Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-10-01 Thread Robin Faichney
Thursday, September 29, 2011, 11:11:36 AM, Michel wrote:

 *** Karl:

[Karl's last paragraph:]
 As to the assertion of a colleague that the term information can not
 be subject to a formal definition: if one wants to use a term in a
 rational, logical discourse, then the term has to be defined. If we
 are to remain in the romantic stage, where information is like
 love, patriotism, morality or so, then of course there is no
 need to connect the term to the basis of rational discourses.
 Otherwise, the need to explicate the roots of a term by showing its
 fundaments in a+b=c is of elementary importance.


 *** My reply to Karl:

 Ok to avoid the mix of the stuff and its reception.

 In the addition table: did you meant that having 5 has a result of
 an addition of two positive integers, the missing information is: was
 it got from 1+4, 2+3, 3+2, or 4+1 ? If yes, that's indeed a very
 simple situation helping to define what is information. If I am wrong,
 please just tell me.

That is also my impression of Karl's contribution: an example of
information, not a definition of it.

 The suggestion you did in the last paragraph is of much interest, too.
 I hope that FISers will post comments about it.

I hope I'm not the colleague mentioned there, because that's most
certainly not my position. I believe I offer one of the clearest
definitions of information (and, of course, the only correct one!) And
I certainly disagree with the implication that all proper definitions
are mathematical in form.

[Gavin:]
 I think the danger is actually there is no such thing as information.

 *** My comment about the inexistence of such information:

 That is a main point to discuss, and again I hope that FISers will
 post their opinions about it.

So do I!

 *** My reply to  Robert:

 It does not shock me that chemical reactions are considered as part of
 physics, even if chemical reactions are often used to separate the two
 fields for pratical purposes.
 Since biology is often viewed as part of chemistry, it can be viewed
 as physics too (still does not shock me!), but I'm quite sure that
 such a conclusion is polemical: this discussion may be postponed to
 the next FIS session, focussing on biology, despite that it is of
 interest here.

I think there's a big difference between saying, as I do, that in
principle all chemical and biological phenomena can be reduced to
physics, and saying, as I most certainly do not, that the disciplines
of chemistry and biology are or should be part of the discipline of
physics. That would be just an academic land grab and I'd want no part
of it.

-- 
Robin Faichney
http://www.robinfaichney.org/

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-29 Thread Pedro C. Marijuan

Dear Michel and FIS colleagues,

Thanks for the excellent discussion, so far. The usual conspiracy of 
bureaucratic things around me have precluded my involvement in the 
important aspects dealt with (and cannot properly refer to the 
individual messages before). Anyhow, three short reflections follow.


When and why chemoinformation appears? I remember that in very early 
90's a new, international society on Molecular Computing was promoted by 
a variety of comp-bio-chem-phys parties, with the leading scientific 
figure of  Michael Conrad (also FIS co-founder!, more or less around the 
same time). The society had a few, important World congresses but 
finally dissolved in late 90's. I suggested to Michael, and presented in 
their 1993 Congress, an integration of the nascent molecular computing 
field under the heading of chemical information and within an ampler 
information sceince --but most of them were working in a more 
technically centered alternative to artificial life and did not get 
interested. Robert Rosen (in a parallel exchange, as he was invited to 
publishing in a Spanish Journal) also agreed with me that there were 
important conceptual differences regarding chemical systems between 
information processing and molecular computing... the relationship 
of information with absence, involving meaning, was part of the 
discussion.


Somehow, what was realized around that time is that different properties 
related to molecules could support new forms of wet processing, or 
provide new views on biological selforganization, and new names for that 
multidisciplinary new effort were looked after. What molecular 
properties? Whatever. This forms part of my comment days ago, once you 
establish the info framework, then the un-definition of information 
dissolves and you can measure it, process it, amplify it, destroy it, 
etc. But not before. The problem is that in order to achieve that 
establishment the different disciplines would act quite differently, 
and in non-communicable ways (among themselves). I discussed some of 
this during Yixin's session, and until now I do not see any elegant way 
to enter meaningful order among the different establishments.


And finally, those efforts and problems of mol. computing and also 
cheminformatics/cheminformation are more or less tractable if you remain 
within highly constrained artificial settings---I remember however the 
very exciting discussions in Paris FIS 2005 between experts working in 
chemical databases, on their tough ontological problems. My contention 
is that without introducing the apophatic path (Bob U., Terry D.), the 
notion of absence  (in my opinion, referring to the bio, within the 
life cycle)  cheminformation will not develop complex enough systems 
or decisive conceptual breakthroughs...  Who knows. Maybe in the 
frontiers between the non-purposive and the purposive chem. entities 
there are valuable informational insights. Could a new approach to 
symmetry be the conceptual-arch key?


best

---Pedro

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-26 Thread karl javorszky
Dear Colleagues,

taking the risk of repeating an idea that has been advanced here in FIS a
number of times, I'd like to offer answers to Michhel's questions:

Michel:  Now, I ask you the following: please can you provide an extremely
simple example (the most simple you could imagine) of situation in
which you can say:  in this situation, information is ... .
Answer: Let me present a numerical table based on a+b=c, consisting of 136
additions (between 1+1=2 and 16+16=32) which is evaluated on 9 aspects of
the additions (namely: a,b,a+b, 2b-a, b-a, 3b-2a, 2a-b, 17-(a+b), 3a-2b) and
ordered on two of these aspects (therefore existing in 72 distinguishable
collections of sequences of distances). This table gives rise to two
concepts of Euclid spaces (consisting of 3 rectangular axes each) and two
planes (with 2 rectangular axes each).
The term information can then be used - as Michel asked for - in a deictic
fashion by pointing to a collection of spatial points in both Euclid spaces
and saying  in this situation, information is:  whether we consider
relevant the connection of these spatial point-collections with  this 
or  that  collection of different spatial points which are connected to
the presently pointed-at collection odf spatial points by either  this 
or  that  re-orderings of the collection. while one points at two
different ways of re-ordering the collection among the 72 ways of
re-ordering the collection, and calling one of them  this  and the other
 that .

It helps if you, dear Colleague, construct the above-mentioned table. Then
it is irrefutalby clear that the meaning of the term information is indeed
contained in the underlying rules that construct a+b=c as a logical
procedure. The only innovation is that one does not ignore the differeneces
between a1+b1=c vs. a2+b2=c (a1 # a2) as one was instructed at Elemenary
School to do.

Michel: 3. The comparison Pedro did with symmetry is of interest: can
anyone
define symmetry ?
Answer: Using the table constructed above, one may point to the two Euclid
spaces and say: The two spaces are  symmetrical  and the term 
symmetrical  is defined by the following: a. the two spaces are
interconnected by a point/plane which we call symmetry centre/axe and each
collection of (a1,b1; a2,b2; a3,b3) which finds a spatial representation in
both of the Euclid spaces is in a symmetrical  relation.

