Is an ionic current a continuant?

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Alan Ruttenberg

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Apr 16, 2007, 1:56:09 AM4/16/07
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Statements in neurondb effectively say that membranes of certain
compartments of certain neurons conduct various ionic currents.
I'm having a little trouble parsing this into BFO.

Suggestions?

http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl

-Alan

Pierre Grenon

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Apr 16, 2007, 3:07:03 AM4/16/07
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aye, this sounds tricky

it must be possible to draw an analogy with rivers, river banks and
dams and river flows

my first reaction is to say:

- membranes et al are substantial of sort, so are the ions

- the ions move, I'd say what we are looking at here with 'ionic
currents'' is a processual of sort, the movement of ions

in any event, my first though would be to say that nothing like a
current distinct from either ions or their movements.

it is even more difficult considering there may be patterns of
movement involved, but you should be fine saying that there are
movements of sorts in which ions are involved in the relevant areas.
the fine grained description of this would probably be too complex for
the purpose

pierre

Matthew Pocock

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Apr 16, 2007, 6:17:04 AM4/16/07
to bfo-d...@googlegroups.com, Pierre Grenon
So, a related question. Is there a mechanism in BFO to associate particulates
with a representation as mass? So - water-as-molecules vs water-as-substance?
This seems relevant for the modelling of these neurons, as individual ions
pass through individual channels in a particular region of membrane. When
viewed in bulk, this movement gives rise to a current, which is itself a
measure that only applies to a bulk, not a particulate.

A similar argument could be made for temperature - the particles have kinetic
energy, and the substance has a temperature exactly under those conditions
where the kinetic energies follow a poison distribution. The temperature is
intimately associated with the moments of that distribution.

The particulate/substance distinction is important in experimental sciences.
Otherwise you end up accidentally claiming that homeophathy realy could work
in the physical world, or being utterly unable to account for the random
motion of pollen in a petri-dish of water.

Matthew

Pierre Grenon

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Apr 16, 2007, 6:28:14 AM4/16/07
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isn't

particle --> object

bulk --> group/population of object --> aggregate

(and, although not specified by BFO but if needed to tidy up things: a
specialzation of parthood (member in group/population))

not enought for this?

William Bug

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Apr 16, 2007, 6:33:38 AM4/16/07
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I think Pierre essentially gets this right.

My background is as a molecular neurophysiologist doing single ion channel, so I can vouch for why the description appears as it does in NeuronDB.

NeuronDB as it's name implies is a database of physiological models - models both at the molecular level (ion channel mechanics if you will) and on the cellular level - e.g., based on the composite ion channels present in the membranes of specific compartments in specific cells, those compartments' collective "ion currents" contribute to the overall spatio-temporal, emergent physiological excitable of the neuron to which they belong.  

These models go back to the original experiments by Alan Hodgkin & Andrew Huxley in the mid-1930's, when the Squid Giant Axon membrane was studied in isolation.  It was extruded like a toothpaste tube, salines on either side of the membrane (in the tube and surrounding the tube) were replaced with known ionic composition, and the propensity of current to flow as the voltage across the membrane was varied was tested under these specific ion conditions.  The result was the characterization of specific Na+, K+, and Cl- conductance that all showed a particular time-course and voltage-dependence.

Soon after that, one of H&H's collaborators, Bernard Katz - and others - began to study the other major family of conductances found in neurons - the neurotransmitter-gated conductances found on the post-synaptic membrane.

Prior to the 1980s when it became possible to study single-ion channels in isolation, most all of the modeling was done at the level of membrane conductances - apart from a variety of noise analysis statistical techniques used to determine smaller units of conductance, such as the "quantum" of current generated when a SINGLE presynaptic transmitter vesicle fuses with the membrane and releases its contents into the synaptic cleft (work first performed by B Katz et al).

Essentially all the modeling of ion conductances in excitable membrane now-a-days cycles back-n-forth between modeling ion channel molecular events leading to individual ion penetration of the channel flowing down it's electrochemical gradient and modeling the emergent behavior of entire cells or portions of cells to macroscopic events such as depolarization or saline ion manipulation (and drug manipulation to study channel populations with specific drug sensitivities).

It's a standard modeling technique to characterize the membrane as essentially a capacitor, resistor, and transistor all wired in parallel.  The lipid bilayer acts a capacitor (with a characteristic capacitance).  There is typically a "passive", non-specific "leakage" current flowing down the resistance, and then there are all the ion channels, which essentially function as voltage-dependent (or transmitter-dependent) current sources (similar to a transistor).  Typically, now that many characteristic measurements have been made on specific ion channel species, models seek to place specific populations of channels into specific compartments with the goal of matching the collective molecular-level conductances with the emergent compartment and cellular-level electrical activity.

That is the typical modeling approach, and that's where this assertion that "ion currents" are contained within the plasma membrane derives from.

If one want's to model ion channels as part of the "electrical excitability machinery" then they could treat them as continuants that are contained with the plasma membrane.  Given the nature of the experimental work done presently, you'd want to be as specific as possible as to exactly WHERE across the cell the given ion conductance and/or ion channels have been identified.

If one wants to model ion channels as contributors to the "electrical excitability process", then you'd need to address the specifics of the role they play in that process.  Simply to say they dwell in the membrane won't be sufficient, but dropping to the level of molecular events won't really suffice either.  The "integrating" performed by the models which matches ions flowing down their electrochemical gradient through molecular channels to the emergent electrical behavior in compartments (very much defined as fiat boundaries) has a lot of unspecified details.  It's certainly pretty meaningless to simply say neuron X has ion currents A,B, & C in its membrane - IF the goal is to effectively describe the electrical activity of the neuron - since SO MUCH of the behavior is based on the specific location, density, and local inter-relatedness of different channel types.

This is really a challenge.

I believe in the end, it will depend on what details one is trying to capture - and to what purpose - that may best guide the process of mapping neuronal ionic currents into BFO classes.

Cheers,
Bill
Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
610 457 0443 (mobile)


Please Note: I now have a new email - Willi...@DrexelMed.edu




Phillip Lord

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Apr 16, 2007, 8:54:23 AM4/16/07
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I believe that neuroweb is talking about conductance, not
conduction. It's not the movement of charge that is being talked
about, but the relationship between voltage and resultant current. Or
a description of how things can move, rather than the fact of their
movement.

Phil


>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> aye, this sounds tricky

[...]

PG> it is even more difficult considering there may be patterns of
PG> movement involved, but you should be fine saying that there are
PG> movements of sorts in which ions are involved in the relevant
PG> areas. the fine grained description of this would probably be
PG> too complex for the purpose

PG> pierre

Pierre Grenon

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Apr 16, 2007, 9:43:02 AM4/16/07
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hear that...

i haven't had time to look at the neuro ontology yet, in my reply I
was trying to parse what I understood of the issue from a BFO
perspective

the way BFO describes how things can move is by speaking of these
things as participating in their movement, possibly by having among
other thigs further specific categories of movements. Conceivably,
moving things would have relevant property particulars (dependent
continuants) which account for their movements being what they are...
possibly you could apply this to a stream of ions as having a given
property particular which would account for whichever physical
property (not immediately in the BFO sense but such as the
quantitative characterizations you find in physics) you are interested
in here

i'll look at the file and see whether I can revise or precise this statement

pierre

Phillip Lord

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Apr 16, 2007, 10:19:44 AM4/16/07
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Well conductance of a membrane would be something which depends on
both the membrane and the ion I would assume.

To give an analogy, the ratio between the speed and pressure for a
fluid travelling down a pipe depends on the pipe (the narrower the
bore, the smaller the ratio) and the fluid (treacle is thicker than
water).

For water under reasonable conditions this relationship will
approximate linear, although this will break down when you get
turbulent flow, when it will probably become quadratic, cubic or some
really weird power function that you only seem in fluid dynamics. I
guess something similar is true with ionic currents as well.

Phil

>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> hear that...

PG> i haven't had time to look at the neuro ontology yet, in my
PG> reply I was trying to parse what I understood of the issue from
PG> a BFO perspective

PG> the way BFO describes how things can move is by speaking of
PG> these things as participating in their movement, possibly by
PG> having among other thigs further specific categories of
PG> movements. Conceivably, moving things would have relevant
PG> property particulars (dependent continuants) which account for
PG> their movements being what they are... possibly you could apply
PG> this to a stream of ions as having a given property particular
PG> which would account for whichever physical property (not
PG> immediately in the BFO sense but such as the quantitative
PG> characterizations you find in physics) you are interested in
PG> here

PG> i'll look at the file and see whether I can revise or precise
PG> this statement

PG> pierre

PG> On 4/16/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>>
>>
>>
>>
>> I believe that neuroweb is talking about conductance, not
>> conduction. It's not the movement of charge that is being talked
>> about, but the relationship between voltage and resultant
>> current. Or a description of how things can move, rather than the
>> fact of their movement.
>>
>> Phil
>>
>>
>> >>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:
>>
PG> aye, this sounds tricky
>>
>> [...]
>>
PG> it is even more difficult considering there may be patterns of
PG> movement involved, but you should be fine saying that there are
PG> movements of sorts in which ions are involved in the relevant
PG> areas. the fine grained description of this would probably be
PG> too complex for the purpose
>>
PG> pierre
>>
PG> On 4/16/07, Alan Ruttenberg <alanrut...@gmail.com> wrote:
>> >>
>> >> Statements in neurondb effectively say that membranes of
>> >> certain compartments of certain neurons conduct various ionic
>> >> currents. I'm having a little trouble parsing this into BFO.
>> >>
>> >> Suggestions?
>> >>
>> >> http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl
>>
>>
>> >
>>

PG>

--
Phillip Lord, Phone: +44 (0) 191 222 7827
Lecturer in Bioinformatics, Email: philli...@newcastle.ac.uk
School of Computing Science, http://homepages.cs.ncl.ac.uk/phillip.lord
Claremont Tower Room 909, skype: russet_apples
Newcastle University,
NE1 7RU

Pierre Grenon

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Apr 16, 2007, 10:32:41 AM4/16/07
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so conductance of a membrabe is a property particular which inheres in
that membrane

I think this would suffice

you could type it as a conductance in relation to the class of ion
say, in order to account for the fact that this is tied (dependent on)
ions. The trick is that it is not specifically dependent on particular
ions, right? It sounds then that conductance would fall under
disposition or tendencies in BFO

Now, you could also attach to ions property particulars of a certain
type which would account for the way they would behave in membranes of
a given sort

- the pipe as a disposition to let fluid of a certain type travel
through it at a certain speed

- the fluid as a disposition of travelling at a certain speed in pipes
of a certain type

These properties are distinct although presumably dependent on various
other properties (shape and rugosity of the pipe, etc)

with respect to the mathematical characterization of these, I gather
this is not an issue specific to the sort of entities at end, anything
which can be quantified and come with a scale will be more or less
treated in teh same way, I gather. So, the treatment of the
quantitaive aspects of conductance will be similar to that of length
or weight say.

does that make sense?

pierre

Phillip Lord

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Apr 16, 2007, 11:04:08 AM4/16/07
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>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> so conductance of a membrabe is a property particular which
PG> inheres in that membrane

PG> I think this would suffice

PG> you could type it as a conductance in relation to the class of
PG> ion say, in order to account for the fact that this is tied
PG> (dependent on) ions. The trick is that it is not specifically
PG> dependent on particular ions, right?


No, I don't think so. You should expect a membrane with for example
Chloride channels to have a very different conductance to chloride
ions than you would to phosphotase ions.


PG> It sounds then that conductance would fall under disposition or
PG> tendencies in BFO

PG> Now, you could also attach to ions property particulars of a
PG> certain type which would account for the way they would behave
PG> in membranes of a given sort

Why would you not attach this to the membrane rather than the ion? It
seems to me that the conductance of a membrane is a mathematical
relationship between voltage and current for a given type of ion over
a given type of membrane. Conductance is a property of two things not
one.


PG> So, the treatment of the quantitaive aspects of conductance will
PG> be similar to that of length or weight say.

PG> does that make sense?


Not entirely. Mass can be specified as force over acceleration -- at
least when the observer has a static frame of reference, although not
in general. This is independent of the entity providing the
force. Likewise length which is dependent only on the entity (although
again not in general).

Conductance is more similar to force producing a velocity against a
friction. It's dependent on the entity being pushed and the entity
causing the friction. And as I said previously, this is all dependent
on the velocity of the entity being pushed -- in general, these
measurements are taken at the linear phase, but it breaks down
eventually if you go fast enough.

Phil

Pierre Grenon

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Apr 16, 2007, 11:38:26 AM4/16/07
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Both membranes and ions have properties but they do not have the same property,

or rather

there is one type of properties for membranes (the property of
alloywing for this and that wrt ions of a certain sort)
and
there is one type of properties for ions (the property of doing this
or that wrt membranes of a certain sort)

Moreover, membranes can have properties of one type in relation to
ions of a given type and properties of another type in relation to
ions of another type, I meant this too

More in line below...

On 4/16/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>

> >>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:
>
> PG> so conductance of a membrabe is a property particular which
> PG> inheres in that membrane
>
> PG> I think this would suffice
>
> PG> you could type it as a conductance in relation to the class of
> PG> ion say, in order to account for the fact that this is tied
> PG> (dependent on) ions. The trick is that it is not specifically
> PG> dependent on particular ions, right?
>
>
> No, I don't think so. You should expect a membrane with for example
> Chloride channels to have a very different conductance to chloride
> ions than you would to phosphotase ions.

This is not what I meant. I didn't ask whether the property in
question of the membrane is the same for all ions, I agree with you
that it could be the most specific properties in questions are likely
or could be different depending on the kind of ions. Although, they
would all be determinates (more specific) of a same determinable (the
family of properties if you want).

I meant, the property of the membrane is not dependent on ion1, ion2,
ion3 etc where these are particular ions (not kinds), but is all
things being equal the same which ever particular ions of a specific
kind (chloride, etc) happen to traverse it.


>
> PG> It sounds then that conductance would fall under disposition or
> PG> tendencies in BFO
>
> PG> Now, you could also attach to ions property particulars of a
> PG> certain type which would account for the way they would behave
> PG> in membranes of a given sort
>
> Why would you not attach this to the membrane rather than the ion? It
> seems to me that the conductance of a membrane is a mathematical
> relationship between voltage and current for a given type of ion over
> a given type of membrane. Conductance is a property of two things not
> one.

I'm saying two things have distinct properties, but there is no one
property of two things. They each have these properties in relation to
the other, of course.

>
> PG> So, the treatment of the quantitaive aspects of conductance will
> PG> be similar to that of length or weight say.
>
> PG> does that make sense?
>
>
> Not entirely. Mass can be specified as force over acceleration -- at
> least when the observer has a static frame of reference, although not
> in general. This is independent of the entity providing the
> force. Likewise length which is dependent only on the entity (although
> again not in general).
>
> Conductance is more similar to force producing a velocity against a
> friction. It's dependent on the entity being pushed and the entity
> causing the friction. And as I said previously, this is all dependent
> on the velocity of the entity being pushed -- in general, these
> measurements are taken at the linear phase, but it breaks down
> eventually if you go fast enough.

I'm not talking about what produces, but what accounts for. It might
be the same thing which does both, but it is another issue.

pierre

>
>
>
> Phil
>
> >
>

Phillip Lord

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Apr 16, 2007, 12:16:41 PM4/16/07
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>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> Moreover, membranes can have properties of one type in relation
PG> to ions of a given type and properties of another type in
PG> relation to ions of another type, I meant this too

Well, that's one way of looking at it. It seems to me a lot clearer
and more straightforward to consider it to be something which is a
feature of both the entities that are interacting. You can have
conductance without a media and you can't have it without a charged
entity.


PG> you could type it as a conductance in relation to the class of
PG> ion say, in order to account for the fact that this is tied
PG> (dependent on) ions. The trick is that it is not specifically
PG> dependent on particular ions, right?
>>
>>
>> No, I don't think so. You should expect a membrane with for
>> example Chloride channels to have a very different conductance to
>> chloride ions than you would to phosphotase ions.


PG> I meant, the property of the membrane is not dependent on ion1,
PG> ion2, ion3 etc where these are particular ions (not kinds), but
PG> is all things being equal the same which ever particular ions of
PG> a specific kind (chloride, etc) happen to traverse it.

Difficult to say till you have tested it. But yes, as a first
approximation, this would make sense. Of course, it's not dependent on
a particular membrane either.

>> Why would you not attach this to the membrane rather than the
>> ion? It seems to me that the conductance of a membrane is a
>> mathematical relationship between voltage and current for a given
>> type of ion over a given type of membrane. Conductance is a
>> property of two things not one.

PG> I'm saying two things have distinct properties, but there is no
PG> one property of two things. They each have these properties in
PG> relation to the other, of course.

Are there not? Mass, length, passage through time, colour. All these
are dependant at least two different things.


>> Not entirely. Mass can be specified as force over acceleration --
>> at least when the observer has a static frame of reference,
>> although not in general. This is independent of the entity
>> providing the force. Likewise length which is dependent only on
>> the entity (although again not in general).
>>
>> Conductance is more similar to force producing a velocity against
>> a friction. It's dependent on the entity being pushed and the
>> entity causing the friction. And as I said previously, this is
>> all dependent on the velocity of the entity being pushed -- in
>> general, these measurements are taken at the linear phase, but it
>> breaks down eventually if you go fast enough.

PG> I'm not talking about what produces, but what accounts for. It
PG> might be the same thing which does both, but it is another
PG> issue.


I am not sure that I understand. Conductance is a description of a
behaviour as is friction. It seems to me to be dependent on the two
entities involved equally and equivalently.

The only difference between two entities in this case (an membrane and
an ion) is that in one case we could distinguish between two
particular membranes and there is no way of distinguishing between two
particular ions. This distinction disappears with friction, at least
in general.

So it seems to me that conductance and friction are properties of the
system, not the individual members of it.

Phil

Pierre Grenon

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Apr 16, 2007, 12:51:16 PM4/16/07
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On 4/16/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>
> >>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:
>
> PG> Moreover, membranes can have properties of one type in relation
> PG> to ions of a given type and properties of another type in
> PG> relation to ions of another type, I meant this too
>
> Well, that's one way of looking at it. It seems to me a lot clearer
> and more straightforward to consider it to be something which is a
> feature of both the entities that are interacting. You can have
> conductance without a media and you can't have it without a charged
> entity.

There is indeed interaction and the properties in question are
realized in the interaction.

in short and rough approximation probably, you need to dissociate the
scientific concept from what is happening

what is happening is that a fluid goes through a pipe. That happening
is actually a processual (occurrent). That entity involves (at least)
two things: fluid and pipe.

In that occurrence, in this process, are realized two things:

the tendency/disposition/property-of-sort of the pipe to allow in a
certain way for the fluid in question to travel thorugh it (correlated
to type of fluid)

the tendency/... of the fluid (some token thereof) to travel in a
ceratin way through the pipe in question (correlated to type of pipe)

Both these properties are relational, but the property of the pipe is
not a property of the fluid and the property of the fluid is not a
property of the pipe.

They are however correlated.

I think it could be possible to make properties of this sort dependent
on specific particular (portions of) fluid and speak of a given
membrane having numerically distinct but similar properties in
relation to different portions of fluid of the same type. This, in
order to achieve the same effect as saying that the membrane has a
single property which is in fact 'generically' dependent (in the sense
that they dependent on the type of entities but not any particular
instance) on the type of fluid, or on the fluid taken as an object
disseminated through teh universe (a property such that any portion of
the fluid going through the pipe would do this and that). The approach
in term of multiple properties of the pipe each tied to distinct
portions of fluid seems very complicated to me, but I admit simplicity
is not necessarily the best criterion here.

>
> PG> you could type it as a conductance in relation to the class of
> PG> ion say, in order to account for the fact that this is tied
> PG> (dependent on) ions. The trick is that it is not specifically
> PG> dependent on particular ions, right?
> >>
> >>
> >> No, I don't think so. You should expect a membrane with for
> >> example Chloride channels to have a very different conductance to
> >> chloride ions than you would to phosphotase ions.
>
>
> PG> I meant, the property of the membrane is not dependent on ion1,
> PG> ion2, ion3 etc where these are particular ions (not kinds), but
> PG> is all things being equal the same which ever particular ions of
> PG> a specific kind (chloride, etc) happen to traverse it.
>
> Difficult to say till you have tested it. But yes, as a first
> approximation, this would make sense. Of course, it's not dependent on
> a particular membrane either.

The property of a given membrane is dependent on this membrane (as it
inheres in it). But it is of a type such that there can be other
instances of it which inhere and are dependent on other membranes and
not the first one.

>
>
> >> Why would you not attach this to the membrane rather than the
> >> ion? It seems to me that the conductance of a membrane is a
> >> mathematical relationship between voltage and current for a given
> >> type of ion over a given type of membrane. Conductance is a
> >> property of two things not one.
>
> PG> I'm saying two things have distinct properties, but there is no
> PG> one property of two things. They each have these properties in
> PG> relation to the other, of course.
>
> Are there not? Mass, length, passage through time, colour. All these
> are dependant at least two different things.

Yes, possibly, but they do not inhere in a multiplicity of instances.

My take on relation property is that:
- they inhere in the entity they are the property of
- they are dependent on some other entity (in which, however, they do
not inhere)

>
> >> Not entirely. Mass can be specified as force over acceleration --
> >> at least when the observer has a static frame of reference,
> >> although not in general. This is independent of the entity
> >> providing the force. Likewise length which is dependent only on
> >> the entity (although again not in general).
> >>
> >> Conductance is more similar to force producing a velocity against
> >> a friction. It's dependent on the entity being pushed and the
> >> entity causing the friction. And as I said previously, this is
> >> all dependent on the velocity of the entity being pushed -- in
> >> general, these measurements are taken at the linear phase, but it
> >> breaks down eventually if you go fast enough.
>
> PG> I'm not talking about what produces, but what accounts for. It
> PG> might be the same thing which does both, but it is another
> PG> issue.
>
>
> I am not sure that I understand. Conductance is a description of a
> behaviour as is friction. It seems to me to be dependent on the two
> entities involved equally and equivalently.

I think conductance is in the end a property of a conductor.

