [See,

for

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> examples, hyphae-producing Streptomyces, akinete
> and/or heterocyst

forming

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> cyanobacteria, iron-scavenging Shewanella
> macrocolonies, or the

wondrous

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> assortment of organisms that comprise e.g.
> thermophilic, alkaline

microbial

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> mats]. Yet the Kolmogorov complexity of the genomes
> from these

organisms

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> are indistinguishable, they all have roughly the
> same number of

genes,

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the

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> degree of their metabolic and protein interaction
> networks are all

scale

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> free (power-law distributed) with nearly identical
> scaling

exponents,

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etc.

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> etc. ad nauseum. Find me some underlying, unifying
> Standard Model

of

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> Complexity that has evaded notice in all studies to
> date, and I'll

pay

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all

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> the publication charges on your paper.

The best-established way of measuring complexity is to
use Kolmogorov complexity.

This:

* Confines discussion to digital phenomena;
* Is difficult to measure;
* Has a subjective element - since it depends on a
choice of descriptive language.

The first is no problem, if we are content to confine
ourselves to the complexity of genomes.

The second is a problem in theory:

* Except in a few trivial cases, you can only put
bounds on the

metric -

Quoted message said:

Quoted message said:

Quoted message said:

rather than measure it exactly (and even then the
lower bound is

rarely

Quoted message said:

Quoted message said:

Quoted message said:

much use). I would suggest ignoring this problem -
and measuring the value using a conventional high-
quality compressor of a type that is capable of
dealing well with repeated sequences.

...and in practice...

* You need to sequence the genome in question before
you can measure its complexity;

The third makes the metric less asethetically
attractive. My approach would probably be to say
something along the lines of:

"Always use FORTRAN-77 as your language".

....]

IMO this third problem -- choosing a language with which
to quantify complexity -- is still *the* showstopper
when it comes to biology.

While we

Quoted message said:

Quoted message said:

might all agree that the primate brain is an incredibly
complex organ,

it's

Quoted message said:

Quoted message said:

not at all agreed upon what it is we mean by this. For
example, a Kolmogorov measure fails miserably in
classifying the brain as complex, after all you're
really only talking about two dozen or so different
recognized cell types stamped out in enormous repetition
with iterated connections between them -- in other
words, a digital representation of

the

Quoted message said:

Quoted message said:

brain is incredibly compressible. I can think of
examples with a

fraction

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of the genes present in a human brain cell that can give
rise to at

least

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that many different recognizeable cell types, and I can
just as easily

think

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of organisms with a vastly larger proteome that show
none of the interactions or differentiation of neural
progenitor cells.

In my mind the obstacle here is that we have not yet
rightly /defined/

the

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problem. Our inherent notion of what is complex is
prominently if not exclusively based on (as evident in
my examples) visual cues, but

prominent

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biological observables such as cell morphology have been
-- at least

thus

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far -- incredibly poor indicators of complexity.

Chaitin suggests that you pick a suitably comprehensive
and capable language - he uses LISP - and stick with it.
So long as you can express or model what you are trying to
comparatively measure, then the results are notionally
commensurate. But the problem here is that this makes
"complexity" a measure of what we can *say* about
something. And this seems right to me - complexity is the
surprisal value, as it were, of our descriptions of
things. The relative scales will change as we are able to
describe more and more, unless we artificially restrict
ourselves to some aspect of the things, like the DNA
(introns or exons? Expressed or regulatory? Methylation or
not?) sequences of organisms, in which case complexity is
a measure of some theoretical quantity and is *still* an
abstract notion. I don't see a way to avoid measuring only
what we know about things in this regard.
--
John Wilkins [email hidden]
wilkins.id.auwilkins.id.auOpen ↗ "Men mark it when they hit, but
do not mark it when they miss"
- Francis
Bacon

I very much agree with this, which is why I advocate
'calling a spade a spade', against Tim Tyler's notion of a
generalized complexity (or complexity metric) applicable
throughout biology and transcending evolution. It's not hard
to find statements saying that human beings are more complex
than bacteria, and while this statement seems palatable
enough, my basic argument is that we need to be absolutely
clear about what it is that we're calling complex.

To the best of our knowledge, the most complex life was much
simpler 3.8 billion years ago than it is today, and so we
have this general idea that complexity increases over time.
But as you point out above, without establishing a rigorous
context within which we can define and measure complexity,
we're doomed to follow the same ill-fated path that lead to
the idea that big brains and opposable thumbs represent some
sort of evolutionary pinnacle towards which all living
things will eventually migrate.

And much like our big brains, complexity to me seems to be
more of a specialized -- as opposed to universal -- solution
that some organisms have arrived at (which I've tried to
outline examples of in the above thread). Clearing this
hurdle in the discussion opens the door to, IMO, a much more
interesting set of questions such as *why* complexity is
only found in a limited number of organisms (for example,
one wonders immediately of the increased necessity for high
fidelity replication -- that is, more parts to copy -- among
more complex organisms).

"chupacabra" <[email hidden]> wrote in message
"]news:[email hidden]...