Here, again, it helps if one constructs the above-mentioned table in
visualising that a symmetry exists.

I hope that these suggestions are both clear and understandable. It is,
however, necessary to construct the table to be able to use the definitions.
(Like one cannot explain the definition of sin(x) without having understood
the construction of a trigonometric table).

Karl


2011/9/23 Michel Petitjean petitjean.chi...@gmail.com

 Dear FISers,

 Pedro raises several points.
 Among them:

 1. Chemoinformatics or Cheminformatics ?
 Both terms are encountered. I would say that unless some authority
 takes a decision, both terms will continue to be used.

 2. Despite I gave an example of what could be cheminformation in a
 concrete case, I did not tell what was exactly cheminformation in this
 concrete case. I just asked the question of what it could be.
 Now, I ask you the following: please can you provide an extremely
 simple example (the most simple you could imagine) of situation in
 which you can say:  in this situation, information is ... .
 Chemical information is welcome, but an example from physics would be
 great, too. However, please, no biology example, that will be dicussed
 at the occasion of a future session.
 These examples are expected to help us to define information in more
 general situations.

 3. The comparison Pedro did with symmetry is of interest: can anyone
 define symmetry ?
 During a long time, symmetry had in common with information that many
 people attempted to define it in its own field, giving raise to many
 particular definitions, but not to a common and widely accepted one.
 Some years ago, although I needed to mention a definition of symmetry
 in one of my papers, I was surprised that I could not find an unifying
 one (symmetry is known since millenaries!!). Even in the book of Weyl
 I did not find the expected one.
 So, I decided to build my own one (Symmetry: Culture and Science,
 2007, 18[2-3], 99-119; free reprint at
 http://petitjeanmichel.free.fr/itoweb.paper.SCS.2007). See also:
 http://petitjeanmichel.free.fr/itoweb.petitjean.html
 In fact, the group structure which is generally a priori imposed, is a
 consequence of several properties that the definition should satisfy
 to be in agreement with some obvious intuitive requirements (and so,
 five different groups appear naturally, none of them being imposed a
 priori). Of course, the proposed unifying definition applies to a
 broad spectrum of situations, not only the geometric one: matrices,
 functions, distributions, graphs, etc.
 But that was possible because I already had 

Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-26 Thread Loet Leydesdorff
Dear Michel, 

It seems to me that Shannon's formulas are mathematical and yet
content-free. By the specification of a system of reference they can be
provided with dimensionality and then also meaning. For example, in the case
of the momenta and positions of particles H is multiplied with k(B) [S =
k(B) *H] and thermodynamic entropy [Watt/Kelvin] can thus be defined.
Momenta and energy are in this case exchanged upon collisions. S measures
the dissipation in the non-ideal case. 

This is a specific (physical) theory of communication. If molecules are
exchanged life can be generated (Maturana); if atoms are exchanged, chemical
evolution can be expected.

It seems to me that the general scheme is the specification of (i) WHAT is
being exchanged -- this specifies the domain theory -- and (ii) HOW one
expects to be exchanged (e.g., dissipative or conservative, recursive or
incursive, etc.), and (iii) WHY. The why question bring us to evolution
theory; for example, the selection environments for the variation
(uncertainty) can then be specified as hypotheses.

Best wishes,
Loet


-Original Message-
From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On
Behalf Of Michel Petitjean
Sent: Monday, September 26, 2011 1:39 PM
To: fis@listas.unizar.es
Subject: Re: [Fis] Chemical information: a field of fuzzy contours ?

Dear FISers,

I thank very much Robin, Xueshan, Stan, and Karl for their examples of
information, that I summarized below:


*** Robin:

Of course, there is no law or formula that relates a bit of information
to, say, quarks, spin, or whatever. These are different ways of looking at
the same thing. Spin is a bit of information (I think it's just one bit, but
I might be wrong, as I said, I'm no
physicist.)

Physical information is a re-conceptualisation of material form that allows
it to be quantified. So, for example, physicists can (and do) say that
information is generally conserved within black holes. (See the Black Hole
Information Paradox, and the bet between physicists concerning it,
http://www.theory.caltech.edu/~preskill/jp_24jul04.html)

Now, there is obviously more to semantic information than material form, but
it is my strongly-held belief that it should be possible to relate all other
concepts of information back to physical information, and, in fact, I have
proposed a way of doing that for semantic information, which I presented at
the DTMD2011 workshop (I've also mentioned it in previous posts on this
list), but I'll say no more about it here, because I think that's going too
far off the current topic.

Michel, maybe that was a bad example, misleading because of its binary
nature. My understanding is that physical information is material form,
re-conceptualised, and so the spin state, like every other physical
attribute, not just the binary ones, IS information (non-semantic
information), as and when it suits us to view it that way, i.e. to focus on
form rather than substance.

Historically, the concept of non-semantic information, or pure pattern,
arose in the context of information theory, but to focus on form is a basic
human capacity, and given the concept of non-semantic information, however
that arises, it is a small step to apply it to material form, which thus
becomes pure pattern whose transformations are governed by the laws of
physics.

So material form is like data and the totality of physical laws is the
program that operates upon it. The operations are, in principle and in
general, reversible, and so physical information is conserved, like matter
and energy. (I believe there is a strong consensus within physics that
physical information is conserved in quantum mechanics.)

In a certain sense the laws of physics stand in for substance, which is
what constrains material form in our ordinary thinking. When we think in
terms of pure patterns constrained by physics, every physical entity
embodies its own description, and (which is to say almost the same thing)
encodes the outcomes of all of its potential interactions.
This is a very powerful way of thinking.

Gavin: I agree with you that there is no such free-standing,
thing-in-itself as information, but that doesn't invalidate the concept,
far from it. Information is, in my view, basically form, and form doesn't
exist without substance, but we work with form, ignoring substance, all the
time, and achieve great things by so doing.