The 'flowability' of a pipe is a property of the pipe. That the pipe
may have different "flowability" for different (types of) fluids, just
means that it has different properties. Not that these are properties
of the fluid as well, although yes, they do depend in one sense or
another on the fluids.

> The only difference between two entities in this case (an membrane and
> an ion) is that in one case we could distinguish between two
> particular membranes and there is no way of distinguishing between two
> particular ions. This distinction disappears with friction, at least
> in general.
>
> So it seems to me that conductance and friction are properties of the
> system, not the individual members of it.

What about saying they are systemic properties of one member of the system?

But being a property of a system is not what you haev suggested
before. You have suggested that conductance was a property of all of
the elements.

If the system is something above more than its member, it is not the
same to say that a property is one which belongs to the system and to
say that it is one which belongs to all the elements of the system.

Actually, if you take systems as objects of sort in their own rights
and wish to say that you are speaking of a property as one of the
system's properties, I might not argue against this. I'm not too sure
what I think of it but it is not as problematic as speaking of a
shared property of all members.

One of the difficulty here is that the members of the system change
and arguably the system as well. Ions once they've travelled one
membrane might not be the same which will travel through it at a later
time. But the property you are lookig at would remain the same. The
membrane would remain the same. For this reason, it seems to me to
make more sense of my suggestion.

pierre

> Phil
>
> >
>

Fabian Neuhaus

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Apr 16, 2007, 3:09:13 PM4/16/07
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Pierre,

As you can imagine I am following your discussion with great interest,
since it is directly connected to our recurring discussion about the
existence of dependent entities that inhere in two (or more) other
entities. I tend to agree with Phillip, but I try to understand your
position. Thus two short question:

> Both these properties are relational, but the property of the pipe is
> not a property of the fluid and the property of the fluid is not a
> property of the pipe.

[...]

>
> My take on relation property is that:
> - they inhere in the entity they are the property of
> - they are dependent on some other entity (in which, however, they do
> not inhere)

I use "relational property" as a name for properties that inhere in two
or more entities -- but that's obviously not intended. Now I try to
understand what you mean 'relational property'. Does the following
capture it? A relational property is a property that inheres on one
entity and depends on at least one other entity?

I am surprised that you believe that the property of the pipe depends
on the fluid. Assume you have two fluids A and B which behave exactly
the same with respect to flowing through pipes, but are different in
some other respect. (E.g. assume that A is water with molecule mass of
19 where the additional neutron is attached to one hydrogen atom, while
B is water with molecule mass of 19 where the additional neutron is
attached to the oxygen atom.) It seems to me that according to your
position if the pipe should have only one tendency/disposition, namely
the disposition to interact with ALL fluids that have some distinct
properties (a certain mass, a certain chemical structure, ...) in a
given way. (By the way, these properties are not realizable entities
themselves.) So my second question is: Do you believe that there are
two properties that inhere in the pipe --one tendency/disposition to
allow in a certain way for fluid A to travel through and another for
fluid B or is there only one tendency/disposition that applies to all
fluids that are similar with respect to 'flow properties'? In the
latter case I don't see how the property of the pipe can depend on a
particular fluid.

Fabian

William Bug

unread,
Apr 17, 2007, 12:58:05 AM4/17/07
to bfo-d...@googlegroups.com
Folks might want to look back at my post to this thread.  

I'm assuming since there was no response to my post, either it was not considered useful or it was incomprehensible.  I'd be glad to follow-up with anyone who has a specific comment or question.  

The discussion that's transpired over the last day is very helpful and gradually converging on a way to use BFO to improve the current NeuronDB.owl representation.

Having said that, my post gives a description of where the NeuronDB content derives from and can help to better inform the analysis of this issue.  In the end, regardless of the current state of the NeuronDB OWL representation - which may or may not be either an optimal representation of the underlying NeuronDB info in OWL - or an optimal mapping to BFO - this representation has as its starting point the model data in NeuronDB.  That is the content the OWL file must reflect, as that content is NOT going to change the way it represents the relevant continuants and occurents in any appreciable manner.

Cheers,
Bill

Matthew Pocock

unread,
Apr 17, 2007, 5:58:42 AM4/17/07
to Pierre Grenon, bfo-d...@googlegroups.com
On Monday 16 April 2007, Pierre Grenon wrote:
> isn't
>
> particle --> object
>
> bulk --> group/population of object --> aggregate
>
> (and, although not specified by BFO but if needed to tidy up things: a
> specialzation of parthood (member in group/population))
>
> not enought for this?

Perhaps this is sufficient. What would the relationship be between water (the
substance) and water (a mass of molecules)? At some point, water stops
behaving (within observational error) like a substance and starts behaving
like it is made up of discrete particles. It is not as if the water molecules
are water-molecule-sized bits of water-substance.

We can say lots of usefull things about water in terms of viewing it as a
substance, and lots of questions that would be intractable at the level of a
particulate model are tractable at the substance level - for example, fluid
dynamics using equations rather than tracing flows of billions of individual
molecules in a discrete-time-state simulator. But, the view of water as a
substance is only valid within certain scale limits, hence homeopathy.

It's not as if substance and particle are the only two models of water as
physical stuff. There's also the atomic/electron high-school view of water as
an oxygen with two hydrogens and the ability to hydrogen-bond. Or there's the
quantum-soup version where we can describe fancy chemistry. I guess what I'm
trying to get at in my groping way is to ask how we can talk about water in
each of these ways and state how these different ways are related to each
other, and what the limitations of each kind of description of water are, so
that we don't apply a way of talking about water to an inappropriate
situation and therefore avoid reaching some classes of wrong conclusions. To
be more general, what kinds of relationships and concepts would we need to
capture this kind of knowledge?

Matthew

Phillip Lord

unread,
Apr 17, 2007, 6:34:41 AM4/17/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> what is happening is that a fluid goes through a pipe. That
PG> happening is actually a processual (occurrent). That entity
PG> involves (at least) two things: fluid and pipe.

PG> In that occurrence, in this process, are realized two things:

PG> the tendency/disposition/property-of-sort of the pipe to allow
PG> in a certain way for the fluid in question to travel thorugh it
PG> (correlated to type of fluid)

PG> the tendency/... of the fluid (some token thereof) to travel in
PG> a ceratin way through the pipe in question (correlated to type
PG> of pipe)

PG> Both these properties are relational, but the property of the
PG> pipe is not a property of the fluid and the property of the
PG> fluid is not a property of the pipe.


Again, I don't think that this makes any sense. Let me recap.

- the ability of a (kind of) pipe to let a (kind of) fluid through it
is the property of a pipe
- the ability of a (kind of) fluid to flow through a (kind of) pipe
is a property of the fluid
- these two properties are different
- but always numerically equal.

PG> I meant, the property of the membrane is not dependent on ion1,
PG> ion2, ion3 etc where these are particular ions (not kinds), but
PG> is all things being equal the same which ever particular ions of
PG> a specific kind (chloride, etc) happen to traverse it.
>>
>> Difficult to say till you have tested it. But yes, as a first
>> approximation, this would make sense. Of course, it's not
>> dependent on a particular membrane either.

PG> The property of a given membrane is dependent on this membrane
PG> (as it inheres in it). But it is of a type such that there can
PG> be other instances of it which inhere and are dependent on other
PG> membranes and not the first one.

Maybe. I think that you are using your conclusions to justify
themselves. I don't think that conductance inheres in the membrane and
is not a property of the membrane alone.

PG> I'm saying two things have distinct properties, but there is no
PG> one property of two things. They each have these properties in
PG> relation to the other, of course.
>>
>> Are there not? Mass, length, passage through time, colour. All
>> these are dependant at least two different things.

PG> Yes, possibly, but they do not inhere in a multiplicity of
PG> instances.

Yes, they do. The mass (length, colour etc) of an entity inheres in
the entity and the thing that is observing it.

PG> My take on relation property is that:
PG> - they inhere in the entity they are the property of
PG> - they are dependent on some other entity (in which, however,
PG> they do
PG> not inhere)

Okay, so in which case you need a new kind of property which is
symmetric, or a principled mechanism for determining which way the
asymmetry works.


>> I am not sure that I understand. Conductance is a description of
>> a behaviour as is friction. It seems to me to be dependent on the
>> two entities involved equally and equivalently.

PG> I think conductance is in the end a property of a conductor

I think that it is not. Conductance has no meaning without a thing
conducted. You can abstract away from this by having a standard
entity conducted. This is how it works for electrical components -- a
200ohm resistor has 200ohm resistance to electrons. Things would be
different if you tried to conductor chloride ions down it.

>> So it seems to me that conductance and friction are properties of
>> the system, not the individual members of it.

PG> What about saying they are systemic properties of one member of
PG> the system?

PG> But being a property of a system is not what you haev suggested
PG> before. You have suggested that conductance was a property of
PG> all of the elements.

PG> If the system is something above more than its member, it is not
PG> the same to say that a property is one which belongs to the
PG> system and to say that it is one which belongs to all the
PG> elements of the system.

Ah, my apologies. Perhaps my English was not as clear as it should
be. I said "conductance is a property of two things not one". By which
I meant, two things considered together at the same time. I was
probably not clear enough in distinguishing between the two
interpretations that you've pointed out.

PG> One of the difficulty here is that the members of the system
PG> change and arguably the system as well. Ions once they've
PG> travelled one membrane might not be the same which will travel
PG> through it at a later time.

As I said before, you can't tell. How can you tell between one ion and
another?

PG> But the property you are lookig at would remain the same. The
PG> membrane would remain the same. For this reason, it seems to me
PG> to make more sense of my suggestion.

You can flow the same piece of water through multiple pipes. I am not
sure what difference this makes.

Phil

Phillip Lord

unread,
Apr 17, 2007, 6:39:15 AM4/17/07
to bfo-d...@googlegroups.com
>>>>> "FN" == Fabian Neuhaus <fneu...@web.de> writes:

FN> So my second question is: Do you believe that there are two
FN> properties that inhere in the pipe --one tendency/disposition to
FN> allow in a certain way for fluid A to travel through and another
FN> for fluid B or is there only one tendency/disposition that
FN> applies to all fluids that are similar with respect to 'flow
FN> properties'? In the latter case I don't see how the property of
FN> the pipe can depend on a particular fluid.


It's worse than this. The pipe will behave differently at different
temperatures and pressures. So in the end, to describe the pipe it
would have a multitude of properties for any possible different fluid
(or indeed solid) and at lots of different temperatures.

Alternatively, you can consider fluid conductance to be a property of
the system. Then the system has one property, the pipe and fluid none
(with respect to conductance). Course, you have a potentially large
number of systems, but it still seems simpler to me.

Phil

Pierre Grenon

unread,
Apr 17, 2007, 7:26:42 AM4/17/07
to bfo-d...@googlegroups.com
Fabian,

sorry for the lag, it took me an enormous amount of energy to refrain
from cribbling the reply with anti german slur,

> > Both these properties are relational, but the property of the pipe is
> > not a property of the fluid and the property of the fluid is not a
> > property of the pipe.
>
> [...]
>
> >
> > My take on relation property is that:
> > - they inhere in the entity they are the property of
> > - they are dependent on some other entity (in which, however, they do
> > not inhere)
>
> I use "relational property" as a name for properties that inhere in two
> or more entities -- but that's obviously not intended.

Right you are, I don't mean multiply inhering

> Now I try to
> understand what you mean 'relational property'. Does the following
> capture it? A relational property is a property that inheres on one
> entity and depends on at least one other entity?

Yes, that is just what I meant.

> I am surprised that you believe that the property of the pipe depends
> on the fluid.

Hold on... I'm confused by the type token ambiguity in your sentence my friend.

> Assume you have two fluids A and B which behave exactly
> the same with respect to flowing through pipes, but are different in
> some other respect. (E.g. assume that A is water with molecule mass of
> 19 where the additional neutron is attached to one hydrogen atom, while
> B is water with molecule mass of 19 where the additional neutron is
> attached to the oxygen atom.)

I assume

A subclass_of Fluid
B subclass_of Fluid
not (A = B)

> It seems to me that according to your
> position if the pipe should have only one tendency/disposition, namely
> the disposition to interact with ALL fluids that have some distinct
> properties (a certain mass, a certain chemical structure, ...) in a
> given way. (By the way, these properties are not realizable entities
> themselves.)

Carefull here

All I said rested on the assumption that the two types of fluids were
distincts. I assume this notion. Whether A and B have similar flowing
properties, if they are distinct then it seems to me there ought to be
distinct even if somewhat similar properties of the pipe.

The risk here is of going from the assumed distinction between A and B
as two different types of fluid to an indistinction of A and B as
having similar "fluidity properties" for lack of better term... your
emphasis on such similar is close to suggests that you are now
defining types of fluids based on their "fluidity property"

Actually, I tried merely to describe a position according to which you
could have:

(1) not (Disp001 = Disp002)
(2) Disp001 inst_of Disposition
(3) Disp001 inst_of Disposition
(4) Disp001 inheres_in Pipe001
(5) Disp002 inheres_in Pipe001
(6) Disp001 depends_on A
(7) Disp002 depends_on B

where you interpret (6) and (7) in a way or another

and I also meant to suggest that it is credible that

(8) Disp001 inst_of DispoTypeC
(9) Disp002 inst_of DispoTypeD
(10) DispoTypeC subclassof Disposition
(11) DispoTypeD subclassof Disposition
(12) intersection_of(DispoTypeC, DispoTypeD) = NULL

I'm not sure but I like to think I tried to leave open the possiblity
which you describe, more likely I meant to say it is credible that the
position you describe is false, i.e. in general it is more credible
that for truly distinct kinds of fluids there will be truly distinct
properties in the same pipe.

Moreover, I meant that it is more credible that for two instances of
A, a1 and a2, there are no two properties of the pipe such that p1
depends on a1 and p2 depends on a2 but just one.

> So my second question is: Do you believe that there are
> two properties that inhere in the pipe --one tendency/disposition to
> allow in a certain way for fluid A to travel through and another for
> fluid B or is there only one tendency/disposition that applies to all
> fluids that are similar with respect to 'flow properties'?

I'm just suggesting one possible take on this which seems to be the
simplest and most consistent with BFO of the ways of approaching the
issue.

It is more credible that pipes have different properties in relation
to different true types of fluids.

You describe two fluids which have similar flowing properties, but you
do not suggest that there is a single property which is that of both
fluids. The same goes for the pipe, it has two similar properties but
they are numerically distinct and even do not belmong to the same
type, as long as the type of fluids are genuinely distinct.

> In the
> latter case I don't see how the property of the pipe can depend on a
> particular fluid.

Well, if we assume that A and B are two distinct types of fluids,
despite all their similarity, if we index dispositions of pipes to a
type of fluid, then the pipe has two disposition, one with resepct to
each fluid, although these might be similar.

If we define a type of fluid as having a particular fluidity property
and allegeldy distinct A and B have that property (os similar
properties) then it sounds more like there is one type of fluid only,
call it AuB, in which case the pipe has only one property which
depends on AuB.

makes sense?
pierre

Pierre Grenon

unread,
Apr 17, 2007, 8:17:38 AM4/17/07
to bfo-d...@googlegroups.com
On 4/17/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>
> >>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:
>
> PG> what is happening is that a fluid goes through a pipe. That
> PG> happening is actually a processual (occurrent). That entity
> PG> involves (at least) two things: fluid and pipe.
>
> PG> In that occurrence, in this process, are realized two things:
>
> PG> the tendency/disposition/property-of-sort of the pipe to allow
> PG> in a certain way for the fluid in question to travel thorugh it
> PG> (correlated to type of fluid)
>
> PG> the tendency/... of the fluid (some token thereof) to travel in
> PG> a ceratin way through the pipe in question (correlated to type
> PG> of pipe)
>
> PG> Both these properties are relational, but the property of the
> PG> pipe is not a property of the fluid and the property of the
> PG> fluid is not a property of the pipe.
>
>
> Again, I don't think that this makes any sense. Let me recap.
>
> - the ability of a (kind of) pipe to let a (kind of) fluid through it
> is the property of a pipe
> - the ability of a (kind of) fluid to flow through a (kind of) pipe
> is a property of the fluid
> - these two properties are different
> - but always numerically equal.
>

I'm not sure I understand "numerically equal"

Suppose we have:

a has_value "Aunit"
b has_value "Bunit"

by "a and b are numerically equal", do you mean:

(1) Aunit = Bunit

or

(2) a = b ?

I use the phrase "a and b are numerically equal" to mean (2). And the
last clause you state is definitely nothing I meant to suggest, on the
contrary.

If you mean (1), I am not sure the last clause makes sense either, as
it is credible that if a and b are the properties in question and they
are quantifiable they might not even be given the same units. Also I
don't think I have suggested so far that the properties in question
had the same value, because I haven't assumed that if they were
quantifiable they would be comparable, if they exist, they are
correlated and so are their value, that's one thing, but they are
probably not numerically identical in neither of the (1) and (2)
senses above.

>
> PG> I meant, the property of the membrane is not dependent on ion1,
> PG> ion2, ion3 etc where these are particular ions (not kinds), but
> PG> is all things being equal the same which ever particular ions of
> PG> a specific kind (chloride, etc) happen to traverse it.
> >>
> >> Difficult to say till you have tested it. But yes, as a first
> >> approximation, this would make sense. Of course, it's not
> >> dependent on a particular membrane either.
>
> PG> The property of a given membrane is dependent on this membrane
> PG> (as it inheres in it). But it is of a type such that there can
> PG> be other instances of it which inhere and are dependent on other
> PG> membranes and not the first one.
>
> Maybe. I think that you are using your conclusions to justify
> themselves. I don't think that conductance inheres in the membrane and
> is not a property of the membrane alone.

wait, I am trying to *describe* a way in which to parse the example in
BFO, but OK, it's possible I misunderstood the example or your own
understanding of the example

The property of a membrane is dependent on the membrane is what BFO says

I'm suggesting a representation according to which the conductance of
a membrane is a property of the membrane

You disagree with this view but I am merely telling you that in BFO
there is no property which is a property of more than one thing -- I
am not considering the recent addition of so-called generically
dependent continuants although to my understanding a property of more
than one thing in the sense you are aiming at would not be a
generically dependent continuant of BFO

> PG> I'm saying two things have distinct properties, but there is no
> PG> one property of two things. They each have these properties in
> PG> relation to the other, of course.
> >>
> >> Are there not? Mass, length, passage through time, colour. All
> >> these are dependant at least two different things.
>
> PG> Yes, possibly, but they do not inhere in a multiplicity of
> PG> instances.
>
> Yes, they do. The mass (length, colour etc) of an entity inheres in
> the entity and the thing that is observing it.

wait, the major assumption here is that this is absurd, there might be
things inhering in an observer but the length of of a rod is something
which exists whether observed or not, so it is not even dependent on
an observer

by dependent, I mean "existentially dependent", I mean to say that the
rod has a property which is an entity,

I do not mean to say anything about the the quantity which can be
associated with this entity, it is credible that the measurement of a
rod is something that depends on (i.e. is functionally related to)
various conditions of measurement, but the length of a rod (in other,
though not quite synonymous, words, the fact that the rod has a
length) is not existentially
dependent on these conditions...

in both case, it is actually not the same kind of dependence we are
talking about (might be arguable, but it would be in the sense that
something that shows in measurement is an entity which is dependent in
the way the length is, not in the sense that the length as an entity
is dependent in the way that measurement values or what have you
aredependent on conditions or observers)

are we clear about this assumption?

> PG> My take on relation property is that:
> PG> - they inhere in the entity they are the property of
> PG> - they are dependent on some other entity (in which, however,
> PG> they do
> PG> not inhere)
>
> Okay, so in which case you need a new kind of property which is
> symmetric, or a principled mechanism for determining which way the
> asymmetry works.

not sure I follow

>
> >> I am not sure that I understand. Conductance is a description of
> >> a behaviour as is friction. It seems to me to be dependent on the
> >> two entities involved equally and equivalently.
>
> PG> I think conductance is in the end a property of a conductor
>
> I think that it is not. Conductance has no meaning without a thing
> conducted. You can abstract away from this by having a standard
> entity conducted. This is how it works for electrical components -- a
> 200ohm resistor has 200ohm resistance to electrons. Things would be
> different if you tried to conductor chloride ions down it.
>

Did I really say anything contradicting what you are saying here?

>
>
>
> >> So it seems to me that conductance and friction are properties of
> >> the system, not the individual members of it.
>
> PG> What about saying they are systemic properties of one member of
> PG> the system?
>
> PG> But being a property of a system is not what you haev suggested
> PG> before. You have suggested that conductance was a property of
> PG> all of the elements.
>
> PG> If the system is something above more than its member, it is not
> PG> the same to say that a property is one which belongs to the
> PG> system and to say that it is one which belongs to all the
> PG> elements of the system.
>
> Ah, my apologies. Perhaps my English was not as clear as it should
> be.

Thanks for your understanding...

> I said "conductance is a property of two things not one".

And I said this is not BFO. I tried to offer you two ways:

1) conductance is a property of the conductor which it has in relation
to the conductee or kind of conductee.

2) conductance is the property of the conductor-conductee system, but
of neither the conductor nor the conductee alone

I think 1) is more credible, but I am just stating two possible
approaches and if I have seemed to suggest that I was holding the
truth about which is right, maybe I should just back off and suspend
any judgement.

The above "So it seems to me that conductance and friction are
properties of the system, not the individual members of it.. " seems
to square with 2)

> By which
> I meant, two things considered together at the same time.

I do not understand this I am afraid. I tought first you were speaking
of a property of two things, and second of a property of a thrid thing
which is composed of the first two.

> I was
> probably not clear enough in distinguishing between the two
> interpretations that you've pointed out.

I didn't mean to berate you if that's the worry

>
> PG> One of the difficulty here is that the members of the system
> PG> change and arguably the system as well. Ions once they've
> PG> travelled one membrane might not be the same which will travel
> PG> through it at a later time.
>
> As I said before, you can't tell. How can you tell between one ion and
> another?

