seems like a good description of e.coli reorganization to me

[From Frank Lenk (2013.12.16.1040 CST)]

Saw this in Science Daily today:

Rapid Evolution of Novel Forms: Environmental Change Triggers Inborn Capacity for Adaptation

http://www.sciencedaily.com/releases/2013/12/131212141938.htm

Provides a mechanism for Bill’s point that e.coli reorganization can produce successful adaptations much more quickly than standard natural selection theory suggests.

Frank

Frank Lenk

Director of Research Services

Mid-America Regional Council

600 Broadway, Suite 200

Kansas City, MO 64105

www.marc.org

Ph. 816.701.8237 (direct)

flenk@marc.org

···

Rupert Young (2013.12.06 20.30 UT)

Not sure if people are already aware of this research, but it seems to verify a prediction of PCT, that reference signals for low level systems can be set by high-level processes. Quelle surprise!

The Eye Pupil Adjusts to Imaginary Light

http://m.pss.sagepub.com/content/early/2013/11/25/0956797613503556

Though I’ve only looked at the abstract as am too stingy to pay for the full text.

Great find, Rupert! Fascinating. Same kind of thing seems to be going on when we jerk out of sleep from an imaginary fall; lower level systems are acting to correct for a disturbance to an imagined perception!

I’ll include this as a reference in the imagination (memory) section of the B:CP course.

Best

Rick


-- Regards,
Rupert


Richard S. Marken PhD

www.mindreadings.com
The only thing that will redeem mankind is cooperation.

                                               -- Bertrand Russell

[Martin Taylor 2013.12.16.12.58]

The linked report doesn't bear on the e-coli form of reorganization.

It only deals with the rate of change. The e-coli form requires that
a beneficial change is continued in the same direction, whereas a
harmful change induces a change of direction. To define direction
you need places that are compared as to location. What is there in
the genetic structure that corresponds to location? In the neural
system, “location” can be specified in a very high-dimensional space
by the strengths of all synapses, and “direction” by the vector of
changes in the strengths of all those synapses. I suppose one could
define a location in genetic space by treating the different amino
acids as having numeric values, but then the idea of direction
becomes a little suspect. How does the substitution of, say, G for C
in one mutation get extended in the same direction, as e-coli
evolution would require?
What the report does support is Bill’s assertion that mutation rate
is responsive to stress (persistent intrinsic error not corrected by
individual reorganization).
Martin

···
      [From Frank

Lenk (2013.12.16.1040 CST)]

      Saw this in

Science Daily today:

Rapid

Evolution of Novel Forms: Environmental Change Triggers
Inborn Capacity for Adaptation

http://www.sciencedaily.com/releases/2013/12/131212141938.htm

        Provides a mechanism for Bill’s

point that e.coli reorganization can produce successful
adaptations much more quickly than standard natural
selection theory suggests.

[Avery Andrews 2013.12.17.8.50 Eastern Oz Daylight Time]

Many statistical learning methods as studied for example in unsupervised grammar acquisition, work in roughly this way. The problem is that navigation in high-dimensional spaces is very hard.

···

[From Frank Lenk (2013.12.16.1040 CST)]

Saw this in Science Daily today:

Rapid Evolution of Novel Forms: Environmental Change Triggers Inborn Capacity for Adaptation

http://www.sciencedaily.com/releases/2013/12/131212141938.htm

Provides a mechanism for Bill’s point that e.coli reorganization can produce successful adaptations much more quickly than standard natural selection theory suggests.

[From Rick Marken (2013.12.16.1520)]

Happy Beethoven's birthday!!

Martin Taylor (2013.12.16.12.58)

Frank Lenk (2013.12.16.1040 CST)

FL: Saw this in Science Daily today:

Rapid Evolution of Novel Forms: Environmental Change Triggers Inborn Capacity for Adaptation

http://www.sciencedaily.com/releases/2013/12/131212141938.htm

Provides a mechanism for Bill�s point that e.coli reorganization can produce successful adaptations much more quickly than standard natural selection theory suggests.

MT: The linked report doesn't bear on the e-coli form of reorganization.

