From engelbert_buxbaum from hotmail.com  Fri Apr  6 10:17:10 2007
From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum)
Date: Fri Apr  6 12:07:14 2007
Subject: [Biophysics] Re: Enthalpy of proteins
References: <1174824065.721759.217440@l77g2000hsb.googlegroups.com>
Message-ID: <57n6hfF29m0ddU1@mid.individual.net>

Jafari wrote:

> My simple question is: is Ha>Hb? or Hb>Ha?

Without further knowledge on what you have to do to get from state A to
state B this question can not be answered. Perhaps you have to break
another ionic bond, or get two equal charges uncomfortably close
together?
From morpheal from yahoo.com  Sat Apr 14 10:52:04 2007
From: morpheal from yahoo.com (Morpheal)
Date: Sat Apr 14 13:38:34 2007
Subject: [Biophysics] A Thought Experiment: Implications of Quantum Physics
	in Genetics - A New Paradigm
Message-ID: <1176565924.921293.226500@p77g2000hsh.googlegroups.com>

Implications of Quantum Physics in Genetics - A New Paradigm

This is a thought experiment with broad implications for the
understanding of genetics
and the relation of genetics to quantum physics.

The fundamental question we are going to consider is whether amino
acids are a sufficient basis for storing all of the necessary
information for the reproduction of an organism.

Those who know what it takes to convey all of the information to build
a relatively simple machine, such as an automobile will have a better
appreciation of the analogy we are going to utilize in attempting to
answer the fundamental question. Every part that comprises the
automobile requries fully detailed drawings. Nowadays parts are often
modeled in three dimensional representations showing all of the
necessary features, to scale, so that the component can be reproduced
accurately. Then the process for its production has to be described in
sufficient detail to enable the component to be produced. Information
about what types of material it is to be made from, and what is to be
done to that material is included along with the representational
model, drawing of digital file. We also have to consider all of the
information necessary for making the machines, and operating them.
This becomes a very large amount of data. Those who work in
engineering, or manufacturing, know how much data, in digital form,
can be required for even the simplest part to be described.  It is
staggering as to how much data would be required to describe all of
the machines and processes going into making that part. It is even
more staggering if one has to add the human element. Whether the part
is made by robots, or with human involvement we have to allow for the
software required to run all of the necessary processes.

Now, compare the complexity of one organ, the human eye, and its
function, with the complexity of our manufactured machines. The eye
and its function is incredibly more complex, in both structure and
function. We now need the representations for every manufacturing
detail and every process necessary to make every component of the eye,
and its related structures enabling effective sensory, perceptual, and
visual memory functions.  Not only do we have to detail every
component but we have to write all of the software to make the system
function. Although we cannot put a meaningful number to the number of
bytes of data that would be required, we know that it is very large.
The software programs necessary to emulate human vision would
themselves be extremely large, and would challenge most computers.
Understanding visual information is not a simple process. Storing
visual memory is not a simple process either. The eye is infinitely
more complex than the most complex automobile. Its function is
similarly infinitely more complex than the function of an automobile.

What we then have to do is to extrapolate that understanding to
include all of the structures and functions of the entire body and the
mind-brain. If we had the means we could attempt a computer simulation
of how much data would be required to define a specific structure and
a function, then extrapolate that to give us a rough idea of how much
data might really be involved.

I am arguing here that amino acid sequences are insufficient means to
store the necessary data required to build a functioning organism.
Similarly, we are faced with the problem of data transmission which at
least cannot fully explain the transfer of sufficient software to
enable function. It is not simply a question of putting the right
molecules into place, the way bricks are mortared together onto a
newly built wall.

What I would suggest is that the amino acid sequences in the DNA helix
are in fact only the filing cabinets for the balance of the necessary
information, which is stored at the quantum level. What we have is the
equivalent of a vast hard drive that stores information at the
subatomic, quantum, level. When we look at the DNA helix, at the
molecular level we look at the file folders, without being able to see
the contents that is stored within those file folders. It is only at
the quantum level that we can find what I suggest must be best
described as a quantum holographic model of structure, linked to its
"software" programs, required for function. A quantum holographic
model would be the most probable paradigm because it appears to be the
only way to reduce the total data requirement for the complete package
of structure and function. Nevertheless, more complex functions
certainly do require complex "software" programs that a traditional,
purely mechanistic, paradigm cannot accomodate.