The point is that I don't have to, though

> PG> But the property you are lookig at would remain the same. The
> PG> membrane would remain the same. For this reason, it seems to me
> PG> to make more sense of my suggestion.
>
> You can flow the same piece of water through multiple pipes. I am not
> sure what difference this makes.

me neither,

I meant to say that the property is dependent on the type or on every
piece of water if you will, but not on any specific piece of water

have I manage explaining better?

pierre

> Phil
>
> >
>

Pierre Grenon

unread,
Apr 17, 2007, 8:36:58 AM4/17/07
to Matthew Pocock, bfo-d...@googlegroups.com
On 4/17/07, Matthew Pocock <matthew...@ncl.ac.uk> wrote:
> On Monday 16 April 2007, Pierre Grenon wrote:
> > isn't
> >
> > particle --> object
> >
> > bulk --> group/population of object --> aggregate
> >
> > (and, although not specified by BFO but if needed to tidy up things: a
> > specialzation of parthood (member in group/population))
> >
> > not enought for this?
>
> Perhaps this is sufficient. What would the relationship be between water (the
> substance) and water (a mass of molecules)?

I seem to recall BFO doesn't make that distinction

> At some point, water stops
> behaving (within observational error) like a substance and starts behaving
> like it is made up of discrete particles. It is not as if the water molecules
> are water-molecule-sized bits of water-substance.
>
> We can say lots of usefull things about water in terms of viewing it as a
> substance, and lots of questions that would be intractable at the level of a
> particulate model are tractable at the substance level - for example, fluid
> dynamics using equations rather than tracing flows of billions of individual
> molecules in a discrete-time-state simulator. But, the view of water as a
> substance is only valid within certain scale limits, hence homeopathy.
>
> It's not as if substance and particle are the only two models of water as
> physical stuff. There's also the atomic/electron high-school view of water as
> an oxygen with two hydrogens and the ability to hydrogen-bond. Or there's the
> quantum-soup version where we can describe fancy chemistry. I guess what I'm
> trying to get at in my groping way is to ask how we can talk about water in
> each of these ways and state how these different ways are related to each
> other, and what the limitations of each kind of description of water are, so
> that we don't apply a way of talking about water to an inappropriate
> situation and therefore avoid reaching some classes of wrong conclusions. To
> be more general, what kinds of relationships and concepts would we need to
> capture this kind of knowledge?

I would suggest you look at the OpenCyc ontology

in particluar, look for

ObjectType
(unfortunately, there is no link to StuffType which might have been helpful)
ExistingObjectType
ExistingStuffType
granuleOfSpatialStuff

here http://www.cyc.com/cycdoc/vocab/top-vocab.html

look also for "stuff" and "substance" related things
here http://www.cyc.com/cycdoc/vocab/chemistry-vocab.html
and maybe
here http://www.cyc.com/cycdoc/vocab/composition-vocab.html

pierre

> Matthew
>

Ingvar Johansson

unread,
Apr 17, 2007, 9:29:28 AM4/17/07
to bfo-d...@googlegroups.com
Pierre Grenon schrieb:

> On 4/17/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>
>> PG> I think conductance is in the end a property of a conductor
>>
>> PL> I think that it is not. Conductance has no meaning without a thing

>> conducted. You can abstract away from this by having a standard
>> entity conducted. This is how it works for electrical components -- a
>> 200ohm resistor has 200ohm resistance to electrons. Things would be
>> different if you tried to conductor chloride ions down it.
>>
>>
>
> PG> Did I really say anything contradicting what you are saying here?
>
First, electrical conductance (G) is the inverse of electrical
resistance (R), i.e., G = 1/R. Resistance is measured by 'ohm', and
conductance is measured by 'siemens'. Let me now talk about resistance.
The fact that there is a *relational* and *dispositional description* of
a property of certain resistor T is quite consistent with the fact *what
is described* inheres in T. Here is a possible dispositional description:

"if an electric current (a stream of electrons) passes through T, then T
makes resistance (of 200 ohm)".

But this can be regarded as being due to the microstructure of T that is
a property of T only.

best,
Ingvar


Phillip Lord

unread,
Apr 17, 2007, 10:47:18 AM4/17/07
to bfo-d...@googlegroups.com

>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> Again, I don't think that this makes any sense. Let me recap.
>>
>> - the ability of a (kind of) pipe to let a (kind of) fluid
>> through it
>> is the property of a pipe
>> - the ability of a (kind of) fluid to flow through a (kind of)
>> pipe
>> is a property of the fluid
>> - these two properties are different
>> - but always numerically equal.
>>

PG> I'm not sure I understand "numerically equal"

PG> Suppose we have:

PG> a has_value "Aunit" b has_value "Bunit"

PG> by "a and b are numerically equal", do you mean:

PG> (1) Aunit = Bunit

PG> or

PG> (2) a = b ?


PG> if they exist, they are correlated and so are their value,
PG> that's one thing, but they are probably not numerically
PG> identical in neither of the (1) and (2) senses above.

The ability of a particular pipe to allow a particular fluid through
it, seems to me, to be the same (or the inverse of) as the ability of
that particular fluid to pass through that particular pipe.

But, to me, it seems that you are saying the former is the property of
a pipe, the latter the property of the fluid.


>> Maybe. I think that you are using your conclusions to justify
>> themselves. I don't think that conductance inheres in the
>> membrane and is not a property of the membrane alone.

PG> wait, I am trying to *describe* a way in which to parse the
PG> example in BFO, but OK, it's possible I misunderstood the
PG> example or your own understanding of the example

PG> The property of a membrane is dependent on the membrane is what
PG> BFO says

PG> I'm suggesting a representation according to which the
PG> conductance of a membrane is a property of the membrane

PG> You disagree with this view but I am merely telling you that in
PG> BFO there is no property which is a property of more than one
PG> thing

But conductance clearly is a property of two things. From which I
conclude that either

- BFO cannot represent conductance
- BFO can represent conductance but we have to make an arbitrary
decision about which of two entities it depends on it inheres in.
- BFO should be extended.


PG> Yes, possibly, but they do not inhere in a multiplicity of
PG> instances.
>>
>> Yes, they do. The mass (length, colour etc) of an entity inheres
>> in the entity and the thing that is observing it.

PG> wait, the major assumption here is that this is absurd, there
PG> might be things inhering in an observer but the length of of a
PG> rod is something which exists whether observed or not, so it is
PG> not even dependent on an observer

Ah, okay, I was indeed thinking of the value of the length.

Now, obviously, by definition we can't know about the length of a rod
(either it's value or it's existence) when there is no observer, so
there's probably no point discussing that. But I would agree that all
observers would believe the rod to have a length, at least if they
could work out a way of distinguishing a length from a width.

So, if we have two observers looking at one rod, does the rod have two
lengths or one? If you are stating that the rod has an existential
relationship to it's length, then I guess that it can have many
different lengths at once.


PG> My take on relation property is that:
PG> - they inhere in the entity they are the property of
PG> - they are dependent on some other entity (in which, however,

PG> they do not inhere)


>>
>> Okay, so in which case you need a new kind of property which is
>> symmetric, or a principled mechanism for determining which way
>> the asymmetry works.

PG> not sure I follow

As we have said, conductance depends on two things. So, how do we work
out which one it inheres in?


>> >> I am not sure that I understand. Conductance is a description
>> >> of a behaviour as is friction. It seems to me to be dependent
>> >> on the two entities involved equally and equivalently.
>>
PG> I think conductance is in the end a property of a conductor
>>
>> I think that it is not. Conductance has no meaning without a
>> thing conducted. You can abstract away from this by having a
>> standard entity conducted. This is how it works for electrical
>> components -- a 200ohm resistor has 200ohm resistance to
>> electrons. Things would be different if you tried to conductor
>> chloride ions down it.
>>

PG> Did I really say anything contradicting what you are saying
PG> here?

I think so. You are claiming that conductance is a property of a
conductor. Therefore it inheres in the conductor. And, therefore, I
think, it does not inhere in the thing conducted. Which I think
contradicts my statement.

>> I said "conductance is a property of two things not one".

PG> And I said this is not BFO. I tried to offer you two ways:

PG> 1) conductance is a property of the conductor which it has in
PG> relation
PG> to the conductee or kind of conductee.

PG> 2) conductance is the property of the conductor-conductee
PG> system, but
PG> of neither the conductor nor the conductee alone

PG> I think 1) is more credible, but I am just stating two possible
PG> approaches and if I have seemed to suggest that I was holding
PG> the truth about which is right, maybe I should just back off and
PG> suspend any judgement.

PG> The above "So it seems to me that conductance and friction are
PG> properties of the system, not the individual members of it.. "
PG> seems to square with 2)

Okay, perhaps we are getting into an English problem again here.

I think that "conductance is a property of two things not one" is the
same as "conductance in the property of the conductor-conductee
system".

But if it is possible to represent this in BFO, it seems the way to go
to me.

Phil

Pierre Grenon

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Apr 17, 2007, 11:35:17 AM4/17/07
to bfo-d...@googlegroups.com
On 4/17/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>
>
> >>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:
>
> >> Again, I don't think that this makes any sense. Let me recap.
> >>
> >> - the ability of a (kind of) pipe to let a (kind of) fluid
> >> through it
> >> is the property of a pipe
> >> - the ability of a (kind of) fluid to flow through a (kind of)
> >> pipe
> >> is a property of the fluid
> >> - these two properties are different
> >> - but always numerically equal.
> >>
>
> PG> I'm not sure I understand "numerically equal"
>
> PG> Suppose we have:
>
> PG> a has_value "Aunit" b has_value "Bunit"
>
> PG> by "a and b are numerically equal", do you mean:
>
> PG> (1) Aunit = Bunit
>
> PG> or
>
> PG> (2) a = b ?
>
>
> PG> if they exist, they are correlated and so are their value,
> PG> that's one thing, but they are probably not numerically
> PG> identical in neither of the (1) and (2) senses above.
>
>
>
> The ability of a particular pipe to allow a particular fluid through
> it, seems to me, to be the same (or the inverse of) as the ability of
> that particular fluid to pass through that particular pipe.

I think you still don't get the distintion I am trying to draw here.

Suppose you have a tunnel between France and England T
Suppose T has a uniform circular section which measures 2 meters

Suppose the French want to invade England for some obscure reason and
commission their German expatriate engineers to design a special
vehicle to travel through T, they are working on vehicle of class V

One of the engineering requirement on V is that the height of V
vehicles be less than 2 meters

T has the property of allowing for vehicle of height inferior to 2
meters to travel through it, call it p1

if v is a V, v has the property of being able to travel through
tunnels which allow for travelling of vehicles of maximal height 2
meters, call it p2

Are you willing to say that there is a single property which is shared
by v (and all V class vehicles) and T?

> But, to me, it seems that you are saying the former is the property of
> a pipe, the latter the property of the fluid.

Yes,

I am saying that p1 is a property of T which depends on some class to
which Vs belong

I am saying that p2 is a property of a v (all Vs have a similar
property more accurately but do not let this bother you here) which
depends on some class of which T is an instance

>
> >> Maybe. I think that you are using your conclusions to justify
> >> themselves. I don't think that conductance inheres in the
> >> membrane and is not a property of the membrane alone.
>
> PG> wait, I am trying to *describe* a way in which to parse the
> PG> example in BFO, but OK, it's possible I misunderstood the
> PG> example or your own understanding of the example
>
> PG> The property of a membrane is dependent on the membrane is what
> PG> BFO says
>
> PG> I'm suggesting a representation according to which the
> PG> conductance of a membrane is a property of the membrane
>
> PG> You disagree with this view but I am merely telling you that in
> PG> BFO there is no property which is a property of more than one
> PG> thing
>
> But conductance clearly is a property of two things. From which I
> conclude that either

before concluding anything, let's see if conductance is the property
of two things

> - BFO cannot represent conductance
> - BFO can represent conductance but we have to make an arbitrary
> decision about which of two entities it depends on it inheres in.
> - BFO should be extended.
>

> >> Yes, they do. The mass (length, colour etc) of an entity inheres


> >> in the entity and the thing that is observing it.
>
> PG> wait, the major assumption here is that this is absurd, there
> PG> might be things inhering in an observer but the length of of a
> PG> rod is something which exists whether observed or not, so it is
> PG> not even dependent on an observer
>
> Ah, okay, I was indeed thinking of the value of the length.

ok, can you apply this to the above as well?

> So, if we have two observers looking at one rod, does the rod have two
> lengths or one? If you are stating that the rod has an existential
> relationship to it's length, then I guess that it can have many
> different lengths at once.

The rod has one length and that is all I am interested in, whether
people can disagree on the measurement is an entirely different issue.

>
> PG> My take on relation property is that:
> PG> - they inhere in the entity they are the property of
> PG> - they are dependent on some other entity (in which, however,
> PG> they do not inhere)
> >>
> >> Okay, so in which case you need a new kind of property which is
> >> symmetric, or a principled mechanism for determining which way
> >> the asymmetry works.
>
> PG> not sure I follow
>
> As we have said, conductance depends on two things. So, how do we work
> out which one it inheres in?

Well, if conductance is the property of a conductor, it should be easy
to figure out which is which, conductors do not travel through ions,
say?

I don't think this is a problem with language of the level you seem to
have in mind, i rather have the feeling to put it simply that we do
not use the word property in the same way.

What I am talking about here is not measurements or values, it is the
thing which is measured if you want. That is a property, let's say.
All you say here seems to indicate to me that you think of the value
as the property.

> I think that "conductance is a property of two things not one" is the
> same as "conductance in the property of the conductor-conductee
> system".

so for you the phrase "the conductor-conductee system" refers to two
things and not one? that is very odd isn't it?

pierre

Phillip Lord

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Apr 17, 2007, 12:43:30 PM4/17/07
to bfo-d...@googlegroups.com
>>>>> "IJ" == Ingvar Johansson <ingvar.j...@ifomis.uni-saarland.de> writes:

IJ> First, electrical conductance (G) is the inverse of electrical
IJ> resistance (R), i.e., G = 1/R. Resistance is measured by 'ohm',
IJ> and conductance is measured by 'siemens'. Let me now talk about
IJ> resistance.

Yes.

IJ> The fact that there is a *relational* and *dispositional
IJ> description* of a property of certain resistor T is quite
IJ> consistent with the fact *what is described* inheres in
IJ> T.

I'm afraid this paragraph doesn't mean anything to me.

IJ> Here is a possible dispositional description:

IJ> "if an electric current (a stream of electrons) passes through
IJ> T, then T makes resistance (of 200 ohm)".

An electric current is not a stream of electrons. It's one way of
making a current. Conductance is defined for current not electrons.

IJ> But this can be regarded as being due to the microstructure of T
IJ> that is a property of T only.

I think not. It's a property of the microstructure of T, the
nature of an electron, and how the two interact.

Phil

Phillip Lord

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Apr 17, 2007, 12:50:17 PM4/17/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> The ability of a particular pipe to allow a particular fluid
>> through it, seems to me, to be the same (or the inverse of) as
>> the ability of that particular fluid to pass through that
>> particular pipe.

PG> I think you still don't get the distintion I am trying to draw
PG> here.

PG> Suppose you have a tunnel between France and England T Suppose T
PG> has a uniform circular section which measures 2 meters

PG> Are you willing to say that there is a single property which is
PG> shared by v (and all V class vehicles) and T?


This is not an equivalent example. You can determine the bore of
tunnel without having to use a vehicle. Likewise, you can determine
the height of the vehicle without having to use tunnel. Hence you can
say that the height in the property of the vehicle and the bore the
property of the tunnel.

This is not true of conductance, which is the difficulty here. There
may be one or more properties of the conductor and one or more
properties of the thing conducted which when all considered give rise
to the property of conductance. However, none of the properties which
inhere solely in either entity is conductance.

PG> wait, the major assumption here is that this is absurd, there
PG> might be things inhering in an observer but the length of of a
PG> rod is something which exists whether observed or not, so it is
PG> not even dependent on an observer
>>
>> Ah, okay, I was indeed thinking of the value of the length.

PG> ok, can you apply this to the above as well?

No. I will try to repeat myself in a different way.

The relationship between conductance and conductor, and the
relationship between conductance and the thing conducted is
equivalent. It makes no sense to me to see what is the primary
relationship, so it makes no to say conductance inheres in one and not
the other.


>> So, if we have two observers looking at one rod, does the rod
>> have two lengths or one? If you are stating that the rod has an
>> existential relationship to it's length, then I guess that it can
>> have many different lengths at once.

PG> The rod has one length and that is all I am interested in,
PG> whether people can disagree on the measurement is an entirely
PG> different issue.

Interesting. I wasn't talking about the measurement as it
happens.

Still, my example doesn't appear to have been a very good one, so
perhaps we should not side track.

>> As we have said, conductance depends on two things. So, how do we
>> work out which one it inheres in?

PG> Well, if conductance is the property of a conductor, it should
PG> be easy to figure out which is which, conductors do not travel
PG> through ions, say?

If conductance is the property of a conductor then you have already
defined that it inheres in the conductor, so you can't use this to
derive where the property inheres.

PG> What I am talking about here is not measurements or values, it
PG> is the thing which is measured if you want. That is a property,
PG> let's say. All you say here seems to indicate to me that you
PG> think of the value as the property.

I don't think so. A property is something that is capable of having a
value. I agree I conflated these a little earlier.

>> I think that "conductance is a property of two things not one" is
>> the same as "conductance in the property of the
>> conductor-conductee system".

PG> so for you the phrase "the conductor-conductee system" refers to
PG> two things and not one? that is very odd isn't it?

conductor-conductee system refers to one system made out of two
things. Conductance depends equally on the two things (which we can
consider to be one system). Still I am pretty sure that we are talking
about English; that English has an imprecise semantics is, I am sure,
a surprise to neither of us.

Phil

Matthias Samwald

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Apr 17, 2007, 1:20:12 PM4/17/07
to BFO Discuss
On Apr 16, 2:54 pm, Phillip Lord <phillip.l...@newcastle.ac.uk> wrote:
> I believe that neuroweb is talking about conductance, not
> conduction. It's not the movement of charge that is being talked
> about, but the relationship between voltage and resultant current.

Incorrect, the Senselab ontology really IS talking about actual
currents ('conduction'), and not conductance.

Pierre Grenon

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Apr 17, 2007, 1:27:20 PM4/17/07
to bfo-d...@googlegroups.com
On 4/17/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:

> This is not an equivalent example.

Right, i was trying to figure what you were talking about. We seem to
be on the same page then.

> No. I will try to repeat myself in a different way.
>
> The relationship between conductance and conductor, and the
> relationship between conductance and the thing conducted is
> equivalent.

This claim just sounds absurd to me.

Earlier you spoke of abilities being inverse or the same.

In both cases, you seem to think about properties in the way we speak
about numerical relations or functions.

> It makes no sense to me to see what is the primary
> relationship, so it makes no to say conductance inheres in one and not
> the other.

you are forgetting that ions too have a correlated property which
makes me fail to grasp the sense of trying to find "the primary
relationship"

> >> So, if we have two observers looking at one rod, does the rod
> >> have two lengths or one? If you are stating that the rod has an
> >> existential relationship to it's length, then I guess that it can
> >> have many different lengths at once.
>
> PG> The rod has one length and that is all I am interested in,
> PG> whether people can disagree on the measurement is an entirely
> PG> different issue.
>
> Interesting. I wasn't talking about the measurement as it
> happens.

So the answer is: the rod has one length only.

> Still, my example doesn't appear to have been a very good one, so
> perhaps we should not side track.

fine

> >> As we have said, conductance depends on two things. So, how do we
> >> work out which one it inheres in?
>
> PG> Well, if conductance is the property of a conductor, it should
> PG> be easy to figure out which is which, conductors do not travel
> PG> through ions, say?
>
> If conductance is the property of a conductor then you have already
> defined that it inheres in the conductor, so you can't use this to
> derive where the property inheres.

really, why would I have to derive anything here? is it in order to
convince you?

> >> I think that "conductance is a property of two things not one" is
> >> the same as "conductance in the property of the
> >> conductor-conductee system".
>
> PG> so for you the phrase "the conductor-conductee system" refers to
> PG> two things and not one? that is very odd isn't it?
>
> conductor-conductee system refers to one system made out of two
> things.

OK, which are these things?

> Conductance depends equally on the two things (which we can
> consider to be one system).

There is nothing to consider. Either there is a system or there are two things.

Even if conductance depends on two things which is something I do not
object to, what does it tells you about inherence?

> Still I am pretty sure that we are talking
> about English;

Clearly not, we are talking about systems here.

What I said earlier was something to the effect that you could say
that conductance is a property of the system if a system is not merely
the plurality of its constituents.

Why do you need speaking of systems if systems are really fictions
which we produce when we consider two things as one?

pierre

Matthias Samwald

unread,
Apr 17, 2007, 1:50:24 PM4/17/07
to BFO Discuss
Hello,

I have a background in cellular electrophysiology and have been
working on the OWL versions for SenseLab databases for the last two
weeks, so I might be able to shed some light on this issue. The
discussion thread seems to have become a bit off-topic, as the
original question was the way ELECTRICAL CURRENTS should be
represented in BFO. Indeed, the SenseLab / NeuronDB ontology makes
statements about the CURRENTS that can be observed over the membrane
of certain neurons and NOT their conductance / electrical resistance.

I have already made a preliminary mapping of the SenseLab / NeuronDB
ontology to BFO (not official and not available for download at this
moment) and I found it quite intuitive to represent electrical
currents (the movement of electrons, in this case through a neuronal
membrane) as a processual entity -- and therefore as an occurent.

The current official version of NeuronDB might be a bit misleading,
because it classifies the currents of a neuron under "neuron
property". It does the same with neuroreceptors and neurotransmitters,
which would of course best be described as physical entities.
Therefore, I think we will remove the "neuron property" class
eventually.

-- Matthias Samwald

William Bug

unread,
Apr 17, 2007, 1:59:23 PM4/17/07
to bfo-d...@googlegroups.com, Matthias Samwald
Please correct me if I'm wrong, Matthias, but I believe the models (in the NeuronDB database - not the ontology) actually model conductance.  The neuronal compartment models are dealing with time- & voltage-dependent conductance in the micro- to nano- Seimen range, whereas the molecular models of ion channel mechanics model conductance in the pico to femto- Siemen range.

If the current (no pun intended) NeuronDB ontology represents the occurent ("conduction"), how is that related to the model parameters as specified in the NeuronDB database - which I presume is somehow represented as instance data in the OWL file.

