Talk:Computing by observing

Section "The Framework"
- In the first sentence it is not clear in which space the trajectories lie.
- Figure 1 does not make clear the fact that one letter corresponds to on configuration (like Fig 3 does)
- Sentence "This allows..." is grammatically not correct and does not make much sense to me.
- Following sentence: sounds like the systems form Turing Machines, which they do not.

Section "Appl..."
"This contrasts..." should only refer to the underlying system, not the observer, which will not be a natural system in general. Anyway, talking about (artificially) "designing natural systems" seems slightly contradictory.

A reference to the recently introduced Observation of Change would be good, as this really seems a step towards realistic restrictions.

Use of links to external sites (e.g. the book DNA Computing on google books) would make the article much more useful. As it is, it does not really use the advantages of internet over printed texts. Also links to those references that are available for download would be very useful.

I have corrected several spelling and minor grammar mistakes.

Reviewer B (Editor):

Section "The framework"

the title of the page is "Computing-by-observation" while the first words in the first section are "Computing by observing" (no dashed between words, -ing forms not consistent). Please, be consistent in the way you refer to this topic (the same inconsistency is present throughout the article).

In the first lines of your article you assume the reared know what 'the framework' is about. You should not make this assumption and say that it is a framework to perform (or something similar) computation. Better than defining it as a framework, I would say something of the kind: "Computing-by-observing refer to ..."

The very first sentence is very confusing as it introduces concepts not previously mentioned: ""Computing by observing" is a framework where the computation is obtained by observing and interpreting the trajectories of an observed system." What is a trajectory? What do you mean with 'observed'? What is a system?

I strongly suggest to rewrite the first paragraphs of this section aiming to explain the concepts to somebody who does not know already them. For instance, the author could start to say a few words on the standard way to regard computation and then introducing new way you propose.

The paragraph goes on with strong assumptions: "an external observer" external in respect to what?

You write: "state (configuration)" a state and a configuration are different things!!! Think to a Turing machine where a configuration includes the state.

"As the observed system progresses" in what?

You use the term "simple" without explaining what "simple" is for you.

Section "Applications and Results" Your way to write is far from being scientific. You keep using terms as "complex", "right" without explaining them.

Section "Observing Formal Grammars" "abstract (idealize)" the meaning of these two words is quite different. Explain yourself.

"is a then device" -> "is then a device"

"singular symbol" -> "single symbol"

You only cite your articles!!!! No citation for Turing machine, no citation for regular expression, no citation for "standard notations used for formal grammars and regular expressions", ... Please, add citations.

"the vertical arrow is the observer mapping" what arrow? in the figure?

Section "Computing by Observing Bio-Systems"

"it can be considered rejected" either it is rejected or it is not. Please, clarify this.

"to to splicing" -> "to splicing"

"predetermined ``type"" what does this mean. Please clarify.

"well known" -> "known"

"special symbols" what makes these symbols special? Remove "special".

"These components can be then composed to constitute" -> "These components can then be put together to constitute"

"It is known in the splicing literature" -> "It is known"

Overall: I like the formal part. The style has to be improved and a longer (and aimed to a not-technical reader) introduction has to be provided.

Second round == Reviewer B: ==

Section "The framework"

There is still an inconsistency between the title of the article "Computing-by-observation" and the way the author refers to the topic: "computing by observing". Be consistent: either change the title or change the way you refer to the topic.

I still thing the the initial sentence is confusing: "Computing by observing is based on the idea" are you describing here 'Computing by observing' or the idea (these are supposed to be 2 different things). I suggest to write: "Computing by observing is a refers to the composition of two distinct computational devices, ..."

Section "Observing formal grammars"

"concrete discrete dynamical system" I know what a discrete dynamical system is but what is a 'concrete' dynamical system? The definition of 'concrete' in not present in the Scholarpedia page for 'dynamical systems'.

Section "Computing by Observing Bio-Systems"

"it is considered accepted, otherwise it is considered rejected" What does 'considered' mean? If something is considered accpted, can then be rejected? I suggest either to remove both 'considered' or to clarify its meaning in this context.

Similarly for "it is considered to be rejected." later in the same section.

I still think that the article would benefit from a longer introduction aimed to a non-technical audience.