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Re: [ontolog-forum] What is the role of an upper level ontology?

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "doug foxvog" <doug@xxxxxxxxxx>
Date: Mon, 20 May 2013 17:11:28 -0400
Message-id: <c994b2ea696a22275f903d91ad56c827.squirrel@xxxxxxxxxxxxxxxxx>
On Sun, May 19, 2013 16:59, Gary wrote:
> I think using leptons and quarks as examples of what is out there could
> tend to a reductionist interpretation. Can we agree on the elements in the
> periodic table, composed from those particles as being out there?    (01)

Structures (patterned groups) of leptons and quarks have a natural
existence.  As do structures of such structures (etc.).  The pattern
of components in a structure can define a type.  Naturally occurring
patterns with numerous instances can be associated with "natural
kinds".  This is what i meant when i said that structures and their
patterns are out there.    (02)

Members of such structures may be replaced with similar entities
such that the modified structure is the same type of thing that the
pre-change structure was.   Whether the new structure is *the
same thing* as the old structure is a matter of definition.  The
appropriate identity criterion for a type may be context dependent.    (03)

This is what i meant by saying that identity for macroscopic structure
is human-defined.    (04)

Quarks form structures of three which include nucleons (as well as
structures of two -- mesons).  Nucleons form structures (atomic nuclei)
with specific patterns.  Electrons (a type of lepton) form standing waves
around atomic nuclei in specific structures (electron shells), the
combined structures of the electron shells and nuclei being
atoms.   Types of atoms with similar nuclei (ignoring excitation state)
are defined as isotopes.  Types of atoms with nuclei with the same
number of protons have similar chemical properties, and are called
elements.  Structures of multiple atoms form molecules and regularly
occurring molecular subcomponents such as monomers and radicals.    (05)

Such patterns are natural kinds as well.    (06)

I consider elements in the periodic table to be types of structures
of nucleons and electrons (thus of quarks and leptons).
An instance of Element, e.g. Carbon, has its own instances.
Elements, as naturally occurring types of structures of subatomic
particles are natural kinds, and their instances are "out there".    (07)

It is clear what is meant for an atom to be an instance of a certain
element: its nucleus has a specific number of protons.  But what
does it mean for a chunk of matter to be an instance of that element?
What proportion of its atoms have to be of that element?    (08)

> Can we also posit larger structures like genes as out there?    (09)

What do you mean by "gene"?  Is it a type defined by a pattern,
like Carbon Dioxide?  Or is it a physical object, like one molecule
of CO2?  If a "gene" is a type, could the type have variations,
alleles, or is it restricted to a specific pattern of nucleotides?    (010)

However you wish to define them, genes (or types of genes) are
natural kinds: complex structures of molecular subcomponents
(and thus ultimately of quarks and leptons).    (011)

With something as simple as a gene, it might be easy to define
identity conditions -- identity is maintained as long as only
specified changes in the identity of specific nucleotides occur,
and nucleotide identity is maintained so long as the elemental
types of the component atoms and the physical pattern of bonds
between atoms of various elemental types does not change.
Atoms gaining or loosing electrons or neutrons does not change
the elemental type of the atom.  A gene could be defined as
a pattern/structure on a single strand of DNA, even though
it defines the pattern on the corresponding part of the opposite
strand.    (012)

However, if a gene (copy) is replicated, is it clear which is the "new"
gene (copy) and which is the "original gene"?   If a gene switches
chromosomes or moves on the same chromosome is it the "same"
gene?  Does it matter if the second chromosome is in the same cell
(organism or organism of a different species)?  If a section of a gene
switches direction on a chromosome, is it the "same" gene (assuming
it can still be decoded)?  If introns between parts of a gene on a
chromosome change, does the gene change?    (013)

There are certainly far larger structures than genes that are natural
kinds.  However, specifying their boundaries, and thus their identity
conditions, ends up being difficult -- which is why i said that identity
is normally human defined.    (014)

-- doug foxvog    (015)