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"Frank Reichenbacher" <[email hidden]> wrote
in message

news:<c5m9ck$30f8

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How large do you think the niche space is, or how many
niche spaces do

you

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think there are, for sentient beings on this planet?
Will the next

sentient

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being have to develop some new structure or function
(say telepathy) in order to out compete us, or find a
new niche space?

Presently, as you know, the most successfull and,
probably, smartest people usually have few offsprings,
and, at least in the developed countries, the birth rate
is much higher in undereducated people with lower
intellectual status So, in modern humans we, in fact, have
a "devolution" where every next generation is, on average,
less "smart" than a previous one. It may be objected by
the Dawkins idea that for the progress of the human
civilization what really matters is not a selection of the
genes but the selection of memes or ideas. But, as humans
will biologically grow more and more stupid, it may once
appear that they simply have not got sufficient brainpower
to command the collected memes.

What does this have to do with your question, "why does
evolution progress from the simple to the complex?"

Frank

Hi Tim,

in article [email hidden], Tim Tyler at
[email hidden] wrote on 4/17/04 2:21 PM:

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Complexity - as everyone agrees - is a scalar property,
not a binary one.

I don't think that "everyone" agrees with this point of
view. Proposed and often used "measures" of complexity are
indeed scalars, but that issue is about estimation rather
than physical reality. I would describe an alternative,
binary view of complexity as the one promoted by Prigogine.
I think that he would have agreed with something like the
following: complexity emerges along with function and
structure from the merely complicated. Emergence is a
process, so there would certainly be a period of ambiguity
as to whether complexity has been achieved, but the concept
would still be essentially binary and not fairly represented
by a scalar parameter.

Guy

chupacabra <[email hidden]> wrote or quoted:

Quoted message said:

Presently, as you know, the most successfull and,
probably, smartest people usually have few offsprings,
and, at least in the developed countries, the birth rate
is much higher in undereducated people with lower
intellectual status. So, in modern humans we, in fact,
have a "devolution" where every next generation is, on
average, less "smart" than a previous one. It may be
objected by the Dawkins idea that for the progress of the
human civilization what really matters is not a selection
of the genes but the selection of memes or ideas. But, as
humans will biologically grow more and more stupid, it may
once appear that they simply have not got sufficient
brainpower to command the collected memes.

The reverse has been happening over the last 5 billion years
- as fairly convincingly demonstrated by skull fossils.

I don't see any good reason to think things have changed in
that department.

Fitness is not about counting offspring - it's about leaving
descendants.

Having many offspring might be an insurance strategy against
hostile local conditions - and should not necessarily be
interpreted as a sign of fitness.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Guy Hoelzer <[email hidden]> wrote or quoted:

Quoted message said:

in article [email hidden], Tim Tyler at
[email hidden]

Quoted message said:

Quoted message said:

Complexity - as everyone agrees - is a scalar property,
not a binary one.

I don't think that "everyone" agrees with this point of
view. Proposed and often used "measures" of complexity are
indeed scalars, but that issue is about estimation rather
than physical reality. I would describe an alternative,
binary view of complexity as the one promoted by
Prigogine. I think that he would have agreed with
something like the following: complexity emerges along
with function and structure from the merely complicated.
Emergence is a process, so there would certainly be a
period of ambiguity as to whether complexity has been
achieved, but the concept would still be essentially
binary and not fairly represented by a scalar parameter.

I don't know what you mean.

For instance, what's this distinction between complexity and
complicated all about:

``complexity emerges along with function and structure from
the merely complicated''

...?

*Maybe* there are some folk somewhere who think complexity
is a binary quantity.

I'd be inclined to show them Kolmogorov complexity - and ask
them the equivalent of "how many hairs make a beard" - i.e.
how they would defend their preferred "complexity
threshold".
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

irr <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

IRR <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

Quoted message said:

> The bacteria are disadvantaged - since they can't
> easily cooperate with one another, and build large
> structures - and such cooperation seems to pay off.
>
> They have been (literally) overshadowed - and
> relegated to the nooks and crannies of the world.
> These days much of the work gets done by macroscopic
> organisms - such as trees.
>
> Once bacteria ruled the world - but now they in the
> middle of a period of decline. Their decline seems
> likely to continue - as much of the world's chemical
> processing gets taken over by machines - who will
> have stolen the bacteria's enzymatic secrets from
> their genomes.

This anthropocentric misinformation that you've
slipped in at multiple points in this thread has no
factual basis and no support in real science. There
have been at least half a dozen articles in just the
past few years in Science and Nature alone that point
towards an inverse scale free relationship between
organism size and organism density. That is, the very
smallest organisms outnumber slightly larger organisms
by orders of magnitude, and outnumber even larger
organisms by many more orders of magnitude.

Well, yes - becuase they are so tiny. I am outnumbered
millions-to-one by my own gut bacteria - but that
doesn't mean that they are more important than I am.

