Re: What are The Logics that Sciences and Medicine need to Model Life?...

[John M <***>]

Dear Ionel B:
thanks for this post which arrived after my Kraxlwerk sent away the previous
reply to your previous post.
I try to be short and abrupt:
1. You whetted my appetite to Grothendiek's book, I wonder if I can get the
URL for the free internet reading. I will try.
2. You phrased YOUR sentence about the Everst, I phrased mine. I have the
habit of looking further and I realized that one can freeze on the descent
as well, not during the climbing up only. No criticism.
3. I have no idea about 'relational biology' so no comments.
4. I don't analyse my logic, can't do it, it would be the target being used
as tool. That's what I have, that's what I love (slogan about the Peoples'
Democracies in the 50s).
5.I don't mind the 'Subject' line (although it may screw up an archive
search match) - it does not fall into MY preferred domain at all.

Regards

John M
----- Original Message -----
From: "Ionel" <***>
To: <***>; "John M" <***>
Cc: "Professor I.C. Baianu" <***>
Sent: Sunday, June 13, 2004 4:22 PM
Subject: Re: What are The Logics that Sciences and Medicine need to Model
Life?...


> Dear John M:
>
> I should re-assure you that Grothendieck's book that I mentioned to you,
> (which is available for free on the Web) is of quite general interest, and
> it is a well-written,--- totally non-mathematical---, highly interesting
> autobiographical, real-facts 'novel'. It begins by describing how he was
> placed at a young age as a refugee in a French camp after WWII. How he
grew
> up always embarassing his teachers with his profound mathematical
questions
> at the age of 12 !  He does not go into what the questions were, or any
> maths whatsoever.
>
> I' m quite sure that your 'common sense' logic has served you well; I 'm
> also equally sure that it's not/ was not ever the Boolean logic.
>
> What I'm not so sure about is that you have seen my point about climbing
> the Everest without freezing, because you propose to re-phrase my sentence
> and I am NOT accepting that! My sentence says what <I> wanted to say, and
> it simply is what my Logic 'says' that I wanted to say.
>
> As for the rest, as they say: "The devil is in the details!", or
> "It's only the details that count."  I have provided the details that you
> asked for in your previous postings, and I believe this was in a quite
> accessible manner; I admit, however, that because of the complexity of the
> problem it does take patience, and also perhaps willingness to keep an
open
> mind, and operate with a logic that is not Boolean, (that is not just
> a "True" and "False", pedestrian 2-value, Logic). As the only alternatives
> available, there are logics in which a double negation is not necessarily
> an affirmation, and this seems to be also your logic even though you seem
> to be reluctant of admitting that. That is, one is using Intuitionistic
> Logics almost all the time even though one might not have been aware of
> that; this may be just as in one of Molliere's famous plays where there is
> a character who spoke, or did, 'prose' all his life without being aware of
> it; when it is pointed out to him, he says: "Gee, I spoke 'PROSE' all my
> life and didn't know it!"
>
> You also wrote:
>
> >>>I am also turned off when I detect in a topic (?!) the reductionist
> >limited model - domain exclusively pursued. Set th. is one.>>
> >>>>>>>>>>
>
> My answer to this specific quote is:
>
> Last-but-not-least, my very important point, that you may have missed in
my
> previous reply, was that-- UNLIKE all the other relational biologists-- I
> have proposed (at 21 !) as early as 1968, and published it in BMB-->
> against fierce opposition (at the time from established relational
> biologists), that mathematical sets/the set-theoretical models and Boolean
> Logic are NOT sufficient for understanding complexity of organisms and
Life
> Itself. Robert Rosen came finally to the same conclusions as mine about
the
> inefficiency of the 'reductionist limited model --Set-theoretical'-&
> Boolean Logic-based-- in his "Essays on Life" published in 2001. The issue
> here is exactly the selection of the logico-mathematical modeling tools
> that are both appropriate and valid for modeling organisms, be they
> biological, ecological or societal, the exact topic of my postings and
also
> of my two replies to your 'helpful' questions.
> ________________________________________________________________________
>
> --------------------------Common-sense logics are fine, but the
> way one applies them logics, or uses them,  makes all the difference!
>
> Please also note the change I made in this posting's title as a result of
> your posted feedbacks, even though you may not be happy with it --as my
> Intuitionistic Logic advises me.
>
> Regards and peace,
>
> Ionel
>
>
> On Sun, 13 Jun 2004 12:20:33 -0400, John M <***> wrote:
>
> >Dear Ionel,
> >reading your text with anticipation where to find connection to my
> questions
> >(and my ways of thinking) I felt like a freshman in some principle he
never
> >heard about and - boy - was I happy that I don't have to go to you for
oral
> >examination!