Cheers,
Bill

Phillip Lord

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Apr 17, 2007, 2:22:35 PM4/17/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> No. I will try to repeat myself in a different way.
>>
>> The relationship between conductance and conductor, and the
>> relationship between conductance and the thing conducted is
>> equivalent.

PG> This claim just sounds absurd to me.

PG> Earlier you spoke of abilities being inverse or the same.

PG> In both cases, you seem to think about properties in the way we
PG> speak about numerical relations or functions.

Again, not really. The values of a property might be specifiable by a
function. The equivalence which I speak of here is that conductance
depends on two things (comprising one system).

>> It makes no sense to me to see what is the primary relationship,
>> so it makes no to say conductance inheres in one and not the
>> other.

PG> you are forgetting that ions too have a correlated property
PG> which makes me fail to grasp the sense of trying to find "the
PG> primary relationship"

I agree it makes no sense. There is no primary
relationship. Conductance is not a property of either thing.


PG> Well, if conductance is the property of a conductor, it should
PG> be easy to figure out which is which, conductors do not travel
PG> through ions, say?
>>
>> If conductance is the property of a conductor then you have
>> already defined that it inheres in the conductor, so you can't
>> use this to derive where the property inheres.

PG> really, why would I have to derive anything here? is it in order
PG> to convince you?


On what grounds do you state that a property inheres in a specific
entity. Seems to me to be a useful question.

PG> so for you the phrase "the conductor-conductee system" refers to
PG> two things and not one? that is very odd isn't it?
>>
>> conductor-conductee system refers to one system made out of two
>> things.

PG> OK, which are these things?

The conductor and conductee.


>> Conductance depends equally on the two things (which we can
>> consider to be one system).

PG> There is nothing to consider. Either there is a system or there
PG> are two things.

It makes sense to talk about the mass of membrane and mass of some
ions independently, but not conductance. So there are two things and
there is a system.


PG> What I said earlier was something to the effect that you could
PG> say that conductance is a property of the system if a system is
PG> not merely the plurality of its constituents.

PG> Why do you need speaking of systems if systems are really
PG> fictions which we produce when we consider two things as one?

To describe conductance I thought.

Phil

Phillip Lord

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Apr 17, 2007, 2:23:38 PM4/17/07
to bfo-d...@googlegroups.com
>>>>> "MS" == Matthias Samwald <sam...@gmx.at> writes:

MS> On Apr 16, 2:54 pm, Phillip Lord <phillip.l...@newcastle.ac.uk> wrote:
>> I believe that neuroweb is talking about conductance, not
>> conduction. It's not the movement of charge that is being talked
>> about, but the relationship between voltage and resultant
>> current.

MS> Incorrect, the Senselab ontology really IS talking about actual
MS> currents ('conduction'), and not conductance.

That's a pity. We wasted a lot of good bandwidth for nothing.

Phil

Matthias Samwald

unread,
Apr 17, 2007, 4:11:03 PM4/17/07
to BFO Discuss
> MS> Incorrect, the Senselab ontology really IS talking about actual
> MS> currents ('conduction'), and not conductance.
>
> That's a pity. We wasted a lot of good bandwidth for nothing.

Oh, I find the discussion about conductance quite important, even
though it does not apply to the NeuronDB ontology. The problems we
have with getting a grip of the phenomenon "conductance" in BFO will
probably also appear for many other biological systems.

Anyways, I would see conductance as a quality of a certain entity, IN
RELATION to several other entities (e.g. certain ions, the temperature
of the object and its surroundings). Does BFO offer a possibility to
describe qualities of an entity in relation to other entities? I know
that the PATO ontology does.

Matthew Pocock

unread,
Apr 17, 2007, 4:51:19 PM4/17/07
to Pierre Grenon, bfo-d...@googlegroups.com
On Tuesday 17 April 2007, Pierre Grenon wrote:
> On 4/17/07, Matthew Pocock <matthew...@ncl.ac.uk> wrote:
> > Perhaps this is sufficient. What would the relationship be between water
> > (the substance) and water (a mass of molecules)?
>
> I seem to recall BFO doesn't make that distinction

OK. Ever mindfull that it's vastly easier to criticise an ontology than to
constructively contribute to it, is this a distinction that BFO
phylosophicaly belives in, and if so, how can we introduce the concepts
and/or relations to formalize this?

> I would suggest you look at the OpenCyc ontology
>
> in particluar, look for
>
> ObjectType
> (unfortunately, there is no link to StuffType which might have been
> helpful) ExistingObjectType
> ExistingStuffType
> granuleOfSpatialStuff
>
> here http://www.cyc.com/cycdoc/vocab/top-vocab.html
>
> look also for "stuff" and "substance" related things
> here http://www.cyc.com/cycdoc/vocab/chemistry-vocab.html
> and maybe
> here http://www.cyc.com/cycdoc/vocab/composition-vocab.html

Thanks. Hours of fun :)

Matthew

>
> pierre
>
> > Matthew


Pierre Grenon

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Apr 17, 2007, 5:26:48 PM4/17/07
to bfo-d...@googlegroups.com

Yes BFO does, that is precisely what BFO does indeed.

Pierre Grenon

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Apr 17, 2007, 5:38:23 PM4/17/07
to Matthew Pocock, bfo-d...@googlegroups.com
On 4/17/07, Matthew Pocock <matthew...@ncl.ac.uk> wrote:
> On Tuesday 17 April 2007, Pierre Grenon wrote:
> > On 4/17/07, Matthew Pocock <matthew...@ncl.ac.uk> wrote:
> > > Perhaps this is sufficient. What would the relationship be between water
> > > (the substance) and water (a mass of molecules)?
> >
> > I seem to recall BFO doesn't make that distinction
>
> OK. Ever mindfull that it's vastly easier to criticise an ontology than to
> constructively contribute to it, is this a distinction that BFO
> phylosophicaly belives in, and if so, how can we introduce the concepts
> and/or relations to formalize this?

Watch out, BFO is not yet capable of believing...

That is a distinction which is ignored, I believe, on purpose and
there is thus no drive to introduce it. I think the sort of issues you
would be looking at are adressed in BFO with the object/aggregate
distinction. To my understand the distinction is at bottom linguistic
junk. Cyc's treatment is a case of an ontology coping interestingly
with it however.

pierre

Pierre Grenon

unread,
Apr 17, 2007, 5:51:04 PM4/17/07
to bfo-d...@googlegroups.com
On 4/17/07, Matthias Samwald <sam...@gmx.at> wrote:
>
> Hello,
>
> I have a background in cellular electrophysiology and have been
> working on the OWL versions for SenseLab databases for the last two
> weeks, so I might be able to shed some light on this issue. The
> discussion thread seems to have become a bit off-topic, as the
> original question was the way ELECTRICAL CURRENTS should be
> represented in BFO. Indeed, the SenseLab / NeuronDB ontology makes
> statements about the CURRENTS that can be observed over the membrane
> of certain neurons and NOT their conductance / electrical resistance.
>
> I have already made a preliminary mapping of the SenseLab / NeuronDB
> ontology to BFO (not official and not available for download at this
> moment)

would you mind sending it to the list? this only might be more helpful
than the ontology itself which is a bit hard to make sense of
considering there are only labels which are not particularly
suggestive

> and I found it quite intuitive to represent electrical
> currents (the movement of electrons, in this case through a neuronal
> membrane) as a processual entity -- and therefore as an occurent.

good move, at least intuitively there is an occurrent which should
play a central role in the representation, whether it should be called
'current' I don't know

> The current official version of NeuronDB might be a bit misleading,
> because it classifies the currents of a neuron under "neuron
> property". It does the same with neuroreceptors and neurotransmitters,
> which would of course best be described as physical entities.
> Therefore, I think we will remove the "neuron property" class
> eventually.

I started earlier another thread as a reply to Alan's original query
after looking at the ontology in question. The neuron_property class
seems indeed to be a bag of wonder in which fall parts of neurons and
possibly some genuine, but few conparatively to what is in there,
properties (bfo:dependent:continuant), it would be a bit worrying to
have occurrents in addition

would you follow up on that mail? would you add to your reply your
mapping to BFO?

pierre

> -- Matthias Samwald
>
>
> >
>

Matthew Pocock

unread,
Apr 17, 2007, 5:57:15 PM4/17/07
to Pierre Grenon, bfo-d...@googlegroups.com
On Tuesday 17 April 2007, Pierre Grenon wrote:
> On 4/17/07, Matthew Pocock <matthew...@ncl.ac.uk> wrote:
> > On Tuesday 17 April 2007, Pierre Grenon wrote:
> > > On 4/17/07, Matthew Pocock <matthew...@ncl.ac.uk> wrote:
> > > > Perhaps this is sufficient. What would the relationship be between
> > > > water (the substance) and water (a mass of molecules)?
> > >
> > > I seem to recall BFO doesn't make that distinction
> >
> > OK. Ever mindfull that it's vastly easier to criticise an ontology than
> > to constructively contribute to it, is this a distinction that BFO
> > phylosophicaly belives in, and if so, how can we introduce the concepts
> > and/or relations to formalize this?
>
> Watch out, BFO is not yet capable of believing...

Perhaps should have asked if the philosophy motivting BFO supports the notion
of, rather than BFO believes in :)

>
> That is a distinction which is ignored, I believe, on purpose and
> there is thus no drive to introduce it. I think the sort of issues you
> would be looking at are adressed in BFO with the object/aggregate
> distinction. To my understand the distinction is at bottom linguistic
> junk. Cyc's treatment is a case of an ontology coping interestingly
> with it however.
>
> pierre

I feel a bit like a dog with a bone, but... what sort of relation do I use to
associate the object with the 'equivalent' aggregate? There are clearly
things I would want to say about the 'object view' that are not applicable to
the 'aggregate view' and vica-versa, so stating that they are the same
individual/particular is not very usefull, and is likely to trigger some
nasty disjoint-class reasoner problem. However, equally obviously, it is both
usefull and correct to state that the 'object view' and 'aggregate view' of
an enty where these are relevant are of the same entity.

Either directly associating one with the other (object-view-of-x
is_object_version_of_aggregate aggregate-view-of-x) or associating both as
descriptions of an underlying 'real' thing (object-view-of-x
is_description_of something; aggregate-view-of-x is_description_of something)
work for me, in a 'getting things down explicity' sort of a way.

Are either or both of these mechanisms contra to the philosphy that motivates
BFO? Or is the entire requrement not within scope?

Matthew

Matthew Pocock

unread,
Apr 17, 2007, 6:03:39 PM4/17/07
to bfo-d...@googlegroups.com, Phillip Lord
We seem to be playing conceptual ping-pong here. Can I be permitted to state
how this could be conceptualised in a way that may possibly be mutually
acceptable to the involved parties?

Any good theory starts of by assuming some stuff. Let's assume that there
realy are things in the 'real' physical world that we would find usefull to
label as conductors and conductees. Let's also assume that their behaviors
are in accordance with how the physical world interacts with itself which we
could call the 'lores of physics'. I am not sure in this case that we can
usefully assume much more about the 'real' world than this.

From this, we can posit that:

* There is a a relation that associates the pair (conductor,conductee) with a
conductance, in accordance with the 'lores of physics'. This is
the 'restriction' of the entailment of the 'lores of physics' to just those
truths relevant to conductors, conductees and conductance.

* The contribution of the conductor (conductee) to this relation has its basis
in the 'real world' properties of the conductor (conductee), as well as
the 'real world' properties of any other relevant entities (perhaps thermal
properties?). If these 'real world' properties where different, then the
relation associating (conductor,conductee) and conductance would be
different.

* If we pick a particular conductee (nominal quantification? e.g.
pick 'electron') then we can identify a sub-relation of the conductance
relation that is the 'restriction' of the relation along these lines. This is
clearly a sub-relation of the original, but is less descriptive of the
system, and captures a strictly smaller part of the 'lores of physics'. If we
then 'project' these relations to discard the non-changing filler (e.g.
electron) and fold this filler into the name of the property then we can
enumerate properties like 'the degree to which it can conduct
electrons", "the degree to which it can conduct sodium ions" and so on. This
is all very lambda in flavor.

* We can do the same thing for conductee, restricting the conductor.

* These projections are in some senses identified with (or perhaps better,
arise from) the 'real world' properties of the conductor (conductee) that
provide the basis for their contribution to conductance. However, they are
not identical with this contribution. As a (potentially happy) side effect,
we have removed all possibility of variation in the other relevant variables,
we have made them eligable for consideration as qualities that inheere in a
single thing.

I would argue that in eliding out the conductee in the case of something
like "conductance of electrons", we loose some degree of understanding about
the 'real world' basis for these qualities. We place an additional layer of
indirection between the 'real world' basis for conductance and the things we
are describing as qualities. If we go too far down this road, then we pass
some point where we cease to be primarily modelling the 'real world' and
start primarily modelling our investigative interests and biases. What I mean
is, at some point somebody interpreting our ontology will gain more
understanding about us and our viewpoint than about the real world we claim
to be decribing. However, going some small way down this road may make
understanding easier, and allow us to conceive of experiments or systems that
rely upon a carefully restricted part of the 'lores of physics'. Such an
example would be silicon-based semi-conductors of electrons.

Now, in all of this, I leave utterly open such questions of if the 'lores of
physics' are mathematical in nature, are processes involving objects, can
ever be known, exist as a single 'objective reality' or as a multi-verse or
structured possibility-tree and so on. I also do not address the basis for or
conceptualisation of the 'real properties' of the conductor (conductee) that
give rise to their contribution conductance, be it pipes and balls,
electrostatics, quantum stuff, pixies with fairy dust-lupricated stars. I'm
not sure making choices like this are actually required or helpful at this
stage. I think all of my points stand regardless of these choices.

Matthew

Pierre Grenon

unread,
Apr 17, 2007, 6:11:36 PM4/17/07
to bfo-d...@googlegroups.com
> On what grounds do you state that a property inheres in a specific
> entity. Seems to me to be a useful question.

i still don't understand useful in what capacity preisely, but nevermind

I can't think of anything more primitive and elementary than a
property being a property of the entity it is a property of

> >> conductor-conductee system refers to one system made out of two
> >> things.
>
> PG> OK, which are these things?
>
> The conductor and conductee.

what is the conductee?

>
> >> Conductance depends equally on the two things (which we can
> >> consider to be one system).
>
> PG> There is nothing to consider. Either there is a system or there
> PG> are two things.
>
> It makes sense to talk about the mass of membrane and mass of some
> ions independently, but not conductance. So there are two things and
> there is a system.

The point is the system is another entity than its members

Is what follows an accurate picture of your view?

There are four things:

A a membrane
B a bunch of ions
C a system made of the membrane A and the bunch of ions B
D the conductance of [please fill in]

D is a property of C
D is not a property of A
D is not a property of B
D is dependent on A
D is dependent on B

Is D dependent on C?

Suppose E is a bunch of you of the same type as B

There are now in addition to A, B, C, and D these entities:

F a system made of membrane A and the bunch of ions E
G the conductance of [please fill in again]

G is a property of F
G is not a property of A
G is not a property of E
G is dependent on A
G is dependent on E

D and G are [please fill in]

>
> PG> What I said earlier was something to the effect that you could
> PG> say that conductance is a property of the system if a system is
> PG> not merely the plurality of its constituents.
>
> PG> Why do you need speaking of systems if systems are really
> PG> fictions which we produce when we consider two things as one?
>
> To describe conductance I thought.

You are telling that you introduce a fictional entity in order to
describe the property of a fictional entity?

> Phil
>

Pierre Grenon

unread,
Apr 17, 2007, 6:40:08 PM4/17/07
to Matthew Pocock, bfo-d...@googlegroups.com
> > Watch out, BFO is not yet capable of believing...
>
> Perhaps should have asked if the philosophy motivting BFO supports the notion
> of, rather than BFO believes in :)

yeah, but then no joke..

what you are describing below seems to be closer to cross granular
parthood (don't think there's anything big behind this)

it is conceptually embedded in BFO to allow for going from one level
of granularity to the other, there have been talks of how to do this
and various suggestions of what it would be a bit exagerated to call a
'mechanism', but to my knowledge there is nothing of extreme maturity
which deals with this

Barry and Thomas Bittner's work on granular partition might contain
the most suggestive elements

> I feel a bit like a dog with a bone, but... what sort of relation do I use to
> associate the object with the 'equivalent' aggregate? There are clearly
> things I would want to say about the 'object view' that are not applicable to
> the 'aggregate view' and vica-versa, so stating that they are the same
> individual/particular is not very usefull, and is likely to trigger some
> nasty disjoint-class reasoner problem. However, equally obviously, it is both
> usefull and correct to state that the 'object view' and 'aggregate view' of
> an enty where these are relevant are of the same entity.

i'd say this would involve making granularity levels explicit and have
a mechanism which allow to index or parameterize categorization to
levels, the logic would have to be a bit different or you would have
to use what we've introduced as meta ontological language (talking of
ontologies)

there should be a discussion on this list of things like that
regarding molecule I seem to recall

> Either directly associating one with the other (object-view-of-x
> is_object_version_of_aggregate aggregate-view-of-x) or associating both as
> descriptions of an underlying 'real' thing (object-view-of-x
> is_description_of something; aggregate-view-of-x is_description_of something)
> work for me, in a 'getting things down explicity' sort of a way.

it's possible x could fall under another category as well, would you
talk of part-view-of-x, say?

i think if you did things like that it would be closer to BFO to link
directly x at different levels of granularity

the link to 'something' could win you the terrible 'Kantian' name calling

> Are either or both of these mechanisms contra to the philosphy that motivates
> BFO? Or is the entire requrement not within scope?

no i think the idea of linking levels is definitely something that BFO expects

pierre

> Matthew
>

Matthew Pocock

unread,
Apr 17, 2007, 7:42:53 PM4/17/07
to Pierre Grenon, bfo-d...@googlegroups.com
On Tuesday 17 April 2007, Pierre Grenon wrote:
> the link to 'something' could win you the terrible 'Kantian' name calling

> pierre

I'm not sure I'd go as far a Kant in saying that we can't know the 'thing in
itself', but I'd certainly agree that in practice we are nearly always
talking of phenomenal things, especially in experimental sciences. The trick
(or our intent?) is to infer something about the things from the phenomenal,
and to state both of these without conflation where we can. The very fact
that perfectly good models of the 'same' bit of reality account for both
similar and different phenomena would seem to support this position e.g.
newtonian mechanics, relativity, qm account quite well for multiple phenomena
arrising from (presumably) the same basis in reality. After all, newtonian
mass is a very different beast to relativity's rest mass or to relativistic
mass, although I presume (but don't know for sure) that they both relate in
some way to the same part of physical reality that underlies the massyness of
things.

Matthew

Alan Ruttenberg

unread,
Apr 17, 2007, 8:35:20 PM4/17/07
to bfo-d...@googlegroups.com, Matthias Samwald
Might be worth looking at this to get closer to what NeuronDB is
talking about.

http://senselab.med.yale.edu/senselab/NeuronDB/ndbRegions.asp?sr=2

On Apr 17, 2007, at 1:20 PM, Matthias Samwald wrote:

William Bug

unread,
Apr 17, 2007, 8:54:53 PM4/17/07
to bfo-d...@googlegroups.com, Matthias Samwald
Good point, Alan.  The discussion should have started with reference to this page.

However, here too there is the lack of distinction between continuant & occurent.

There is no doubt the evidence from the literature used by SenseLab curators to construct the data repository is focussed mostly on ion currents - using physiological techniques to measure currents at both the cellular and molecular (single-channel) level (for some of the receptors & transmitters - they measure membrane voltage).

However, the statement at the top of this page mentions "membrane channels" - clearly continuants.  Click on that link and you are presented with a thorough listing (based on the IUPHAR ion channel classification scheme - http://www.ebi.ac.uk/iuphar-ic/ionChannel.html) of the related continuants.

More and more, I'm thinking bfo:function may best capture the underlying evidence in NeuronDB, while also providing a link to the relevant continuants, which clearly we all hope to be able to link into (genes, transcripts, macro-molecular receptor & channel complexes - hopefully pathways, too - e.g., transmitter metabolism and 2nd messenger systems (for G-protein Coupled Receptors)).  Those continuants are all very important to link to in the context of using information such as NeuronDB and BrainPharm in the context of neurological disease informatics.

Cheers,
Bill

On Apr 17, 2007, at 8:35 PM, Alan Ruttenberg wrote:

http://senselab.med.yale.edu/senselab/NeuronDB/ndbRegions.asp?sr=2


Chris Mungall

unread,
Apr 17, 2007, 10:39:00 PM4/17/07
to bfo-d...@googlegroups.com, Georgios V. Gkoutos (Genetics)

definitely not.. I think this discussion will help us improve the
"conductance" sub-hierarchy in PATO (which is currently named and
defined as if it were the process, conduction, which I think should
be changed).

>
> Phil
>
> >
>

Ingvar Johansson

unread,
Apr 18, 2007, 3:57:13 AM4/18/07
to bfo-d...@googlegroups.com
Phillip Lord schrieb:

>>>>>> "IJ" == Ingvar Johansson <ingvar.j...@ifomis.uni-saarland.de> writes:
>>>>>>
>
>
> IJ> The fact that there is a *relational* and *dispositional
> IJ> description* of a property of certain resistor T is quite
> IJ> consistent with the fact *what is described* inheres in
> IJ> T.
>
> I'm afraid this paragraph doesn't mean anything to me.
>
A new brief attempt then, but with another example. When I am saying
that I am 1,75 m tall, I am describing a property (length) that
*inheres* in me. Nonetheless I am using a *relational description* in
order to denote this length of mine; I am relating my length to the
standard unit for lengths.

> IJ> Here is a possible dispositional description:
>
> IJ> "if an electric current (a stream of electrons) passes through
> IJ> T, then T makes resistance (of 200 ohm)".
>
> An electric current is not a stream of electrons.
Come on! I adopted my example to your words. You wrote: "a 200ohm
resistor has 200 ohm resistance *to electrons*".

