On Thu, July 7, 2011 16:08, Gary Berg-Cross said: (01)
extract:
> Did this earlier view reflect biological reality? Which of the
> alternatives discussed above reflects reality now? (02)
The reality is that there are physical things that reproduce (create things
similar to themselves) by combining physical materials from outside
themselves into new structures with different chemistry from that which
they originally had. We CLASSIFY these types of objects as forms of
living things (possibly excluding some). We similarly classify subsets
of this large class of objects due to various properties which we can
observe that they have. I.e., we create models of the reality based
on properties which we deem important. (03)
The various alternatives discussed below all reflect reality -- although
different aspects of it. Some categories have recently been found to be
useful, so they have been defined, membership criteria have been
determined, and whether previously defined classes are subclasses of the
more general classes have been determined. In the case of
Plant0 = Plant1 U Fungi & Plant1 /\ Fungi = 0
the English word "Plant" has been reassigned from its previous meaning
to a subclass of the class which had been its previous meaning. (04)
You ask about "reality". Note that what is changing is models of that
reality, not the reality itself. Both the old and new models have uses.
Biologists have found the new models to be more useful. What is confusing
is the re-use of English words for new concepts which are similar to, but
not identical with concepts they previously denoted. [Of course, this is
in addition to the totally different meanings which the words already have
(physical plant, plant a flag, ...).] (05)
> This discussion on classifying things reminds me of the discussion thread
> back about 4 years ago on Models and Confounded models. I wrote as part
> of
> this discussion this about biological classifications based on unique
> properties etc. as Doug noted earlier:
>
>>> There are many gradations of wetlands reaching from soggy ground to
>>> standing shallow water. A rigid division between land and water is
>>> quite
>>> arbitrary. Fungi used to be classified as plants, but now they are a
>>> different kingdom. (06)
> Here's what I noted in the earlier discussion on Models of reality.
>
>>(G B-C) I've suggested that there are alternative biological models that
> serve
> as the basis for biological "reality". I think that this has
> implications for what the ontology represents (independent of the
> model-theoretic underlying the ontology). (07)
I don't see that this needs to be a problem for computerized ontologies.
An ontology can have different classes for the different meanings discussed
below. The ontology should clearly specify the meaning of its terms. The
difficulty may reside in a user taking the time to carefully read the
definitions of the classes in order to select the intended one. (08)
-- doug f (09)
> Here is an example of what troubles me.
> (05)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid05>
>
> Recent Linneus' hierarchical classification system, have (generally)
> adopting five kingdoms of living organisms - as discussed in Purves et
> al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
> (www.sinauer.com). In this view Viruses, are not considered living. Ok
> leave that aside for this discussion it's an explicit assumption.
> (06)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid06>
>
> But recent studies suggest that there might be a sixth Kingdom, the
> Archaea.
> (07)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid07>
>
> As discussed in the Wikipedia:
> (08)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid08>
>
> "currently in textbooks from the United States, a system of six kingdoms
> (Animalia, Plantae, Fungi, Protoctista, Archaea and Prokaryota), while
> in British and Australian textbooks, five kingdoms (Animalia, Plantae,
> Fungi, Protist, Bacteria) are used."
> (09)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid09>
>
> Above these in the (also in Wikipedia ) there is a simple phylogenetic
> representation of three Domains of life: Archaea, Bacteria (Eubacteria),
> and Eukaryota -
>
>(010)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid010>
>
> But in the hierarchical classification system (also in Wikipedia) there
> are 2 "superkingdoms" and 4 kingdoms.
> http://en.wikipedia.org/wiki/Kingdom_(biology)#Two_superkingdoms.2C__Fou
> r_kingdomsAssociates
>
>(011)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid011>
>
> Now, if I had relied on earlier biological understanding I would have a
> different taxonomy of life, kingdoms etc. No superkingdoms at all.
>
>(012)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid012>
>
> Did this earlier view reflect biological reality? Which of the
> alternatives discussed above reflects reality now?
>
>(013)<http://ontolog.cim3.net/forum/ontolog-forum/2007-07/msg00137.html#nid013>
>
> Gary Berg-Cross
> SOCoP
> Knowledge Strategies
>
> On Thu, Jul 7, 2011 at 3:40 PM, AzamatAbdoullaev
> <abdoul@xxxxxxxxxxxxxx>wrote:
>
>>
>> > Rich wrote: "Suppose there is a universe of "PRIMITIVE" properties..."
>> This is all the science is to pursue, to discover the universe of
>> basic/simple/primitive properties as a universal hierarchy of
>> properties,
>> generating the standard pyramid of classes of entities.
>> Azamat
>> PS: To extend the idea, go for basic states or fundamental
>> properties/quantities, like in QM the quantum numbers are used to define
>> a
>> quantum system. So the question is how many states/properties are
>> needed
>> to
>> describe any given thing or system.