*** Xueshan:

1. Chmoinformatics: A study about how to manage and compute chemical
information, such as management of chemical abstracts, retrieval of chemical
information through internet, molecules represented by graphs, data mining
etc. there are many books like this in the bookstore. Of course, this may
not be a subject that could arouse real interests among true information
researchers, because there are thousands of applications of information
technology in different areas, it is difficult for us to call all these
applications of information technology

Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-24 Thread Michel Petitjean
Dear FISers,

Many thanks to Xueshan Yan for these three examples of cheminformation.
I agree that among the various cheminformation concepts, some are technological.
E.g., the Infonortics conferences (the 2011 one held in Barcelona:
http://www.infonortics.com/call-11.html, http://www.haxel.com/icic/)
are oriented to professional information, rather in the sense of
publishing. That should be of interest for professional information
people in a broader sense, not only in a technology of publication one
and related.
On the other hand, cheminformatics conferences and workshops organized
in various countries, such as in USA (by CINF division of the ACS,
mentioned in a previous post), in Germany
(https://www.gdch.de/index.php?id=780), in UK
(http://cisrg.shef.ac.uk/shef2010/), in France
(http://infochim.u-strasbg.fr/spip.php?rubrique12), etc., seem to
target attendees mainly interested in a different technolgical
cheminformation, closer to the one mentioned in case 1 by Xueshan Yan.
It seems to me that the two respective scopes of these two classes of
conferences have a reduced intersection.
Nevertheless, none of them should be ignored.
Regarding cases 2 and 3 mentioned by Xueshan Yan, I would like to read
more from FISers before commenting.

Thanks also to Robin Faichney for the example of information in
physics, that I would comment a bit (not joking).
I can understand that a two states system such as a spin can be viewed
as carrying a bit of information.
This is a good example of application of information theory to a
physical system. This class of examples is nice because it takes
benefit from the rigorous definitions available in the field, which
can be found in textbooks (Cover, Renyi, etc.).
However, since we assumed that information theory is a subfield of
information science (in addition to be a subfield of probability
theory), we also need very simple examples of information outside the
field of information theory.

Best regards,

Michel.

2011/9/24 Xueshan Yan y...@pku.edu.cn:
 Dear Michel,

 It is very interesting for you telling us so many stories about the study of
 chemical information which took place in France and your university.

 As an information researcher, I once was invited to deliver a speech on
 Information Science at a meeting about chmoinformatics here a few years ago;
 I found their interests are far different from mine. Their main concerns are
 what information technology can be applied to chemistry――It seems as if you
 like this one according to your introductory post.But what we are eager to
 know is where the chemical information exists and how it functions between
 two molecules or supermolecules. As a matter of fact, I found there are
 three kinds of studies about information in chemistry.

 1. Chmoinformatics: A study about how to manage and compute chemical
 information, such as management of chemical abstracts, retrieval of chemical
 information through internet, molecules represented by graphs, data mining
 etc. there are many books like this in the bookstore. Of course, this may
 not be a subject that could arouse real interests among true information
 researchers, because there are thousands of applications of information
 technology in different areas, it is difficult for us to call all these
 applications of information technology as informatics or information
 science.

 2. Chmoinformatics: A study about how chemical information function between
 two molecules or two supermolecules, according to the terms in biology and
 chemistry: between substrate and receptor, or in coordination chemistry:
 between donor and acceptor, or host and guest, we can only consider this
 thought as a conjecture which proposed by Jean-Marie Lehn of University
 Louis Pasteur――the noble prize winner of 1987. As a matter of fact, we all
 know that in the process of molecule reaction and recognition, an
 intelligent is in esse. This has been proved by Fischer’s lock-and-key model
 early in 1894.

 3. Semiochemistry: A study about chemical information materials that mediate
 interactions between members of different species. This study consider
 pheromone, quinonyl compounds etc. as messengers. It is an interdiscipline
 of chemistry and biology.

 We especially want to know what advance about the second study about
 chemical information in chemists has made recent years. Because Lehn said in
 many places: “Supramolecular chemistry (chmoinformatics) has paved the way
 toward apprehending chemistry as an information science”.

 Best wishes,
 Xueshan Yan
 Peking University, FIS Beijing Group


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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-23 Thread Michel Petitjean
Dear FISers,

Pedro raises several points.
Among them:

1. Chemoinformatics or Cheminformatics ?
Both terms are encountered. I would say that unless some authority
takes a decision, both terms will continue to be used.

2. Despite I gave an example of what could be cheminformation in a
concrete case, I did not tell what was exactly cheminformation in this
concrete case. I just asked the question of what it could be.
Now, I ask you the following: please can you provide an extremely
simple example (the most simple you could imagine) of situation in
which you can say:  in this situation, information is ... .
Chemical information is welcome, but an example from physics would be
great, too. However, please, no biology example, that will be dicussed
at the occasion of a future session.
These examples are expected to help us to define information in more
general situations.

3. The comparison Pedro did with symmetry is of interest: can anyone
define symmetry ?
During a long time, symmetry had in common with information that many
people attempted to define it in its own field, giving raise to many
particular definitions, but not to a common and widely accepted one.
Some years ago, although I needed to mention a definition of symmetry
in one of my papers, I was surprised that I could not find an unifying
one (symmetry is known since millenaries!!). Even in the book of Weyl
I did not find the expected one.
So, I decided to build my own one (Symmetry: Culture and Science,
2007, 18[2-3], 99-119; free reprint at
http://petitjeanmichel.free.fr/itoweb.paper.SCS.2007). See also:
http://petitjeanmichel.free.fr/itoweb.petitjean.html
In fact, the group structure which is generally a priori imposed, is a
consequence of several properties that the definition should satisfy
to be in agreement with some obvious intuitive requirements (and so,
five different groups appear naturally, none of them being imposed a
priori). Of course, the proposed unifying definition applies to a
broad spectrum of situations, not only the geometric one: matrices,
functions, distributions, graphs, etc.
But that was possible because I already had knowledge of the many
definitions in particular domains or situations.

Thus I expect that that you will post several examples of information
in very simples cases.
From the analysis of these situations we should move forward.

E.g., for symmetry, one of the simple examples I gave was the set of
three points of the real line: if one point is the mid of the two
other, there is symmetry (in fact, it is a case of achirality, i.e.
indirect symmetry, because here we deal with reflections rather than
with rotations).
It would be great to have so simple situations for information in
chemistry or physics.

Thanks by advance,
ll my best,

Michel.

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-23 Thread Robin Faichney
Friday, September 23, 2011, 1:07:07 PM, Michel wrote:

 Now, I ask you the following: please can you provide an extremely
 simple example (the most simple you could imagine) of situation in
 which you can say:  in this situation, information is ... .
 Chemical information is welcome, but an example from physics would be
 great, too.

I'm no physicist but I'm interested in physical information. It
continues to amaze me how little attention is paid by most
non-physicists to the very well established concept of information in
physics.

Of course, there is no law or formula that relates a bit of
information to, say, quarks, spin, or whatever. These are different
ways of looking at the same thing. Spin is a bit of information (I
think it's just one bit, but I might be wrong, as I said, I'm no
physicist.)