> It's one way of
> making a current. Conductance is defined for current not electrons.
>
> IJ> But this can be regarded as being due to the microstructure of T
> IJ> that is a property of T only.
>
> I think not. It's a property of the microstructure of T, the
> nature of an electron, and how the two interact.
The point you miss is that (in relation to my example above) by means of
a relational description one can describe *both* a property inhering in
an object (my lenght inheres in me) *and* the relation between this
property and another property (I am 1.75 times the standard meter).
Similarly, by means of a dispositional description one can describe
*both* a property inhering in an object (a *capacity* to transmit, with
a certain resistance, electric current) *and* the relation between this
property/capacity and other entities (electric currents) with which the
capacity interacts.

Ingvar
>
>
> Phil
>
> >


--
Ingvar Johansson
IFOMIS, Saarland University
home site: http://ifomis.org/
personal home site:
http://hem.passagen.se/ijohansson/index.html


Phillip Lord

unread,
Apr 18, 2007, 8:45:12 AM4/18/07
to bfo-d...@googlegroups.com

>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> On what grounds do you state that a property inheres in a
>> specific entity. Seems to me to be a useful question.

PG> I can't think of anything more primitive and elementary than a
PG> property being a property of the entity it is a property of

Okay.


>> >> conductor-conductee system refers to one system made out of
>> >> two things.
>>
PG> OK, which are these things?
>>
>> The conductor and conductee.

PG> what is the conductee?

The ions or electrons. You know this, so I am presumably missing
something in your question.


>> It makes sense to talk about the mass of membrane and mass of
>> some ions independently, but not conductance. So there are two
>> things and there is a system.

PG> The point is the system is another entity than its members

PG> Is what follows an accurate picture of your view?


A a membrane
B a bunch of ions
C a system made of the membrane A and the bunch of ions B

D the conductance of [A in this case]

D is a property of C
D is not a property of A
D is not a property of B
D is dependent on A
D is dependent on B

Is D dependent on C? Yes.

F a system made of membrane A and the bunch of ions E

G the conductance of [F in this case]

G is a property of F
G is not a property of A
G is not a property of E
G is dependent on A
G is dependent on E

D and G are [please fill in -- again I don't know what you are after
here. They are ions, a collection of things, charged...and so on]

PG> What I said earlier was something to the effect that you could
PG> say that conductance is a property of the system if a system is
PG> not merely the plurality of its constituents.
>>
PG> Why do you need speaking of systems if systems are really
PG> fictions which we produce when we consider two things as one?
>>
>> To describe conductance I thought.

PG> You are telling that you introduce a fictional entity in order
PG> to describe the property of a fictional entity?

You bought in the notion of fictional entities. I am suggesting that
we need to be able to describe a system, which is actually a set of
things considered together as a coherent entity. Is this fictional?
Not something I am worried about.

The idea that you can sometimes consider several things at once as one
thing seems straight forward enough though. A membrane is after all a
collection of different things put together, which considered together
have some properties.

Again maybe I am missing your point.

Phil

Phillip Lord

unread,
Apr 18, 2007, 9:07:05 AM4/18/07
to bfo-d...@googlegroups.com

>>>>> "IJ" == Ingvar Johansson <ingvar.j...@ifomis.uni-saarland.de> writes:

IJ> The fact that there is a *relational* and *dispositional
IJ> description* of a property of certain resistor T is quite
IJ> consistent with the fact *what is described* inheres in
IJ> T.
>>
>> I'm afraid this paragraph doesn't mean anything to me.
>>

IJ> A new brief attempt then, but with another example. When I am
IJ> saying that I am 1,75 m tall, I am describing a property
IJ> (length) that *inheres* in me. Nonetheless I am using a
IJ> *relational description* in order to denote this length of mine;
IJ> I am relating my length to the standard unit for lengths.


Yes, but that is not the case here. For a length, the existence of the
length is independent of the unit of measure, although clearly the
value of the length is not.

On the other hand, it might also be possible to ask whether you are
taller or shorter than me. This depends on me as much as it depends on
you. You might also ask whether you are taller or shorter than
average. This, of course, depends on everybody.

Perhaps not a good analogy, but conductance is of the latter form. I
can demonstrate this. Given your height in metres, I can work out your
height in feet and inches, hands or cubits or any other unit. All I
need to have done is compare one unit with the other, and I can do
this independent of the measure of you.

On the other hand, if I plug you into the mains, and measure your
resistance to electrons, it tells me nothing at all about how you will
behave if I immerse you in brine and try and conduct chloride and
sodium ions though you.

Of course, we still need a relational description to describe the
system -- that we measure the resistance in ohms rather than any other
measure.


IJ> is a possible dispositional description:


>>
IJ> "if an electric current (a stream of electrons) passes through
IJ> T, then T makes resistance (of 200 ohm)".
>>
>> An electric current is not a stream of electrons.

IJ> Come on! I adopted my example to your words. You wrote: "a
IJ> 200ohm resistor has 200 ohm resistance *to electrons*".

If you read the example back you will see that the point of the
example was to describe a simplification. The point is simple -- for
an electrical component the only conductee you are going to be
interested in is an electron. The usage of the entity means that this
is intuitive simplification. For a membrane, it's ions you are going
to be interested in, but what kind of ion?


>> It's one way of making a current. Conductance is defined for
>> current not electrons.
>>
IJ> But this can be regarded as being due to the microstructure of T
IJ> that is a property of T only.
>>
>> I think not. It's a property of the microstructure of T, the
>> nature of an electron, and how the two interact.

IJ> The point you miss is that (in relation to my example above) by
IJ> means of a relational description one can describe *both* a
IJ> property inhering in an object (my lenght inheres in me) *and*
IJ> the relation between this property and another property

I think I have already explained why this is not relevant in this
case.

Phil

Pierre Grenon

unread,
Apr 18, 2007, 9:24:45 AM4/18/07
to bfo-d...@googlegroups.com
> >> >> conductor-conductee system refers to one system made out of
> >> >> two things.
> >>
> PG> OK, which are these things?
> >>
> >> The conductor and conductee.
>
> PG> what is the conductee?
>
> The ions or electrons. You know this, so I am presumably missing
> something in your question.

the question is whether its all electrons in the world or some only,
or something else, is it always the same, can this change, etc

this is the sense of the questions below


> A a membrane
> B a bunch of ions
> C a system made of the membrane A and the bunch of ions B
> D the conductance of [A in this case]

we will need another round of clarification, are you sure you mean A
(the membrane) and not C (the system) ?

> D is a property of C
> D is not a property of A
> D is not a property of B
> D is dependent on A
> D is dependent on B
>
> Is D dependent on C? Yes.
>
>
>
> F a system made of membrane A and the bunch of ions E
> G the conductance of [F in this case]

why not A?

> G is a property of F
> G is not a property of A
> G is not a property of E
> G is dependent on A
> G is dependent on E
>
> D and G are [please fill in -- again I don't know what you are after
> here. They are ions, a collection of things, charged...and so on]

D and G are conductances, respectively of A (the membrane) and F (the
system made of A and E a bunch of ions, say)

Here you need saying what is the relation between D and G

But first you need to confirm your other answers, please

D is the conductance of [?]
G is the conductance of [?]
D and G are [?]


>
> PG> What I said earlier was something to the effect that you could
> PG> say that conductance is a property of the system if a system is
> PG> not merely the plurality of its constituents.

> Again maybe I am missing your point.

The point is that you are not clear when you say that there is a
system made of two elements wether in terms of entities whic exist we
are in situation 1 or 2 below:

situation 1: there are two entities
Element-1
Element-2

situation 2: there are three entities
Element-1
Element-2
System

If conductance is a property of a system then we need to agree that we
are looking at situation 2 (fine, a system is a bfo:aggregate if you
want then), but I can't elicit from your talk of "two things as one
but two things and not one" whether you even agree to this.

pierre

Phillip Lord

unread,
Apr 18, 2007, 11:35:22 AM4/18/07
to bfo-d...@googlegroups.com

>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> what is the conductee?
>>
>> The ions or electrons. You know this, so I am presumably missing
>> something in your question.

PG> the question is whether its all electrons in the world or some
PG> only, or something else, is it always the same, can this change,
PG> etc

Well it's any electrons (or of the same type of ions). This stems from
the fact that all electrons (or all ions of one type) are exactly
alike. This is not true, of course, of membranes but it is still a
useful abstraction.

So, for example, you can talk about the conductance of the squid giant
axon membrane (in general) or about the conductance of this specific
giant axon membrane but only with respect to the type of sodium ions,
rather than these specific ions.

Now this isn't true of all circumstances which appear to be
analogous. For example, take a copper pipe and water. We could measure
the resistance of a specific pipe or pipes in general, as the
manufacture of copper pipes is such that each pipe is alike. Water is
not alike however. Water from Newcastle is soft for instance and
contains different things than water from anywhere else (real world
water, not pure H20). So, we might refer to the specific water.

>> A a membrane B a bunch of ions C a system made of the membrane A
>> and the bunch of ions B D the conductance of [A in this case]

PG> we will need another round of clarification, are you sure you
PG> mean A (the membrane) and not C (the system) ?

Sorry, made a mistake. I mean C, yes.


>> F a system made of membrane A and the bunch of ions E G the
>> conductance of [F in this case]

PG> why not A?

Cause "A" was a mistake:-)


PG> But first you need to confirm your other answers, please

PG> D is the conductance of [?] G is the conductance of [?] D and
PG> G are [?]

Again, sorry for the mistake.

>> Again maybe I am missing your point.

PG> The point is that you are not clear when you say that there is a
PG> system made of two elements wether in terms of entities whic
PG> exist we are in situation 1 or 2 below:

PG> situation 1: there are two entities Element-1 Element-2

PG> situation 2: there are three entities Element-1 Element-2 System

PG> If conductance is a property of a system then we need to agree
PG> that we are looking at situation 2 (fine, a system is a
PG> bfo:aggregate if you want then), but I can't elicit from your
PG> talk of "two things as one but two things and not one" whether
PG> you even agree to this.


Okay. Well, I don't know, is the answer. I am not sure what you mean
by "exist". Clearly from the point of view of describing conductance
we need to have the notion of the two things (conductor, conductee)
considered together.

But I am not sure that I can distinguish your two situations. I mean
if there are three entities existing, then there are also two existing
as well. So I would say that both situations are true.

Phil

Pierre Grenon

unread,
Apr 18, 2007, 12:14:19 PM4/18/07
to bfo-d...@googlegroups.com
On 4/18/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>
>
> >>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:
>
> PG> what is the conductee?
> >>
> >> The ions or electrons. You know this, so I am presumably missing
> >> something in your question.
>
> PG> the question is whether its all electrons in the world or some
> PG> only, or something else, is it always the same, can this change,
> PG> etc
>
> Well it's any electrons (or of the same type of ions). This stems from
> the fact that all electrons (or all ions of one type) are exactly
> alike. This is not true, of course, of membranes but it is still a
> useful abstraction.
>
> So, for example, you can talk about the conductance of the squid giant
> axon membrane (in general) or about the conductance of this specific
> giant axon membrane but only with respect to the type of sodium ions,
> rather than these specific ions.
>
> Now this isn't true of all circumstances which appear to be
> analogous. For example, take a copper pipe and water. We could measure
> the resistance of a specific pipe or pipes in general, as the
> manufacture of copper pipes is such that each pipe is alike. Water is
> not alike however. Water from Newcastle is soft for instance and
> contains different things than water from anywhere else (real world
> water, not pure H20). So, we might refer to the specific water.
>

ok with all of this, but that's not my question, I am asking you to
tell me what exactly is this conductee that the conductance depends on
and which forms a system with the membrane in which (the system) you
say conductance inheres

the conductance with respect to sodium ions of a particular squid
giant axon membrane, the one on your table, is dependent on sodium
ions? all ions? some ions? the answer depends on the time at which I
ask the question? do we have to look at the membrane to figure out
which sodium ions are involved? is there an entity which is the type
sodium ion on which the conductance in question depends? if there were
no sodium ions in the world would the conductance exist?

the questions below are still intended to help in discussion these questions

> PG> D is the conductance of [?] G is the conductance of [?] D and
> PG> G are [?]
>
> Again, sorry for the mistake.

No proble, but you left a blank:

D is the conductance of C
G is the conductance of F


D and G are [?]

> >> Again maybe I am missing your point.


>
> PG> The point is that you are not clear when you say that there is a
> PG> system made of two elements wether in terms of entities whic
> PG> exist we are in situation 1 or 2 below:
>
> PG> situation 1: there are two entities Element-1 Element-2
>
> PG> situation 2: there are three entities Element-1 Element-2 System
>
> PG> If conductance is a property of a system then we need to agree
> PG> that we are looking at situation 2 (fine, a system is a
> PG> bfo:aggregate if you want then), but I can't elicit from your
> PG> talk of "two things as one but two things and not one" whether
> PG> you even agree to this.
>
>
> Okay. Well, I don't know, is the answer. I am not sure what you mean
> by "exist".

I don't know what to tell you, I mean it is an entity, it falls
somewhere in the ontology

in this case I also mean it is not something I dream or fancy is there
while believing that it's not really there...

> Clearly from the point of view of describing conductance
> we need to have the notion of the two things (conductor, conductee)
> considered together.
>
> But I am not sure that I can distinguish your two situations. I mean
> if there are three entities existing, then there are also two existing
> as well. So I would say that both situations are true.


Rename in the above:

Element-1 -> E1
Element-2 -> E2
System -> S

Surely, if like in situation 2, E1, E2 and S exist, then E1 and E2
exist. But this doesn't mean that situation 1 is included in situation
2.

Situation 1 is such that E1 and E2 only exist, S does not exist in situation 1.

Situation 2 is such that E1 and E2 exist, And in addition S exists.
E1, E2 and S are distinct entities.

Suppose you have a bag of candies.
Situation 1: you have (no more no less than) 2 candies
Situation 2: you have no more no less than 3 candies.

Don't tell me the example is not analogous because the tird candy is
not a system...

Do you see what I mean?

It needs to be the case that if conductance is the property of a
system that the system is an entity in its own rights on top of its
elements.

In other words, if D is the conductance of C, then C is an exists

Agreed?

pierre

> Phil
>
> >
>

Phillip Lord

unread,
Apr 19, 2007, 5:50:49 AM4/19/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> ok with all of this, but that's not my question, I am asking you
PG> to tell me what exactly is this conductee that the conductance
PG> depends on and which forms a system with the membrane in which
PG> (the system) you say conductance inheres

PG> the conductance with respect to sodium ions of a particular
PG> squid giant axon membrane, the one on your table, is dependent
PG> on sodium ions? all ions? some ions? the answer depends on the
PG> time at which I ask the question? do we have to look at the
PG> membrane to figure out which sodium ions are involved? is there
PG> an entity which is the type sodium ion on which the conductance
PG> in question depends? if there were no sodium ions in the world
PG> would the conductance exist?


As I have said, there is no "some" sodium ions. All sodium ions are
alike, and we can't distinguish them.

So is conductance dependant on

sodium ions -- yes

all ions -- all measures of conductance would be yes, but you can
measure some of the values of conductance without measuring all of
them.

time -- to my knowledge, no.

do we have to look at the membrane -- which sodium ions has little
meaning as all are alike.

it there an entity -- I don't know, not sure what you mean by
entity in this context, but perhaps yes.

if there were no sodium ions -- no, not with respect to sodium ions,
but yes with respect to other entities bearing of charge.


PG> No proble, but you left a blank:

PG> D is the conductance of C G is the conductance of F D and G are
PG> [?]

Oh, thought I answered that one. Don't know, as I am not sure what you
are asking. They are conductances.

>>
>> Okay. Well, I don't know, is the answer. I am not sure what you
>> mean by "exist".

PG> I don't know what to tell you, I mean it is an entity, it falls
PG> somewhere in the ontology

Not sure this is what you meant to say. Yes, it will become an entity
if you put it in the ontology.

PG> in this case I also mean it is not something I dream or fancy is
PG> there while believing that it's not really there...

Well conductance is a thing that we can attach a particular kind of
value to. It derives from other things that we could potentially also
place a value on, although we probably don't know how to the
derivation, nor measure these other things.

PG> Suppose you have a bag of candies. Situation 1: you have (no
PG> more no less than) 2 candies Situation 2: you have no more no
PG> less than 3 candies.

PG> Don't tell me the example is not analogous because the tird
PG> candy is not a system...

Thanks for the clarification. I am afraid that I don't have any choice
but to tell you this.

PG> Do you see what I mean?

PG> It needs to be the case that if conductance is the property of a
PG> system that the system is an entity in its own rights on top of
PG> its elements.

I really can't answer this question as I am not sure what you mean. If
I may be so bold, let me answer it with another question.

If I have a bag of sweeties (if I may use British English), then the
sweeties exist and so do the bag. Is "bag of sweeties" an entity in
its own rights? "bag of sweeties" will have a weight, length and so
on which are properties of "bag of sweeties" and not the individual
components. Some of these (weight, mass) are easy to derive from the
equivalent property of the sweets and the bag, while some of them (the
length) are not.

Now from your question, that "bag of sweeties" has some properties
means that it has to be a entity in it's own right. Likewise, as
conductor-conductee has properties I would conclude that it's also an
entity in it's own right. Does this make sense?

Phil

Pierre Grenon

unread,
Apr 19, 2007, 7:55:31 AM4/19/07
to bfo-d...@googlegroups.com
On 4/19/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>
> >>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:
>
> PG> ok with all of this, but that's not my question, I am asking you
> PG> to tell me what exactly is this conductee that the conductance
> PG> depends on and which forms a system with the membrane in which
> PG> (the system) you say conductance inheres
>
> PG> the conductance with respect to sodium ions of a particular
> PG> squid giant axon membrane, the one on your table, is dependent
> PG> on sodium ions? all ions? some ions? the answer depends on the
> PG> time at which I ask the question? do we have to look at the
> PG> membrane to figure out which sodium ions are involved? is there
> PG> an entity which is the type sodium ion on which the conductance
> PG> in question depends? if there were no sodium ions in the world
> PG> would the conductance exist?
>
>
> As I have said, there is no "some" sodium ions. All sodium ions are
> alike, and we can't distinguish them.

There might be an ambiguity here because this worry seems irrelevant
to me. I am not asking whether there are different types of sodium
ions.

So, here suppose SodiumIon is a let's say atomic or most specific
type, there are no substypes and ok, all sodium ions are similars...
Now I am asking you whether the entire population of sodium ions in
the world or some subpopulation of sodium ions in the world are what
the sodium ion conductance of the membrane on your table depends on.

In other words, since you think there is a system involved here which
carries the conductance as a property, I am asking whether this system
is made of, in addition to the membrane, the entire population of
sodium ions or only a subpopulation

> So is conductance dependant on
>
> sodium ions -- yes

all of them then

> all ions -- all measures of conductance would be yes, but you can
> measure some of the values of conductance without measuring all of
> them.

I am not asking about measurement, I am asking on what the conductance
which is an entity and not a measure depends on

> time -- to my knowledge, no.

ok, so this rules out scenarios in which a membrane has numerically
distinct (in the sense I have explained earlier) conductances over
time each depending, for example, on the population of ions that was
involved during a given time (to link up to your measurement worries,
say all the ions that went through the membrane during
experiementation)

> do we have to look at the membrane -- which sodium ions has little
> meaning as all are alike.

see just above the parenthetic phrase and the ambiguity I tried to warn against

> it there an entity -- I don't know, not sure what you mean by
> entity in this context, but perhaps yes.

having a specific dependence on all the sodium ions might cause
problem if you think that 'all the sodium ions' does not refer to the
same thing all the type

BFO might speak of the aggregate of all the sodium ions as a whole
which can change and reject what is called mereological essentialism
(i.e. if A looses parts it is no longer A)

an alternative is to say that there is an entity on top of the sodium
ion population which is their type, a universal and index dependence
on this type

> if there were no sodium ions -- no, not with respect to sodium ions,

at least we confirm dependence on something here

> but yes with respect to other entities bearing of charge.

this should have been irrelevant, you must be speaking on another conductance,

this also suggests that even you think of conductance as a property of
the conductor because you are speaking of conductances of the
conductor with respect to different 'conductees',

so I you should be receptive to the idea that conductance is a
property of a conductor and not a property of a conductor-conductee
system since if the conductees are distinct you also have distinct
systems and your remark should come across as even more irrelevant

do you see my point here?

>
> PG> D is the conductance of C G is the conductance of F D and G are
> PG> [?]
>
> Oh, thought I answered that one. Don't know, as I am not sure what you
> are asking. They are conductances.


I am not asking you what they are because we agreed on this. I am
asking you the relation in which they enter. I really didn't want to
make suggestions myself, but for example:

D and G are identical?
--> trouble

D and G are not identical but similar?
--> in what way?
...

> >>
> >> Okay. Well, I don't know, is the answer. I am not sure what you
> >> mean by "exist".
>
> PG> I don't know what to tell you, I mean it is an entity, it falls
> PG> somewhere in the ontology
>
> Not sure this is what you meant to say. Yes, it will become an entity
> if you put it in the ontology.

forget about entity and ontologies

I mean by exist what exist means, I am not aware of an ambiguity
concerning this term

I exist, you exist, unicorns do not exist

>
> PG> It needs to be the case that if conductance is the property of a
> PG> system that the system is an entity in its own rights on top of
> PG> its elements.
>
> I really can't answer this question as I am not sure what you mean. If
> I may be so bold, let me answer it with another question.

Can you answer the following question?

Do you agree that if unicorns do not exist, then there are no unicorn
riders in the world?


> If I have a bag of sweeties (if I may use British English),

Please do, I love British vernacular, I would prefer Newcastle slang
ideally but this might be better off list

> then the
> sweeties exist and so do the bag.

ok, a bag is among other things a container, right? it's not Newcastle
lingo, eh?

> Is "bag of sweeties" an entity in
> its own rights?

It is a bag, which is an entity containing sweeties

> "bag of sweeties" will have a weight, length and so
> on which are properties of "bag of sweeties" and not the individual
> components.

In that case, the most adventurous thing to say is that the bag has
properties which may change depending on whether it is empty or
contains sweeties, for instance the material might be strecthed or
under such mechanical constraints

The bag and the sweeties form an aggregate (this is going to be the
way to look at it in BFO) which indeed has properties that the bag or
the sweeties do not have and lacks of properties that the bag or the
sweeties have

> Some of these (weight, mass) are easy to derive from the
> equivalent property of the sweets and the bag, while some of them (the
> length) are not.

length might not be a good example

> Now from your question, that "bag of sweeties" has some properties
> means that it has to be a entity in it's own right.

yes

> Likewise, as
> conductor-conductee has properties I would conclude that it's also an
> entity in it's own right.

yes

> Does this make sense?