A further implication includes inherent knowledge, learned by
predecessor organisms, providing information for survival, not having
to be relearned with each new, successive, generation. Plato's
anamnesis, recollection of knowledge outside of immediate experience,
is then a reality, as some information could be conveyed on the DNA
helix beyond what is necessary to provide for basic structure and
function. (As a footnote, citing unpublished experiments performed
almost two decades ago, we have experimental indications that provide
some strong indications that inherent information of that type does
exist and plays a role in human reactions to their lived environments.
This accounts for such phenomena as "collective unconscious" mind,
where there is a sharing of some common threads of similar information
inherent from past generations indicating historic socio-cultural
group affinities as being definitive of its variants. We may also have
the answer to some instances of alleged "reincarnation" where entire,
historically verifiable, memories can be idenfitied without that
information being learned within an individual's own lifetime. Our
expectation is that such instances do occur, and that experiences that
are deemed more significant to survival, having had what is felt to be
a strong  impact on the previous generation organism's survival, and
potentially an impact on species survival, tend to be the type of
experiences that are recorded onto the DNA helix. Studies of
"reincarnation" anomalies  support that contention.)

Bob Ezergailis
Hamilton, Canada
April 13, 2007

From reanimater_2000 from yahoo.com  Sat Apr 14 12:45:32 2007
From: reanimater_2000 from yahoo.com (Immortalist)
Date: Sat Apr 14 13:38:35 2007
Subject: [Biophysics] Re: A Thought Experiment: Impications of Quantum
	Physics in Genetics - A New Paradigm
In-Reply-To: <1176565505.232893.196150@n59g2000hsh.googlegroups.com>
References: <1176565505.232893.196150@n59g2000hsh.googlegroups.com>
Message-ID: <1176572732.049877.148630@y5g2000hsa.googlegroups.com>

On Apr 14, 8:45 am, "Morpheal" <morph...@yahoo.com> wrote:
> Implications of Quantum Physics in Genetics - A New Paradigm
>
> This is a thought experiment with broad implications for the
> understanding of genetics
> and the relation of genetics to quantum physics.
>
> The fundamental question we are going to consider is whether amino
> acids are a sufficient basis for storing all of the necessary
> information for the reproduction of an organism.
>
> Those who know what it takes to convey all of the information to build
> a relatively simple machine, such as an automobile will have a better
> appreciation of the analogy we are going to utilize in attempting to
> answer the fundamental question. Every part that comprises the
> automobile requries fully detailed drawings.

If we take a sand castle and somehow could measure the quantum
distribution of effects and fields, and then scattered the structure,
leaving different arrangements of distribution and effects, then
brought it back together, would this arrangement of sand micro rocks,
subsume the same field arrangment as before?

If we gather matter together could it be possible to remotely arrange
quantum fields and particle through subsumption architecture by
influence scaler phenonemon?

A subsumption architecture is a way of decomposing complicated
intelligent behaviour into many "simple" behaviour modules, which are
in turn orgnized into layers. Each layer implements a particular goal
of the agent, and higher layers are increasingly more abstract. Each
layer's goal subsumes that of the underlying layers, e.g. the decision
to move forward by the eat-food layer takes into account the decision
of the lowest obstacle-avoidance layer.

http://en.wikipedia.org/wiki/Subsumption_architecture

Genghis - Subsumption Architecture.

...Brooks's ideas gelled in a cockroachlike contraption the size of a
football called "Genghis." Brooks had pushed his downsizing to an
extreme. Genghis had six legs but no "brain" at all. All of its 12
motors and 21 sensors were distributed in a decomposable network
without a centralized controller. Yet the interaction of these 12
muscles and 21 sensors yielded an amazingly complex and lifelike
behavior.