Certainly not what I meant to imply -- I'm not even sure
if Kolmogorov had a metric by which we could start to
categorize importance 🙂. But I would maintain that the
enormous numbers of microorganisms that are out there
argue they aren't in any sort of period of decline. In
fact in the middle of this 6th mass extinction we've
apparently instigated, I'd say they are in better shape
than anyone.

Once they were the only form of life - but now they are
excluded from many large and significant niches by
competition from plants.

The rise of complex organisms seems destined to continue -
and if life remains confined on Earth, as complex organisms
rise, bacteria practically must fall back - and give up
their carbon atoms to make more room.

Quoted message said:

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In fact the largest organisms on Earth (ourselves
among them) make up only a minute fraction of the
global biomass.

A *lot* of the global biomass is in the form of trees
- e.g.:

``The ongoing enrichment of the atmosphere with CO2
raises the question of whether growth of forest trees,
which represent close to 90% of the global biomass
carbon, is still carbon limited at current
concentrations of close to 370 p.p.m.''

...most of which are much bigger than us.

Unfortunately these very dated statistics are only valid
if you're on Bush's Science Advisory Board. See for
example Whitman et. al's "Prokaryotes: The unseen
majority" (Proc. of the National Academy of Sciences, 95:
6578-83. 1998) for a starter read and follow the trail of
references therein.

It seems that agrees that plants have equal or greater
biomass than procaryotes. Does it really support the idea
that complex organisms make up only a minute fraction of the
global biomass?

Quoted message said:

Notice that this article is already 6 years old and so
predates recent major discoveries into the "deep
subsurface" biosphere (e.g. Lidy hot springs and similar
studies) that we've only scratched the surface of, and
that may represent an unseen microbial contingency larger
than all combined terrestrial life.

*Maybe* there's an "unseen microbial contingency larger than
all combined terrestrial life". Maybe not.

Even if true, that wouldn't make the biomess of organisms
larger than us "a minute fraction of the global biomass".
Trees really are pretty significant carbon sinks - and I
think they do not deserve dismissal.

Quoted message said:

And of course I'd argue that the counting is already
biased -- every cell from every macroscopic organism has
anywhere from one to a few dozen mitochondria (and quite a
good number have chloroplasts) that were unjustly abducted
from the microbial domain and now count towards the
eukaryotic total!

These are systemtically surrounded by their clones - with
whom they cooperate in order to perpetuate themselves.

ISTM that they should be counted among the cooperators -
rather than as among the "free livers".

True, they once worked for the other side - but allegiances
can change...
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

John Wilkins <[email hidden]> wrote or quoted:

Quoted message said:

irr said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

Quoted message said:

Quoted message said:

The best-established way of measuring complexity is to
use Kolmogorov complexity.

This:

* Confines discussion to digital phenomena;
* Is difficult to measure;
* Has a subjective element - since it depends on a
choice of descriptive language.

The first is no problem, if we are content to confine
ourselves to the complexity of genomes.

The second [...]

The third makes the metric less asethetically
attractive. My approach would probably be to say
something along the lines of:

"Always use FORTRAN-77 as your language". [...]

IMO this third problem -- choosing a language with which
to quantify complexity -- is still *the* showstopper
when it comes to biology. [...]

Chaitin suggests that you pick a suitably comprehensive
and capable language - he uses LISP - and stick with
it. [...]

My suggestion exactly [OK - except for the bit about
"LISP" ;-)].

Complexity metrics are dependent on the language used
to specify them with ... but not all languages are
created equal.

You can build a FORTH interpreter in a smaller physical
space than you can build a Java interpreter. Picking small,
simple languages with efficient hardware implementations
makes the choice of language *much* less arbitrary.

Instead of "length of description", you could use "size of a
computer made entirely of NAND gates" - and this would get
you pretty close to the goal of getting a fundamental
complexity metric.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

irr <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

irr <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message
> IRR <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

Quoted message said:

> * You need to sequence the genome in question before
> you can measure its complexity;
>
> The third makes the metric less asethetically
> attractive. My approach would probably be to say
> something along the lines of:
>
> "Always use FORTRAN-77 as your language". [...]

IMO this third problem -- choosing a language with
which to quantify complexity -- is still *the*
showstopper when it comes to biology.

I like the answer I gave.

I almost always give this answer.

So far - IMO - I have had no serious complaints ;-)

Better check your audience ;-).

Do you have an objection? If so, what is it?

Quoted message said:

Quoted message said:

Quoted message said:

While we might all agree that the primate brain is an
incredibly complex organ, it's not at all agreed upon
what it is we mean by this. For example, a Kolmogorov
measure fails miserably in classifying the brain as
complex, after all you're really only talking about
two dozen or so different recognized cell types
stamped out in enormous repetition with iterated
connections between them -- in other words, a digital
representation of the brain is incredibly
compressible.

IMO - this makes no sense at all :-|

An acceptable digital version of the brain would handle
the same I/O - and produce similar inputs from similar
outputs. This sounds like a job for a huge computer with
an *extremely* lengthy description to me - and of course
a correspondingly enormous Kolmogorov complexity.