Physical information is a re-conceptualisation of material form that
allows it to be quantified. So, for example, physicists can (and do)
say that information is generally conserved within black holes. (See
the Black Hole Information Paradox, and the bet between physicists
concerning it,
http://www.theory.caltech.edu/~preskill/jp_24jul04.html)

Now, there is obviously more to semantic information than material
form, but it is my strongly-held belief that it should be possible to
relate all other concepts of information back to physical information,
and, in fact, I have proposed a way of doing that for semantic
information, which I presented at the DTMD2011 workshop (I've also
mentioned it in previous posts on this list), but I'll say no more
about it here, because I think that's going too far off the current
topic.

-- 
Robin Faichney
http://www.robinfaichney.org/

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-23 Thread Xueshan Yan
Dear Michel,

It is very interesting for you telling us so many stories
about the study of chemical information which took place in
France and your university.

As an information researcher, I once was invited to deliver
a speech on Information Science at a meeting about
chmoinformatics here a few years ago; I found their
interests are far different from mine. Their main concerns
are what information technology can be applied to
chemistry――It seems as if you like this one according to
your introductory post.But what we are eager to know is
where the chemical information exists and how it functions
between two molecules or supermolecules. As a matter of
fact, I found there are three kinds of studies about
information in chemistry.

1. Chmoinformatics: A study about how to manage and compute
chemical information, such as management of chemical
abstracts, retrieval of chemical information through
internet, molecules represented by graphs, data mining etc.
there are many books like this in the bookstore. Of course,
this may not be a subject that could arouse real interests
among true information researchers, because there are
thousands of applications of information technology in
different areas, it is difficult for us to call all these
applications of information technology as informatics or
information science.

2. Chmoinformatics: A study about how chemical information
function between two molecules or two supermolecules,
according to the terms in biology and chemistry: between
substrate and receptor, or in coordination chemistry:
between donor and acceptor, or host and guest, we can only
consider this thought as a conjecture which proposed by
Jean-Marie Lehn of University Louis Pasteur――the noble
prize winner of 1987. As a matter of fact, we all know that
in the process of molecule reaction and recognition, an
intelligent is in esse. This has been proved by Fischer’s
lock-and-key model early in 1894.

3. Semiochemistry: A study about chemical information
materials that mediate interactions between members of
different species. This study consider pheromone, quinonyl
compounds etc. as messengers. It is an interdiscipline of
chemistry and biology.

We especially want to know what advance about the second
study about chemical information in chemists has made recent
years. Because Lehn said in many places: “Supramolecular
chemistry (chmoinformatics) has paved the way toward
apprehending chemistry as an information science”.

Best wishes,
Xueshan Yan
Peking University, FIS Beijing Group


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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-22 Thread Pedro C. Marijuan
Dear Michel and FIS colleagues,

Thanks for the very accurate Intro. I am reluctant to discuss about 
biological information right now, as there are other aspects you have 
dealt with that deserve further discussion. The story itself is funny: 
the way new fields of multidisciplinary origins have to swim against the 
strong forces of institutional viscosity --probably the stunning 
success of bioinformatics also contributed to the revival of cheminfo in 
France (and elsewhere). That's fodder for my scientomics perspective, 
the interpenetration or recombination of fields as the usual origin of 
new disciplines ...  by the way, the proper term in English should be 
Chemoinformatics or Cheminformatics? I have seen both in the literature.

The relationship  between scientific practice, Data Mining (DM) and 
Knowledge Discovery in Databases (KDD) is another crucial informational 
aspect you enter. Where is information? For my taste, every major 
discipline has provided its own answer, but implicitly, and that 
contributes to the impossibility to give a consistent answer to your 
questions about that. The discussion could be too long, beyond my typing 
possibilities today... I think however that bioinformation can give some 
serious points precisely by means of DM and KDD related tools --my bet 
is that the technology of microarrays in systems biology and 
bionformatics will be able to tell us what is meaning at the cellular 
scale. But an in depth discussion of the chemical background would be 
needed.

Continuing with Gavin's --there is a grain of truth in some of his 
rejections-- precisely I see Info Science as the attempt to achieve 
multidisciplinary consistency around the whole familiy of info concepts, 
even probably assuming that info itself cannot be defined, although you 
can measure it, process it,  etc.  That's not pejorative, can anyone 
define time, or symmetry? Biologically speaking there is not much to 
discuss: metabolism is what our cells eat, signaling is about the 
information they read from the environment. It is written in 
chemicals, like our newspapers (in ink), but cells do not eat it, the 
same way we do not eat newspapers (unless in onion paper!). Veteran 
Fisers will remember a funny exchange with Igor many years ago, Father 
Brown related...

best wishes

--Pedro

-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Avda. Gómez Laguna, 25, Pl. 11ª
50009 Zaragoza, Spain
Telf: 34 976 71 3526 ( 6818) Fax: 34 976 71 5554
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-21 Thread Igor Gurevich
2011/9/16 Michel Petitjean petitjean.chi...@gmail.com:
 Chemical information: a field of fuzzy contours ?
 -

 Before turning to chemistry, I would recall some facts that I noticed
 on the FIS forum:
 although many people consider that a unifying definition of
 information science is possible (to be constructed),
 a number of other people consider that there are many concepts of
 information which are not necessarily
 the facets of an unique concept, so that it could be better to speak
 about information scienceS,
 and not about information science.
 I can read on http://en.wikipedia.org/wiki/Information_science
  Information science is an interdisciplinary science primarily
 concerned with the
 analysis, collection, classification, manipulation, storage, retrieval
 and dissemination of information. 
 and some fewer lines above:
  Information Science consists of having the knowledge and
 understanding on how to collect, classify, manipulate, store, retrieve
 and disseminate any type of information. 
 Clearly, collecting, storing, and retrieving information let us think
 that we must deal with databases.
 The question where is information is neglected, although answering
 it is enlighting:
 no doubt that much information is stored in data banks.
 There are strong connections of Information Science(s) with Data
 Mining (DM) and Knowledge Discovery in Databases (KDD).

 Is the situation clearer in chemistry ?

 Undoubtly there is a field of chemical information.

 The ACS (American Chemical Society) has a Division of Chemical
 Information (CINF),
 named as such in 1975, but which in fact goes back to 1943
 (http://www.acscinf.org/).
 CINF is active and organizes various meetings which can be retrieved on the 
 web.
 Visit also http://www.libsci.sc.edu/bob/chemnet/chchron.htm, an
 informative website.

 The ACS publishes the Journal of Chemical Information and Modeling
 renamed so in 2005
 after having been named Journal of Chemical Information and Computer
 Sciences from 1975 to 2004,
 itself being the continuation of the Journal of Chemical
 Documentation from 1961 to 1974.
 In fact, it is the same journal (one volume per year), which turned to
 chemical information the same year that CINF received his actual name.