RM: I think it does. The report says that "stress" leads to depletion
of HSP90. Since HSP90 suppresses genetic variation, a reduction in
HSP90 leads to an increase in genetic variation. Left out of this
explanation, of course, is a definition of "stress"; that is, a
definition of stress that allows it to have a functional relationship
to HSP90 concentration. The e-coli reorganization (and evolution)
model would say that stress is an error signal. The the question then
becomes "what is the perception that is not being kept at the
reference". The authors suggest that the perception under control is
the physiological state of the organism, which corresponds to some of
the "intrinsic" perceptual variables of PCT. The degree of difference
between intrinsic reference and intrinsic perception then determines
the concentration of HSP90 which determines the degree of genetic
protien folding and, thus, the probability of new genetic variants in
the offspring of each parent.

If this analysis is right, then the concentration of HSP90 is the
output of the e-coli reorganization/ evolution process, determining
the frequency of new variants in a breeding population. By increasing
the frequency of new variants in a high stress (large error)
population you increase the chances of offsring with variants that
will reduce allow the organism to stress (error) and the variation in
their offspring will then be less. Evolutoin still works by random
variation and selective retection, it's just that the variety of
variants to choose from increases when change (adaptation) is needed.

I think what is needed now in this research is to test whether this
e-coli analysis is correct. And this would involve trying to find the
functional conection between stress (error) and HSP90 concentration.
That is, they shoudl try to identify the control organization whose
output is the concentration of HSP90.

Best

Rick

···

--
Richard S. Marken PhD
www.mindreadings.com

The only thing that will redeem mankind is cooperation.
                                                   -- Bertrand Russell

[Martin Taylor 2013.12.16.23.04]

Rick,

What you say about the effect of the stress (error magnitude) on the rate of mutation is correct, and I said as much. But the essence of e-coli reorganization is the maintenance of the _direction_ of change when a move reduces error and an alteration of the _direction_ of change when the reorganization move makes things worse. Changes in the rate of mutation are only half the story, and not the half that distinguishes e-coli from random hill-climbing.

The other thing to note is that mutations can cause jumps to new parts of the fitness landscape, which e-coli does not do (neither the bacterium nor the metaphoric process).

Martin

···

[From Rick Marken (2013.12.16.1520)]

Happy Beethoven's birthday!!

Martin Taylor (2013.12.16.12.58)

Frank Lenk (2013.12.16.1040 CST)

FL: Saw this in Science Daily today:

Rapid Evolution of Novel Forms: Environmental Change Triggers Inborn Capacity for Adaptation

  http://www.sciencedaily.com/releases/2013/12/131212141938.htm

Provides a mechanism for Bill�s point that e.coli reorganization can produce successful adaptations much more quickly than standard natural selection theory suggests.
MT: The linked report doesn't bear on the e-coli form of reorganization.

RM: I think it does. The report says that "stress" leads to depletion
of HSP90. Since HSP90 suppresses genetic variation, a reduction in
HSP90 leads to an increase in genetic variation. Left out of this
explanation, of course, is a definition of "stress"; that is, a
definition of stress that allows it to have a functional relationship
to HSP90 concentration. The e-coli reorganization (and evolution)
model would say that stress is an error signal. The the question then
becomes "what is the perception that is not being kept at the
reference". The authors suggest that the perception under control is
the physiological state of the organism, which corresponds to some of
the "intrinsic" perceptual variables of PCT. The degree of difference
between intrinsic reference and intrinsic perception then determines
the concentration of HSP90 which determines the degree of genetic
protien folding and, thus, the probability of new genetic variants in
the offspring of each parent.

  If this analysis is right, then the concentration of HSP90 is the
output of the e-coli reorganization/ evolution process, determining
the frequency of new variants in a breeding population. By increasing
the frequency of new variants in a high stress (large error)
population you increase the chances of offsring with variants that
will reduce allow the organism to stress (error) and the variation in
their offspring will then be less. Evolutoin still works by random
variation and selective retection, it's just that the variety of
variants to choose from increases when change (adaptation) is needed.

I think what is needed now in this research is to test whether this
e-coli analysis is correct. And this would involve trying to find the
functional conection between stress (error) and HSP90 concentration.
That is, they shoudl try to identify the control organization whose
output is the concentration of HSP90.