That was, regarding systems (let's not build too much on the bag
analogy), the sense of my question, you earlier seemed to want have
your sweeties and eat them too

pierre

> Phil
>
> >
>

Phillip Lord

unread,
Apr 19, 2007, 12:08:06 PM4/19/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> the conductance with respect to sodium ions of a particular
PG> squid giant axon membrane, the one on your table, is dependent
PG> on sodium ions? all ions? some ions? the answer depends on the
PG> time at which I ask the question? do we have to look at the
PG> membrane to figure out which sodium ions are involved? is there
PG> an entity which is the type sodium ion on which the conductance
PG> in question depends? if there were no sodium ions in the world
PG> would the conductance exist?
>>
>>
>> As I have said, there is no "some" sodium ions. All sodium ions
>> are alike, and we can't distinguish them.


PG> In other words, since you think there is a system involved here
PG> which carries the conductance as a property, I am asking whether
PG> this system is made of, in addition to the membrane, the entire
PG> population of sodium ions or only a subpopulation

Ah, okay. Well, I think I would say, the system in question consists
of only a subpopulation. The conductance of is respect to this
membrane and those ions. However, given that our best theory is that
all sodium ions are alike, we can infer that the conductance of this
system will have the same conductance as another system containing the
same membrane and different sodium ions.

Obviously it's important that we are able to make this
inference. Without it, conductance becomes a description of how a
particular membrane behaved at a particular time, with some particular
ions. With it, conductance becomes a property from the value of which
we can infer how some ions will behave with respect to a membrane (or
with less accuracy a particular type of membrane).

> So is conductance dependant on
>
> sodium ions -- yes

PG> all of them then

Don't know. I have described the situation as I see it in terms of
properties. Have I given you enough information to determine whether
conductance is dependent on all or some sodium ions? I'm just
concerned that you are using "dependent" in a way I don't fully
understand.

>> time -- to my knowledge, no.

PG> ok, so this rules out scenarios in which a membrane has
PG> numerically distinct (in the sense I have explained earlier)
PG> conductances over time each depending, for example, on the
PG> population of ions that was involved during a given time (to
PG> link up to your measurement worries, say all the ions that went
PG> through the membrane during experiementation)

Yeah, I think so. Obviously, some membranes do change conductance over
time, but not because of the which ions are passing.

>> do we have to look at the membrane -- which sodium ions has
>> little meaning as all are alike.

PG> see just above the parenthetic phrase and the ambiguity I tried
PG> to warn against

Ok. Still not sure how to answer this, in the light of that
knowledge.

>> it there an entity -- I don't know, not sure what you mean by
>> entity in this context, but perhaps yes.

PG> an alternative is to say that there is an entity on top of the
PG> sodium ion population which is their type, a universal and index
PG> dependence on this type

Not sure I fully understand this, but I think so.


>> if there were no sodium ions -- no, not with respect to sodium
>> ions,

PG> at least we confirm dependence on something here

Wey, hey, rock and roll.


>> but yes with respect to other entities bearing of charge.

PG> this should have been irrelevant, you must be speaking on
PG> another conductance,

PG> this also suggests that even you think of conductance as a
PG> property of the conductor because you are speaking of
PG> conductances of the conductor with respect to different
PG> 'conductees',

PG> so I you should be receptive to the idea that conductance is a
PG> property of a conductor and not a property of a
PG> conductor-conductee system since if the conductees are distinct
PG> you also have distinct systems and your remark should come
PG> across as even more irrelevant

PG> do you see my point here?

Well I have already said that under some circumstances, it's very
useful to consider that conductance (or resistance) is a property of
conductor, for example with electrical components.

Of course, it's easy to slip into this usage of terminology, which I
think that I have here. But your question was leading in this way. A
membrane-sodium ion system can't exist if there are no sodium ions, so
there is no sense in asking about the conductance of such a
non-existent system. Likewise, conductance would not exist if no
membranes in the world existed. Of course, other systems with
conductance and involving sodium ions would.


>>
PG> D is the conductance of C G is the conductance of F D and G are
PG> [?]
>>
>> Oh, thought I answered that one. Don't know, as I am not sure
>> what you are asking. They are conductances.

PG> I am not asking you what they are because we agreed on this. I
PG> am asking you the relation in which they enter. I really didn't
PG> want to make suggestions myself, but for example:

PG> D and G are identical? --> trouble

PG> D and G are not identical but similar? --> in what way?

Okay, think we have covered this now, in my first paragraph
above. Based on my best understanding of your terms, I think that they
would not be identical, but would have the same numerical value.


PG> I don't know what to tell you, I mean it is an entity, it falls
PG> somewhere in the ontology
>>
>> Not sure this is what you meant to say. Yes, it will become an
>> entity if you put it in the ontology.

PG> forget about entity and ontologies

PG> I mean by exist what exist means, I am not aware of an ambiguity
PG> concerning this term

PG> I exist, you exist, unicorns do not exist

I don't mean to be picky here. I've been an building data models, and
logic based representations of knowledge for a long time. What I have
discovered is that you should always be scared when people think that
a word is self-describing and clear and that "everyone knows what that
means".

Mathematicians like to say "there exists an $x$ such that $Q(x) = 1$"
for instance. Does the value of x fulfilling $Q(x) = 1 exist in this
same way that, I presume, you do?

Does the system exist? Well, I would find it useful if it did, as it
would give me a property of which to hang the numerical value of
conductance off. This is assume that you have to exist to hang a
property of something.


>> I really can't answer this question as I am not sure what you
>> mean. If I may be so bold, let me answer it with another
>> question.

PG> Can you answer the following question?

PG> Do you agree that if unicorns do not exist, then there are no
PG> unicorn riders in the world?

If by unicorn riders you mean people who have ridden a unicorn, then
no. You could also mean people who are capable of riding a unicorn,
and they do exist I think, though it's hard to be sure.

>> If I have a bag of sweeties (if I may use British English),

PG> Please do, I love British vernacular, I would prefer Newcastle
PG> slang ideally but this might be better off list

Sadly, I'm not a geordie.

>> then the sweeties exist and so do the bag.

PG> ok, a bag is among other things a container, right? it's not
PG> Newcastle lingo, eh?

Yeah, a paper bag, with sweets in it.


>> Is "bag of sweeties" an entity in its own rights?

PG> It is a bag, which is an entity containing sweeties

No, you miss my meaning. I agree that the bag is an entity. Is the
"bag of sweeties" the system an entity that exists?


PG> The bag and the sweeties form an aggregate (this is going to be
PG> the way to look at it in BFO) which indeed has properties that
PG> the bag or the sweeties do not have and lacks of properties that
PG> the bag or the sweeties have

Right, so this aggregate thing is an entity that exists and which
can bear properties.

>> Some of these (weight, mass) are easy to derive from the
>> equivalent property of the sweets and the bag, while some of them
>> (the length) are not.

PG> length might not be a good example

Maybe, cause a bag of sweeties doesn't have an intuitive
orientation. What about volume? This depends on the bag, the volume of
the sweeties and the packing qualities of the sweeties wrt to the
shape of the bag -- it would be hard to derive a priori.

>> Now from your question, that "bag of sweeties" has some
>> properties means that it has to be a entity in it's own right.

PG> yes

>> Likewise, as conductor-conductee has properties I would conclude
>> that it's also an entity in it's own right.

PG> yes

Okay. So this seems fine to me. In which case, we conclude that what
we actually have is an aggregate of conductor-conductee and a property
of that aggregate which is conductance?


>> Does this make sense?

PG> That was, regarding systems (let's not build too much on the bag
PG> analogy), the sense of my question, you earlier seemed to want
PG> have your sweeties and eat them too

Always, my friend, always.

Phil

Pierre Grenon

unread,
Apr 19, 2007, 1:22:26 PM4/19/07
to bfo-d...@googlegroups.com
> PG> In other words, since you think there is a system involved here
> PG> which carries the conductance as a property, I am asking whether
> PG> this system is made of, in addition to the membrane, the entire
> PG> population of sodium ions or only a subpopulation
>
> Ah, okay. Well, I think I would say, the system in question consists
> of only a subpopulation. The conductance of is respect to this
> membrane and those ions.

Can you elaborate on which population is involved for a given membrane
and a given conductance?

Suppose there are 3 sodium ions in the world and one membrane. How
many sodium ions conductances does the membrane have?

Since what will allow for a distinction between conductance is the
subpopulation involved this becomes our issue now.

> However, given that our best theory is that
> all sodium ions are alike, we can infer that the conductance of this
> system will have the same conductance as another system containing the
> same membrane and different sodium ions.

ok, I understand what you are saying but forget about this, this is
irrelevant, we are trying to find a way of securing the fact that the
conductance of the membrane with respect to population A is not the
same entity as the conductance of the membrane with respect to
population B. That they are similar in some way is very conforting
under your view, but does not help answering the question.

> Obviously it's important that we are able to make this
> inference. Without it, conductance becomes a description of how a

remember, conductance is not a description, we are speaking about an
entity, the description you speak of could be a description of this
entity

> particular membrane behaved at a particular time, with some particular
> ions.

this said... that they behave similarly all things being equal with
the same ions suggests to me that it does not matter which population
is involved

> > So is conductance dependant on
> >
> > sodium ions -- yes
>
> PG> all of them then
>
> Don't know. I have described the situation as I see it in terms of
> properties. Have I given you enough information to determine whether
> conductance is dependent on all or some sodium ions? I'm just
> concerned that you are using "dependent" in a way I don't fully
> understand.

Here 'dependence' is to be understood in the way of BFO, this has
nothing to do with possible quantitative variation, say, it is just
'existential dependence' between two entities (you seemed to have no
trouble earlier in answering whether if there were no sodium ions
there would be conductance... this is the relevant sense of
"dependence")

> >> time -- to my knowledge, no.
>
> PG> ok, so this rules out scenarios in which a membrane has
> PG> numerically distinct (in the sense I have explained earlier)
> PG> conductances over time each depending, for example, on the
> PG> population of ions that was involved during a given time (to
> PG> link up to your measurement worries, say all the ions that went
> PG> through the membrane during experiementation)
>
> Yeah, I think so. Obviously, some membranes do change conductance over
> time, but not because of the which ions are passing.

So a membrane can have many similar conductances depending on which
population of ions is involved but it has them at all time (provided
the population exists). Right?

> >> do we have to look at the membrane -- which sodium ions has
> >> little meaning as all are alike.
>
> PG> see just above the parenthetic phrase and the ambiguity I tried
> PG> to warn against
>
> Ok. Still not sure how to answer this, in the light of that
> knowledge.

I was wondering whether it is important to know where are the ions
involved in sustaining the conductance in existence. Do they need to
be somewhere in the membrane?

> >> it there an entity -- I don't know, not sure what you mean by
> >> entity in this context, but perhaps yes.
>
> PG> an alternative is to say that there is an entity on top of the
> PG> sodium ion population which is their type, a universal and index
> PG> dependence on this type
>
> Not sure I fully understand this, but I think so.

Do you understand the difference between frogs and their frogness,
say? It would be better to say 'the universal: Frog'. I am not asking
you whether you actually believe that there is a universal frog which
is instantiated by frogs. Here the idea would be that there are frogs,
these are entities, and there is another entity, their type, say Frog,
such that all frogs are in the instantiation relation with Frog.

>
> >> if there were no sodium ions -- no, not with respect to sodium
> >> ions,
>
> PG> at least we confirm dependence on something here
>
> Wey, hey, rock and roll.

ok so you see the meaning of dependence now

>
> >> but yes with respect to other entities bearing of charge.
>
> PG> this should have been irrelevant, you must be speaking on
> PG> another conductance,
>
> PG> this also suggests that even you think of conductance as a
> PG> property of the conductor because you are speaking of
> PG> conductances of the conductor with respect to different
> PG> 'conductees',
>
> PG> so I you should be receptive to the idea that conductance is a
> PG> property of a conductor and not a property of a
> PG> conductor-conductee system since if the conductees are distinct
> PG> you also have distinct systems and your remark should come
> PG> across as even more irrelevant
>
> PG> do you see my point here?
>
> Well I have already said that under some circumstances, it's very
> useful to consider that conductance (or resistance) is a property of
> conductor, for example with electrical components.

ah, you said this? I'll look up but this is not something that is
circumstances dependent or we really have two kinds of conductance
here

> Of course, it's easy to slip into this usage of terminology, which I
> think that I have here. But your question was leading in this way.

maybe but to my defence, I am not German

> A
> membrane-sodium ion system can't exist if there are no sodium ions, so
> there is no sense in asking about the conductance of such a
> non-existent system. Likewise, conductance would not exist if no
> membranes in the world existed. Of course, other systems with
> conductance and involving sodium ions would.

ok, now let's focus, my friend

> PG> D and G are not identical but similar? --> in what way?
>
> Okay, think we have covered this now, in my first paragraph
> above. Based on my best understanding of your terms, I think that they
> would not be identical, but would have the same numerical value.

yes, covered

>
> PG> I mean by exist what exist means, I am not aware of an ambiguity
> PG> concerning this term
>
> PG> I exist, you exist, unicorns do not exist
>
> I don't mean to be picky here. I've been an building data models, and
> logic based representations of knowledge for a long time. What I have
> discovered is that you should always be scared when people think that
> a word is self-describing and clear and that "everyone knows what that
> means".

But you have been aware that things exist since long before data
modeling got the better of you, I mean that sense of existence.

> Mathematicians like to say "there exists an $x$ such that $Q(x) = 1$"
> for instance. Does the value of x fulfilling $Q(x) = 1 exist in this
> same way that, I presume, you do?

this has nothing to do with whether an equation has a solution

> Does the system exist? Well, I would find it useful if it did, as it
> would give me a property of which to hang the numerical value of
> conductance off.

What if I gave you a conductor to hang the numerical value of conductance off?

> This is assume that you have to exist to hang a
> property of something.

Absolutely, so far the only reason why we are considreing that system
of the sort we discuss exist is because you want to hang a numerical
value off them. This does not mean however that if conductance is a
property of a conductor and not a conductor-conductee system, the
system would not exist.

>
> >> I really can't answer this question as I am not sure what you
> >> mean. If I may be so bold, let me answer it with another
> >> question.
>
> PG> Can you answer the following question?
>
> PG> Do you agree that if unicorns do not exist, then there are no
> PG> unicorn riders in the world?
>
> If by unicorn riders you mean people who have ridden a unicorn, then
> no. You could also mean people who are capable of riding a unicorn,
> and they do exist I think, though it's hard to be sure.

I don't mean people who would have the capability of being unicorn
riders would unicorn exist.

What do you mean by horse riders?

Don't answer, I mean by unicorn riders the same thing you mean with
horse riders but with unicorns not horses.

> >> If I have a bag of sweeties (if I may use British English),
>
> PG> Please do, I love British vernacular, I would prefer Newcastle
> PG> slang ideally but this might be better off list
>
> Sadly, I'm not a geordie.

there is even a name for this! waow

> >> Some of these (weight, mass) are easy to derive from the
> >> equivalent property of the sweets and the bag, while some of them
> >> (the length) are not.
>
> PG> length might not be a good example
>
> Maybe, cause a bag of sweeties doesn't have an intuitive
> orientation. What about volume? This depends on the bag, the volume of
> the sweeties and the packing qualities of the sweeties wrt to the
> shape of the bag -- it would be hard to derive a priori.

I would go for weirder things for the sake of the argument, not
physical, say a price

> Okay. So this seems fine to me. In which case, we conclude that what
> we actually have is an aggregate of conductor-conductee and a property
> of that aggregate which is conductance?

We conclude nothing of this sort, we conclude that if you believe this
then we have identified your beliefs about conductance.

We conclude therefore that:

you do not believe that conductance is the property of two things but
that it is the property of a complex made of two things.

Now that we have agreed that property of two things is not the right
view (which recall is how this sweeties thing started), we have the
following basic alternative:

Solution 1: Conductance inheres in a conductor and depends on the condutee.

Solution 2: Conductance inheres in the conductor-conductee aggregate.

These two possibilities branch depending on what the conductee is in
term of the following alternatives:

- entire population of thingies
- subpopulation of thingies
- type which thingies instantiate

> Always, my friend, always.

I too start experiencing some great impression of communion here
pierre

William Bug

unread,
Apr 19, 2007, 2:46:29 PM4/19/07
to bfo-d...@googlegroups.com
(Please let me know if this is not helpful and I will stop posting to the list on this issue).

Not to slight the delectable discussion of sweets and General Relativity, in regards to the relations at hand, I think we should reconnoiter a bit, going back to the original artifact - neuron_ontology.owl - a repesentation of the content in NeuronDB (and indirectly - ModelDB - http://senselab.med.yale.edu/senselab/)

With that in mind:
1) The ionic currents being described (and the receptors and transmitters, as well), ultimately need to link to distinct molecular entities, even if they don't do it explicitly in neuron_ontology.owl (which they probably will soon - at least some subset of those properties).  With that in mind, we will ultimately need a representation of the continuants related to ionic current, receptor, and transmitter that lends itself to that task.

2) Even more importantly, when considering the dependancies/relations/properties of ionic currents, there are two ways to break it down - both necessary - both somewhat interdependent
a) "passive" electrochemistry:
The ionic currents are dependent on the Na+ ion electrochemical transmembrane gradient.  This means the CURRENTS will be a function of:
 i) the Na+ (Na+ activity in typical saline - the "chemical" part)
ii) the other contributing charged species:
A) some freely moving (ions in solution such as K+, Ca++, Cl-), and;
B) "immobilized" charges such as the predominantly negative charge contributed by the exposed Phosphate groups extending form the heads of the phospholipids that make up the external, exposed face on both sides of the bilayer.  
When we start thinking of Na+ ions moving through the channels that underly the transmembrane conductances, the "screening" and "concentrating" effects of this accumulation of negative charge are important to consider.  All of these "electrical" contributors to the electrochemical gradient will contribute to the overall transmembrane voltage, which is the driving force they contribute to the flow of Na+ ions through the transmembrane channels.
b) "active" conductance change
This derives from the ion channel macromolecular complex having a conformation that is dependent on the transmembrane voltage.  When I say "active" here, I'm making reference to the distinction made in electronics between "active" and "passive" components.  In the case of these molecules underlying the transmembrane ionic currents - molecules we want to related to many other continuants - this dependency on membrane voltage is an important one to take into account.

So - the particular transmembrane ionic current species (say the fast, transient Na+ current responsible for the depolarizing phase of the action potential) is very much dependent on:
I)  the two COLLECTIONs of charged moieties ("free" and "immobilized") contributing to the electrical environment
ii) the SPECIFIC ion species the underlying ion channels "select" for
iii) the nature of the voltage-dependence of the underlying channels

In the case of the receptors which are also being represented here (included in NeuronDB, as well as a critical element in the BrainPharm ontology Matthias just referenced), the case is very much similar.  For the receptor/channel complexes (Ach-R, ionotropic glutamate receptors, etc.) the conductance is a function of the conformation of the associated ion channel which in this case is altered allosterically when a particular neurotransmitter binds to the receptor.

For G-protein coupled receptors (GPCR) such as the metabolomic glutamate receptor, binding to the receptor first leads to a state change in an intracellular 2nd messenger enzyme system, leading to a change in some intracellular signaling molecule such as IP3 or cAMP which then leads to a change in the pore conformation of one or more types of ion channel (and associated ionic conductance).

These are the underlying continuants, occurents, and relations that need to be addressed in neuron_ontology.owl (and BrainPharm) - at least in the context of the ionic currents and receptors described in those ontologies (and transmitters, too, indirectly).

Cheers,
Bill

Phillip Lord

unread,
Apr 20, 2007, 9:29:39 AM4/20/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> Ah, okay. Well, I think I would say, the system in question
>> consists of only a subpopulation. The conductance of is respect
>> to this membrane and those ions.

PG> Can you elaborate on which population is involved for a given
PG> membrane and a given conductance?

PG> Suppose there are 3 sodium ions in the world and one
PG> membrane. How many sodium ions conductances does the membrane
PG> have?

Well, if there were only 3 sodium ions you'd be unable to measure
conductance in a sane way. It's kind of a mass action feature.

But to not use this to duck the question, again, I am not sure. My gut
feeling is that there would be 3 conductance's all with the same
numerical value. But because sodium ions are all alike, the numerical
value would be exactly the same, so I am not sure that this
distinction makes that much difference.


>> Obviously it's important that we are able to make this
>> inference. Without it, conductance becomes a description of how a

PG> remember, conductance is not a description, we are speaking
PG> about an entity, the description you speak of could be a
PG> description of this entity

>> particular membrane behaved at a particular time, with some
>> particular ions.

PG> this said... that they behave similarly all things being equal
PG> with the same ions suggests to me that it does not matter which
PG> population is involved

I think I have answer this question above. Yes, I agree it doesn't
matter in this case.


>> Don't know. I have described the situation as I see it in terms
>> of properties. Have I given you enough information to determine
>> whether conductance is dependent on all or some sodium ions? I'm
>> just concerned that you are using "dependent" in a way I don't
>> fully understand.

PG> Here 'dependence' is to be understood in the way of BFO, this
PG> has nothing to do with possible quantitative variation, say, it
PG> is just 'existential dependence' between two entities (you
PG> seemed to have no trouble earlier in answering whether if there
PG> were no sodium ions there would be conductance... this is the
PG> relevant sense of "dependence")

Well the quantification is different. You are asking about all the
sodium ions. In our example, imagine that one sodium ion in the world
undergoes radioactive decay and ceases to exist. Now there is one less
sodium ion. But the conductance exists just the same.

>> Yeah, I think so. Obviously, some membranes do change conductance
>> over time, but not because of the which ions are passing.

PG> So a membrane can have many similar conductances depending on
PG> which population of ions is involved but it has them at all time
PG> (provided the population exists). Right?

Yes, I think so.

>> Ok. Still not sure how to answer this, in the light of that
>> knowledge.

