Hi Sang Ho Lee,

Yes, I acknowledge the (wilful) naive question ! Thank you for the references and the nice summary on the "state of art" of the issue in biology.

I was already amazed of the fantastic discoveries of the last century in biology on how information is accurately exchanged, handled, developed with such high level of accuracy and reliability (DNA, RNA, genetic code, cell organization, mitosis, meiosis, regulation, operons, promoters, repressors, 3D-complexity of proteins, etc, etc.) so many times in a second to allow life to thrive in billions of cells, organisms, ....during millions of years. So indeed this is the question everybody asks : how is it possible ? What is the secret of such high information quality at all levels ? How can we grasp  it, measure it ?

And now, since 2-3 decades, we see the progress of epigenetics (the "how genes are expressed ..") with the precise timely methylations, demethylations, transposable elements, mobile DNA, reprogramming, return to pluripotency, epigenetic barriers, Polycomb, Trithorax, .... somatic, germinal memory, even epigenetic heritability of learned behaviours etc. etc. (all the work since the pioneer work of Barbara Mc Clintock).

Of course it takes time and it is an huge work all over the world to discover, describe and prove all this.

But the  "information problem" is still there !

I have found following article : maybe a starting point for further thinking ?

Hi, Guibert.

For the educational points, there are references to start below.

Context as a source of information in rating depth of interpretation. J Gen Psychol 63(1), 133-143 (1960): Published online: 06 Jul 2010

Effect of depth of information processing on students’ ability to acquire and retrieve information related to different instructional objectives. Innov Educ Training Int'l 24(4), 264-279 (1987): Published online: 19 Aug 2006

Performance Approach, Performance Avoidance and Depth of Information Processing: A fresh look at relations between students' academic motivation and cognition. Int'l J of Exp Educ Psychol 22(5), 571-589 (2010): 2002 Published online: 01 Jul 2010

 As a biologist’s explanation;

It is a truly fundamental, but a naïve question that everyone would like to know. The query in the last paragraph especially reminds a lot. Comparable questions to the “how the molecules work together” have similarly been being raised in young biology classrooms and upper Biomed research labs all over the world. No philosophy nor the physics can explain the incredible accuracy and amazing cellular events. It is also definitely true that biology is unable to explain the whole picture of information processing occurring in the cell. What we can do or are doing right now in textbooks or research papers, however, is combining small bits and pieces of research results in a told story context with further human imagination and guessing some of the events. Biology, these days, demands endless and untiring imaginations what may be happening in the cell. Surely, no one can directly see the molecules without modern tricks of techniques. Only the experimental and analytical researchers help us put them together into the connected way. Thus, a story is born. Then, the next generation of scientists is trying to demonstrate that the incomplete and descriptive story existed already is evident in both indirect or direct ways of molecular events. Now, younger scientists take a more imaginative story on top of the older colleagues. These continue. Even if we may understand a full story about the moment of transcriptional process on a certain gene promoter. No one will have experienced to see all the reality of molecules bumping into each other, binding of a specific promoter sequence, TFs, co-factors and repressors at the dimensions of time and space.

Hi Sang Ho Lee,

Yes, I acknowledge the (wilful) naive question ! Thank you for the references and the nice summary on the "state of art" of the issue in biology.

I was already amazed of the fantastic discoveries of the last century in biology on how information is accurately exchanged, handled, developed with such high level of accuracy and reliability (DNA, RNA, genetic code, cell organization, mitosis, meiosis, regulation, operons, promoters, repressors, 3D-complexity of proteins, etc, etc.) so many times in a second to allow life to thrive in billions of cells, organisms, ....during millions of years. So indeed this is the question everybody asks : how is it possible ? What is the secret of such high information quality at all levels ? How can we grasp  it, measure it ?