Best

Rick

[From Rick Marken (2013.12.17.0925)]

Martin Taylor (2013.12.16.23.04)

MT: What you say about the effect of the stress (error magnitude) on the rate of
mutation is correct, and I said as much. But the essence of e-coli
reorganization is the maintenance of the _direction_ of change when a move
reduces error and an alteration of the _direction_ of change when the
reorganization move makes things worse. Changes in the rate of mutation are
only half the story, and not the half that distinguishes e-coli from random
hill-climbing.

RM: Actually, I think it is. But I think we have to develop a
simulation to see how (or whether) this works.

Best

Rick

···

The other thing to note is that mutations can cause jumps to new parts of
the fitness landscape, which e-coli does not do (neither the bacterium nor
the metaphoric process).

Martin

[From Rick Marken (2013.12.16.1520)]

Happy Beethoven's birthday!!

Martin Taylor (2013.12.16.12.58)

Frank Lenk (2013.12.16.1040 CST)

FL: Saw this in Science Daily today:

Rapid Evolution of Novel Forms: Environmental Change Triggers Inborn
Capacity for Adaptation

  http://www.sciencedaily.com/releases/2013/12/131212141938.htm

Provides a mechanism for Bill�s point that e.coli reorganization can
produce successful adaptations much more quickly than standard natural
selection theory suggests.
MT: The linked report doesn't bear on the e-coli form of reorganization.

RM: I think it does. The report says that "stress" leads to depletion
of HSP90. Since HSP90 suppresses genetic variation, a reduction in
HSP90 leads to an increase in genetic variation. Left out of this
explanation, of course, is a definition of "stress"; that is, a
definition of stress that allows it to have a functional relationship
to HSP90 concentration. The e-coli reorganization (and evolution)
model would say that stress is an error signal. The the question then
becomes "what is the perception that is not being kept at the
reference". The authors suggest that the perception under control is
the physiological state of the organism, which corresponds to some of
the "intrinsic" perceptual variables of PCT. The degree of difference
between intrinsic reference and intrinsic perception then determines
the concentration of HSP90 which determines the degree of genetic
protien folding and, thus, the probability of new genetic variants in
the offspring of each parent.

  If this analysis is right, then the concentration of HSP90 is the
output of the e-coli reorganization/ evolution process, determining
the frequency of new variants in a breeding population. By increasing
the frequency of new variants in a high stress (large error)
population you increase the chances of offsring with variants that
will reduce allow the organism to stress (error) and the variation in
their offspring will then be less. Evolutoin still works by random
variation and selective retection, it's just that the variety of
variants to choose from increases when change (adaptation) is needed.

I think what is needed now in this research is to test whether this
e-coli analysis is correct. And this would involve trying to find the
functional conection between stress (error) and HSP90 concentration.
That is, they shoudl try to identify the control organization whose
output is the concentration of HSP90.

Best

Rick

--
Richard S. Marken PhD
www.mindreadings.com

The only thing that will redeem mankind is cooperation.
                                                   -- Bertrand Russell

Lol… that was refreshingly random…

*barb

[From Rick Marken (2013.12.17.0940)]

Rick Marken (2013.12.16.1520)--

RM: Happy Beethoven's birthday!!

Barb Powers

BP: Lol... that was refreshingly random...

RM: I was once disappointed that I am not a genius but I have learned
that it's just as valuable to be a good audience for genius -- without
an audience genius would pretty much be wasted, eh? Hence my almost
savage appreciation of Beethoven, Bach, Mozart, Shakespeare, Austen,
Galileo, Newton and Powers.

Best

Rick

···

--
Richard S. Marken PhD
www.mindreadings.com

The only thing that will redeem mankind is cooperation.
                                                   -- Bertrand Russell

You have to be a genius of sorts to recognize and understand it. And thank you for including “Powers” at the end of such a lofty list!

···

On Tue, Dec 17, 2013 at 10:40 AM, Richard Marken rsmarken@gmail.com wrote:

[From Rick Marken (2013.12.17.0940)]

Rick Marken (2013.12.16.1520)–

RM: Happy Beethoven’s birthday!!

