[Fis] what is information

Emanuel Diamant emanl.245 at gmail.com
Sun Oct 4 07:54:17 CEST 2015


Dear all,

 

I apologize for the delayed response and fragmented personal replies. 

 

I apologize that not all of your responses were selected for further
comments, only those that were the first to come and those that look as the
most relevant ones.

 

I apologize that not all topics of these responses are regarded in my
answers, only these that look to me as the most relevant ones.

  

I apologize that the style of my answers is not always elegant and polite,
(that is one of my problems), but the reason is not my bad character or bad
temper, the reason is my bad knowledge of English. Sorry.

 

And here are the replies:  

 

=====================================  

To Krassimir Markov, (September 24, 2015).

 

Thank you for your response. Yet I don’t like it – you force me to repeat
commonplace banalities again and again. I have no stomach for this sort of
things, but you insist – and so I have to repeat:

 

Every scientific discourse or dialogue begins with establishing some initial
basic assumptions, which do not need to be solid or substantial (therefore,
I dare to call them axioms). In the course of a subsequent reasoning, the
initial assumptions are being transformed into a set of hypotheses, which
are being applied to explain the existence or to predict results of
observations of some natural phenomenon. If the hypotheses successfully pass
this trial, the initial assumptions become regarded as true and sustainable.
Then the next round of hypotheses ramification and complication comes into
being until a full-blown new theory has become available.

 

This is the way of thinking and reasoning which I am familiar with. Your
question “What is data?” does not meet the conventions of such a discourse.
Reading some of your previously published papers, I can guess what are the
basic assumptions that you adhere to. But you do not declare them by
yourself. Why should I do that instead of you? Do that, defend their
validity by making prediction tests (as it is described above), and do not
ask “smart” questions.

 

Meanwhile I will ignore and discard your response. 

 

========================================  

To Günther Witzany, (September 24, 2015).

 

Thank you very much for your response. I am a great admirer of your
publications. Long before they become available on the Research Gate, I was
really a stubborn hunter for them, happy with any piece of text (mainly
abstracts) that I was lucky to catch (I am an engineer and thus biological
publications usually are not accessible to me). 

 

As it was just stated above (in my answer to Krassimir), the only way to
develop a new theory is to validate and justify its initial assumptions by
applying them to an explanatory description of an observable natural
phenomenon. In this regard, your publications were exactly what I was
needed. (Although long before your papers become available to me, I gained
my inspirations from the papers of Eshel Ben-Jacob, published a couple of
years earlier). Never mind, his and your explorations were thought
provoking, inspiring and really helpful to me. However, some reservations
regarding their subject would be worth to mention here.

 

In Eshel’s and your early publications, the term “model”/“modeling” is often
encountered on various occasions. In contemporary science, the term has a
pure mathematical connotation and usually implies data modeling. What
follows from this is that “modeling” (and your engagement with it)
explicitly presumes mandatory data processing. In the context of my
assumptions-speculations, data processing is tightly bound to physical
information processing. And that is the point – you all all the time are
busy with physical information processing, despite you even don’t recognize
the notion of it. (Semantic information processing also remains a terra
incognita for you). 

 

In this regard, your description of the marvels and the mysteries of the
“chemical Auxin” are missing their argument strength. First, Auxin is not a
chemical (as you call it); it is a plant hormone (Wikipedia), a hormonal
messenger. The message that a messenger is carrying is actually a piece of
text written in a language (which is still unknown to us) with a chemical
alphabet (that is also unknown to us). The message as a rule contains
physical and semantic information subparts (text pieces).

 

I apologize for drawing you into this mishmash, but the time is ripe to
clarify some of the matters.

For a long time, you Gunter, on various occasions assert the following
statement: 

 

“The Modern Synthesis regards the genetic code as a lineup of molecules that
can be investigated through physics and chemistry and mathematics (for
sure). And this is it. However, we know the genetic content of organisms is
about communication, which cannot be reduced simply to physics and
chemistry. Since the 1970s, Manfred Eigen has insisted that the genetic code
is really a language, not just metaphorically, but a real language”. (In an
Interview given to Susan Mazur, 2015).

 

On another occasion: “Today, everyone speaks about the genetic code – genes
encoded in DNA that serve as the information-bearing molecules for all
biological entities
 In the 1970s, Manfred Eigen insisted that the genetic
code really represents a natural language and is not just metaphorical
”
(Life is physics, and chemistry, and communication
<http://onlinelibrary.wiley.com/doi/10.1111/nyas.12570/full> , 2015, p. 1). 