>> > ----- Original Message -----
>> > From: "Rich Cooper" <rich@xxxxxxxxxxxxxxxxxxxxxx>
>> > To: <doug@xxxxxxxxxx>; "'John F. Sowa'" <sowa@xxxxxxxxxxx>;
>> > <ontolog-forum-bounces@xxxxxxxxxxxxxxxx>; "Christopher Menzel"
>> > <cmenzel@xxxxxxxx>; "AzamatAbdoullaev" <abdoul@xxxxxxxxxxxxxx>
>> > Sent: Thursday, July 07, 2011 12:29 AM
>> > Subject: RE: [ontolog-forum] Why most classifications are fuzzy
>> >
>> >
>> >> Doug, Azamat, John,
>> >>
>> >> Let me propose an alternative that uses some of Azamat's ideas and
>> some
>> >> of
>> >> Doug's responses.
>> >>
>> >> Suppose there is a universe of "PRIMITIVE" properties, i.e. those
>> that
>> >> are
>> >> terminal, not decomposable into other properties. That is, there are
>> >> terminal and nonterminal properties, as there are terminal and
>> >> nonterminal
>> >> symbols in an ontology, or a language, or a group of logical
>> expressions,
>> >> as
>> >> Chris alluded to. This should be easy to agree on for most, but is
>> still
>> >> the context of whatever metrics have been chosen to separate the
>> entities
>> >> into classes.
>> >>
>> >> I'll call them the P[i] properties.
>> >>
>> >> Classification is the process of choosing (with whatever method you
>> wish)
>> >> unique properties that are to be used in dividing a given sample
>> group
>> >> into
>> >> classes by the classification scheme. I will only use terminal
>> >> properties
>> >> in the classification scheme, whatever their origin.
>> >>
>> >> Then there is some list of such P[i] which serve to make a
>> distinction
>> >> among
>> >> the samples. That distinction is, by my definition, whatever
>> primitive
>> >> properties separate according the values of each entity with each
>> >> property
>> >> in the chosen list.
>> >>
>> >> For example, in a relational database, there are columns which serve
>> this
>> >> purpose, and for which select statements can be written that refer to
>> >> exactly those properties. The group-by clause specifies the precise
>> >> logical
>> >> combination of property values to be used in sorting the various
>> entities
>> >> returned by the select statement.
>> >>
>> >> Any further specification of how those properties are combined or
>> grouped
>> >> is
>> >> part of an arbitrary (read subjective) classification theory.
>> >>
>> >> JMHO,
>> >> -Rich
>> >>
>> >> Sincerely,
>> >> Rich Cooper
>> >> EnglishLogicKernel.com
>> >> Rich AT EnglishLogicKernel DOT com
>> >> 9 4 9 \ 5 2 5 - 5 7 1 2
>> >>
>> >> -----Original Message-----
>> >> From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx
>> >> [mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] On Behalf Of doug
>> foxvog
>> >> Sent: Wednesday, July 06, 2011 1:20 PM
>> >> To: [ontolog-forum]
>> >> Subject: Re: [ontolog-forum] Why most classifications are fuzzy
>> >>
>> >> On Wed, July 6, 2011 14:38, AzamatAbdoullaev said:
>> >>> John wrote
>> >>>> "And a warning: Unless you can find an immutable law of nature
>> >>>> that creates a classification, don't expect it to be a solid
>> >>>> foundation for a "standard ontology".
>> >>
>> >>> Agree. Here are five methodogical rules from the standard ontology:
>> >>> 1. Class is determined by a single property;
>> >>
>> >> This definition would block many subclasses, unless the property
>> >> is defined as membership in the class.
>> >>
>> >>> 2. Kind is determined by a set of properties;
>> >>
>> >> Is this a useful distinction?
>> >>
>> >>> 3. Natural Kind is determined by a set of lawfully related
>> properties
>> >>> (laws);
>> >>> 4. Natural Genus is the set of things sharing a basic law;
>> >>
>> >> I haven't heard this term except in the context of Linneaen taxonomy.
>> >>
>> >>> 5. Natural Species is the set of things sharing a particular law.
>> >>
>> >> The term has a useful meaning in biology; but what is its use
>> otherwise?
>> >>
>> >>> Many classifications are mostly at the level one, like the five
>> >>> classifications for natural resources, such as land, water, soils,
>> >>> plants,
>> >>> animals, solar power, etc, divided by a single property: origin;
>> >>> renewability, availability, development stage or distribution scope.
>> >>
>> >> There are many gradations of wetlands reaching from soggy ground to
>> >> standing shallow water. A rigid division between land and water is
>> quite
>> >> arbitrary. Fungi used to be classified as plants, but now they are a
>> >> different kingdom.
>> >>
>> >>> A more
>> >>> scientific understanding of resources is asking for reaching higher
>> >>> levels.
>> >>
>> >> Even at this level there are difficulties.