Each of Genghis's six tiny legs worked on its own, independent of the
others. Each leg had its own ganglion of neural cells-a tiny
microprocessor-that controlled the leg's actions. Each leg thought for
itself! Walking for Genghis then became a group project with at least
six small minds at work. Other small semiminds within its body
coordinated communication between the legs. Entomologists say this is
how ants and real cockroaches cope-they have neurons in their legs
that do the leg's thinking.

In the mobot Genghis, walking emerges out of the collective behavior
of the 12 motors. Two motors at each leg lift, or not, depending on
what the other legs around them are doing. If they activate in the
right sequence-Okay, hup! One, three, six, two, five, four!-walking
"happens."

No one place in the contraption governs walking. Without a smart
central controller, control can trickle up from the bottom. Brooks
called it "bottom-up control." Bottom-up walking. Bottom-up smartness.
If you snip off one leg of a cockroach, it will shift gaits with the
other five without losing a stride. The shift is not learned; it is an
immediate self-reorganization. If you disable one leg of Genghis, the
other legs organize walking around the five that work. They find a new
gait as easily as the cockroach.

In one of his papers, Rod Brooks first laid out his instructions on
how to make a creature walk without knowing how:

There is no central controller which directs the body where to put
each foot or how high to lift a leg should there be an obstacle ahead.
Instead, each leg is granted a few simple behaviors and each
independently knows what to do under various circumstances. For
instance, two basic behaviors can be thought of as "If I'm a leg and
I'm up, put myself down, " or "If I'm a leg and I'm forward, put the
other five legs back a little."

These processes exist independently, run at all times, and fire
whenever the sensory preconditions are true. To create walking then,
there just needs to be a sequencing of lifting legs (this is the only
instance where any central control is evident). As soon as a leg is
raised it automatically swings itself forward, and also down. But the
act of swinging forward triggers all the other legs to move back a
little. Since those legs happen to be touching the ground, the body
moves forward.

Once the beast can walk on a flat smooth floor without tripping, other
behaviors can be added to improve the walk. For Genghis to get up and
over a mound of phone books on the floor, it needs a pair of sensing
whiskers to send information from the floor to the first set of legs.
A signal from a whisker can suppress a motor's action. The rule might
be, "If you feel something, I'll stop; if you don't, I'll keep
going."

While Genghis learns to climb over an obstacle, the foundational
walking routine is never fiddled with. This is a universal biological
principle that Brooks helped illuminate-a law of god: When something
works, don't mess with it; build on top of it. In natural systems,
improvements are "pasted" over an existing debugged system. The
original layer continues to operate without even being (or needing to
be) aware that it has another layer above it.

http://www.kk.org/outofcontrol?/ch3-b.html

There are three kinds of "scopes" we can look through at one time and
one scale of observation;

Microscope
Mesoscope
Macroscope

Pretext: will become "mico-scale"
Text: will become "root-scale" or "middle-scale"
Context: will become "macr-scale"

THREE SCALES:

(-1) - Micro-scale: A prefix denoting very small size; e.g.
microgamete, micronucleus.

( 0) - Meso-scale: In meteorology, describing systems, or patterns of
systems between small and synoptic [The term means 'simultaneous']
scale; dimensions of between about 10 and 100 km across, in the
horizontal, have been suggested.

(+1) - Macro-scale: Large-scale. Thus, a macroclimate is the general
climate of a region extending across several hundred kilometres, such
as the Great Plains of North America, macrometeorology is the study of
large scale meteorological phenomena which can cover hundreds of
kilometres or may encompass the whole globe, from monsoons to the
general circulation of the atmosphere, and macro-economics is the
study of an economy as a whole.

Shifting focus upon different "scales" (attention to one area of a
hierarchy) can be illustrated with an analogy from grammatical
stucture and hierarchy. [In music theory a scale is those notes within
a group that don't repeat the same tone at a higher of lower octives.
When the same note is reached in a different scale of a higher or
lower pitch then it is another octive. (you can ignore this part)]

If we focus upon a word it becomes the "meso-scale" in which the micro-
scale is letters it consists (reductionism) and the macro-scale is the
sentence in which it might fit (productionism or synductionism).