 Interestingly, still in 1975, the main cheminformatics lab in France
 (in fact the only one in France at this time) was renamed.
 The old name was LCOP (Laboratoire de Chimie Organique Physique),
 and the new name was ITODYS, still in vigor,
 meaning until 2001: Institut de TOpologie et de DYnamique des
 Systemes. This name, which can be understood in English due
 to the close similarity between the French and the English words, was
 partly due to the existence of a distance in the molecular graphs
 (this distance is the smaller number of chemical bonds separating two
 atoms), and as known, a distance induces a topology:
 it clearly acknowledged the cheminformatics aspects of the research
 performed in the lab.

 Chemical Information Science, which is sometimes named Chemical Informatics
 (http://www.indiana.edu/~cheminfo/acs800/soced_wash.html)
 can be reasonably considered to be a part of the Cheminformatics field.
 This latter is defined on Wikipedia
 (http://en.wikipedia.org/wiki/Cheminformatics):
 Chemoinformatics is the mixing of those information resources to
 transform data into information and
 information into knowledge for the intended purpose of making better
 decisions faster in the area of
 drug lead identification and optimization.
 This definition, dated from 1998, clearly acknowledges the extraction
 of information from data,
 but it is restrictive since it discards all pioneering works about
 computerization of chemical databases,
 including structural formulas coding and structural motifs retrieval,
 which historically cannot be denied
 to be the core of the cheminformatics field.

 Now let me write more lines about the story of cheminformatics in France,
 which is a bit funny but enlights the debate on the definition on the
 field of chemical information.
 The French pioneer was Jacques-Emile Dubois (1920-2005), founder of
 the LCOP and of the ITODYS,
 who published his first cheminformatics paper in 1966. One of his main
 ideas was to use the concept
 of concentric layers in the molecular graphs: the nodes are the atoms
 and the edges are the bonds,
 the neighbours of a node constitute the first concentric layer around this 
 node,
 the next neighbours constitute the second layer, and so on.
 This concept was known to mathematicians such as Cayley and Polya.
 Here, the challenge was to explain to experimental chemists that in a
 number of applications, such as QSAR
 (Quantitative Structure-Activity Relationship), the use of sets of two
 concentric layers around focus atoms
 may be more efficient that the usually taught approaches based on
 squeletons and substituents.
 Dubois also thought that this concept could help to 

Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-19 Thread Loet Leydesdorff
Dear Michel, 

 

Ø  Stating that information does not exist may be compared to stating that a
cloud does not exist: it is hard to define it rigorously and its frontiers
are highly fuzzy, but everybody is sure that it exists.

 

The problem is here the “exist”. This easily lead to reification. For
example, you formulate: 

 

Ø  Thus I would not seek information here.

 

In my opinion, “information” can be entertained as a concept in a discourse.
It can then also be defined, for example, as probabilistic entropy. I like
Husserl’s term “cogitatum” which he added in “the Cartesian Meditations” to
Descartes distinction between res extensa and res cogitans. Information
cannot to be found as res extensa. 

 

Best wishes, 

Loet

 

 

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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-19 Thread Loet Leydesdorff
Dear Michel, 

The model allows us to entertain descriptions of future states in the
present. Thus, it makes the discursive system strongly anticipatory in the
sense of Daniel Dubois: a strongly anticipatory system uses its future state
for its shaping itself in the present. 

The strong antipation in the discourse can also be typified as discursive
knowledge. Unlike personal (e.g., tacit) knowledge, the further codification
of the communication (of information and meaning) thus can be considered as
an evolutionary mechanism. 

Res extensa is only historical; not evolutionary. As the retention of
previous information flows; footprints. Evolutionary mechanisms such as in
the res cogitans are not confined by the historical dimension, but can
operate with future states.

So: this was my second penny for this week!

Best wishes, 
Loet



-Original Message-
From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On
Behalf Of Michel Petitjean
Sent: Monday, September 19, 2011 4:44 PM
To: fis@listas.unizar.es
Subject: Re: [Fis] Chemical information: a field of fuzzy contours ?

Dear Loet,
Thanks for your very good reply.
Yes information cannot be found as res extensa, justs as mathematics:
mathematics exist in our head, and can be communicated, can be taught, etc.,
but do not exist as concrete objects.
However, starting from data (and databanks), we can extract knowledge and
produce mathematical models, the so-called physical laws (note that many
math demonstrated math theorems still not apply to any physical situation).
They do not exist as objects, but they do exists as models of physical
situations.
Some years ago on a chemistry forum there was a debate about orbitals:
some tell that they do exist because they can be measured etc. (even void
orbitals ?), and some tell that it is just a current math model of the
reality with an acceptable degree of simplification. I am in favor of the
latter view: they exist, but as a model.
Information is as knowledge: it can be extracted and as such it exists, but
yes the exists is ambiguous, just as for orbitals.
All my best,
Michel.

2011/9/19 Loet Leydesdorff l...@leydesdorff.net:
 Dear Michel,

 Ø  Stating that information does not exist may be compared to stating 
 that a cloud does not exist: it is hard to define it rigorously and 
 its frontiers are highly fuzzy, but everybody is sure that it exists.

 The problem is here the “exist”. This easily lead to reification. For 
 example, you formulate:

 Ø  Thus I would not seek information here.

 In my opinion, “information” can be entertained as a concept in a
discourse.
 It can then also be defined, for example, as probabilistic entropy. I 
 like Husserl’s term “cogitatum” which he added in “the Cartesian 
 Meditations” to Descartes distinction between res extensa and res 
 cogitans. Information cannot to be found as res extensa.

 Best wishes,

 Loet


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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-18 Thread Michel Petitjean
Dear Stan,
I would not insert an 'organic realm' in the hierarchy: it is part of
the chemical realm, but it is broader than expected.
The rules of Organic Chemistry are not universal as the theorems of
mathematics are: many exceptions exist, at least due to the existence
of multifunctional compounds. Even increasing the length of an alkyl
chain can give surprising results. It is why patents covering
syntheses of an infinite number of compounds should never have been
accepted, although they were. At the occasion of a course, we learned
the main rules needed to face to the realm of Organic Chemistry, but
the complexity of structural formulas we face (often natural products)
is incredibly vast, and each year we discover more. In parallel,
Organic Chemists establish new syntheses and reactions, and the
catalog of rules we have is now too large to be likely known by only
one Organic Chemist.
But compared to Biology, even Organic Chemistry remains simple !!
It means that we are as the midge trying to understand a computer: it
is unlikely that we will be successful.
But the challenge is so exciting, and we can take benefits from any
increase of knowledge.
Best,
Michel.