> Gary Berg-Cross
> Sent from my iPad
> On May 18, 2013, at 10:47 PM, "doug  foxvog" <doug@xxxxxxxxxx> wrote:
>> On Sat, May 18, 2013 04:53, rrovetto@xxxxxxxxxxx wrote:
>>> Comments inline after RR:
>>> On Sat, May 18, 2013 at 1:28 AM, doug foxvog <doug@xxxxxxxxxx> wrote:
>>>> On Fri, May 17, 2013 00:14, John F Sowa wrote:
>>>>> GBC
>>>>>> Examples are Semantic Theories of:
>>>>>>  parts & wholes,
>>>>>>  essence & identity,
>>>>>>  composition and constituency.
>>>>> I agree that many people who propose an upper ontology like to
>>>>> include
>>>>> such things.  Unfortunately, those are among the most complex issues
>>>>> that have been debated in philosophy for millennia -- with no
>>>> consensus.
>>>> Identity is the crux of all of the above.   And the problem is that
>>>> identity for some spatio-temporal entity
>>>> is human defined and human created.
>>> RR: Doug, fellow Terp here. Ireland and photography are two of my
>>> favorites as well.
>> Hi, Terp!
>>> RR: To the extent that "identity" has to do with *distinguishing*,
>>> then yes there is a certain degree of fiat involved.
>>> And to the extent that it is confined to (or formulated into)
>>> some logical or mathematical formalism the
>>> same holds. But to the extent that identity involves that which makes
>>> some
>>> putative unity or whole separate/distinct (in a mind-external sense)
>>> from
>>> another, it's not human defined and created.
>> As long as you don't get too specific, yes.  General concepts of
>> identity
>> work for macroscopic objects for various purposes.  And depending upon
>> the purpose, different senses of identity are used.  What is part and
>> what
>> is not part of an object depend upon the purpose.  And depending upon
>> the purpose, different identity criteria are used.  Think Theseus's
>> ship,
>> a double-trunk tree whose underground connection between the two
>> trunks are disconnected, when a human being starts, ....
>>> Reality affords minds to distinguish,
>>> and so some reality outside of minds grounds these unities.
>> Agreed.
>>>> What is out "there" are a bunch of quarks, leptons, and photons that
>>>> interact in various ways.  Patterns of groups of them have
>>>> "interesting"
>>>> properties and various of the properties last for those patterns
>>>> (which
>>>> are continually gaining and losing members) for macroscopic periods of
>>>> time.
>>>> RR: This reflects one reductive view of the world.
>> I didn't say there are ONLY elementary particles.  I refer to patterned
>> groups of them (which include at various scales atoms, molecules, rocks
>> life forms, buildings, planets, ...) which have some stability.   It is
>> these
>> patterned groups that have the slippery sort of identity that we are
>> discussing.
>>> Whether it's true is another question.
>>> What's important is that "interesting" does not mean "arbitrary",
>> Of course not.
>>> but whether (some of) the "interesting" properties/patterns
>>> mark the so-called natural kinds, lead to formulations and discoveries
>>> of
>>> general scientific principles, and ideally result in some practical and
>>> beneficial use or manipulation of what's being studied.
>> Certainly they do.
>>>> The meaning of "identity" seems clear.  As one Supreme Court
>>>> justice said about pornography:
>>>> "I know what it is when i see it."
>>>> However, identity turns out to be extremely context and viewer
>>>> dependent.  Even identity of subatomic particles can be assured
>>>> only by following them (i.e., constantly interacting with each
>>>> thereby changing its properties).
>>> RR: The quote makes a good point.
>>> These are general and basic notions that
>>> resist precise description so well. It's no surprise since they are so
>>> general and perhaps in the background of our psyche.
>>> Perhaps two different senses of 'identity' are being used, here?
>> As John said in a later post, many.
>>> One about describing what the justice was trying to identify,
>>> the other about individuating (particles).
>>> Generally speaking, when including social
>>> matters, like this and a child-to-adult, things become much more
>>> complicated and, perhaps less likely to have a mind-independent answer
>>> (assuming you're trying to find one rather than simply prescribe). For
>>> the
>>> social-related or social-type of identity questions it might be best to
>>> appeal to normative considerations: is it *good* to define identity in
>>> this way, what good will it do?
>> This seems to agree with my initial comment:
>>>> the problem is that
>>>> identity for some spatio-temporal entity
>>>> is human defined and human created.
>>>> Unless one can define "identity" in a reasonable way, one can't
>>>> define non-instantaneous types of parthood, essence, composition,
>>>> and constituency reasonably.
>>>>> JS: For parts & wholes, the following is a classic:...
>>>>> But look at the following list of 16 more recent books on
>>>>> mereology: ...
>>>>> For essence, the situation is even more hopeless.  Plato and
>>>>> Aristotle
>>>>> couldn't agree on how to define essence, how to recognize it, or how
>>>>> to reason about it.  Today, all the debates between P & A are just as
>>>>> hot as ever.  There's much more detail, much more debate, and even
>>>>> less agreement.  There are also skeptics from Sextus Empiricus to
>>>>> Quine who debunk the very idea.
>>>>> Identity is another swamp.  The = sign in logic and mathematics looks
>>>>> very clear and simple, but outside of mathematics identity is *never*
>>>>> fundamental.  You can observe similarity, but identity is *always*
>>>>> a context-dependent inference for a particular purpose.
>>>> Exactly.
>>>>> ... And how can you recognize identity?  By a continuous
>>>>> trajectory in space-time?  Perhaps in theory, but certainly not
>>>>> in practice.  ...
>>>>> Fundamental principle:  All the options are important and
>>>>> can be useful for various applications.
>>>>> But they belong in an open-ended family of *microtheories*.
>>>>> None of them belong in an upper level ontology.
>>>> Here i beg to disagree.  Since the options are important and can be
>>>> useful, it *is* useful to define them in an upper level ontology.
>>>> HOWEVER, such properties should not belong to classes of spatio-
>>>> temporal things in a mid level ontology.  [I suggest only the broadest
>>>> s-tclasses belong in an upper level ontology.]
>>>> So i agree with John that relating such properties
>>>>>>  parts & wholes,
>>>>>>  essence & identity,
>>>>>>  composition and constituency
>>>> to spatio-temporal things belong in specific theory microtheories.
>>>> -- doug f
>>>>> ...
>>>>> John
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