At the next level up the scale the sentence would become the "meso-
scale" with words being micro-scale in which the sentence consists
(reductionism) and a paragraph would be a macro-scale, where a
sentence is a part (productionism or synductionism).

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

If a morpheme is the smallest language unit that carries a semantic
interpretation I am wondering what the morpheme_root "duction" means.

The root is the primary lexical unit of a word, which carries the most
significant aspects of semantic content and cannot be reduced into
smaller constituents.

Duction: The act of leading, bringing, or conducting.

re: backa, gain, repeatedly

meso: middle

syn: together, united, at the same time

Making this up today but I need the meaning of the ;

re-duction-ism
meso-duction-ism
syn-duction-ism

micro-analysis
meso-analysis
macro-analysis

super-structure
root-structure
sub-structure

Why hasn't this awesome perspective elaborated in current metaphysics?

http://www.virtualsalt.com/roots.htm
http://en.wikipedia.org/wiki/List_of_prefixes_in_the_English_language
http://en.wikipedia.org/wiki/Morpheme

http://xrefer.com/entry/462106
http://xrefer.com/entry.jsp?xrefid=610070
http://xrefer.com/entry.jsp?xrefid=609978

Microtubules are cylindrical molecules made by gluing together 13
strands of the protein, tubulin, to make a tube 25 nanometres across,
with a central channel about 15 nanometres wide. Each microtubule is
covered by a fuzz of protein stubs, known as MAPs (microtubule
associated proteins), and these can be used to hook clusters of
microtubules together into larger lattices. Both microtubules and MAPs
seem to be capable of a certain amount of movement, meaning that they
can be woven into plastic structures, able to give and bend.

The structural properties of microtubule assemblies make them a
valuable building material within cells. For example, a bundle of 20
microtubules form the beating, hair-like cilia that coat the surface
of many small single-celled animals, allowing them to swim. However
the main use for microtubules appears to be to make an internal
skeleton for cells-an intricate scaffolding that gives a cell its
shape but also can deform and bend enough to allow it to move.

The existence of the microtubule cytoskeleton was discovered only
relatively recently in the 1970s-previously the fixative chemicals
used in electron microscopy was having the unfortunate effect of
dissolving the tubules-so biologists still have much to learn about
what the cytoskeleton does and how it operates. Yet biologists believe
that it not only holds a cell in shape but also plays an important
role in cell metabolism, acting as a piping system or an internal
highway to move plasma and other essential cell products about the
cell. Some have suggested microtubules might do this by using their
MAP spurs to drag cell protoplasm along, hand over hand, in a
miniature bucket brigade running up the sides of a tubule.

There is also evidence that the cytoskeleton could serve as a
primitive brain. Biologists have long been puzzled how a simple single-
celled animal, like the slipper-shaped paramecium, could behave so
intelligently when it has no nervous system. A paramecium is
surprisingly nimble as it swims about in pond-bottom detritus,
twisting in and out of tight spaces in search of its dinner. Somehow
the protozoan manages to respond swiftly to information coming in from
a light-sensitive eyespot and its touch-sensitive cilia to co-ordinate
its swimming action. Several biologists have speculated that the
cytoskeleton could serve as the communication and information
processing link needed to organise such relatively complex behaviour.

This suggestion that the cytoskeleton could be a "brain within a
brain" has particularly excited the quantum theorists. In casting
around for a suitable cell structure to operate as a go-between,
connecting the sub-atomic realm with the macroscopic world of firing
brain cells, some theorists had considered that the membranes at the
synaptic junctions between nerve cells might be the site of quantum
interactions. Others had wondered whether the ion channels down the
flanks of neurons could be ruled by quantum effects. But quickly,
microtubules began to look a far better bet. While microtubules are
not unique to neurons, they are found there in particular abundance (a
fact that does not surprise neurologists given that nerve cells are so
metabolically-active and microtubules seem essential to metabolic
activity). Furthermore, the speed at which microtubules can switch
state between relaxation and contraction is believed to be of the
order of a nanosecond. This may be slow by the usual time scales of
quantum events, but it is about a million times faster than the cell
firing events usually believed to underlie consciousness and so at
least appears to get the biology of the system within striking
distance of a quantum explanation.