Certainly a huge computer, but really an extremely lengthy
description? Check out the top 500 list (top500.org) --
the fastest computers in the world are and will continue
to be iterations of the single processor system you're
likely reading this reply on right now. While such
massively parallel systems -- including the human brain --
are increadibly impressive to look at, they are remarkably
regular. [...]

The human brain is not "remarkably regular" - and as such
requires a lengthy description.

Some computer systems are very regular - at least when they
are turned on - but they are not very much like brains.
--
__________
|im |yler timtyler.orgtimtyler.orgOpen ↗ [email hidden] Remove
lock to reply.

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

chupacabra <[email hidden]> wrote or quoted:

Quoted message said:

Presently, as you know, the most successfull and,
probably, smartest people usually have few offsprings,
and, at least in the developed countries, the birth rate
is much higher in undereducated people with lower
intellectual status. So, in modern humans we, in fact,
have a "devolution" where every next generation is, on
average, less "smart" than a previous one. It may be
objected by the Dawkins idea that for the progress of
the human civilization what really matters is not a
selection of the genes but the selection of memes or
ideas. But, as humans will biologically grow more and
more stupid, it may once appear that they simply have
not got sufficient brainpower to command the collected
memes.

The reverse has been happening over the last 5 billion
years - as fairly convincingly demonstrated by skull
fossils.

I don't see any good reason to think things have changed
in that department.

In our society success of people is usually measured by
their status, money, education etc. You just look up some
relevant demographic statistics tables: more successive,
educated, rich people definitely have less offspring. This
means that human evolution has either reversed or is guided
precently by other factors less known to scientists.

Quoted message said:

Fitness is not about counting offspring - it's about
leaving descendants.

Having many offspring might be an insurance strategy
against hostile local conditions - and should not
necessarily be interpreted as a sign of fitness.

You are right, what matters is the offring that managed to
survive to the reproductive age. Yes, in underdeveloped
countries and among less successive social groups child
mortality is usually higher. Yet, as this is often not too
high in modern society almost everywhere, anyway less
successive groups will leave more reproductive offspring and
progress through generations.

On Wed, 21 Apr 2004 03:34:27 +0000 (UTC), Tim Tyler <[email hidden]>

Quoted message said:

irr <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

IRR <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

> > The bacteria are disadvantaged - since they can't
> > easily cooperate with one another, and build large
> > structures - and such cooperation seems to pay off.
> >
> > They have been (literally) overshadowed - and
> > relegated to the nooks and crannies of the world.
> > These days much of the work gets done by
> > macroscopic organisms - such as trees.
> >
> > Once bacteria ruled the world - but now they in the
> > middle of a period of decline. Their decline seems
> > likely to continue - as much of the world's
> > chemical processing gets taken over by machines -
> > who will have stolen the bacteria's enzymatic
> > secrets from their genomes.
>
> This anthropocentric misinformation that you've
> slipped in at multiple points in this thread has no
> factual basis and no support in real science. There
> have been at least half a dozen articles in just the
> past few years in Science and Nature alone that point
> towards an inverse scale free relationship between
> organism size and organism density. That is, the very
> smallest organisms outnumber slightly larger
> organisms by orders of magnitude, and outnumber even
> larger organisms by many more orders of magnitude.

Well, yes - becuase they are so tiny. I am outnumbered
millions-to-one by my own gut bacteria - but that
doesn't mean that they are more important than I am.

Certainly not what I meant to imply -- I'm not even sure
if Kolmogorov had a metric by which we could start to
categorize importance 🙂. But I would maintain that the
enormous numbers of microorganisms that are out there
argue they aren't in any sort of period of decline. In
fact in the middle of this 6th mass extinction we've
apparently instigated, I'd say they are in better shape
than anyone.

Once they were the only form of life - but now they are
excluded from many large and significant niches by
competition from plants.

The rise of complex organisms seems destined to continue -
and if life remains confined on Earth, as complex organisms
rise, bacteria practically must fall back - and give up
their carbon atoms to make more room.

Quoted message said:

Quoted message said:

> In fact the largest organisms on Earth (ourselves
> among them) make up only a minute fraction of the
> global biomass.

A *lot* of the global biomass is in the form of trees -
e.g.:

``The ongoing enrichment of the atmosphere with CO2
raises the question of whether growth of forest trees,
which represent close to 90% of the global biomass
carbon, is still carbon limited at current
concentrations of close to 370 p.p.m.''

...most of which are much bigger than us.

Unfortunately these very dated statistics are only valid
if you're on Bush's Science Advisory Board. See for
example Whitman et. al's "Prokaryotes: The unseen
majority" (Proc. of the National Academy of Sciences, 95:
6578-83. 1998) for a starter read and follow the trail of
references therein.

It seems that agrees that plants have equal or greater
biomass than procaryotes. Does it really support the idea
that complex organisms make up only a minute fraction of
the global biomass?