 

Although you do not completely support Manfred Eigen’s claim (and you even
propose a refinement for it in your Pragmatic turn in biology, 2014), your
primary assumption remains unchanged:

“The question remains how to define nucleic acid sequences as a real natural
language/code
” (ibid, p. 6).

 

Sorry, but this is a wrong and a misleading statement: nucleic acid
sequences are not real natural language/code – they are pieces of text
bearing an information description. They are pieces of text written in some
certain language using some certain alphabet (codes).

 

To clarify further my claim, I would like to propose a gedanken experiment:
imagine you have to provide a description of the water molecule structure.
In English language using Latin alphabet letters, this description (text)
would look like this: “Water is made up of two hydrogen atoms and an atom of
oxygen”.

 

Then you can decide to re-write this text using another alphabet, say, a
chemical alphabet. Craig Venter has done such a thing inserting English text
messages written as a sequence of letters C, G, A, and T (he called them
“watermark” messages) into the DNA sequence of a bacterial genome. The
purpose of the watermarks was to distinguish the synthetic genome from its
natural counterpart. But what is interesting to us is that the bacterium and
its watermarks were viable, that is, capable to replicate themselves in the
course of bacterial reproduction and multiplication. That is, English text
messages have behaved exactly the same way as all other genetic information
sequences.

 

I hope my basic assumption endorsed by Craig Venter’s experiments is quite
clear to you now: the current wave of gene screening experiments is busy
with high-throughput data (code) gathering only. It has nothing to do with
information texts embedded in the code sequences. Therefore, text meaning is
out of reach of contemporary gene screening experiments.

 

In context of my basic assumptions (speculations), the bottom line can be
summarized like this: contemporary biological research is busy with physical
information processing only. Semantic information processing is out of its
scope.

 

I apologize again for such a long and late response.

 

===================================================  

To Pedro C. Marijuan, (September 25, 2015).

 

Dear Pedro, I do not wish to be in a discord with you, but I do not share
your praise for the Gunter’s response (the reasons for that I hope are
somehow explained above). I also disagree with your assessment of the Encode
project. Because my arguments on this subject overlap with comments to
Howard Bloom’s response, I would further expand my explanation (on this
subject) in the following comments upon the Bloom’s letter.

 

========================================  

To Howard Bloom, (September 26, 2015).

 

Dear Howard, I disagree with your assessment of Gunter’s “wonderful
description of auxin's many functions”, but I am in accordance with you when
you declare that the Encode project is an ambitious and primitive (however,
I disagree with you about its necessity). 

 

As it was explained above (in my reply to Gunter), contemporary biological
science does not accept the notion of information. It does not recognize the
duality of information, its physical and semantic subdivision. And
therefore, it is doomed to fall into the trap of its own unawareness –
continue to put extensive money and effort resources in data/code gathering
(that is, physical information processing) hoping to arrive in such a way at
the encoded texts meaning/interpretation (semantic information). Functional
features of the code are the declared goals of the Encode project. They
cannot be and never would be reached in a frame of mind of data processing.

 

A similar situation is in the Human Brain Project launched by the European
Community in 2014. The HBP has proudly declared that one of its prime goals
is neuron communication study. A special line of research is devoted to
neuron communication modeling, that is – to an endless and exhausting data
processing enterprise. 

 

The data gathered in neuron communication studies are the action potential
pulse train propagation records. But if “the brain is processing
information” what information is conveyed in the course of interneuron
communication? What information is carried by action potentials pulse train?


 

In my view, the pulse train of action potentials could be equated with noise
following an actual train passage, a passage of heavy freight train. From
the train noise records, would you like to extract the knowledge about the
nature of the train’s payload? Are you serious? That does not work and never
would not (work). 

 

It would be nice if FIS discussions would help the Human Brain Project
participants to overcome their generic cognitive biases. (“Cognitive” as you
remember is an ability to process information).

 

===================================================  

I apologize again for such a long and unbalanced reply.

 

Best regards,

Emanuel.

