2008-06-14 email for archive - DNA as information entity, features associated with Information

[Alan Ruttenberg]

---------- Forwarded message ----------
From: Alan Ruttenberg <alanrut...@gmail.com>
Date: Sat, Jun 14, 2008 at 8:41 AM
Subject: Re: Reminder: First Information Entity Ontology Workshop, this Monday June 9, 2008, 9AM
To: Barry Smith <phis...@buffalo.edu>
Cc: Darren Natale <da...@georgetown.edu>, Rees Jonathan <j...@creativecommons.org>, Tom Knight <t...@csail.mit.edu>, g...@mit.edu, Fabian Neuhaus <fneu...@web.de>, Bjoern Peters <bpe...@liai.org>, "K. Krasnow Waterman" <k...@mit.edu>

On Jun 11, 2008, at 11:35 AM, Barry Smith wrote:

Alan and I ponder rebaptizing 'Information Entity Ontology' and calling it the 'Information Artifact Ontology' -- thus narrowing the focus, and ideally leaving open the issue of whether DNA molecules are carriers of information
This choice is motivated by the prime need at the moment, which is to support OBI, and to support the annotation of publications, results, databases, etc., all of which are information artifacts.

Here is a list of features of information as Alan and I see it:

I would say: these are the features that we have associated with the term "information". They are the pieces from which we will be building various definitions.

...

2. communication, thus the potential for remote control, action at a distance

There's a little complication on this one, as communication is a process. At the beginning you have some information, and at the end you have some information in a different place. Sometimes this is accomplished by moving around an information bearing object. But sometimes it is manifestly conveyed by a process - talking, pulsing light, etc.

3. preservation over time
4. small occupation on space of possibilities
5. low noise ('perfect') copyability
6. formulated in a background language marked by
       6a, compositionality, which involves also a high degree of
       6b. free associability (providing I follow the rules of grammar (or analogous rules in music?) I have a gigantic degree of freedom to create new things which are still language)
       6c a distinction between the grammatical and the non-grammatical (between the well-formed and the ill-formed), resting on widespread consensus
       6d substitutability of synonyms (thus an idea of shared meaning -- whereby it is meaning which gets communicated)
7. aboutness (every information artifact is intended to be about something)
Optional criteria:
8. potential for logical complexity; narrative objects (e.g. journal articles) always have 8.
9. potential for normativity (some information artifacts convey oughtness, also governed by logic and aboutness)

Interestingly, most types of Shannon-Weaver information, and bird songs, do not count as information because they fall short already on 5. and 6.

That would suggest, in this analysis, that 5 and 6 are "optional", as certainly one sense in which "information" is used is in such cases. The bird songs are not pointless - they function in reproductive activity.

When we say that primates do not have command of language we are addressing something like their inability to master anything like a language satisfying 6.

This speaks more about language, than about information per se, no?

How is it with DNA? Is there anything like mastery, or freedom to create new strings by composition, in the world of DNA (I mean in the world of DNA as it is before human beings start to create DNA artifacts)?

There is the immune system's ability to generate new antibodies

Photographs lack 6. I think the same goes for pixellated images.
Absolute music and dance lack 7.

Much music is intentionally evocative (though not always successfully so) as is dance. When doing so, would we not say that they are about what they intend to invoke?

Proposal: Information artifacts have to be bearers of information in the sense which involves satisfaction of at least criteria 1-7.

Need to think about this.

To be information artifacts in our sense, databases have to be ABOUT something (a string of random numbers is not an information artifact)

Could they (the databases) not be about a process of generating random numbers in the sense of recording some sequence of random numbers (for example for later analysis to see if they actually contain some shannon information?)

The following are information artifacts in this sense:

serial number
batch number
grant number
person number
name
address
email address
URI
protocol
lab note
ontology
gene list
publication
result
license
document granting permission
contract
novel
textbook
newspaper
timetable
recipe
map
objective specification