Barb Powers

BP: Lol… that was refreshingly random…

RM: I was once disappointed that I am not a genius but I have learned

that it’s just as valuable to be a good audience for genius – without

an audience genius would pretty much be wasted, eh? Hence my almost

savage appreciation of Beethoven, Bach, Mozart, Shakespeare, Austen,

Galileo, Newton and Powers.

Best

Rick

Richard S. Marken PhD

www.mindreadings.com

The only thing that will redeem mankind is cooperation.

                                               -- Bertrand Russell

Rick,

I agree with your list, but would add Einstein, as well as Gandhi and Mandela, whose understanding and use of social dynamics rivalled that of the geniuses you mentioned in their fields. (And the anonymous constructor of the Antikythera mechansim!)

Martin

···

On 2013/12/17 12:40 PM, Richard Marken wrote:

[From Rick Marken (2013.12.17.0940)]

Rick Marken (2013.12.16.1520)--

RM: Happy Beethoven's birthday!!
Barb Powers

BP: Lol... that was refreshingly random...

RM: I was once disappointed that I am not a genius but I have learned
that it's just as valuable to be a good audience for genius -- without
an audience genius would pretty much be wasted, eh? Hence my almost
savage appreciation of Beethoven, Bach, Mozart, Shakespeare, Austen,
Galileo, Newton and Powers.

Best

Rick

[From Mike Acree (2013.12.17.1050 PST)]

···

Lol… that was refreshingly random…

*barb

On Mon, Dec 16, 2013 at 4:22 PM, Richard Marken rsmarken@gmail.com wrote:

[From Rick Marken (2013.12.16.1520)]

Happy Beethoven’s birthday!!

And today is Arthur Fiedler’s birthday . . . and Chelsea Manning’s 26th.

Mike

[From Rick Marken (2013.12.17.1050)]

MT: I agree with your list, but would add Einstein, as well as Gandhi and
Mandela, whose understanding and use of social dynamics rivalled that of the
geniuses you mentioned in their fields. (And the anonymous constructor of
the Antikythera mechansim!)

RM: I agree. Mine was quite an abbreviated list.

Best

Rick

···

On Tue, Dec 17, 2013 at 10:32 AM, Martin Taylor <mmt-csg@mmtaylor.net> wrote:

On 2013/12/17 12:40 PM, Richard Marken wrote:

[From Rick Marken (2013.12.17.0940)]

Rick Marken (2013.12.16.1520)--

RM: Happy Beethoven's birthday!!
Barb Powers

BP: Lol... that was refreshingly random...

RM: I was once disappointed that I am not a genius but I have learned
that it's just as valuable to be a good audience for genius -- without
an audience genius would pretty much be wasted, eh? Hence my almost
savage appreciation of Beethoven, Bach, Mozart, Shakespeare, Austen,
Galileo, Newton and Powers.

Best

Rick

--
Richard S. Marken PhD
www.mindreadings.com

The only thing that will redeem mankind is cooperation.
                                                   -- Bertrand Russell

[Martin Taylor 2013.12.17.23.28]

[From Rick Marken (2013.12.17.0925)]

Martin Taylor (2013.12.16.23.04)

MT: What you say about the effect of the stress (error magnitude) on the rate of
mutation is correct, and I said as much. But the essence of e-coli
reorganization is the maintenance of the _direction_ of change when a move
reduces error and an alteration of the _direction_ of change when the
reorganization move makes things worse. Changes in the rate of mutation are
only half the story, and not the half that distinguishes e-coli from random
hill-climbing.

RM: Actually, I think it is. But I think we have to develop a
simulation to see how (or whether) this works.

There are three separate issues here:
     (1) What did Bill Powers define as "e-coli reorganization". For that I refer you to Chapter 7 in LCSIII, particularly pp66 (in the review version -- I think my paper version must be at my cottage) and Demo 7-1. He emphasises the fact that e-coli keeps going in the same direction when things are getting better, but tumbles quickly when they are getting worse. He discusses how just changing the rate at which changes are made got him nowhere until he thought of the directional constancy of e-coli that is going "the right way". So rate changes are indeed only half the story that is e-coli reorganization.
     (2) Whether mutation rate changes in a stressed population decrease the likelihood of the population going extinct and increase the likelihood that changed descendants will have reduced stress.
     (3) How one might simulate a test of (2). What kind of "rough" fitness landscape would induce stress in a way that the descendant population might reduce stress, and under what conditions would the evolving population change fast enough to survive without too rapid mutations preventing any new population stabilizing.