Quoted message said:

Notice that this article is already 6 years old and so
predates recent major discoveries into the "deep
subsurface" biosphere (e.g. Lidy hot springs and similar
studies) that we've only scratched the surface of, and
that may represent an unseen microbial contingency larger
than all combined terrestrial life.

*Maybe* there's an "unseen microbial contingency larger
than all combined terrestrial life". Maybe not.

Even if true, that wouldn't make the biomess of organisms
larger than us "a minute fraction of the global biomass".
Trees really are pretty significant carbon sinks - and I
think they do not deserve dismissal.

Quoted message said:

And of course I'd argue that the counting is already
biased -- every cell from every macroscopic organism has
anywhere from one to a few dozen mitochondria (and quite
a good number have chloroplasts) that were unjustly
abducted from the microbial domain and now count towards
the eukaryotic total!

These are systemtically surrounded by their clones - with
whom they cooperate in order to perpetuate themselves.

ISTM that they should be counted among the cooperators -
rather than as among the "free livers".

True, they once worked for the other side - but allegiances
can change...

Tim, I am afraid the facts indicate that prokaryotes really
do outweigh everything else. The PNAS paper by Whitman,
Coleman, and Wiebe which was cited above
(pnas.org6578Open ↗ does
indicate that the total carbon fixed in prokaryotes was of
the same order of magnitude, but somewhat less, than the
carbon fixed in plants. That is as you say. But carbon and
total biomass is a poor measure of biological abundance.
Virtually all the carbon content of plants is inert
cellulose in the cell wall. If you look at functional
material, the proteins as measured by the nitrogen content
or nucleic acids (plus many other active metabolites) as
measured by phosphorous content, then prokaryotes overwhelm
the plants. Yes, trees are nice, but the oceanic bigger and
richer and the soil even more so. And all this doesn't even
begin to count the enormous mass of archaea that were
discovered since that paper. You don't mention that the
title of that paper is "Prokaryotes: the unseen majority".

You say that prokaryotes are "but now they are excluded from
many large and significant niches by competition from
plants". Perhaps you don't realize that the only reason
plants can grow in these "large and significant niches" is
that they are supported (both physically and metabolically)
by the soil which is totally dependent on the microbes
living there. Yes, the terrestrial world we live in is
dominated by eukaryotes. But we live in only a small
fraction of the earth. Several people have repeatedly
pointed out to you that aquatic and soil/substrate ecology
is dominated by microbes and that these form by far the
largest component of the biosphere.

I'll accept your argument that counting mitochondria and
plastids as part of the "prokaryotic" side is a bit of a
stretch. But given that these organelles are a small
fraction of the biomass in eukaryotes (although they
outnumber the eukaryotic cells) and that the eukaryotic
biomass is a small fraction of the total prokaryotic
biomass, it really doesn't make that much of a difference.

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

Quoted message said:

irr <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

irr <[email hidden]> wrote or quoted:
> "Tim Tyler" <[email hidden]> wrote in message
> > IRR <[email hidden]> wrote or
> > quoted:

Quoted message said:

Quoted message said:

> > * You need to sequence the genome in question
> > before you can

measure

Quoted message said:

Quoted message said:

Quoted message said:

> > its complexity;
> >
> > The third makes the metric less asethetically
> > attractive. My

approach

Quoted message said:

Quoted message said:

Quoted message said:

> > would probably be to say something along the lines
> > of:
> >
> > "Always use FORTRAN-77 as your language". [...]
>
> IMO this third problem -- choosing a language with
> which to quantify complexity -- is still *the*
> showstopper when it comes to biology.

I like the answer I gave.

I almost always give this answer.

So far - IMO - I have had no serious complaints ;-)

Better check your audience ;-).

Do you have an objection? If so, what is it?

Quoted message said:

Quoted message said:

> While we might all agree that the primate brain is
> an incredibly complex organ, it's not at all agreed
> upon what it is we mean by

this.

Quoted message said:

Quoted message said:

Quoted message said:

> For example, a Kolmogorov measure fails miserably in
> classifying the brain as complex, after all you're
> really only talking about two

dozen

Quoted message said:

Quoted message said:

Quoted message said:

> or so different recognized cell types stamped out in
> enormous repetition with iterated connections
> between them -- in other words,

a

Quoted message said:

Quoted message said:

Quoted message said:

> digital representation of the brain is incredibly
> compressible.

IMO - this makes no sense at all :-|

An acceptable digital version of the brain would
handle the same I/O -

and

Quoted message said:

Quoted message said:

Quoted message said:

produce similar inputs from similar outputs. This
sounds like a job

for

Quoted message said:

Quoted message said:

Quoted message said:

a huge computer with an *extremely* lengthy
description to me - and of course a correspondingly
enormous Kolmogorov complexity.

Certainly a huge computer, but really an extremely
lengthy description? Check out the top 500 list
(top500.org) -- the fastest computers in the world are
and will continue to be iterations of the single
processor

system

Quoted message said:

Quoted message said:

you're likely reading this reply on right now. While
such massively parallel systems -- including the human
brain -- are increadibly

impressive

Quoted message said:

Quoted message said:

to look at, they are remarkably regular. [...]