2011/9/17 Stanley N Salthe ssal...@binghamton.edu:
 Michel -- Organic chemistry was known to be the most difficult course in
 Columbia University.  But I got interested in it, worked very hard
 constantly, and I achieved an  'A'.  But what you say here indicates several
 orders of magnitude more difficulty than what I played with in university.
  For me this raises a question about the 'realms of nature', as in the
 subsumptive hierarchy: {physical realm {chemical realm {biological realm}}.
  Do you think one should place an 'organic realm' between chemical and
 biological?  Or, otherwise, do you think it possible that there might be
 organic realms out in the universe not entrained into biology?
 STAN


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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-18 Thread Gavin Ritz
Hi there Joseph

Can you show me where information is in chemistry?

 

What part of chemistry is chemical information?

 

I’m less concerned about a unifying definition of information but rather I
would like to see some evidence and experiments for biological information.

 

So far I haven’t seen one piece of evidence to suggest that information
exits at all.

 

I see a lot of conjecture, assumptions, propositions but not a whole lot of
actual evidence and actual tests.

 

Kind regards

Gavin

 

-Original Message-
From: fis-boun...@listas.unizar.es [mailto:fis-boun...@listas.unizar.es] On
Behalf Of joe.bren...@bluewin.ch
Sent: Sunday, 18 September 2011 2:50 a.m.
To: petitjean.chi...@gmail.com; fis@listas.unizar.es
Subject: Re: [Fis] Chemical information: a field of fuzzy contours ?

 

Dear Michel and FIS Colleagues,

 

This will be an interesting discussion, since the core nature and role of
information will be involved. Here is just one first point: to me, as a

chemist, chemical information is only secondarily an object capable of
being formalized, archived, etc. A formula has meaning for me in terms

of the potential reactions the molecule to which it refers can undergo, what
it looked like when crystallized for the first time and so on.

 

Cheminformatics seems not to deal with such aspects of chemical information
as part of a process of doing chemistry. Can this be captured by 

another system?

 

Best wishes,

 

Joseph

 

Ursprüngliche Nachricht
Von: petitjean.chi...@gmail.com
Datum: 16.09.2011 09:44
An: fis@listas.unizar.es
Betreff: [Fis] Chemical information: a field of fuzzy contours ?

Chemical information: a field of fuzzy contours ?
-

Before turning to chemistry, I would recall some facts that I noticed
on the FIS forum:
although many people consider that a unifying definition of
information science is possible (to be constructed),
a number of other people consider that there are many concepts of
information which are not necessarily
the facets of an unique concept, so that it could be better to speak
about information scienceS,
and not about information science.
I can read on http://en.wikipedia.org/wiki/Information_science
 Information science is an interdisciplinary science primarily
concerned with the
analysis, collection, classification, manipulation, storage, retrieval
and dissemination of information. 
and some fewer lines above:
 Information Science consists of having the knowledge and
understanding on how to collect, classify, manipulate, store, retrieve
and disseminate any type of information. 
Clearly, collecting, storing, and retrieving information let us think
that we must deal with databases.
The question where is information is neglected, although answering
it is enlighting:
no doubt that much information is stored in data banks.
There are strong connections of Information Science(s) with Data
Mining (DM) and Knowledge Discovery in Databases (KDD).

Is the situation clearer in chemistry ?

Undoubtly there is a field of chemical information.

The ACS (American Chemical Society) has a Division of Chemical
Information (CINF),
named as such in 1975, but which in fact goes back to 1943
(http://www.acscinf.org/).
CINF is active and organizes various meetings which can be retrieved on the
web.
Visit also http://www.libsci.sc.edu/bob/chemnet/chchron.htm, an
informative website.

The ACS publishes the Journal of Chemical Information and Modeling
renamed so in 2005
after having been named Journal of Chemical Information and Computer
Sciences from 1975 to 2004,
itself being the continuation of the Journal of Chemical
Documentation from 1961 to 1974.
In fact, it is the same journal (one volume per year), which turned to
chemical information the same year that CINF received his actual name.

Interestingly, still in 1975, the main cheminformatics lab in France
(in fact the only one in France at this time) was renamed.
The old name was LCOP (Laboratoire de Chimie Organique Physique),
and the new name was ITODYS, still in vigor,
meaning until 2001: Institut de TOpologie et de DYnamique des
Systemes. This name, which can be understood in English due
to the close similarity between the French and the English words, was
partly due to the existence of a distance in the molecular graphs
(this distance is the smaller number of chemical bonds separating two
atoms), and as known, a distance induces a topology:
it clearly acknowledged the cheminformatics aspects of the research
performed in the lab.

Chemical Information Science, which is sometimes named Chemical Informatics
(http://www.indiana.edu/~cheminfo/acs800/soced_wash.html)
can be reasonably considered to be a part of the Cheminformatics field.
This latter is defined on Wikipedia
(http://en.wikipedia.org/wiki/Cheminformatics):
Chemoinformatics is the mixing of those information resources to
transform data into information and
information into knowledge for the intended

Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-17 Thread joe.bren...@bluewin.ch





Dear Michel and FIS Colleagues,


This will be an interesting discussion, since the core nature and role of 
information will be involved. Here is just one first point: to me, as a
chemist, chemical information is only secondarily an object capable of being 
formalized, archived, etc. A formula has meaning for me in terms

of the potential reactions the molecule to which it refers can undergo, what it 
looked like when crystallized for the first time and so on.



Cheminformatics seems not to deal with such aspects of chemical information as 
part of a process of doing chemistry. Can this be captured by 
another system?


Best wishes,


Joseph



Ursprüngliche Nachricht
Von: petitjean.chi...@gmail.com
Datum: 16.09.2011 09:44
An: fis@listas.unizar.es
Betreff: [Fis] Chemical information: a field of fuzzy contours ?

Chemical information: a field of fuzzy contours ?
-

Before turning to chemistry, I would recall some facts that I noticed
on the FIS forum:
although many people consider that a unifying definition of
information science is possible (to be constructed),
a number of other people consider that there are many concepts of
information which are not necessarily
the facets of an unique concept, so that it could be better to speak
about information scienceS,
and not about information science.
I can read on http://en.wikipedia.org/wiki/Information_science
 Information science is an interdisciplinary science primarily
concerned with the
analysis, collection, classification, manipulation, storage, retrieval
and dissemination of information. 
and some fewer lines above:
 Information Science consists of having the knowledge and
understanding on how to collect, classify, manipulate, store, retrieve
and disseminate any type of information. 
Clearly, collecting, storing, and retrieving information let us think
that we must deal with databases.
The question where is information is neglected, although answering
it is enlighting:
no doubt that much information is stored in data banks.
There are strong connections of Information Science(s) with Data
Mining (DM) and Knowledge Discovery in Databases (KDD).

Is the situation clearer in chemistry ?

Undoubtly there is a field of chemical information.