 

===========================================  

From: HowlBloom at aol.com [mailto:HowlBloom at aol.com] 
Sent: Saturday, September 26, 2015 6:40 AM
To: pcmarijuan.iacs at aragon.es; witzany at sbg.at
Cc: rose at howardbloom.net; fis at listas.unizar.es; emanl.245 at gmail.com
Subject: Re: [Fis] Information is a linguistic description of structures

 

wonderful description of auxin's many functions, gunther.  

 

may i suggest that auxin--or gaba and glutamate in animals--is like the word
"a" in the english language.  the meaning of "a" depends entirely on
context.  just as Gunther has said in many of his papers.

 

and context changes as developmental stages pass by, just as pedro has
emphasized.

 

a project like ENCODE is ambitious and necessary, but primitive.  it's the
equivalent of breaking down Shakespeare to its component words, then putting
those words in a list. doing that to shakespeare would lose everything for
the sake of gaining almost nothing.

 

this reductionist approach, while of value, is what babara ehrenreich in her
introduction to the upcoming paperback version of my book the god problem:
how a godless cosmos creates, calls "unacknowledged necrophilia."  her
quote:

 

I was educated in this scientific tradition, ending up in cell biology,
which proposed that you cannot understand, say, the flight of a hummingbird
until you have killed the bird, cut its wing muscles into slices a few
microns thick, and subjected them to electron microscopy. Thus a kind of
unacknowledged necrophilia runs through modern laboratory biology: to study
something you first have to kill it. You know you have “understood” it when
you arrive at a theoretical description that contains no hint of agency—just
a series of mechanisms involving organelles, which you have isolated through
high-speed centrifugation, and molecules, identified by a series of
fractionation processes. The hummingbird’s speed and grace is explained by
the density of mitochondria in its wing muscles, leading to an abundant flow
of ATP to the myosin.

to reduce shakespeare to a list of words would be to kill it.  our task is
to understand its life.

 

with warmth and oomph--howard

 

===========================================  

From: Pedro C. Marijuan [mailto:pcmarijuan.iacs at aragon.es]        (6)
Sent: Friday, September 25, 2015 2:38 PM
To: Günther Witzany
Cc: Emanuel Diamant; farah at howardbloom.net; 'fis'
Subject: Re: Information is a linguistic description of structures

 

Dear FISers and all,

I include below another response to Immanuel post (from Guenther). I think
he has penned an excellent response--my only addition is to expostulate a
doubt. Should our analysis of the human (or cellular!) communication with
the environment be related to linguistic practices? In short, my argument is
that biological self-production becomes "la raison d'etre" of communication,
both concerning its evolutionary origins and the continuous opening towards
the environment along the different stages of the individual's life cycle.
It is cogent that the same messenger plays quite different roles in
different specialized cells --we have to disentangle in each case how the
impinging "info" affects the ongoing life cycle (the impact upon the
transcriptome, proteome, metabolome, etc.) There is no shortcut to the
endless work necessary--wet lab & in silico. So I think that Encode and
other big projects are quite useful in the continuous exploration of
biological complexity and provide us valuable conceptual stuff--but looking
for hypothetical big formalisms (I quite agree) is out sight. Molecular
recognition which is the at the  fundamentals of biological organization can
only provide modest guidelines about the main informational architectures of
life... beyond that, there is too much complexity, endless complexity to
contemplate, particularly when we try to study multicellular organization.
Anyhow, this topic of the essential informational openness of the
individual's life cycle appears to me as the Gordian knot to be cut for the
advancement of our field: otherwise we will never connect meaningfully with
the endless info flows that interconnect our societies, generated from the
life cycles of individuals and addressed to the life cycles of other
individuals. Info sources, channels for info flows, and info receptors are
not mere Shannonian overtones, they symbolically refer to the very info
skeleton of our societies; or looking dynamically it is the engine of social
history and of social complexity. 

Well, sorry that I could not express myself better.

all the best--Pedro 



==================================================  

From: Günther Witzany [mailto:witzany at sbg.at]       (1)
Sent: Thursday, September 24, 2015 11:21 AM
To: Emanuel Diamant
Cc: Pedro C. Marijuan; farah at howardbloom.net
Subject: Re: Information is a linguistic description of structures 

 

Dear all!

 

What is the opposite of a linguistic description? a non-linguistic
description? Please tell me one possible explanation of a non-linguistic
description. So Im not convinced of the sense of the term "information". 