The human brain is not "remarkably regular" - and as such
requires a lengthy description.

Some computer systems are very regular - at least
when they are turned on - but they are not very much
like brains.
--
__________
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lock to reply.

Quoted message said:

From Erdi's "The Complexity of the Brain: Structural,
Functional and Dynamic

Modules": "Experimental facts from anatomy, physiology,
embriology, and psychophysics give evidence of highly
ordered structure composed of 'building blocks' of
repetitive structures in the vertebrate nervous system. The
building block according to the modular architectonic
principle is rather common in the nervous system. Modular
architecture is a basic feature of the spinal cord, the
brain stem reticular formation, the hypothalamus, the
subcortical relay nuclei, the cerebellar and especially
cerebral cortex." and on and on....

Going back to my original message, the neurohistology and
neuroanatomy (that is, the number of differentiated cell
types and their organization) is incredibly well laid out
with astonishing regularity and organization. This is not
remarkable. What is remarkable is that such a regular
structure can exhibit amazingly complex features (look at,
e.g. any of Christof Koch or Francis Crick's recent work,
among a wide field of other 'computational
neuroscientists'😉.

These complex features that arise from a regular structure
are very real and active points of interest these days. This
is popularly referred to as emergence, and one major
question is if this emergence corresponds to the appearance
of language, consciousness, etc. Now going back to my
'original original' message, none of these complex features
are apparent when looking at the characteristic
neuroanatomical structure, and so here again is another
example where a swath of different complexity metrics will
fail to meet our standards.

On the other hand, we could look instead at other features,
such as the interconnectiveness of various parts of the
nervous system (scale free? I'm not sure) and perhaps get a
better measure of complexity for a given metric. I wouldn't
argue against this, and Koch and many others argue
convincingly for this. But the bottom line is, as I've been
trying to convince you of, the solution depends entirely on
how you define your space and choose to measure the
complexity of that space.

Though it might apply great in theory or in determining
regularity of strings of numbers, your argument of "though
the definitions may differ in detail... it tends not to
matter which one you use" just flat out fails when it comes
to applications in biology.

IRR <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message

Quoted message said:

irr <[email hidden]> wrote or quoted:

Quoted message said:

"Tim Tyler" <[email hidden]> wrote in message
> irr <[email hidden]> wrote or quoted:
> > "Tim Tyler" <[email hidden]> wrote in message
> > > IRR <[email hidden]> wrote or
> > > quoted:

Quoted message said:

Quoted message said:

Quoted message said:

Certainly a huge computer, but really an extremely
lengthy description? Check out the top 500 list
(top500.org) -- the fastest computers in the world are
and will continue to be iterations of the single
processor system you're likely reading this reply on
right now. While such massively parallel systems --
including the human brain -- are increadibly
impressive to look at, they are remarkably regular.
[...]

The human brain is not "remarkably regular" - and as
such requires a lengthy description.

Some computer systems are very regular - at least when
they are turned on - but they are not very much like
brains.

Quoted message said:

From Erdi's "The Complexity of the Brain: Structural,
Functional and Dynamic

Modules": "Experimental facts from anatomy, physiology,
embriology, and psychophysics give evidence of highly
ordered structure composed of 'building blocks' of
repetitive structures in the vertebrate nervous system.
The building block according to the modular architectonic
principle is rather common in the nervous system. Modular
architecture is a basic feature of the spinal cord, the
brain stem reticular formation, the hypothalamus, the
subcortical relay nuclei, the cerebellar and especially
cerebral cortex." and on and on....

Repetition does not signifiy simplicity. The Encyclopaedia
Brittanica has many copies of the letter "e" in it - but has
no short description nontheless.

You need repetition *without* much variation for there to
exist a short description.

The adult brain is *very* complex. The argument that there's
a short description of it - and so its Kolmogorov complexity
is very low - and so such metrics give a counter-intuitive
low value for the complexity of the brain falls down -
because no such short description exists.

What there /might/ be a short description of is the
infant brain.

Instructions to build this are contained in the genetic
program - which fits on a CD or so.

*If* you are arguing about the brain of a child, then
perhaps we can agree that its Kolmogorov complexity doesn't
exceed a few hundred megabytes or so - at least early on.

However, after birth the complexity of the brain explodes -
as it accumulates information from its environment - and
encodes this information in irregular patterns of neural
weights - rapidly producing stupendous levels of complexity.
--
__________
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lock to reply.

chupacabra <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

chupacabra <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

Quoted message said:

Presently, as you know, the most successfull and,
probably, smartest people usually have few offsprings,
and, at least in the developed countries, the birth
rate is much higher in undereducated people with lower
intellectual status. So, in modern humans we, in fact,
have a "devolution" where every next generation is, on
average, less "smart" than a previous one. It may be
objected by the Dawkins idea that for the progress of
the human civilization what really matters is not a
selection of the genes but the selection of memes or
ideas. But, as humans will biologically grow more and
more stupid, it may once appear that they simply have
not got sufficient brainpower to command the collected
memes.