And now, since 2-3 decades, we see the progress of epigenetics (the "how genes are expressed ..") with the precise timely methylations, demethylations, transposable elements, mobile DNA, reprogramming, return to pluripotency, epigenetic barriers, Polycomb, Trithorax, .... somatic, germinal memory, even epigenetic heritability of learned behaviours etc. etc. (all the work since the pioneer work of Barbara Mc Clintock).

Of course it takes time and it is an huge work all over the world to discover, describe and prove all this.

But the  "information problem" is still there !

I have found following article : maybe a starting point for further thinking ?

Dear Aleš,

Nice to hear from you !

And yes, your work as reflected in the recent article « Inventive processes in nature: from information origin in chemical evolution to technological exhaustion » on your RG page should certainly be part of the basic references to the issue.

As already noticed in the past, we have similar interests. You are more seeing the question of useful information gathering from the « artificial » (AI) side with focus on invention while I’m considering it from the « empirical » side with focus on what nature tells us (a.o. following recently acquired additional knowledge on epigenetics).

There are filters in both approaches.

Dear Aleš,

>> I would like to point out that epigenetics is remnant of chemical evolution still running in parallel to the genetics.

This is the interpretation you probably are rushing into as a chemist ! Of course, when it’s about life, biochemistry (and physics, and …. depending on the focus) is always involved. But with all respect  I doubt that epigeneticians would fully agree with the rather “reducing” view expressed above ….Don't forget that epigenetics is much with transposable elements (in DNA), complex sets of proteins, organization, timing .....

And suggesting that all chemical which is not genetic in E-coli would be epigenetic is a bit going too quickly to a conclusion (in my opinion) … !. 

Dear Guibert, you can get to the maximum-compact representation of information (from the point of view of entropy), while you always have a system (strictly and globally speaking - the universe) "behind your shoulders", into which the semantics of what you are viewing under the information incorporated. In addition, my replics from another discussion...

"Information is an alternation of something. The information is invariant with respect to any carriers (bearers), including the information itself. In order to process the information (that is, interpret it as data, which includes structure and form, among others), a "standard" of information or measure is required; in which semantics will be included within any choice (i.e. standard is information itself)!

Semantics is an inavoidable self-reference that does not allow reach complete closing (insulation) of any system (irrespective of the formal proofs of Gödel's incompleteness theorem).

Any categories, such as space, byte, structure, form, etc... are secondary. They can exist only within SYSTEM on the basis of (objectively, i.e. given, i.e. already) existing semantics - the mentioned system with standard and interrelations, which automatically implies presence of alphabet (language) and information carrier (bearer) in the form of a covering, deeper (fundamental) system.

Any thoughts/computation/processing of something (information), can only occur within an objectively (already) existing (dynamical) system (objectively existing semantics), for example, given human (physical) body with present brain physical structure. Any expression, statement, word, symbol of language, axiom or other meme/element of (formal, strictly speaking, any) system is a semantics in the form of knowledge (i.e. information, i.e. the physical structure of the system) of the subject that is the bearer of the elements of given (formal) system.

...

It is impossible to avoid the concept of the system when considering something (including information) at any level of abstraction."

So (in my opinion) in your question, one should take into account the semantics and the entire physical system involved in its implementation as a minimum. This is information too, without which the considered part of information is meaningless. I do not think that one will manage to circumvent the self-reference and successfully answer your question, the opposite, of course, forces to peer into the abyss of Zeno's paradox. But is there really a choice?

This is evident even from the connection between the structure of the alphabet and the size of messages being formed. It is impossible to consider the latter in isolation from the first, the first in isolation from the physical structure of the carrier of the semantics of the alphabet (brain, etc.), etc...

Dear Aleš,

I think to see your point : in a bottom up approach, what you call « chemical evolution » is pursuing its own way and may have been (and may still be) at the root of epigenetic phenomena.

Dear Vasiliy,

Thank you for the clarification. Information depth should be evaluated together with the system (/context) it is used for (/with). This appears also from the references of above post of Sang Ho Lee : « Context as a source of information », « depth of interpretation », « depth of information processing » vs « students’ ability to acquire » it, …. There is the source of the information and the recipient of it. The scale of “information depth” could then reflect the information content as assessed by an expert (system) while the optimal information for efficient use in a given context would be somewhere in between on the scale.    