PG> I was wondering whether it is important to know where are the
PG> ions involved in sustaining the conductance in existence. Do
PG> they need to be somewhere in the membrane?

No. They could be outside. But they will need to be within the
electrical field while measuring the conductance.

PG> an alternative is to say that there is an entity on top of the
PG> sodium ion population which is their type, a universal and index
PG> dependence on this type
>>
>> Not sure I fully understand this, but I think so.

PG> Do you understand the difference between frogs and their
PG> frogness, say? It would be better to say 'the universal:
PG> Frog'. I am not asking you whether you actually believe that
PG> there is a universal frog which is instantiated by frogs. Here
PG> the idea would be that there are frogs, these are entities, and
PG> there is another entity, their type, say Frog, such that all
PG> frogs are in the instantiation relation with Frog.


Yes, okay. So I will make a careful answer here. In this case, yes, it
depends on the type of sodium ion rather than the instantiations of
it. But the reason for this is because of the nature of sodium ions as
a atom (well ion), not from it's nature as the conductee in this
system. There could be conductees which are not atomic and for which
this is not true.

Did you ever do the experiment with a metal painted ping-pong ball on
a string? You stick it between two electrically charged plates, and it
pendulates between the two. The conductee in this case can be
considered to be the ball, and the conductor, well a combination of
components.


>> Well I have already said that under some circumstances, it's very
>> useful to consider that conductance (or resistance) is a property
>> of conductor, for example with electrical components.

PG> ah, you said this? I'll look up but this is not something that
PG> is circumstances dependent or we really have two kinds of
PG> conductance here

Yeah I said this. Whether it is useful to describe conductance as a
property of the conductor is, yes, circumstance dependent. For an
electrical component, by only considering it in the context of an
electrons. For membranes, no, unless they have a natural conductee
which they always use.

>> Of course, it's easy to slip into this usage of terminology,
>> which I think that I have here. But your question was leading in
>> this way.

PG> maybe but to my defence, I am not German

Is okay, didn't think you were doing it deliberately.

PG> But you have been aware that things exist since long before data
PG> modeling got the better of you, I mean that sense of existence.

Yes, I was aware of many straight-forward and simple things before I
started building data models which I am no longer aware of.


>> Does the system exist? Well, I would find it useful if it did, as
>> it would give me a property of which to hang the numerical value
>> of conductance off.

PG> What if I gave you a conductor to hang the numerical value of
PG> conductance off?

I would say, wrt to which conductee am I calculating the value? And
can I hang many conductances off one conductor? And wouldn't it make
more sense to hang it of the conductor-conductee system?


>> This is assume that you have to exist to hang a property of
>> something.

PG> Absolutely, so far the only reason why we are considreing that
PG> system of the sort we discuss exist is because you want to hang
PG> a numerical value off them. This does not mean however that if
PG> conductance is a property of a conductor and not a
PG> conductor-conductee system, the system would not exist.

Yes, of course. It's a one way implication. Just because conductance
(in your example) might not be a property of the system does not mean
that it has no properties.


PG> Do you agree that if unicorns do not exist, then there are no
PG> unicorn riders in the world?
>>
>> If by unicorn riders you mean people who have ridden a unicorn,
>> then no. You could also mean people who are capable of riding a
>> unicorn, and they do exist I think, though it's hard to be sure.

PG> I don't mean people who would have the capability of being
PG> unicorn riders would unicorn exist.

PG> What do you mean by horse riders?

Someone who rides a horse, or who has ridden a horse. The reason I
hedged by bets a little is this: a court judge becomes a judge was he
comes to the bar -- he doesn't have to have judged anything. I am not
sure that this distinction makes any difference in this case.

PG> Please do, I love British vernacular, I would prefer Newcastle
PG> slang ideally but this might be better off list
>>
>> Sadly, I'm not a geordie.

PG> there is even a name for this! waow

Oh yeah. The word "geordie" is several hundred years old.


>> Okay. So this seems fine to me. In which case, we conclude that
>> what we actually have is an aggregate of conductor-conductee and
>> a property of that aggregate which is conductance?

PG> We conclude nothing of this sort, we conclude that if you
PG> believe this then we have identified your beliefs about
PG> conductance.

PG> We conclude therefore that:

PG> you do not believe that conductance is the property of two
PG> things but that it is the property of a complex made of two
PG> things.

Well, I would say that I would be happy describing it in either way.


PG> Now that we have agreed that property of two things is not the
PG> right view (which recall is how this sweeties thing started), we
PG> have the following basic alternative:

PG> Solution 1: Conductance inheres in a conductor and depends on
PG> the condutee.

PG> Solution 2: Conductance inheres in the conductor-conductee
PG> aggregate.

PG> These two possibilities branch depending on what the conductee
PG> is in term of the following alternatives:

PG> - entire population of thingies
PG> - subpopulation of thingies
PG> - type which thingies instantiate

Well, given my previous example of the ping pong ball, I would say
that in general, we can only conclude that conductance relates to the
subpopulation of thingies, and MAY relate to type. I am not sure about
the entire population.


>> Always, my friend, always.

PG> I too start experiencing some great impression of communion here


Normally I would say, we should go for a beer sometime. But I fear we
would argue all night, I would drink far too much and wake with a very
bad case of hangover.

Phil

Pierre Grenon

unread,
Apr 20, 2007, 10:23:06 AM4/20/07
to bfo-d...@googlegroups.com
> Well, if there were only 3 sodium ions you'd be unable to measure
> conductance in a sane way. It's kind of a mass action feature.

Suppose it is doable so we don't worry about that sort of thing unless
there truly is something important for our issue here (i.e. number of
conductances in relation to number of ions).

The question is not about measurement but the existence of conductance.

> My gut
> feeling is that there would be 3 conductance's all with the same

Why not just 1?

Why not 6?

> >> Don't know. I have described the situation as I see it in terms
> >> of properties. Have I given you enough information to determine
> >> whether conductance is dependent on all or some sodium ions? I'm
> >> just concerned that you are using "dependent" in a way I don't
> >> fully understand.
>
> PG> Here 'dependence' is to be understood in the way of BFO, this
> PG> has nothing to do with possible quantitative variation, say, it
> PG> is just 'existential dependence' between two entities (you
> PG> seemed to have no trouble earlier in answering whether if there
> PG> were no sodium ions there would be conductance... this is the
> PG> relevant sense of "dependence")
>
> Well the quantification is different. You are asking about all the
> sodium ions. In our example, imagine that one sodium ion in the world
> undergoes radioactive decay and ceases to exist. Now there is one less
> sodium ion. But the conductance exists just the same.

Really? So there is 1 conductance then, not 3 in the example above.

> >> Yeah, I think so. Obviously, some membranes do change conductance
> >> over time, but not because of the which ions are passing.
>
> PG> So a membrane can have many similar conductances depending on
> PG> which population of ions is involved but it has them at all time
> PG> (provided the population exists). Right?
>
> Yes, I think so.

This is contradictory with what you have just said although this is
consistent with you saying there were 3 conductances in the example.
Which is right?

> PG> I was wondering whether it is important to know where are the
> PG> ions involved in sustaining the conductance in existence. Do
> PG> they need to be somewhere in the membrane?
>
> No. They could be outside. But they will need to be within the
> electrical field while measuring the conductance.

The conductance exists only when it is measured? or only once it has
been measured?

Is this something you really mean here?

> PG> an alternative is to say that there is an entity on top of the
> PG> sodium ion population which is their type, a universal and index
> PG> dependence on this type
> >>
> >> Not sure I fully understand this, but I think so.
>
> PG> Do you understand the difference between frogs and their
> PG> frogness, say? It would be better to say 'the universal:
> PG> Frog'. I am not asking you whether you actually believe that
> PG> there is a universal frog which is instantiated by frogs. Here
> PG> the idea would be that there are frogs, these are entities, and
> PG> there is another entity, their type, say Frog, such that all
> PG> frogs are in the instantiation relation with Frog.
>
>
> Yes, okay.

Fine, settled, so in the 3 ions case, there is only one conductance, not 3.

And conductance (it's existence, if you prefer, not it's measurement,
recall these are a priori distcnt affairs) does not depend on where
the ions happen to be.

> So I will make a careful answer here. In this case, yes, it
> depends on the type of sodium ion rather than the instantiations of
> it. But the reason for this is because of the nature of sodium ions as
> a atom (well ion), not from it's nature as the conductee in this
> system. There could be conductees which are not atomic and for which
> this is not true.
>
> Did you ever do the experiment with a metal painted ping-pong ball on
> a string? You stick it between two electrically charged plates, and it
> pendulates between the two. The conductee in this case can be
> considered to be the ball, and the conductor, well a combination of
> components.

But if there is a notion of conductance here, I could replace the ball
with any perfectly similar ball. This is completely analogous then.
Here the conductance depends on the type of ball in question.

Is that OK? (It should be.)

>
> >> Well I have already said that under some circumstances, it's very
> >> useful to consider that conductance (or resistance) is a property
> >> of conductor, for example with electrical components.
>
> PG> ah, you said this? I'll look up but this is not something that
> PG> is circumstances dependent or we really have two kinds of
> PG> conductance here
>
> Yeah I said this. Whether it is useful to describe conductance as a
> property of the conductor is, yes, circumstance dependent. For an
> electrical component, by only considering it in the context of an
> electrons. For membranes, no, unless they have a natural conductee
> which they always use.

I don't understand, conductance of an electrical component is
electron-conductance of that component. That something can have
different types of conductances depending on what is conducted doesn't
suggest to me that conductance is not a property of the conductor,
only taht it is also dependent on the conductee. In the case of
membranes as well as in the case of electrical components.

I think I see why you feel there needs to be something else in certain
cases (a system), but you fail to see that actually there is no need
of something else, the conductances as properties of conductors are
differentiated by the types of conductees. There is no need to bring
in systems to secure the differentiation.

>
> >> Does the system exist? Well, I would find it useful if it did, as
> >> it would give me a property of which to hang the numerical value
> >> of conductance off.
>
> PG> What if I gave you a conductor to hang the numerical value of
> PG> conductance off?
>
> I would say, wrt to which conductee am I calculating the value?

Well if we're speaking about the sodium ion conductance of the giant
sea monster axon mombrane, the conductee is sodium ions, not
electrons, not cheesecake...

> And
> can I hang many conductances off one conductor?

Why not? You speak English and Georgie say, is that a problem?

> And wouldn't it make
> more sense to hang it of the conductor-conductee system?

no

> >> This is assume that you have to exist to hang a property of
> >> something.
>
> PG> Absolutely, so far the only reason why we are considreing that
> PG> system of the sort we discuss exist is because you want to hang
> PG> a numerical value off them. This does not mean however that if
> PG> conductance is a property of a conductor and not a
> PG> conductor-conductee system, the system would not exist.
>
> Yes, of course. It's a one way implication. Just because conductance
> (in your example) might not be a property of the system does not mean
> that it has no properties.

certainly

>
> PG> Do you agree that if unicorns do not exist, then there are no
> PG> unicorn riders in the world?
> >>
> >> If by unicorn riders you mean people who have ridden a unicorn,
> >> then no. You could also mean people who are capable of riding a
> >> unicorn, and they do exist I think, though it's hard to be sure.
>
> PG> I don't mean people who would have the capability of being
> PG> unicorn riders would unicorn exist.
>
> PG> What do you mean by horse riders?
>
> Someone who rides a horse, or who has ridden a horse. The reason I
> hedged by bets a little is this: a court judge becomes a judge was he
> comes to the bar -- he doesn't have to have judged anything. I am not
> sure that this distinction makes any difference in this case.

Good, conductances exist even if they are not measured as long as you
have conductors and conductees (or their type).

Unicorn riders do not exist.

> Oh yeah. The word "geordie" is several hundred years old.

Come on, English is not that old. French scholars are quite positive
that it did not evolve from grunting noises before the late 19th
century possibly even more recently.


> PG> you do not believe that conductance is the property of two
> PG> things but that it is the property of a complex made of two
> PG> things.
>
> Well, I would say that I would be happy describing it in either way.

then stop arguing!

>
> PG> Now that we have agreed that property of two things is not the
> PG> right view (which recall is how this sweeties thing started), we
> PG> have the following basic alternative:
>
> PG> Solution 1: Conductance inheres in a conductor and depends on
> PG> the condutee.
>
> PG> Solution 2: Conductance inheres in the conductor-conductee
> PG> aggregate.
>
> PG> These two possibilities branch depending on what the conductee
> PG> is in term of the following alternatives:
>
> PG> - entire population of thingies
> PG> - subpopulation of thingies
> PG> - type which thingies instantiate
>
> Well, given my previous example of the ping pong ball, I would say
> that in general, we can only conclude that conductance relates to the
> subpopulation of thingies, and MAY relate to type. I am not sure about
> the entire population.

well, I'm not sure either, for BFO I'd go either for the type which
would be more straightforward (and might require some change, not too
sure) or its 'extension' as the aggregate of all of its instances
(which can change its members but remains one thing). I don't think
your ping pong example suggests population thingies, it is to me
completely analogous to the sodium ions example.

> Normally I would say, we should go for a beer sometime. But I fear we
> would argue all night, I would drink far too much and wake with a very
> bad case of hangover.

hear!

you can argue, if you let me drink,

pierre

> Phil
>
> >
>

Phillip Lord

unread,
Apr 23, 2007, 7:25:23 AM4/23/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> Well, if there were only 3 sodium ions you'd be unable to measure
>> conductance in a sane way. It's kind of a mass action feature.

PG> Suppose it is doable so we don't worry about that sort of thing
PG> unless there truly is something important for our issue here
PG> (i.e. number of conductances in relation to number of ions).

Pierre


I started to reply to this, but I've now decided not to; please
forgive me for this discourtesy, but I've thought about the whole
debate for over the weekend. I had a moment of what I hope is
clarity. As a result, I think that a direct reply to this email would
be wasteful.


As you will remember, we were arguing about the conductance of
membranes and whether conductance is a property of the membrane (the
conductor) or the thing conducted (conductee).

I've come to a number of conclusions, one of which is that I am
wrong in at least one way. I'll start with my conclusions and then
explain how I got there. They are

a) conductance is a property of the conductor only
b) a conductor is not a physical entity, but rather a role that a
physical entity (and even no physical entity) can play.
c) a membrane is not a conductor.


Please remember that in the following I am attempting to describe the
key entities involved and their interactions. I've generally avoiding
using BFO terms, until near the end, as I am not sure enough that I
will use these correctly.

I start off with two scenarios:

1) a membrane, in physiological solution with salt as the main
component.

2) Two metal plates with a silvered ping pong ball operating as a
pendulum between them.

3) An electron gun.

In our previous discussion we had the membrane as a conductor and
sodium ions as the charged entity (the conductee). I was thinking
about how to apply these to the second example. The charged entity in
this case is either the ping pong ball or the electrons. But what is
the conductor? Well I can't think of one. It's clear that it's not the
air (cause we could remove it, and the system would work better), it's
clear that it's not the string. Perhaps it could be considered to be
the ball which could be both conductee and conductor. But I don't
think that this makes sense either.

Taking things a bit further, we can also use the example of an
electron gun. In this case, there are electrons flowing from a
filament through vacuum toward a +ve charged plate. Now in this case,
nothing in the middle betwen the electron gun and +ve charged plate,
other than the charged entity. So clearly, we don't need what we have
previously been calling the conductor.

So I think we have our terms wrong. In the case of the membrane, what
we have is a matrix, with ions moving through it. This whole thing is
the conductor. You can't lose any aspect of it, without it ceasing to
be a conductor (in this example, not in general). Hence my conclusion
that a membrane is not a conductor -- it's part of one.

We have also reached the conclusion that in general, the matrix is not
required. We can move a charged entity across a vacuum quite
happily. This would lead us to the conclusion, therefore, that
electrons in a vacuum are a conductor.

But what about the charged entity? Well, take the ping pong ball
example. Now remove the ping pong ball. We now have two plates, in a
vacuum. No current. No conductor. But this is not true. If we apply a
AC current across the two plates, which are now acting as a capacitor,
the current will flow fine. In otherwords, we still have a
conductance. And critically, there is nothing physical flowing between
the plates -- their interaction is purely at the level of electrical
fields; neither matter nor, I think, energy is flowing between the
two. Conclusion, the charged entity is also optional.


So how would I model all of this? If we think of conductance in the
following way, I think life becomes easier. It's a property of the
conductor, but the conductor is a role of some system (maybe
comprising of a single entity).

Now, those things that make the system a conductor do not always
require the same relationship with each other and the system. So, in
the case of the ping pong ball, it seems clear that the conductive
properties arise dependant on the individual ball, string and
plates.

In the case of the membrane scenario, it's clearly the type of sodium
ion which is important not the individual ion. Hence, if we take the
membrane/sodium system and replace all the sodium ions we have the
same system, the same conductance property and it will have the same
numerical value. If we replace the ping pong ball with another, on the
other hand, then we have a different system.

We don't even need to know about the parts of a system to know that it
has conductance -- we could have a black box with some stuff inside
it. We would not need to know whether there was a membrane, ping pong
ball or wire inside. If you replaced the box with another box, then
you would have a different system, as the conductance is a property of
the individual system, rather than the general box-nature of our black
box.


Does this make sense? I am not suggesting that my model is one that
would fit into BFO, just saying it's how I would produced a model.


Phil

Pierre Grenon

unread,
Apr 23, 2007, 11:36:54 AM4/23/07
to bfo-d...@googlegroups.com
> As you will remember, we were arguing about the conductance of
> membranes and whether conductance is a property of the membrane (the
> conductor) or the thing conducted (conductee).
>
> I've come to a number of conclusions, one of which is that I am
> wrong in at least one way. I'll start with my conclusions and then
> explain how I got there. They are
>
> a) conductance is a property of the conductor only

i woudl agree but this is becoming somewhat of a vacuous claim

> b) a conductor is not a physical entity, but rather a role that a
> physical entity (and even no physical entity) can play.

i disagree, being a conductor is at bottom a role, it seems to me
credible to say it is tied to a disposition measured by conductance...

I cannot make sense of non physical entities being involved here

> c) a membrane is not a conductor.

i think i see where you want to go, i'm also wondering whether this is
not taking 'conductance' to be more general than it is

>
> Please remember that in the following I am attempting to describe the
> key entities involved and their interactions. I've generally avoiding
> using BFO terms, until near the end, as I am not sure enough that I
> will use these correctly.
>
> I start off with two scenarios:
>
> 1) a membrane, in physiological solution with salt as the main
> component.
>
> 2) Two metal plates with a silvered ping pong ball operating as a
> pendulum between them.
>
> 3) An electron gun.
>
> In our previous discussion we had the membrane as a conductor and
> sodium ions as the charged entity (the conductee). I was thinking
> about how to apply these to the second example. The charged entity in
> this case is either the ping pong ball or the electrons. But what is
> the conductor? Well I can't think of one. It's clear that it's not the
> air (cause we could remove it, and the system would work better), it's
> clear that it's not the string. Perhaps it could be considered to be
> the ball which could be both conductee and conductor. But I don't
> think that this makes sense either.

One possibility is that this is just not an example of conduction. You
describe something which happens when a ping pong ball is in the
electrical field generated by a condensator, right? Maybe this is
pushing the notion of conduction a bit far, I dunno for sure.

> Taking things a bit further, we can also use the example of an
> electron gun. In this case, there are electrons flowing from a
> filament through vacuum toward a +ve charged plate. Now in this case,
> nothing in the middle betwen the electron gun and +ve charged plate,
> other than the charged entity. So clearly, we don't need what we have
> previously been calling the conductor.

Yes, but then again, maybe you are shooting at something so general --
e.g. movement -- that we are not talking of conduction either.

> So I think we have our terms wrong. In the case of the membrane, what
> we have is a matrix,

I don't understand, I don't know what a matrix is

> with ions moving through it. This whole thing is
> the conductor. You can't lose any aspect of it, without it ceasing to
> be a conductor (in this example, not in general). Hence my conclusion
> that a membrane is not a conductor -- it's part of one.

I think I sort of see what you mean, this sounds odd

> We have also reached the conclusion that in general, the matrix is not
> required. We can move a charged entity across a vacuum quite
> happily.

but you are just saying that there are different sort of
translocation, if conduction is a translocation in a
medium/conductor/matrix, translocation in vaccuum is just some other
sort of thing

> This would lead us to the conclusion, therefore, that
> electrons in a vacuum are a conductor.

I don't think this follows

> But what about the charged entity? Well, take the ping pong ball
> example. Now remove the ping pong ball. We now have two plates, in a
> vacuum. No current. No conductor. But this is not true. If we apply a
> AC current across the two plates, which are now acting as a capacitor,
> the current will flow fine. In otherwords, we still have a
> conductance.

I'm not sure i understand, where does the current flow in your example?

> And critically, there is nothing physical flowing between
> the plates -- their interaction is purely at the level of electrical
> fields; neither matter nor, I think, energy is flowing between the
> two. Conclusion, the charged entity is also optional.

I don't understand

>
> So how would I model all of this? If we think of conductance in the
> following way, I think life becomes easier. It's a property of the
> conductor, but the conductor is a role of some system (maybe
> comprising of a single entity).

No you mean conductance is a property of an entity which has the role
of being a conductor in certain circumstances.

OK, let me anticipate on where I wanted to go. Seeing conductance as a
disposition of the conductor would also mean that this disposition is
realized when the conductor actually has its role, i.e. when it
conducts. I am not particularly confortable with this, but this is the
intuition.

> Now, those things that make the system a conductor do not always
> require the same relationship with each other and the system. So, in
> the case of the ping pong ball, it seems clear that the conductive
> properties arise dependant on the individual ball, string and
> plates.
>
> In the case of the membrane scenario, it's clearly the type of sodium
> ion which is important not the individual ion. Hence, if we take the
> membrane/sodium system and replace all the sodium ions we have the
> same system, the same conductance property and it will have the same
> numerical value. If we replace the ping pong ball with another, on the
> other hand, then we have a different system.