> >I picked out one (shorter? - [remember the "fog" index]. it has 68 words)
> >sentence to discuss first:
> >>..." So the real statement that I made contained  implicitely the fact
> >>that I am talking about the Logic(s) that one has to utilize/employ/ >or
> >develop in order to be able to : 1. produce valid models of living
> >systems,
> >and 2. predict and select correctly the important >aspects/processes/
> >interaction and measurement modes with >living systems, etc., that would
> >allow us to make progress in >Biology and Medicine. "<
> >From the end: mentioning Med is a cheap shot. It is not a science and
since
> >the time of the ancient Aegyptian 'curing-priests - looking in the
eyes -'
> >it is a perfectly reductionistic technology we ALL rely on very heavily.
I
> >like #1 because it "provides valid models" - validity of course in our
> >reduced terms, in #2 the "important" has the same role. Then again your
> >"...Logic(s) that one has to utilize/employ/..." is a "says who?" order.
> >Same position in the use of "correctly".
> >I don't like to use such imperatives, because who am I to prescribe to
> >others how to think?
> >(A little blip: my 'common-sense' logic would change in your insert about
> >climbing the Everest
> >the phrase ..."to do so"... into: "to be able to return".  That may be
> >personal.)
> >The thought of thinking brings me to the "Logic" systems you keep in so
> high
> >repute. I mentioned my own 'common sense' thinking and several people
> >flattered me by calling it 'logical'. It is not 'virgin', it has been
> >screwed in college by 'science-thinking' brainwashing.  I wonder if a
click
> >to my piece on my mock website-URL would enlighten this position of mine?
> >(http://pages.prodigy.net/jamikes/SciRelMay00.html) - just referring to
> >religions and science, both as belief systems.
> >Thanks for introducing me to Grothendiek. I am very choozy in my reading,
> >most books have less courtesy than to 'answer' my questions emerging
> >immediately when I start reading a book and that makes me upset so I stop
> >reading. Especially when it is in a topic I don't WANT to read by all
> means.
> >Alas, after several attempts, 'formal (math?) logical systems' is not one
> of
> >those. This deficiency of mine is age-related, before 80 I was a
voracious
> >reader. I am also turned off when I detect in a topic (?!) the
reductionist
> >limited model - domain exclusively pursued. Set th. is one.
> >
> >I still don't know what do you consider 'life' or 'living system' to
derive
> >whether your 'logic' applies to an identification of it.
> >
> >Thanks for your remarks, it was a "READING" to go through it.
> >
> >John M
> >
> >
> >
> >
> >----- Original Message -----
> >From: "Ionel" <***>
> >To: <***>
> >Sent: Saturday, June 12, 2004 5:12 PM
> >Subject: Re: What is /are The Logic(s) of Life?...
> >
> >
> >> Dear John M:
> >>
> >> I love simple and direct, or basic, questions such as those that you
are
> >> asking now in your posting because I have a chance of providing you
with
> >> simple, or complex, answers as the case may be, without straining my
> logic
> >> or thinking (and also 'leave the 100 running foxes alone') as some
people
> >> do; (NO reference here to any of the Rosen Forum members. As the
> >> great 'Bill' would have said : "Brutus is an Honorable man, but Brutus
> >> says that my dear friend Caesar ..."; he left you all in his will, but
I
> >> cannot read the will least should I offend any Honorable men..." They
> said
> >> excitedly... PLEASE do read Caesar's will!!! , and so on... Marc
Anthony
> >> read Caesar's  last Will...). As we are attempting to understand things
> >and
> >> processes in Nature, or within ourselves, the way of Science has been
and
> >> still is, that of using 'Logic', or Logics, as the case may be. If one
> >> wishes to renounce all Logic(s), than one may be involved in something
> >else
> >> than Science, such as various Religions and myths based on belief
alone,
> >> and then, there will for sure as many beliefs as there are people, or
> >> religions. I will not take this any further to its 'logical' conclusion
> as
> >> it would clearly imply a sort of 'anarchy'-- or complete chaos-- in
> >> thinking; thus, such renouncement of Logic(s)will prevent one from
> >> obtaining any Rational solutions to any deep questions about Nature. If
> >one
> >> were to give up all Logic(s) in understanding Nature and living
> >> organisms in particular further progress in our understanding of all
> >Nature
> >> would cease very, very quickly, a thing that we cannot afford to do. So
> >the
> >> real statement that I made contained  implicitely the fact that I am
> >> talking about the Logic(s) that one has to utilize/employ/ or develop
in
> >> order to be able to : 1. produce valid models of living systems, and 2.