>> >>
>> >> -- doug foxvog
>> >>
>> >>
>> >>> Azamat Abdoullaev
>> >>>
>> >>> ----- Original Message -----
>> >>> From: "John F. Sowa" <sowa@xxxxxxxxxxx>
>> >>> To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
>> >>> Sent: Wednesday, July 06, 2011 7:45 PM
>> >>> Subject: [ontolog-forum] Why most classifications are fuzzy
>> >>>
>> >>>
>> >>>> This forum has been quiet for a while, and I'd like to stir the pot
>> >>>> with a controversial issue.
>> >>>>
>> >>>> Two widely known rigid classifications established a paradigm,
>> >>>> which some people mistakenly consider the norm: the periodic
>> >>>> table in chemistry and the Linneaen taxonomy of living things.
>> >>>> But the rigid boundaries of those categories are the result of
>> >>>> underlying laws of nature that explain why intermediate cases are
>> >>>> impossible (periodic table) and rare (taxonomy of species).
>> >>>>
>> >>>> For physics and chemistry, quantum mechanics implies discrete
>> steps,
>> >>>> which create discrete classifications of elementary particles.
>> >>>> At the next level up, it also implies discrete combinations of
>> >>>> such particles -- combinations of quarks to form baryons (protons
>> >>>> and neutrons) and combinations of atoms to form molecules.
>> >>>>
>> >>>> For biology, discrete molecular operations support the stable
>> >>>> molecules needed for life and the mechanisms for replicating the
>> >>>> huge molecules needed for DNA. But those mechanisms are only
>> >>>> weakly stable -- that leads to random mutations.
>> >>>>
>> >>>> For the next level up, natural selection creates fuzzy boundaries
>> >>>> among interbreeding populations, but crisp boundaries between
>> >>>> isolated populations. For example, look at the sharp distinction
>> >>>> between foxes and wolves, but fuzzy boundaries among dogs. When
>> >>>> humans allow dogs to "do their own thing", the breeds quickly
>> >>>> revert to a generic ur-dog -- which is usually healthier and
>> >>>> more robust than many breeds.
>> >>>>
>> >>>> Some biological classifications are not based on DNA. Examples
>> >>>> are trees and berries. For example, the family Rosaceae includes
>> >>>> rose bushes, apple trees, and raspberries. Biologically, all
>> >>>> berries are fruit, but apples are more likely to be grouped with
>> >>>> oranges as "typical" fruit than with raspberries.
>> >>>>
>> >>>> By height and woodiness, an apple tree is more likely to be
>> >>>> classified with a remotely related spruce tree than with
>> >>>> a rose bush. And many evergreens become bushes or trees
>> >>>> at the whim of some human with a pair of shears.
>> >>>>
>> >>>> There is even a debate in India whether bamboo should be
>> >>>> classified as grass or tree: "Recently there was a controversy
>> >>>> when the union ministry of environment and forests asked states
>> >>>> across India to recognise bamboo as a minor forest produce."
>> >>>>
>> >>>> See http://www.bbc.co.uk/nature/life/Bamboo
>> >>>>
>> >>>> In general, what makes any classification rigid is some *law*,
>> >>>> which could be a law of nature or some human rule. Since it's
>> >>>> a lot easier to change human laws, such classifications are
>> >>>> likely to change with culture, technology, or fads.
>> >>>>
>> >>>> Summary: Fuzzy boundaries are the norm in most classifications.
>> >>>> Whenever a boundary seems to be sharp, look for some axiom, law,
>> >>>> principle, or convention that creates the distinction. Those
>> >>>> laws are more fundamental than any grouping by "similarity".
>> >>>>
>> >>>> And a warning: Unless you can find an immutable law of nature
>> >>>> that creates a classification, don't expect it to be a solid
>> >>>> foundation for a "standard ontology".
>> >>>>
>> >>>> John Sowa
>> >>>>
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>> >>
>> >>
>> >> =============================================================
>> >> doug foxvog doug@xxxxxxxxxx http://ProgressiveAustin.org
>> >>
>> >> "I speak as an American to the leaders of my own nation. The great
>> >> initiative in this war is ours. The initiative to stop it must be
>> ours."
>> >> - Dr. Martin Luther King Jr.
>> >> =============================================================
>> >>
>> >>
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>
>
> --
> Gary Berg-Cross, Ph.D.
> gbergcross@xxxxxxxxx
> http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross
> NSF INTEROP Project
> http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0955816
> SOCoP Executive Secretary
> Knowledge Strategies
> Potomac, MD
> 240-426-0770
>
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=============================================================
doug foxvog doug@xxxxxxxxxx http://ProgressiveAustin.org (011)
"I speak as an American to the leaders of my own nation. The great
initiative in this war is ours. The initiative to stop it must be ours."
- Dr. Martin Luther King Jr.
============================================================= (012)
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