The ACS (American Chemical Society) has a Division of Chemical
Information (CINF),
named as such in 1975, but which in fact goes back to 1943
(http://www.acscinf.org/).
CINF is active and organizes various meetings which can be retrieved on the web.
Visit also http://www.libsci.sc.edu/bob/chemnet/chchron.htm, an
informative website.

The ACS publishes the Journal of Chemical Information and Modeling
renamed so in 2005
after having been named Journal of Chemical Information and Computer
Sciences from 1975 to 2004,
itself being the continuation of the Journal of Chemical
Documentation from 1961 to 1974.
In fact, it is the same journal (one volume per year), which turned to
chemical information the same year that CINF received his actual name.

Interestingly, still in 1975, the main cheminformatics lab in France
(in fact the only one in France at this time) was renamed.
The old name was LCOP (Laboratoire de Chimie Organique Physique),
and the new name was ITODYS, still in vigor,
meaning until 2001: Institut de TOpologie et de DYnamique des
Systemes. This name, which can be understood in English due
to the close similarity between the French and the English words, was
partly due to the existence of a distance in the molecular graphs
(this distance is the smaller number of chemical bonds separating two
atoms), and as known, a distance induces a topology:
it clearly acknowledged the cheminformatics aspects of the research
performed in the lab.

Chemical Information Science, which is sometimes named Chemical Informatics
(http://www.indiana.edu/~cheminfo/acs800/soced_wash.html)
can be reasonably considered to be a part of the Cheminformatics field.
This latter is defined on Wikipedia
(http://en.wikipedia.org/wiki/Cheminformatics):
Chemoinformatics is the mixing of those information resources to
transform data into information and
information into knowledge for the intended purpose of making better
decisions faster in the area of
drug lead identification and optimization.
This definition, dated from 1998, clearly acknowledges the extraction
of information from data,
but it is restrictive since it discards all pioneering works about
computerization of chemical databases,
including structural formulas coding and structural motifs retrieval,
which historically cannot be denied
to be the core of the cheminformatics field.

Now let me write more lines about the story of cheminformatics in France,
which is a bit funny but enlights the debate on the definition on the
field of chemical information.
The French pioneer was Jacques-Emile Dubois (1920-2005), founder of
the LCOP and of the ITODYS,
who published his first cheminformatics paper in 1966. One of his main
ideas was to use

Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-17 Thread Michel Petitjean
Dear Joe, dear FISErs,

An organic chemist is able to predict a number of properties from the
structural formula, including much about reactivity of the compound.
But as you know, doing that properly is extremely difficult in a
number of cases, because the rules governing reactivity are much more
complicated that the ones which are taught at Universities, and the
number of rules expands rapidly each year. In fact, an experienced
Organic Chemist has in his head a so extraordinary rich collection of
rules and a so enormous knowledge that even many chemists which are
not Organicians cannot imagine the extent of this knowledge.
It is clear that the doing chemistry process derives from these
rules (these rules are chemical information), not only from the
formulas.
Since the 70's, some cheminformaticians tried to store that in
databases: reactions databases plus databases of reactivity rules for
computer sssisted synthesis or retrosynthesis, etc., then built
programmes intended to output proposals supposed to help the chemist.
As far as I know, the brain of the Organician is still by far much
more efficient than the best softwares which were produced.
So, I may tell that the information available in the brain of the
Organician is extremely difficult to store on computer, and it is even
very difficult to teach it, apart the very beginning.
There are examples other than reactivity. A huge of QSAR studies were
done in order to predict various physico-chemical properties of simple
chemical compounds, e.g., predicting from the structural formulas the
boiling temperatures of monofunctional compounds such as alcohols,
cetones, etc. at 20 C under 1 atm. But even in these apparently simple
cases, the chemical information we need to do that with an acceptable
accuracy is difficult to extract: the conclusions of such QSAR studies
cannot be applied to any alcohol or cetone (still assumed to be
monofunctional compounds), and it is even difficult to know the extent
of validity of the published empirical rules, concretely often
summarized by some regression coefficients.
The example of spectroscopic databases is also of interest. How
simulate spectras (infrared, NMR, mass spectras, etc.) of chemical
compounds ? Starting from the structural formula, it is really hard to
simulate, e.g. a low resolution mass spectra. Most time, it was
attempted to extract rules from spectroscopic databases, then try to
predict the spectra of a compound absent from the database, or
conversely, retrieving the structural formula of a compound from its
spectra(s). Many such softwares were developped since the 70's (one of
the oldest ones is STIRS), but really the chemical information needed
to do that properly is very difficult to extract.
To conclude, I retain your example of crystallization: for sure when
we will able to retrieve from the structural formula H-O-H that water
under 1 atm should crystallize at 0 C, then for sure we will be ready
to predict more about crystallization of chemicals.

Best regards,

Michel.

2011/9/17 joe.bren...@bluewin.ch joe.bren...@bluewin.ch:
 Dear Michel and FIS Colleagues,

 This will be an interesting discussion, since the core nature and role of
 information will be involved. Here is just one first point: to me, as a
 chemist, chemical information is only secondarily an object capable of
 being formalized, archived, etc. A formula has meaning for me in terms
 of the potential reactions the molecule to which it refers can undergo, what
 it looked like when crystallized for the first time and so on.

 Cheminformatics seems not to deal with such aspects of chemical information
 as part of a process of doing chemistry. Can this be captured by  another 
 system?

 Best wishes,

 Joseph


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Re: [Fis] Chemical information: a field of fuzzy contours ?

2011-09-17 Thread Stanley N Salthe
Michel -- Organic chemistry was known to be the most difficult course in
Columbia University.  But I got interested in it, worked very hard
constantly, and I achieved an  'A'.  But what you say here indicates several
orders of magnitude more difficulty than what I played with in university.
 For me this raises a question about the 'realms of nature', as in the
subsumptive hierarchy: {physical realm {chemical realm {biological realm}}.
 Do you think one should place an 'organic realm' between chemical and
biological?  Or, otherwise, do you think it possible that there might be
organic realms out in the universe not entrained into biology?