http://www.btinternet.com/~neuronaut/webtwo_articles.html


> Nowadays parts are often
> modeled in three dimensional representations showing all of the
> necessary features, to scale, so that the component can be reproduced
> accurately. Then the process for its production has to be described in
> sufficient detail to enable the component to be produced. Information
> about what types of material it is to be made from, and what is to be
> done to that material is included along with the representational
> model, drawing of digital file. We also have to consider all of the
> information necessary for making the machines, and operating them.
> This becomes a very large amount of data. Those who work in
> engineering, or manufacturing, know how much data, in digital form,
> can be required for even the simplest part to be described.  It is
> staggering as to how much data would be required to describe all of
> the machines and processes going into making that part. It is even
> more staggering if one has to add the human element. Whether the part
> is made by robots, or with human involvement we have to allow for the
> software required to run all of the necessary processes.
>
> Now, compare the complexity of one organ, the human eye, and its
> function, with the complexity of our manufactured machines. The eye
> and its function is incredibly more complex, in both structure and
> function. We now need the representations for every manufacturing
> detail and every process necessary to make every component of the eye,
> and its related structures enabling effective sensory, perceptual, and
> visual memory functions.  Not only do we have to detail every
> component but we have to write all of the software to make the system
> function. Although we cannot put a meaningful number to the number of
> bytes of data that would be required, we know that it is very large.
> The software programs necessary to emulate human vision would
> themselves be extremely large, and would challenge most computers.
> Understanding visual information is not a simple process. Storing
> visual memory is not a simple process either. The eye is infinitely
> more complex than the most complex automobile. Its function is
> similarly infinitely more complex than the function of an automobile.
>
> What we then have to do is to extrapolate that understanding to
> include all of the structures and functions of the entire body and the
> mind-brain. If we had the means we could attempt a computer simulation
> of how much data would be required to define a specific structure and
> a function, then extrapolate that to give us a rough idea of how much
> data might really be involved.
>
> I am arguing here that amino acid sequences are insufficient means to
> store the necessary data required to build a functioning organism.
> Similarly, we are faced with the problem of data transmission which at
> least cannot fully explain the transfer of sufficient software to
> enable function. It is not simply a question of putting the right
> molecules into place, the way bricks are mortared together onto a
> newly built wall.
>
> What I would suggest is that the amino acid sequences in the DNA helix
> are in fact only the filing cabinets for the balance of the necessary
> information, which is stored at the quantum level. What we have is the
> equivalent of a vast hard drive that stores information at the
> subatomic, quantum, level. When we look at the DNA helix, at the
> molecular level we look at the file folders, without being able to see
> the contents that is stored within those file folders. It is only at
> the quantum level that we can find what I suggest must be best
> described as a quantum holographic model of structure, linked to its
> "software" programs, required for function. A quantum holographic
> model would be the most probable paradigm because it appears to be the
> only way to reduce the total data requirement for the complete package
> of structure and function. Nevertheless, more complex functions
> certainly do require complex "software" programs that a traditional,
> purely mechanistic, paradigm cannot accomodate.
>
> A further implication includes inherent knowledge, learned by
> predecessor organisms, providing information for survival, not having
> to be relearned with each new, successive, generation. Plato's
> anamnesis, recollection of knowledge outside of immediate experience,
> is then a reality, as some information could be conveyed on the DNA
> helix beyond what is necessary to provide for basic structure and
> function. (As a footnote, citing unpublished experiments performed
> almost two decades ago, we have experimental indications that provide
> some strong indications that inherent information of that type does
> exist and plays a role in human reactions to their lived environments.
> This accounts for such phenomena as "collective unconscious" mind,
> where there is a sharing of some common threads of similar information
> inherent from past generations indicating historic socio-cultural
> group affinities as being definitive of its variants. We may also have
> the answer to some instances of alleged "reincarnation" where entire,
> historically verifiable, memories can be idenfitied without that
> information being learned within an individual's own lifetime. Our
> expectation is that such instances do occur, and that experiences that
> are deemed more significant to survival, having had what is felt to be
> a strong  impact on the previous generation organism's survival, and
> potentially an impact on species survival, tend to be the type of
> experiences that are recorded onto the DNA helix. Studies of
> "reincarnation" anomalies  support that contention.)
>
> Bob Ezergailis
> Hamilton, Canada
> April 13, 2007