Your question about the information depth may be partially addressed by considering the theory of graph/network complexity (http://pubsonline.informs.org/doi/abs/10.1287/mnsc.21.2.172?journalCode=mnsc).

However, this depth thing seems to be irrelevant to the specific biological question you pose in the end. First, the premise "promoter recognizes a given DNA sequence" does not make any sense. Promoter IS a DNA sequence. Then, if you mean "how a transcription factor recognizes its target DNA sequence?", then again this has little to do with the information depth. The apparent mystery here arises from an incomplete description of the system. In the physical world, the transcription factor does not recognize a sequence of letters (it cannot read), but it recognizes a three-dimensional structure resulting from a particular base-pair sequence. Due to its own spatial architecture, the transcription factor has a higher probability (free energy) to bind this specific 3D DNA structure than any other DNA region. So, the mystery gets easily explained.

Dear Dmitri,

Thank you for the given reference and the comments.

Yes I agree with you that in biology the “promoter” is a DNA sequence. I used the word in a conceptual way trying to hold the wide scope of the question. But as you show it, this can be at cost of accuracy ! “Transcription factor” is the correct wording so I’ve slightly changed the text of the question accordingly.

The idea of this biological part of the question is indeed about “recognizing” the right place to initiate and proceed with transcription.

Of course I agree with your comment that “the transcription factor …. recognizes a three-dimensional structure resulting from a particular base-pair sequence”.

But I’d be less affirmative that this solves the “mystery”.

What I allude to in the biological part of the question could indeed be reduced to chemical interactions between macromolecules (DNA, RNA, proteins) showing precise 3D-structures. But one should hold in mind that this must occur systematically, in due time, in a continuously changing environment, under unforeseeable and varying external constraints, …. Not just “this configuration matches that one, so let chemistry combine them !”. As you put it “the transcription factor has a higher probability ….”. Indeed “a higher probability”, not a “very high or 100 % probability”. And nevertheless, this works in due time, often many times a second, in billions of cells, since millions of years (ok, these figures are just to fix ideas …!).

Similarly about repressor protein “recognizing” where to place itself to hinder that transcription takes place. Or e.g. the Trithorax- Polycomb-groups proteins activating / repressing gene expression during embryonic development. And also these several “inherited” behaviours in epigenetics. All this very precise regulating stuff widely observed in biology seems to me more than just resulting from local best fitting of 3D-macromolecules.

Can’t we say that in the general framework of “exchange of information of high quality with high content”, living entities and their biological organization prove particularly efficient ?

Also, high content and high quality information can be transferred through literature. Just to mention Homer, The Three Kingdoms, Shakespeare or Tolstoï and so many essays, textbooks for teaching, learning, poetry, etc.

Finally, it must be noted that the question is asked with the intention to be as wide open as possible, not limited to literature or biology.

There are surely other fields where the question of how to quantify information content has been raised.

Actually the aim is not to solve the issue. Rather to find paths of thinking !

Dear Aleš,

Thank you for this additional contribution and the corresponding link. I didn’t know Khazzoom – Brookes postulate.

You sketch an interesting dynamic process :  “… increase in (exergy) efficiency means better adaptation”…”replicators will proliferate” ….with “higher quality of information contained in the replicators”…. “Energy (exergy) efficiency is fitness advantage in itself.”

On this basis, sequences of the kind :

→ further experimentation → exergy efficiency increase → gain of knowledge → more replicators with more embedded knowledge → higher information quality

could probably prove helpful as a general scheme for the assessment of information quality (*).

This could indeed apply to biological phenomena too.

(*) Notwithstanding other potential pathways which could next be revealed ...

Yes indeed England was in the limelight (newspapers, ...) several months ago.