STAN

On Sat, Sep 17, 2011 at 1:53 PM, Michel Petitjean 
petitjean.chi...@gmail.com wrote:

 Dear Joe, dear FISErs,

 An organic chemist is able to predict a number of properties from the
 structural formula, including much about reactivity of the compound.
 But as you know, doing that properly is extremely difficult in a
 number of cases, because the rules governing reactivity are much more
 complicated that the ones which are taught at Universities, and the
 number of rules expands rapidly each year. In fact, an experienced
 Organic Chemist has in his head a so extraordinary rich collection of
 rules and a so enormous knowledge that even many chemists which are
 not Organicians cannot imagine the extent of this knowledge.
 It is clear that the doing chemistry process derives from these
 rules (these rules are chemical information), not only from the
 formulas.
 Since the 70's, some cheminformaticians tried to store that in
 databases: reactions databases plus databases of reactivity rules for
 computer sssisted synthesis or retrosynthesis, etc., then built
 programmes intended to output proposals supposed to help the chemist.
 As far as I know, the brain of the Organician is still by far much
 more efficient than the best softwares which were produced.
 So, I may tell that the information available in the brain of the
 Organician is extremely difficult to store on computer, and it is even
 very difficult to teach it, apart the very beginning.
 There are examples other than reactivity. A huge of QSAR studies were
 done in order to predict various physico-chemical properties of simple
 chemical compounds, e.g., predicting from the structural formulas the
 boiling temperatures of monofunctional compounds such as alcohols,
 cetones, etc. at 20 C under 1 atm. But even in these apparently simple
 cases, the chemical information we need to do that with an acceptable
 accuracy is difficult to extract: the conclusions of such QSAR studies
 cannot be applied to any alcohol or cetone (still assumed to be
 monofunctional compounds), and it is even difficult to know the extent
 of validity of the published empirical rules, concretely often
 summarized by some regression coefficients.
 The example of spectroscopic databases is also of interest. How
 simulate spectras (infrared, NMR, mass spectras, etc.) of chemical
 compounds ? Starting from the structural formula, it is really hard to
 simulate, e.g. a low resolution mass spectra. Most time, it was
 attempted to extract rules from spectroscopic databases, then try to
 predict the spectra of a compound absent from the database, or
 conversely, retrieving the structural formula of a compound from its
 spectra(s). Many such softwares were developped since the 70's (one of
 the oldest ones is STIRS), but really the chemical information needed
 to do that properly is very difficult to extract.
 To conclude, I retain your example of crystallization: for sure when
 we will able to retrieve from the structural formula H-O-H that water
 under 1 atm should crystallize at 0 C, then for sure we will be ready
 to predict more about crystallization of chemicals.

 Best regards,

 Michel.

 2011/9/17 joe.bren...@bluewin.ch joe.bren...@bluewin.ch:
  Dear Michel and FIS Colleagues,
 
  This will be an interesting discussion, since the core nature and role of
  information will be involved. Here is just one first point: to me, as a
  chemist, chemical information is only secondarily an object capable of
  being formalized, archived, etc. A formula has meaning for me in terms
  of the potential reactions the molecule to which it refers can undergo,
 what
  it looked like when crystallized for the first time and so on.
 
  Cheminformatics seems not to deal with such aspects of chemical
 information
  as part of a process of doing chemistry. Can this be captured by
 another system?
 
  Best wishes,
 
  Joseph
 

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[Fis] Chemical information: a field of fuzzy contours ?

2011-09-16 Thread Michel Petitjean
Chemical information: a field of fuzzy contours ?
-

Before turning to chemistry, I would recall some facts that I noticed
on the FIS forum:
although many people consider that a unifying definition of
information science is possible (to be constructed),
a number of other people consider that there are many concepts of
information which are not necessarily
the facets of an unique concept, so that it could be better to speak
about information scienceS,
and not about information science.
I can read on http://en.wikipedia.org/wiki/Information_science
 Information science is an interdisciplinary science primarily
concerned with the
analysis, collection, classification, manipulation, storage, retrieval
and dissemination of information. 
and some fewer lines above:
 Information Science consists of having the knowledge and
understanding on how to collect, classify, manipulate, store, retrieve
and disseminate any type of information. 
Clearly, collecting, storing, and retrieving information let us think
that we must deal with databases.
The question where is information is neglected, although answering
it is enlighting:
no doubt that much information is stored in data banks.
There are strong connections of Information Science(s) with Data
Mining (DM) and Knowledge Discovery in Databases (KDD).

Is the situation clearer in chemistry ?

Undoubtly there is a field of chemical information.

The ACS (American Chemical Society) has a Division of Chemical
Information (CINF),
named as such in 1975, but which in fact goes back to 1943
(http://www.acscinf.org/).
CINF is active and organizes various meetings which can be retrieved on the web.
Visit also http://www.libsci.sc.edu/bob/chemnet/chchron.htm, an
informative website.

The ACS publishes the Journal of Chemical Information and Modeling
renamed so in 2005
after having been named Journal of Chemical Information and Computer
Sciences from 1975 to 2004,
itself being the continuation of the Journal of Chemical
Documentation from 1961 to 1974.
In fact, it is the same journal (one volume per year), which turned to
chemical information the same year that CINF received his actual name.

Interestingly, still in 1975, the main cheminformatics lab in France
(in fact the only one in France at this time) was renamed.
The old name was LCOP (Laboratoire de Chimie Organique Physique),
and the new name was ITODYS, still in vigor,
meaning until 2001: Institut de TOpologie et de DYnamique des
Systemes. This name, which can be understood in English due
to the close similarity between the French and the English words, was
partly due to the existence of a distance in the molecular graphs
(this distance is the smaller number of chemical bonds separating two
atoms), and as known, a distance induces a topology:
it clearly acknowledged the cheminformatics aspects of the research
performed in the lab.

Chemical Information Science, which is sometimes named Chemical Informatics
(http://www.indiana.edu/~cheminfo/acs800/soced_wash.html)
can be reasonably considered to be a part of the Cheminformatics field.
This latter is defined on Wikipedia
(http://en.wikipedia.org/wiki/Cheminformatics):
Chemoinformatics is the mixing of those information resources to
transform data into information and
information into knowledge for the intended purpose of making better
decisions faster in the area of
drug lead identification and optimization.
This definition, dated from 1998, clearly acknowledges the extraction
of information from data,
but it is restrictive since it discards all pioneering works about
computerization of chemical databases,
including structural formulas coding and structural motifs retrieval,
which historically cannot be denied
to be the core of the cheminformatics field.

Now let me write more lines about the story of cheminformatics in France,
which is a bit funny but enlights the debate on the definition on the
field of chemical information.
The French pioneer was Jacques-Emile Dubois (1920-2005), founder of
the LCOP and of the ITODYS,
who published his first cheminformatics paper in 1966. One of his main
ideas was to use the concept
of concentric layers in the molecular graphs: the nodes are the atoms
and the edges are the bonds,
the neighbours of a node constitute the first concentric layer around this node,
the next neighbours constitute the second layer, and so on.
This concept was known to mathematicians such as Cayley and Polya.
Here, the challenge was to explain to experimental chemists that in a
number of applications, such as QSAR
(Quantitative Structure-Activity Relationship), the use of sets of two
concentric layers around focus atoms
may be more efficient that the usually taught approaches based on
squeletons and substituents.
Dubois also thought that this concept could help to retrieve rapidly a
chemical motif in a large
database of structural formulas. An efficient solution of this rapid
retrieval problem was found
by Roger Attias