The reverse has been happening over the last 5 billion
years - as fairly convincingly demonstrated by skull
fossils.

I don't see any good reason to think things have changed
in that department.

In our society success of people is usually measured by
their status, money, education etc.

Well - that's not nature's metric. Nature rewards
reproductive success - not financial independence.

Quoted message said:

You just look up some relevant demographic statistics
tables: more successive, educated, rich people definitely
have less offspring. This means that human evolution has
either reversed or is guided precently by other factors
less known to scientists.

That goes to prove material wealth is not the only factor -
not that evolution has reversed course.

Quoted message said:

Quoted message said:

Fitness is not about counting offspring - it's about
leaving descendants.

Having many offspring might be an insurance strategy
against hostile local conditions - and should not
necessarily be interpreted as a sign of fitness.

You are right, what matters is the offring that managed to
survive to the reproductive age. Yes, in underdeveloped
countries and among less successive social groups child
mortality is usually higher. Yet, as this is often not too
high in modern society almost everywhere, anyway less
successive groups will leave more reproductive offspring
and progress through generations.

You meant to say "less successful"?

If they leave more offspring, they are probably not "less
successful".

Regarding intelligence - maybe the most intellectual are
reproductively handicapped (I agree there is evidence to
support this).

...but the least intellectual are *also* reproductively
handicapped.

To argue that mankind is getting stupider is to argue
that the first effect is more significant than the second
one - but I don't know of any evidence to suggest that
that is true.
--
__________
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lock to reply.

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

Guy Hoelzer <[email hidden]> wrote or quoted:

Quoted message said:

in article [email hidden], Tim Tyler
at [email hidden]

Quoted message said:

Quoted message said:

Complexity - as everyone agrees - is a scalar
property, not a binary one.

I don't think that "everyone" agrees with this point of
view. Proposed and often used "measures" of complexity
are indeed scalars, but that issue is about estimation
rather than physical reality. I would describe an
alternative, binary view of complexity as the one
promoted by Prigogine. I think that he would have agreed
with something like the following: complexity emerges
along with function and structure from the merely
complicated. Emergence is a process, so there would
certainly be a period of ambiguity as to whether
complexity has been achieved, but the concept would
still be essentially binary and not fairly represented
by a scalar parameter.

I don't know what you mean.

Tim,

I'm surprised at you. I just did a Google search of the WEB
for "complex", "more complex", "less complex", etc. It
appears that most people use "complex" without modifiers. It
is binary. The people have spoken. Get with it. ;-)

Guy may have a tough sell, though, convincing the
Kolmogoroff fans on this thread, especially since most of
them probably learned of the existence of Kolmogoroff
through the writings of the Brussels school. One can
speculate that Guy prefers the term "complex" for the state
that the Belgians refer to as "chaotic".

He will have an even tougher sell convincing Edser that
"dependent level of fitness" and "independent level of
fitness" are NOT binary - since Guy is doing this on a
thread where Edser has just complained that no one besides
himself uses these terms. It will be fun to watch these two
threads play out.

Still, one must admire the man's independent thought. Or,
should I say complex? Or perhaps chaotic?

Jim

in article [email hidden], Tim Tyler at [email hidden]
wrote on 4/20/04 8:34 PM:

Quoted message said:

Guy Hoelzer <[email hidden]> wrote or quoted:

Quoted message said:

in article [email hidden], Tim Tyler
at [email hidden]

Quoted message said:

Quoted message said:

Complexity - as everyone agrees - is a scalar property,
not a binary one.

I don't think that "everyone" agrees with this point of
view. Proposed and often used "measures" of complexity
are indeed scalars, but that issue is about estimation
rather than physical reality. I would describe an
alternative, binary view of complexity as the one
promoted by Prigogine. I think that he would have agreed
with something like the following: complexity emerges
along with function and structure from the merely
complicated. Emergence is a process, so there would
certainly be a period of ambiguity as to whether
complexity has been achieved, but the concept would still
be essentially binary and not fairly represented by a
scalar parameter.

I don't know what you mean.

For instance, what's this distinction between complexity
and complicated all about:

``complexity emerges along with function and structure
from the merely complicated''

The term "complexity" is appropriately used to describe a
complex. In this context I would define a complex as a
coherently structured network parts that primarily interact
with each other and are less well connected to the external
environment. Webster's simply defines it as a "unified
grouping." In effect, when complex and systemic dynamics
emerge, things become LESS complicated. Complexity breeds
simplicity. I think that some things appear to be far more
complicated than they really are, because we haven't yet
recognized the wholeness of the system or the wholenesses of
subsystems. The existence of macroscopic wholes
significantly reduces apparent complicatedness. There would
be no value, for example, in drilling down
reductionistically to the level of quarks to gain a better
understanding of animal behavior.

Quoted message said:

*Maybe* there are some folk somewhere who think complexity
is a binary quantity.