Martin

[From Rick Marken (2013.12.18.1530)]

Martin Taylor (2013.12.17.23.28)--

MT: There are three separate issues here:
    (1) What did Bill Powers define as "e-coli reorganization". For that I
refer you to Chapter 7 in LCSIII, particularly pp66 (in the review version
-- I think my paper version must be at my cottage) and Demo 7-1. He
emphasises the fact that e-coli keeps going in the same direction when
things are getting better, but tumbles quickly when they are getting worse.
He discusses how just changing the rate at which changes are made got him
nowhere until he thought of the directional constancy of e-coli that is
going "the right way". So rate changes are indeed only half the story that
is e-coli reorganization.

RM: I can't find that in my copy of LCS III. But I think (having
writtin some e.coli simulatons myself -- see
http://www.mindreadings.com/ControlDemo/Select.html) that directional
constancy (or lack thereof) is a side effect of the rate of tumbling
(directional changes). When the rate of tumbling is low (long times
between tumbles) there is directional constancy during the
inter-tumble interval. So I can't believe that Bill talked about how
changing the rate of tumbling got him nowhere unless he was talking
about how it was not rate per se but rate as a function of error that
made the difference; inter-tumble intervals are short (high rate of
tumbling -- or in the case of evolution, high rate of mutation) when
error is increasing and long (low rate of tumbling or mutation) when
error is decreasing.

MT: (2) Whether mutation rate changes in a stressed population decrease the
likelihood of the population going extinct and increase the likelihood that
changed descendants will have reduced stress.

RM: Yes, we need a model to answer that!

MT: (3) How one might simulate a test of (2). What kind of "rough" fitness
landscape would induce stress in a way that the descendant population might
reduce stress, and under what conditions would the evolving population
change fast enough to survive without too rapid mutations preventing any new
population stabilizing.

RM: That is indeed the big question. We need a computer simulation of
e-coli reorganization in a population that experiences varying levels
of stress due to environmental change. I have some ideas about how to
model this and I will try to cobble something together soon. But it
would be great if you would beat me to it, Martin!

Best

Rick

···

--
Richard S. Marken PhD
www.mindreadings.com

The only thing that will redeem mankind is cooperation.
                                                   -- Bertrand Russell

[Martin Taylor 2013.12.19.00.44]

[From Rick Marken (2013.12.18.1530)]

Martin Taylor (2013.12.17.23.28)--
MT: There are three separate issues here:
     (1) What did Bill Powers define as "e-coli reorganization". For that I
refer you to Chapter 7 in LCSIII, particularly pp66 (in the review version
-- I think my paper version must be at my cottage) and Demo 7-1. He
emphasises the fact that e-coli keeps going in the same direction when
things are getting better, but tumbles quickly when they are getting worse.
He discusses how just changing the rate at which changes are made got him
nowhere until he thought of the directional constancy of e-coli that is
going "the right way". So rate changes are indeed only half the story that
is e-coli reorganization.

RM: I can't find that in my copy of LCS III. But I think (having
writtin some e.coli simulatons myself -- see
http://www.mindreadings.com/ControlDemo/Select.html) that directional
constancy (or lack thereof) is a side effect of the rate of tumbling
(directional changes).

I think you have that backward, at least as Bill thought about it. It was the directional idea that solved his problem. You can't even have the concept of a tumble if you don't first have a direction. Here is the relevant section of LCS3, pp 65-66 of the review version PDF (retyped by me, so there may be typos that are not in the book). The elisions are irrelevant side comments.

--------quote Powers LCSIII pp65-66-------
P65: If there is some condition in the organism that causes changes in
behavioural organization to occur, and if removing this condition stops
those changes, then of course the organization of behaviour will remain
as it was just before the condition was removed. It will look as if
removing that condition is reinforcing because that removal, or the
positive occurrence of whatever removed it, seemed to strenghten the
tendency to produce that behaviour from then on. What is really
happening, according to reorganization theory, is that the tendency to
change the behaviour is reduced. The idea of reinforcement is the
opposite of the process that I called reorganization.

