Re: [Fis] fis Digest, Vol 564, Issue 3

2012-10-16 Thread Steven Ericsson-Zenith 

For a "Whole-Cell Computational Model" this paper, an interesting pulling 
together of the pieces as it is, says precious little about the membrane 
behavior and dynamic structure of the cell - something that I expect from a 
paper that claims to be a "whole-cell" model. The title of the paper appears to 
be missing the word "Toward …"

Steven

--
  Dr Steven Ericsson-Zenith
  Institute for Advanced Science & Engineering
  http://iase.info



On Oct 16, 2012, at 1:19 PM, Kevin Clark  wrote:

> "A Whole-Cell 
> Computational Model Predicts Phenotype from Genotype"


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Re: [Fis] fis Digest, Vol 564, Issue 3

2012-10-16 Thread Kevin Clark 
Pedro, thank you for the citations of the Science and Cell articles. I find the 
paper "The Connectome of a Decison-Making Neural Network" by Jerrall et al. a 
technical achievement. However, the authors present no new concepts in terms of 
the role of neural networks in decision making, knowledge, etc.

Best regards,

Kevin





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Today's Topics:

   1. The Information Flow (Pedro C. Marijuan)


--

Message: 1
Date: Mon, 15 Oct 2012 17:56:45 +0200
From: "Pedro C. Marijuan" 
Subject: [Fis] The Information Flow
To: fis@listas.unizar.es
Message-ID: <507c323d.5000...@aragon.es>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear FIS Colleagues,

Thanks to Zhao Chuan for the Computer Poem/Song. It is a soft way to 
retake our discussions. These weeks there have been a couple of 
important achievements in the bio-information field. On the one side, 
the first 'complete' model of a prokaryotic cell ("A Whole-Cell 
Computational Model Predicts Phenotype from Genotype", by Karr et al., 
Cell, 150, 389-401, 2012). On the other, there was the report of another 
'complete' scheme, that of the C. elegans nervous system, now at the 
level of individual synaptic contacts, which was able to explain the 
mating behavior of the worm ("The Connectome of a Decision-Making Neural 
Network", by Jarrell et al., Science, 337, 437-444, 2012). It contained 
several references to the "information flow" through interneurons and 
sensorimotor circuits, and a very curious definition of knowledge (as 
"the set of activity weights in an adjacency matrix of a neural network, 
upon which the network's input-output function in part depends...").

Both papers are very interesting, relatively consistent with each other, 
and I think both represent symbolic milestones in the bio-information 
field. The point on information flows left me thinking on the larger 
perspective beyond single information items that we rarely focus on. 
Actually the first Shannonian information metaphor was about "sources" 
and "channels" --wasn't it? Particularly thinking on social information 
matters, how many aspects of contemporary life relate to the maintenance 
of the information flows intertwining and directing the economic flows. 
No doubt that the "forces of communication" have definitely won the 
upper hand upon the "forces of production ".

Somehow, Zhao Chuan's poem is but a celebration of the central role that 
computers have come to play in the gigantic information flows of our time.

best wishes

--Pedro

-- 
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta X
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-



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End of fis Digest, Vol 564, Issue 3
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Re: [Fis] The Information Flow (From Bob Ulanowicz)

2012-10-16 Thread Pedro C. Marijuan 
(From Bob Ulanowicz)

*

Dear Pedro,

I am not familiar with either model. I am made uneasy, however, by the
deterministic nature of the model descriptions.

My concern is that networks in general are metaphors for the
amalgamation of constraint and indeterminacy. There are, of course,
degenerate forms of networks that are deterministic, or almost so.
Ontogeny in general is "almost deterministic" and that would be
reflected in their corresponding network descriptors. My worry is
that by focusing upon these degenerate cases we lose sight of the fact
that in living systems considered more broadly (e.g., ecological,
social and economic systems), the indeterminate plays a larger and
*obligatory* role in the persistence of the system.

The best,
Bob



- End forwarded message -


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Re: [Fis] The Information Flow

2012-10-16 Thread Bill Seaman 

How about Knowing Through…

How can we embody a neural network/learning system through multi-modal sensing?
b



Bill Seaman
Professor, Department of Art, Art History & Visual Studies
DUKE UNIVERSITY 
114 b East Duke Building
Box 90764   
Durham, NC 27708, USA   
+1-919-684-2499 
http://billseaman.com/
http://fds.duke.edu/db/aas/AAH/faculty/william.seaman
http://www.dibs.duke.edu/research/profiles/98-william-seaman




On Oct 15, 2012, at 2:38 PM, Stanley N Salthe  wrote:

> On that "curious definition of knowledge", it looks like 'knowing how' rather 
> than 'knowing that'.
> 
> STAN 
> 
> On Mon, Oct 15, 2012 at 11:56 AM, Pedro C. Marijuan 
>  wrote:
> Dear FIS Colleagues,
> 
> Thanks to Zhao Chuan for the Computer Poem/Song. It is a soft way to
> retake our discussions. These weeks there have been a couple of
> important achievements in the bio-information field. On the one side,
> the first 'complete' model of a prokaryotic cell ("A Whole-Cell
> Computational Model Predicts Phenotype from Genotype", by Karr et al.,
> Cell, 150, 389-401, 2012). On the other, there was the report of another
> 'complete' scheme, that of the C. elegans nervous system, now at the
> level of individual synaptic contacts, which was able to explain the
> mating behavior of the worm ("The Connectome of a Decision-Making Neural
> Network", by Jarrell et al., Science, 337, 437-444, 2012). It contained
> several references to the "information flow" through interneurons and
> sensorimotor circuits, and a very curious definition of knowledge (as
> "the set of activity weights in an adjacency matrix of a neural network,
> upon which the network's input-output function in part depends...").
> 
> Both papers are very interesting, relatively consistent with each other,
> and I think both represent symbolic milestones in the bio-information
> field. The point on information flows left me thinking on the larger
> perspective beyond single information items that we rarely focus on.
> Actually the first Shannonian information metaphor was about "sources"
> and "channels" --wasn't it? Particularly thinking on social information
> matters, how many aspects of contemporary life relate to the maintenance
> of the information flows intertwining and directing the economic flows.
> No doubt that the "forces of communication" have definitely won the
> upper hand upon the "forces of production ".
> 
> Somehow, Zhao Chuan's poem is but a celebration of the central role that
> computers have come to play in the gigantic information flows of our time.
> 
> best wishes
> 
> --Pedro
> 
> --
> -
> Pedro C. Marijuán
> Grupo de Bioinformación / Bioinformation Group
> Instituto Aragonés de Ciencias de la Salud
> Centro de Investigación Biomédica de Aragón (CIBA)
> Avda. San Juan Bosco, 13, planta X
> 50009 Zaragoza, Spain
> Tfno. +34 976 71 3526 (& 6818)
> pcmarijuan.i...@aragon.es
> http://sites.google.com/site/pedrocmarijuan/
> -
> 
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Re: [Fis] The Information Flow

2012-10-16 Thread John Collier 


Good point, Stan. I think that it can be used to create a notion of
'knowing that', but it will require at least another level. I review some
ways to do this in

Explaining Biological Functionality: Is Control Theory Enough? South
African Journal of Philosophy. 2011, 30(4): 53-62. The main references
are more directly related to 'knowing that', but I would see 'knowing
that' as fulfilling a particular functional role,. and requiring
something like explicit representations, both of which I deal with in the
paper. I can see that there is a further paper to be written that takes
the step to the specific case of 'knowing that'.
Cheers,
John
At 03:38 PM 2012/10/15, Stanley N Salthe wrote:
On that "curious definition
of knowledge", it looks like 'knowing how' rather than 'knowing
that'. 
STAN 
On Mon, Oct 15, 2012 at 11:56 AM, Pedro C. Marijuan
<
pcmarijuan.i...@aragon.es> wrote:


Dear FIS Colleagues,

Thanks to Zhao Chuan for the Computer Poem/Song. It is a soft way
to

retake our discussions. These weeks there have been a couple of

important achievements in the bio-information field. On the one
side,

the first 'complete' model of a prokaryotic cell ("A
Whole-Cell

Computational Model Predicts Phenotype from Genotype", by Karr
et al.,

Cell, 150, 389-401, 2012). On the other, there was the report of
another

'complete' scheme, that of the C. elegans nervous system, now at
the

level of individual synaptic contacts, which was able to explain
the

mating behavior of the worm ("The Connectome of a
Decision-Making Neural

Network", by Jarrell et al., Science, 337, 437-444, 2012). It
contained

several references to the "information flow" through
interneurons and

sensorimotor circuits, and a very curious definition of knowledge
(as

"the set of activity weights in an adjacency matrix of a neural
network,

upon which the network's input-output function in part
depends...").

Both papers are very interesting, relatively consistent with each
other,

and I think both represent symbolic milestones in the
bio-information

field. The point on information flows left me thinking on the
larger

perspective beyond single information items that we rarely focus
on.

Actually the first Shannonian information metaphor was about
"sources"

and "channels" --wasn't it? Particularly thinking on social
information

matters, how many aspects of contemporary life relate to the
maintenance

of the information flows intertwining and directing the economic
flows.

No doubt that the "forces of communication" have definitely
won the

upper hand upon the "forces of production ".

Somehow, Zhao Chuan's poem is but a celebration of the central role
that

computers have come to play in the gigantic information flows of our
time.

best wishes

--Pedro

--

-

Pedro C. Marijuán

Grupo de Bioinformación / Bioinformation Group

Instituto Aragonés de Ciencias de la Salud

Centro de Investigación Biomédica de Aragón (CIBA)

Avda. San Juan Bosco, 13, planta X

50009 Zaragoza, Spain

Tfno. +34 976 71 3526
(& 6818)


pcmarijuan.i...@aragon.es



http://sites.google.com/site/pedrocmarijuan/

-

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Professor John
Collier
colli...@ukzn.ac.za
Philosophy and Ethics, University of KwaZulu-Natal, Durban 4041 South
Africa
T: +27 (31) 260 3248 / 260 2292   F:
+27 (31) 260 3031
http
://web.ncf.ca/collier



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