> >> predict and select correctly the important aspects/processes/
interaction
> >> and measurement modes with living systems, etc., that would allow us to
> >> make progress in Biology and Medicine. At stake is not only the
survival
> >of
> >> huge multitudes of cancer or heart patients our fellow Americans--that
I
> >do
> >> care very much about-- but also perhaps the  survival of Homo sapiens
> >> sapiens. Please note the 'sapiens sapiens': it strongly implies : <No
> >> thinking--and implicitely -- No Logic> means no Human species, as a
> >> distinguishable species! Please also note the very last
> >> sentence in my previous posting which really leaves open the question
of
> >> the choice of the/our appropriate Logic(s) that we need to understand
> >> living organisms.
> >> The only thing that we do know for sure now is that the simple Boolean
> >> Logic of machines, automata, robots, etc. is NOT sufficient to allow us
> to
> >> understand complex systems such as living organisms.  And there are
still
> >> very many scientists who would argue even now that just Boolean Logic
is
> >> sufficient to understand everything. Boolean Logic is at the Foundation
> of
> >> Set Theory, which was --and is still is considered by many-- at the
> >> Foundation of Mathematics  and our Thinking Itself!!
> >>
> >> As for the other 'Logics' that you were specifying, Except for the
> Baesian
> >> one, not being an expert on the History of Religions and ancient Logics
I
> >> cannot comment on with any reliable expertise. I can only refer you to
> >> Mircea Eliade's (fmrly. at UIC) extremely valuable, published and  very
> >> extensive/ thorough work on Comparative Religions and their 'internal
> >> logics.'  I'm quite sure you'd enjoy reading his work, if you had not
> done
> >> so already. He had a real literary talent --and lots of practice--that
I
> >> only wish I had. I am glad I am able to read some of his works in
> >original,
> >> not in translation that loses much of his charming style.
> >>
> >> As to the Baesian, it is contained as a particular case of both
> >Lukasiewicz
> >> and Heyting, intuitionistic Logics. There are published papers (not
mine)
> >> that prove this fact!
> >>
> >> So the selection of Logics that I suggested in my posting IS our only
> real
> >> gain/progress in the selection of Logic(s) for modeling living
organisms
> >> and biological processes since the publication in 1945 of the
MacCullogh
> >> and Pitts paper in BMB claiming to specify "the neural circuits that
can
> >> implement the 'Boolean' Logic of Human Thought". In my 1977 paper in
BMB
> >on
> >> Genetic Activities in Nonlinear Dynamic Networks, I proposed that
Boolean
> >> Logic is NOT enough, and that a much better model is provided by
n-valued
> >> Lukasiewicz Logics. Many others have recently 'borrowed' my idea and
used
> >> it for improved the modeling of the neuronal networks in the Human
Brain.
> >>
> >> Modern maths has gone even further: ----------------------------
> >> it has now adopted for its foundations--avoiding both 'structureless'
> Sets
> >> and Boolean Logic-- Intuitionistic (Brouwer-Heyting) Logics
> >> that is NOT limited to just 2 logical values, and takes on instead an
> >> infinite range of logical values--------------------------- in a
> >> generalized mathematical  'structure' , or 'space', defined both
> >> mathematically and logically as a Topos. I  was, and am, strongly
> >> advocating that the logical power of Intuitionistic (Heyting algebra)
> >> Logics and Topoi is a very important means, or tool, for vastly
improving
> >> our models of Living Organisms, Ecology and Human Societies. It offers
> for
> >> the first time strong possibilities to get closer to the biological
> >> Complexity than we have had in our entire scientific Thinking History--
> >> that always utilzed and utilizes Logic(s)-- the kinds that I have
> >specified
> >> in my previous and current posting.
> >>
> >> What is new here is that I specified-- FOR THE FIRST TIME --the best
> >> Logical  possibilities and Fundamental Mathematical 'Structures' THAT
WE
> >DO
> >> HAVE NOW, for Modeling Living Organisms and
Nature. ---------------------
> >> This is a very important new idea that I have not seen anywhere
else.----
> -
> >> -----------------------------------------------------------------------
> >>
> >> If one wished to climb the Everest, one would better make sure that one
> >has
> >> BOTH the tools and the TEAM that will enable one to do so, instead of
> >> ending up as a frozen block on the mountain's slope.
> >> ______________________________________________________________
> >>
> >> There are some sad stories in Science: thus Alexander Grothendieck--
> a/the
> >> mathematical genius that introduced in France what is now called the
> first
> >> Topos-- a Grothendieck Topos, and completely 'revolutionized'
> mathematical
> >> thinking in this century; he withdrew from human contact and
disappeared
> >> upon his retirement in 1988. This sad act has no Logic, except his own
> >> internal one-- it is being said he was 'disgusted' with science
politics
> >> and unfair treatments. His reminiscences --in literary style--no
maths--
> >> are published on the web and it's possible that you'd find it very
> >> interesting and you might even 'resonate' strongly with Alexander
> >> Grothendieck's 'retiring logic' , and thinking, after his
quasi-complete
> >> withdrawal from society and human contacts upon his retirement, as he
is
> >> said "to have become a Buddhist monk". To me, it's a very, very sad
story
> >> thinking of the great many things such a genius mathematical mind could
> >> produce, especially in the logico-mathematical modeling of Life. Maybe
> >> you'd disagree with me: obviously, Alexander Grothendieck--formerly one
> of
> >> the greatest mathematicians on this planet-- does! That does not change
> >> the nature of things and the logics that we need to employ in order to
> >> understand Life Itself-- to borrow that expression from both Francis
> Crick
> >> and Robert Rosen(in the order their books were published).