...

While this was not quite a workable model, it did contain the seeds of
one. It showed that if an error signal in some sort of very basic
control system could cause outputs that randomly altered the
organization of behaviour, this reorganization would continue until a
behavioural organization was produced that would bring the error signal
to zero. ... I more or less abandoned this model because on second and
third thought it just didn't seem efficient enough.

...

In 1980 Daniel Koshland published a little book called "Bacterial
Chemotaxis" (1980) which provided the missing feature of the model of
reorganization. ... When all these flagellae spin at the same time in
the same direction, E.coli swims in a straight line. (P66)... When the
motors are synchronized again, E.Coli takes off in a new direction that
has been shown to be unrelated to the former direction.

The trick is that when E.COli is swimming up a gradient of some good
chemical in its surroundings, or down a gradient of a bad one, tumbling
is delayed, while if the direction is toward the bad or away from the
good, the time to the next tumble is shortened. ... On average, it (or
rather a simulation based on this principle) makes its way toward the
source of the good substance or away from the bad one over hal;f as fast
as it could do if it could just turn and swim the right way.

Suddenly random reorganization didn't look as inefficient as I thought
it would have to be. The key idea is that what is change by a
reorganization is not a position, not the value of some behavioural
parameter, but the rate of change of position or value. And what was
sensed was not the degree of goodness or badness, but the first
derivative of goodness or badness�whether the result was getting better
or worse. ...

In E. Coli what is reorganized is its direction of swimming...But the
direction of swimming through space can be treated as analogous to the
direction of altering a set of control system parameters in some
abstract multidimensional space, and a tumble can be trreated as an
alteration in the proportions by which the parameters are being changed,
so the direction of metaphorical swimming in this multidimensional space
changes.

···

--------------

Martin

[From Rick Marken (2013.12.19.0850)]

Martin Taylor (2013.12.19.00.44)--

RM: . But I think (having writtin some e.coli simulatons myself -- see
http://www.mindreadings.com/ControlDemo/Select.html) that directional
constancy (or lack thereof) is a side effect of the rate of tumbling
(directional changes).

MT: I think you have that backward, at least as Bill thought about it. It was
the directional idea that solved his problem.

RM: OK, this is really getting us nowhere. I'm trying to develop a
model of E. coli evolution and having no luck so far. Perhaps what is
missing is the directional idea. What do you think corresponds to
direction in an evolutionary model?

Best

Rick

···

--
Richard S. Marken PhD
www.mindreadings.com

The only thing that will redeem mankind is cooperation.
                                                   -- Bertrand Russell

[Martin Taylor 2013.12.19.15.21]

[From Rick Marken (2013.12.19.0850)]
Martin Taylor (2013.12.19.00.44)--

RM: . But I think (having writtin some e.coli simulatons myself -- see
) that directional
constancy (or lack thereof) is a side effect of the rate of tumbling
(directional changes).
MT: I think you have that backward, at least as Bill thought about it. It was
the directional idea that solved his problem.
RM: OK, this is really getting us nowhere. I'm trying to develop a
model of E. coli evolution and having no luck so far. Perhaps what is
missing is the directional idea. What do you think corresponds to
direction in an evolutionary model?

[Martin Taylor 2013.12.16.12.58]

    In the neural system, "location" can be specified in a very

high-dimensional space by the strengths of all synapses, and
“direction” by the vector of changes in the strengths of all
those synapses. I suppose one could define a location in genetic
space by treating the different amino acids as having numeric
values, but then the idea of direction becomes a little suspect.
How does the substitution of, say, G for C in one mutation get
extended in the same direction, as e-coli evolution would
require?
In other words, I don’t think there is an obvious way to define
direction in the gene structure. That was my point in entering this
thread initially.

It might be possible to do it at some level involving gene

expression and activation, but I don’t know enough about that even
to speculate where it might be.

Martin
···

http://www.mindreadings.com/ControlDemo/Select.html