 

Concerning the "difference" of physical and semantic information: What would
you prefer in the case of plant communication. Does the chemical Auxin
represent a physical or a semantic information? Auxin is used in hormonal,
morphogenic, and transmitter pathways. As an extracellular signal at the
plant synapse, auxin serves to react to light and gravity. It also serves as
an extracellular messenger substance to send electrical signals and
functions as a synchronization signal for cell division. At the
intercellular, whole plant level, it supports cell division in the cambium,
and at the tissue level, it promotes the maturation of vascular tissue
during embryonic development, organ growth as well as tropic responses and
apical dominance. In intracellular signaling, auxin serves in organogenesis,
cell development, and differentiation. Especially in the organogenesis of
roots, for example, auxin enables cells to determine their position and
their identity. These multiple functions of auxin demonstrate that
identifying the momentary usage (its semantics) is extremely difficult
because the context (investigation object of pragmatics) of use can be very
complex and highly diverse, although the chemical property remains the same.

Yes, mathematics is an artificial language. Last century the Pythagorean
approach, mathematics represents material reality, (if we use mathematics we
reconstruct creators thoughts) was reactivated: Exact science must represent
observations as well as theories in mathematical equations. Then it would be
sure to represent reality, because brain synapse logics then could express
its own material reality. But this was proven as error. Prior to all
artificial languages we learned how to interconnect linguistic utterances
with practical behavior in socialisation; therefore the ultimate
meta-language is everyday language with its visible superficial grammar and
its invisible deep grammar that transports the intended meaning. How should
computers extract deep grammar structures out of measurable superficial
syntax structures? In the case of ENCODE project (to find the human genome
primary data structures) this was the aim which got financial support of 3
billion dollars with the result of detecting the superficial grammar only,
nothing else.

 

Best Wishes

Guenther

 

=========================================== 

From: Krassimir Markov [mailto:markov at foibg.com]      (2)
Sent: Thursday, September 24, 2015 11:40 AM
To: Emanuel Diamant; fis at listas.unizar.es
Cc: farah at howardbloom.net; witzany at sbg.at
Subject: Re: [Fis] Information is a linguistic description of structures

 

Dear Emanuel,

What is DATA?

Best regards

Krassimir

 

=========================================== 

From: Emanuel Diamant [mailto:emanl.245 at gmail.com]   (0)
Sent: Thursday, September 24, 2015 8:47 AM
To: 'fis at listas.unizar.es'
Cc: 'pcmarijuan.iacs at aragon.es'; 'witzany at sbg.at'; 'farah at howardbloom.net'
Subject: Information is a linguistic description of structures 

 

Dear FIS colleagues,

 

As a newcomer to FIS, I feel myself very uncomfortable when I have to
interrupt the ongoing discourse with something that looks for me quite
natural but is lacking in our current public dialog. What I have in mind is
that in every discussion or argument exchange, first of all, the grounding
axioms and mutually agreed assumptions should be established and declared as
the basis for further debating and reasoning. Maybe in our case, these
things are implied by default, but I am not a part of the dominant
coalition. For this reason, I would dare to formulate some grounding axioms
that may be useful for those who are not FIS insiders:

 

1. Information is a linguistic description of structures observable in a
given data set

2. Two types of data structures could be distinguished in a data set:
primary and secondary data structures.

3. Primary data structures are data clusters or clumps arranged or occurring
due to the similarity in physical properties of adjacent data elements. For
this reason, the primary data structures could be called physical data
structures.

4. Secondary data structures are specific arrangements of primary data
structures. The grouping of primary data structures into secondary data
structures is a prerogative of an external observer and it is guided by his
subjective reasons, rules and habits. The secondary data structures exist
only in the observer’s head, in his mind. Therefore, they could be called
meaningful or semantic data structures. 

5. As it was said earlier, Description of structures observable in a data
set should be called “Information”. In this regard, two types of information
must be distinguished – Physical Information and Semantic Information. 

6. Both are language-based descriptions; however, physical information can
be described with a variety of languages (recall that mathematics is also a
language), while semantic information can be described only by means of
natural human language.

 

This is a concise set of axioms that should preface all our further
discussions. You can accept them. You can discard them and replace them with
better ones. But you can not proceed without basing your discussion on a
suitable and appropriate set of axioms.

 

That is what I have to say at this moment.

My best regards to all of you,

Emanuel.

 

====================================================  

 

 

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