> >> --------------------------------------------------------------------
> >> Hope this answer has addressed your questions cited below. Other
> questions
> >> that you asked may have to wait for a second round, until you have seen
> my
> >> first response.
> >>
> >> Regards,
> >>
> >> Ionel
> >>
> >> On Sat, 12 Jun 2004 11:24:54 -0400, John M <***> wrote:
> >>
> >> >Dear Ionel,
> >> >
> >> >excuse me for 'talking into the discussion of the adults': .... have
no
> >> idea about most of the things you seem to be an expert in (yet so far
> >> conducted my plain life quite efficiently) -
> >> >you raise two points in your post (which I don't pretend to follow in
> its
> >> >intricacies - don't even copy the entire text here) - and I have
> >questions
> >> >to the second one:
> >>
> >> >JMQ#1: With all the uncertainty (cf: learned discussions without a
> >> >generally acceptable consent) about the term and meaning "LIFE" is it
so
> >> >sure that "it" has a logic?
> >> >
> >> >Q#1A: Even if the answer is positive: yes, is it assured that WE can
> know
> >> >that logic? Do we comprehend nature, the total, with all its
> intricacies,
> >> >logic, being a (matter)-restricted little part of it?
> >> >
> >> >JMQ#2 refers to the term 'logic': there is XYZ, RST, LMN, etc. systems
> of
> >> >logic, all formalized into aspects galore. Buddhism has a different
one
> >> from
> >> >westerners' common sense. Baesian etc. are also different from them.
The
> >> >Navajos etc. have special ones.
> >> >I see the problem to identify an answer in an unudentified system
about
> >an
> >> >unidentified concept.
> >> >So I cannot valuate your conclusions below in my (1st person) mind.
> >> >....
> >> ________________John M.
> >??_________________________________________________
> >>
> >> >Regards,
> >> >JohnM
> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> >>
> >>
> >>
> >> ---Original Message -----
> >> >From: "I. C. Baianu" <***>
> >> >To: <***>
> >> >Sent: Friday, June 11, 2004 2:22 PM
> >> >Subject: Re: What is /are The Logic(s) of Life?... and Adjointness is
> >> >Fundamental in Categories and Topoi of Biological Systems
> >> >
> >> >
> >> >> Tim:
> >> >>
> >> >> Robert Rosen provides new answers to in "Life Itself" and his
"Essays
> >on
> >> >> Life.":  ------What is /are The Logic(s) of Life? -----.
> >> >>[JM]:SNIP
> >> >>....thus we need to re-phrase the question as : "What are the
>possible
> >> >candidates for 'The Logic of Life'? "--
> >> >>the title of this post.<
> >> >>
> >> >>[JM]:Snip including #1 >
> >> >_______________________________________________
> >> >> 2.What is /are The Logic(s) of Life?
> >> >>
> >> >> characterized through adjunctions/adjoint functors (as discussed
> >> >above),...
> >> >[JM]:SNIP
> >> >Your well-readness and applicational skills of those 100,000 books
which
> >I
> >> >have not read makes me skip the above reputable lines and
> >> >return to my simple common-sense logic. (see later on this).
> >> >The 'logic' of what?
> >> >This may well be RR's question, in which case I understand it with his
> >> >remark I read some time ago (online): "The question 'what is life' is
a
> >> >wrongly formulated question" and I always agreed with this position.
> >> >
> >>
>
>>;>> ----------------------------------------------------------------------
> -
> >> --
> >> >> Therefore, one concludes that the Logic of Life INVOLVES fundamental
> >> >> Adjunctions in Ord(T),( with T being a Topos), that can occur in
> either
> >> >the
> >> >> category of Lukasiewicz (n-valued)Logics or the Category of
> >> Intuitionistic
> >> >> Heyting Logic Algebras. It would, thus seem also that the Logics of
> >> >Complex
> >> >> Systems in the Rosennean sense is Lukasiewicz (n-valued), or
> >> >> Heyting Logic , or other related possible Logics that one may
consider
> >> >> (notably among them, as an example, the Fuzzy Relational Logic).
> >> >>
> >_________________________________________________________________________