I'd be inclined to show them Kolmogorov complexity - and
ask them the equivalent of "how many hairs make a beard" -
i.e. how they would defend their preferred "complexity
threshold".

I would distinguish between a measure like this and its
underlying concept.

Guy

Tim Tyler <[email hidden]> wrote in
:"]news:[email hidden]:

Quoted message said:

irr <[email hidden]> wrote or quoted:

Quoted message said:

Quoted message said:

While we might all agree that the primate brain is an
incredibly complex organ, it's not at all agreed upon
what it is we mean by this. For example, a Kolmogorov
measure fails miserably in classifying the brain as
complex, after all you're really only talking about two
dozen or so different recognized cell types stamped out
in enormous repetition with iterated connections between
them -- in other words, a digital representation of the
brain is incredibly compressible.

Quoted message said:

IMO - this makes no sense at all :-|

Quoted message said:

An acceptable digital version of the brain would handle
the same I/O - and produce similar inputs from similar
outputs. This sounds like a job for a huge computer with
an *extremely* lengthy description to me
- and of course a correspondingly enormous Kolmogorov
complexity.

I agree with Tim that a digital computer that mimics the
brain would be huge by today's standards. I however also
agree that this capability is achieved using a relatively
small amount of genetic code. Part of the secret is that
brain development relies on input from the environment - in
other words much of the data needed to code for a brain
resides outside of the genes. Trying to capture this
complexity entirely in a computer program would in fact
require specifying a lot of data that the actual developing
brain doesn't include as different cell types but gathers as
input to the neural net.

Yours,

Bill Morse

Jim Menegay <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in message
news:<[email hidden]>...

Quoted message said:

Guy Hoelzer <[email hidden]> wrote or quoted:

Quoted message said:

in article [email hidden], Tim
Tyler at [email hidden]

Quoted message said:

Quoted message said:

Quoted message said:

> Complexity - as everyone agrees - is a scalar
> property, not a binary one.

I don't think that "everyone" agrees with this point
of view. Proposed and often used "measures" of
complexity are indeed scalars, but that issue is about
estimation rather than physical reality. I would
describe an alternative, binary view of complexity as
the one promoted by Prigogine. I think that he would
have agreed with something like the following:
complexity emerges along with function and structure
from the merely complicated. Emergence is a process,
so there would certainly be a period of ambiguity as
to whether complexity has been achieved, but the
concept would still be essentially binary and not
fairly represented by a scalar parameter.

I don't know what you mean.

I'm surprised at you. I just did a Google search of the
WEB for "complex", "more complex", "less complex", etc. It
appears that most people use "complex" without modifiers.
It is binary. The people have spoken. Get with it. ;-)

Touche.
--
__________
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lock to reply.

Tim Tyler <[email hidden]> wrote in message news:<c69ku1$8kp$1

Quoted message said:

Regarding intelligence - maybe the most intellectual are
reproductively handicapped (I agree there is evidence to
support this).

...but the least intellectual are *also* reproductively
handicapped.

To argue that mankind is getting stupider is to argue
that the first effect is more significant than the second
one - but I don't know of any evidence to suggest that
that is true.

Do you mean that humanity is progressing towards ordinarity
and mediocrity?

By the way, how would you explain significant changes in
human phenotype during the last century, I mean people have
become much taller, weigh more, are less susceptible to some
diseases etc. These changes were apparently too fast to be
explained by the natural selection.

William Morse <[email hidden]> wrote or quoted:

Quoted message said:

Tim Tyler <[email hidden]> wrote in

Quoted message said:

Quoted message said:

An acceptable digital version of the brain would handle
the same I/O - and produce similar inputs from similar
outputs. This sounds like a job for a huge computer with
an *extremely* lengthy description to me
- and of course a correspondingly enormous Kolmogorov
complexity.

I agree with Tim that a digital computer that mimics the
brain would be huge by today's standards. I however also
agree that this capability is achieved using a relatively
small amount of genetic code. Part of the secret is that
brain development relies on input from the environment -
in other words much of the data needed to code for a brain
resides outside of the genes. Trying to capture this
complexity entirely in a computer program would in fact
require specifying a lot of data that the actual
developing brain doesn't include as different cell types
but gathers as input to the neural net.

See:

``Epigenesis:

The ontogenetic program is limited in the amount of
information that can be stored, thereby rendering the
complete specification of the organism impossible. A well-
known example is that of the human brain with some 10^10
neurons and 10^14 connections, far too large a number to
be completely specified in the four-character genome of
length approximately 3 x 10^9. Therefore, upon reaching a
certain level of complexity, there must emerge a different
process that permits the individual to integrate the vast
quantity of interactions with the outside world. This
process is known as epigenesis, and primarily includes the
nervous system, the immune system, and the endocrine
system. These systems are characterized by the possession
of a basic structure that is entirely defined by the
genome (the innate part), which is then subjected to
modification through lifetime interactions of the
individual with the environment (the acquired part). The
epigenetic processes can be loosely grouped under the
heading of learning systems.''

- cs.bgu.ac.ilpoe.htmlOpen ↗
--
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