From shijun from bic-ta.org  Thu Apr 19 09:54:41 2007
From: shijun from bic-ta.org (bicta2007)
Date: Thu Apr 19 13:08:14 2007
Subject: [Biophysics] Final Call for Papers--BIC-TA2007
Message-ID: <200704191659.l3JGxKc07734@net.bio.net>

I'd like to apologize if you receive multiple emails.


****************************************************************************


                            CALL FOR PAPERS


                    2nd International Conference on
 
      BIO-INSPIRED COMPUTING: THEORIES AND APPLICATIONS (BIC-TA2007)


         Zhengzhou University of Light Industry, Zhengzhou, China


                        September 14-17, 2007


****************************************************************************


BIC-TA2007 paper submission Deadline has been extended to May 10, 2007


****************************************************************************


Organized by    

Peking University, China 
Zhengzhou University of Light Industry, China 
Huazhong University of Science & Technology, China 


Hosted by    

Zhengzhou University of Light Industry, China 


Co-Hosted by 

Zhengzhou University, China 
Zhongyuan University of Technology, China 


Sponsors    

National Natural Science Foundation of China 
Henan Engineering Research Center for Biotechnology 

****************************************************************************


BIC-TA2007 aims to provide a high-level international forum for researchers 
working in the main areas of natural computing inspired from biology to 
present their recent results and exchange ideas.

The conference includes, but not limited to the following topics:

A. Theories and Methodologies
A1 Neural Networks
A2 Evolutionary Computing and Genetic Algorithms
A3 DNA and Molecular Computing
A4 Membrane Computing
A5 Biological Computing
A6 Swarm Intelligence
A7 Autonomy-Oriented Computing
A8 Cellular and Molecular Automata

B. Applications
B1 Bioinformatics and Cheminformatics
B2 Computational Biology and Drug Design
B3 Systems Biology and Synthetic Biology
B4 Computational Genomics and Proteomics
B5 Computational Neuroscience
B6 Artificial Life and Artificial Immune Systems
B7 Signal Processing and Pattern Recognition
B8 Financial Engineering and Electronic Commerce
B9 Data Fusion, Knowledge Discovery and Data Mining
B10 Natural Language Processing and Expert Systems
B11 Computer Security and Computer Vision
B12 Circuit Design and Signal Processing
B13 Biological Implementation and Molecular Implementation
B14 DNA Nanotechnology
B15 Web and Network Application
B16 Multi-Objective Optimization
B17 Other Applications


****************************************************************************


Deadlines

Submission Deadline: 10 May, 2007
Notification of Acceptance: 10 June, 2007
Final Version for the Pre-proceedings: 25 June, 2007


****************************************************************************


Authors should submit a soft copy of their manuscripts with pdf format only 
to the conference via the online submission systems.

The submission of a paper implies that the paper is original and has not been 
submitted to elsewhere for possible publication. All submissions will be 
peer-reviewed by experts in the field based on originality, significance, 
quality and clarity. The papers will be prepared in LNCS style (available at 
http://www.springer.de or our website) with no more than 12 pages.

A pre-proceedings volume will be available during the conference. The expanded 
and revised version of all accepted papers at BIC-TA 2007 will be published 
after the conference in international journals indexed by SCI-Expanded.

The latest information on BIC-TA2007 and related Special Issues of journals are
available at: http://www.bic-ta.org

 
****************************************************************************


Tel: +86-371-63627289

Fax: +86-371-63556791 

Email: bicta2007@gmail.com; sec@bic-ta.org