No, it doesn't work like that, or I don't see what you mean because
the terms 'same' and 'different' are ambiguous, we've talked about
that. I can't be quite sure what you mean. It seems however that
dependence on particular instances versus type is another issue. Well,
it depends really, I am not sure it makes sense to speak of conduction
in the case of the ball and if it is not conduction we are talking
about, maybe that it is one ball and not an entirely similar one which
is involved is important. But I doubt this.

> We don't even need to know about the parts of a system to know that it
> has conductance -- we could have a black box with some stuff inside
> it. We would not need to know whether there was a membrane, ping pong
> ball or wire inside. If you replaced the box with another box, then
> you would have a different system, as the conductance is a property of
> the individual system, rather than the general box-nature of our black
> box.
>
>
> Does this make sense?

Not really

> I am not suggesting that my model is one that
> would fit into BFO, just saying it's how I would produced a model.
>

understood

pierre

> Phil
>
> >
>

Phillip Lord

unread,
Apr 23, 2007, 1:22:52 PM4/23/07
to bfo-d...@googlegroups.com

>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> a) conductance is a property of the conductor only

PG> i woudl agree but this is becoming somewhat of a vacuous claim

Not sure whether this is good or bad!

>> But what is the conductor? Well I can't think of one. It's clear
>> that it's not the air (cause we could remove it, and the system
>> would work better), it's clear that it's not the string. Perhaps
>> it could be considered to be the ball which could be both
>> conductee and conductor. But I don't think that this makes sense
>> either.

PG> One possibility is that this is just not an example of
PG> conduction. You describe something which happens when a ping
PG> pong ball is in the electrical field generated by a condensator,
PG> right? Maybe this is pushing the notion of conduction a bit far,
PG> I dunno for sure.

I had to look "condensator" up on wikipedia! I would normally use
"capacitor".

Yes, this is the setup. Obviously, with this set up, the current
would jump up and down a bit, so the conductance would not be entirely
smooth over time. If you put say 10 balls however it would smooth a
lot. Inside a black box, you wouldn't be able to tell (well, except
for the noise).

>> Taking things a bit further, we can also use the example of an
>> electron gun. In this case, there are electrons flowing from a
>> filament through vacuum toward a +ve charged plate. Now in this
>> case, nothing in the middle betwen the electron gun and +ve
>> charged plate, other than the charged entity. So clearly, we
>> don't need what we have previously been calling the conductor.

PG> Yes, but then again, maybe you are shooting at something so
PG> general -- e.g. movement -- that we are not talking of
PG> conduction either.

*shrugs*. Well, you can measure the conductance of such a system.

>> So I think we have our terms wrong. In the case of the membrane,
>> what we have is a matrix,

PG> I don't understand, I don't know what a matrix is

Matrix -- something other stuff is embedded in. Extracellular matrix,
nuclear matrix, agarose gel matrix.


>> with ions moving through it. This whole thing is the
>> conductor. You can't lose any aspect of it, without it ceasing to
>> be a conductor (in this example, not in general). Hence my
>> conclusion that a membrane is not a conductor -- it's part of
>> one.

PG> I think I sort of see what you mean, this sounds odd

I'm an odd sort of chap.

>> We have also reached the conclusion that in general, the matrix
>> is not required. We can move a charged entity across a vacuum
>> quite happily.

PG> but you are just saying that there are different sort of
PG> translocation, if conduction is a translocation in a
PG> medium/conductor/matrix, translocation in vaccuum is just some
PG> other sort of thing

>> This would lead us to the conclusion, therefore, that electrons
>> in a vacuum are a conductor.

PG> I don't think this follows

With an electron gun, and a positive plate. You need the whole
system. A bunch of electrons sitting there in space minding their own
business would not be, I think.

>> But what about the charged entity? Well, take the ping pong ball
>> example. Now remove the ping pong ball. We now have two plates,
>> in a vacuum. No current. No conductor. But this is not true. If
>> we apply a AC current across the two plates, which are now acting
>> as a capacitor, the current will flow fine. In otherwords, we
>> still have a conductance.

PG> I'm not sure i understand, where does the current flow in your
PG> example?

If you have a capacitor connecting to an AC current, then it will
transmit this current continuously. Nothing is flowing across the
dielectric (the vacuum in this case) in the middle, except an
electrical field (or some kind of photon if you want to go
quantum). But it will move around the rest of the circuit.

In this case, incidentally, you would be able to tell inside a black
box, because the capacitor pushes the current out of phase wrt to the
voltage, and the apparent conductance varies with the frequency of the
current. More strictly, you might want to measure the impedance, but
this is just going to bring another electrical property, and will
confuse the issue.

>> And critically, there is nothing physical flowing between the
>> plates -- their interaction is purely at the level of electrical
>> fields; neither matter nor, I think, energy is flowing between
>> the two. Conclusion, the charged entity is also optional.

PG> I don't understand

You can conduct current without a charged entity moving, is what I am
saying, at least for the over the full loop within space that the
current appears to be moving.


>> So how would I model all of this? If we think of conductance in
>> the following way, I think life becomes easier. It's a property
>> of the conductor, but the conductor is a role of some system
>> (maybe comprising of a single entity).

PG> No you mean conductance is a property of an entity which has the
PG> role of being a conductor in certain circumstances.

Yeah, that might be clearer. Either works I think. I tend to prefer
mine, I think, but yours might be more straightforward.


PG> OK, let me anticipate on where I wanted to go. Seeing
PG> conductance as a disposition of the conductor would also mean
PG> that this disposition is realized when the conductor actually
PG> has its role, i.e. when it conducts. I am not particularly
PG> confortable with this, but this is the intuition.

Yeah, that would cover it. I guess with your representation any entity
which was capable of becoming a conductor would have a conductance,
where as in mine, it doesn't, unless it actually is conducting. Mine
representation makes more sense to me, but is counter to the way that
most electricians and scientists would think of it.


>> Now, those things that make the system a conductor do not always
>> require the same relationship with each other and the system. So,
>> in the case of the ping pong ball, it seems clear that the
>> conductive properties arise dependant on the individual ball,
>> string and plates.
>>
>> In the case of the membrane scenario, it's clearly the type of
>> sodium ion which is important not the individual ion. Hence, if
>> we take the membrane/sodium system and replace all the sodium
>> ions we have the same system, the same conductance property and
>> it will have the same numerical value. If we replace the ping
>> pong ball with another, on the other hand, then we have a
>> different system.

PG> No, it doesn't work like that, or I don't see what you mean
PG> because the terms 'same' and 'different' are ambiguous, we've
PG> talked about that. I can't be quite sure what you mean.

Well, identity is always a bit of a sod. I am not sure that I have got
to grips with exactly how you are referring to it. Of all the issues
we have discussed, I have been most confused by those relating to
whether conductance depends on these particular sodium ions, or the
type of sodium.

PG> It seems however that dependence on particular instances versus
PG> type is another issue.

I think that it is.

PG> Well, it depends really, I am not sure it makes sense to speak
PG> of conduction in the case of the ball and if it is not
PG> conduction we are talking about, maybe that it is one ball and
PG> not an entirely similar one which is involved is important. But
PG> I doubt this.

>> We don't even need to know about the parts of a system to know
>> that it has conductance -- we could have a black box with some
>> stuff inside it. We would not need to know whether there was a
>> membrane, ping pong ball or wire inside. If you replaced the box
>> with another box, then you would have a different system, as the
>> conductance is a property of the individual system, rather than
>> the general box-nature of our black box.
>>
>>
>> Does this make sense?

PG> Not really

One black box, and another black box are not alike, at least with
respect to conductance. All black boxes are alike in that they are all
boxes, black and we don't know what is inside them.


Hmmm. I hoped that my weekend brain wave would simplify the
situation. Perhaps, it has not.

Phil

William Bug

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Apr 23, 2007, 2:30:24 PM4/23/07
to bfo-d...@googlegroups.com
All right - I give in.  I think we're getting closer to a discussion that is immediately relevant to the NeuronDB neuron_ontology.owl.

To the best of our knowledge, what are the continuants involved in these Neuronal_current classes defined in neuron_ontology?  21 of the 22 classes defined in that ontology are in fact pores formed by macromolecular complexes (derived from a variety of genes) which are integral membrane proteins that collectively produce a pore through the lipid bilayer - a region into which saline can penetrate and not come into direct contact with the lipids making up the membrane. The remainder of the 22 - the I.K.leak current - is in fact a current that flows even in vitro in pure, artificial bilayers devoid of any exogenously added protein - e.g., see PubMed ID 9336176.  I'm not going to deal with I.K.leak below.

Here's why I've started to think Pierre's description of conductance as a disposition may in fact fit best to the real entities we are trying to model in this case.  Considering the pore-forming macromolecular complexes in hand, as studied (and modeled), they are thought of as having multiple conformational states (true of all proteins, correct?).  In the context of ion channel macromolecular complexes, single-channel recording enables us to observe the state transitions of individual pores.  With relatively rare exceptions, the typical pore in this case has two states - "open" (i.e., conducting) and "closed" (i.e., non-conducting).  For the voltage-dependent ion channels, change in the transmembrane voltage alters the equilibrium ratio of these states. The "open" state tends to be favored by more depolarized potentials (inside the membrane relatively more positive relative to outside), where as the "closed" state is typically more favored by at hyperpolarized potentials (inside the membrane relatively more negative relative to outside ).  The "inactivating" channels (I.K, I.K.A, I.Na.transient, and many others) have a third "inactive" state - a state that leads to the channel becoming unavailable to "open".  The "inactivate" state is favored by more depolarized potentials but the kinetics of transitions to this state tend to be slower than the transitions to the "open" state.  The direct effect on channels that possess an "inactive" state is they briefly open, the specific ions that match their "selectivity filter" start to flow down their electrochemical gradient, and then the channels "inactivate" - shutting off the flow.

You can observe all of this behavior directly - state transitions as represented by the rapid (< 200 microsecond) turning on and off of currents of a fixed size in the 100 fA - 10 pA range - with single-channel physiological recording.

Channels linked to neurotransmitter receptors can be thought of in much the same way, where in that case, the state transitions are a function of the conformational changes induced by ligand binding via allosteric interactions.  Here too there is typically a "closed", "open" and "inactive" state.  The latter is referred to as receptor "accommodation" whereby the receptor-linked channels even in the presence of bound ligand shift to a non-conducting state and remain there for a certain time even after the ligand has been released.

I'd also stress though we're working on neurons here, this issue is of general importance to nearly ALL cells, including prokaryotes.  You find voltage-dependent & receptor dependent channels in most epithelial and glandular secretory cells, in hepatocytes, chondrocytes, in E. coli and paramecium - all over - not just in what would conventionally be thought of as eukaryotic "excitable" cells such as neurons and myocytes.

Back to the point.

Why does disposition sound a like a good way to characterize ionic conductance to me? 

1) multiple-states
As described above, the "open" or conducting state is just one of many for the continuants involved.

2) context dependence
In addition to the "open" state being dependent on transmembrane voltage and/or the presence of ligands (both of which are really a context for these continuants - not an intrinsice property of the continuants themselves), even when "open", whether these channels conduct a current - and what ionic species carries that current - is completely dependent on the saline composition.  One can actually remove most of the primary conducting species from the salines - and/or block the selectivity filter pharmacologically - and still observe the transitions between "closed" and "open" - even though no significant current is flowing.  These experiments were done in the 1970s to measure what are called "gaiting" currents of voltage-dependent ion channels - essentially the shifting in dipole moment of the channel macromolecular complexes observed as the conformation shifts from "closed" to "open" to "inactive" and eventually back to "closed" again.  The hypothesis being tested there was if the voltage-dependent channels shift their confirmation as the electric field changes, there must be charged moieties on their peptide constituents that are responding to the change in electric field.  The conformation change is the result of dissipating the "strain" on these moieties introduced by the change in electric field.  If this is true, one should be able to measure some small re-arrangement of charges as the state transitions occur from  "closed" to "open" thereby opening the "gait", allowing ions to flow through the pore - hence the name "gaiting" current.

Taken together, I'm thinking - and I could be misinterpreting the BFO class definitions here - disposition fits better for ionic conductance than does function.  Reasonable people could differ on this, and there may still be a need for a related function.  Function as defined by BFO appears to be THE primary activity in which a continuant is involved.  Once could certainly argue both for voltage-dependent and ligand-dependent ion channels, their PRIMARY BIOLOGICAL FUNCTION is to conduct ionic currents.  I'd be hard-pressed to come up with any counter-argument to that claim.  But I can see how disposition may be the more fitting BFO representation in this case.

Cheers,
Bill

Phillip Lord

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Apr 24, 2007, 7:12:26 AM4/24/07
to bfo-d...@googlegroups.com
>>>>> "WB" == William Bug <Willi...@DrexelMed.edu> writes:

WB> Why does disposition sound a like a good way to characterize
WB> ionic conductance to me?

WB> 1) multiple-states
WB> As described above, the "open" or conducting state is just one
WB> of
WB> many for the continuants involved.

WB> 2) context dependence
WB> In addition to the "open" state being dependent on
WB> transmembrane
WB> voltage and/or the presence of ligands (both of which are really
WB> a context for these continuants - not an intrinsice property of
WB> the continuants themselves)


Bill

I'm largely in agreement with your analysis here, although I am not
really sure what is meant by "disposition" in the BFO sense. As you
say, conductance of a membrane or single channel will vary as a result
of many different things.

WB> Function as defined by BFO appears to be THE primary activity in
WB> which a continuant is involved. Once could certainly argue both
WB> for voltage- dependent and ligand-dependent ion channels, their
WB> PRIMARY BIOLOGICAL FUNCTION is to conduct ionic currents. I'd
WB> be hard-pressed to come up with any counter-argument to that
WB> claim. But I can see how disposition may be the more fitting
WB> BFO representation in this case.


I'm not sure about THE primary biological function. For instance, a
chloride channel in the gut would appear to have a very different
function from one in an axon -- in one case to enable transmission of
messages and one to ingest.

Phil

William Bug

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Apr 24, 2007, 11:21:13 AM4/24/07
to bfo-d...@googlegroups.com
You make an excellent point here, Phil, which I believe helps to clarify how one would define a bfo:function for ion channels (or their macroscopic equivalents - ionic currents), one that fits much better to the examples provided in the bfo.owl file for function.  Chloride channels in airway epithelial cells, gut epithelial cells, and CNS neurons MAY all exhibit indistinguishable biophysical and molecular characteristics.  In each case, however, their higher biological function will differ considerably - control of mucous secretion, digestion, and nerve cell activation.  Chloride channels in airway epithelial cells and glandular (gland as in sebaceous gland) epithelial cells, on the other hand, might be considered to have related or nearly identical function in this sense - i.e., osmosis-driven fluid secretion.  

This potentially provides a nice example of how underlying molecular continuants that MAY be defined identically and have identical continuant dispositions can contribute to completely different functions.  It can help to illustrate how BFO could be used to describe some of the more subtle, contextually-dependent complexity of biological systems - IF in fact our interpretation of how BFO classes should be applied in this case is correct.

I stress MAY above, because in the example I give above, one would want to examine the specific experimental evidence to determine whether such biomaterial molecular continuants should be considered to be identical at some fundamental level.

Cheers,
Bill



Matthias Samwald

unread,
Apr 24, 2007, 1:35:17 PM4/24/07
to BFO Discuss
I just saw that the rdfs:comment for the dispostion class gives
several examples for dispositions, one of them is "the disposition of
metal to conduct electricity." (quote). So I guess it has already been
decided?


Phillip Lord

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Apr 25, 2007, 8:51:05 AM4/25/07
to bfo-d...@googlegroups.com
>>>>> "MS" == Matthias Samwald <sam...@gmx.at> writes:

MS> I just saw that the rdfs:comment for the dispostion class gives
MS> several examples for dispositions, one of them is "the
MS> disposition of metal to conduct electricity." (quote). So I
MS> guess it has already been decided?

Matthias

As I think the discussion has shown, this isn't generalisable to a
membrane.

It's also worth mentioning that conductance is NOT the disposition to
conduct electricity. It's the ratio between voltage and current, when
passed over a conductor. Metal might have a disposition to conduct
electricity but this is not the same thing as a numerical value
associated with this tendency.

Phil

Pierre Grenon

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Apr 25, 2007, 9:10:22 AM4/25/07
to bfo-d...@googlegroups.com
On 4/25/07, Phillip Lord <philli...@newcastle.ac.uk> wrote:
>
> >>>>> "MS" == Matthias Samwald <sam...@gmx.at> writes:
>
> MS> I just saw that the rdfs:comment for the dispostion class gives
> MS> several examples for dispositions, one of them is "the
> MS> disposition of metal to conduct electricity." (quote). So I
> MS> guess it has already been decided?
>
>
>
> Matthias
>
> As I think the discussion has shown, this isn't generalisable to a
> membrane.

tut tut tut

not generalizable perhaps, but possibly similar...

> It's also worth mentioning that conductance is NOT the disposition to
> conduct electricity. It's the ratio between voltage and current, when
> passed over a conductor. Metal might have a disposition to conduct
> electricity but this is not the same thing as a numerical value
> associated with this tendency.

right, though the disposition is the anchor in the ontology for such a value

pierre

> Phil
>
> >
>

Pierre Grenon

unread,
Apr 25, 2007, 9:27:01 AM4/25/07
to bfo-d...@googlegroups.com
> >> a) conductance is a property of the conductor only
>
> PG> i woudl agree but this is becoming somewhat of a vacuous claim
>
> Not sure whether this is good or bad!

I'm not known for my optimism at the local biergarten, it's just that
we seem to have lost the notion of conductor

> I had to look "condensator" up on wikipedia! I would normally use
> "capacitor".

sorry, 'condensateur' in French, I tend to put -or wherever I can,

> Yes, this is the setup. Obviously, with this set up, the current
> would jump up and down a bit, so the conductance would not be entirely
> smooth over time. If you put say 10 balls however it would smooth a
> lot. Inside a black box, you wouldn't be able to tell (well, except
> for the noise).

this doesn't mean anything to me. Where does the current jump up and
down? Is it the balls moving in the field that you are calling the
current?

>
> >> Taking things a bit further, we can also use the example of an
> >> electron gun. In this case, there are electrons flowing from a
> >> filament through vacuum toward a +ve charged plate. Now in this
> >> case, nothing in the middle betwen the electron gun and +ve
> >> charged plate, other than the charged entity. So clearly, we
> >> don't need what we have previously been calling the conductor.
>
> PG> Yes, but then again, maybe you are shooting at something so
> PG> general -- e.g. movement -- that we are not talking of
> PG> conduction either.
>
> *shrugs*. Well, you can measure the conductance of such a system.

really you can? oh wait I think I see what you mean with the balck box.

Suppose there is something which produces a beam of elctrons A and
it's directed toward the plate B, the electrons start from A and
arrive in B. We have:

A-Vacuum-B

This is you black box, right? You plug something in A and you get some
detection device linked to B, or something along those lines. Then you
are saying we can measure the conductance of the blackbox based on
waht gets in at A and what gets out at B.

Is this something close to what you are having in mind?

This is mostly for the effect, but this sounds wrong.

Really, you are making things complicated, we have to start with an
homogeneous system, for lack of better word, better some simple, non
composite, 'conductor' (where this will mean a medium in which
something can move). Then we can worry about composites and black
boxes

> >> So I think we have our terms wrong. In the case of the membrane,
> >> what we have is a matrix,

...


> >> with ions moving through it. This whole thing is the
> >> conductor.

no this is just not analogous, maybe we should not speak about
conductance in the electrical circuit sense and try to adapt it to
other things, such as objects moving in sites or matrixes (is that the
plural?) of sort

> >> You can't lose any aspect of it, without it ceasing to
> >> be a conductor (in this example, not in general). Hence my
> >> conclusion that a membrane is not a conductor -- it's part of
> >> one.

But we have just lost the use of a notion of conductor here, replaced
with one of matrix. In both cases, the question arises of whether the
specific objects moving are what the feature of the thing in which
they move depend on

> >> We have also reached the conclusion that in general, the matrix
> >> is not required. We can move a charged entity across a vacuum
> >> quite happily.

wouldn't you say that vacuum is a medium of sort with some correlated
feature then? all of this seems circular

> With an electron gun, and a positive plate. You need the whole
> system. A bunch of electrons sitting there in space minding their own
> business would not be, I think.

yeah, but the case is not analogous, you want to deal with too many
things at once

> >> But what about the charged entity? Well, take the ping pong ball
> >> example. Now remove the ping pong ball. We now have two plates,
> >> in a vacuum. No current. No conductor. But this is not true. If
> >> we apply a AC current across the two plates, which are now acting
> >> as a capacitor, the current will flow fine. In otherwords, we
> >> still have a conductance.
>
> PG> I'm not sure i understand, where does the current flow in your
> PG> example?
>
> If you have a capacitor connecting to an AC current, then it will
> transmit this current continuously. Nothing is flowing across the
> dielectric (the vacuum in this case) in the middle, except an
> electrical field (or some kind of photon if you want to go
> quantum). But it will move around the rest of the circuit.

Right, no conduction between the plates of the capacitor, conduction
in the rest of the circuit:

capacitor: not conductor
rest of the circuit: conductor

sometimes capacitors endure 'claquage', in which case this seems
analogous to the electron beam, but then the conductor is whatever is
between the plates. In fact, there might even be a circuit here with
three conductors: plate A, medium, plate B.

> In this case, incidentally, you would be able to tell inside a black
> box, because the capacitor pushes the current out of phase wrt to the
> voltage, and the apparent conductance varies with the frequency of the
> current.

the apparent conductance varies? this is getting, well, strange

> More strictly, you might want to measure the impedance, but
> this is just going to bring another electrical property, and will
> confuse the issue.

no please,it's good to precise things strictly, you were speaking of
something else then, i understand the strangeness

> >> And critically, there is nothing physical flowing between the
> >> plates -- their interaction is purely at the level of electrical
> >> fields; neither matter nor, I think, energy is flowing between
> >> the two. Conclusion, the charged entity is also optional.
>
> PG> I don't understand
>
> You can conduct current without a charged entity moving, is what I am
> saying, at least for the over the full loop within space that the
> current appears to be moving.

I still don't understand

there is an electrical field, are you speaking about a field ? are you
being non strict again in speaking of current then?

>
> >> So how would I model all of this? If we think of conductance in
> >> the following way, I think life becomes easier. It's a property
> >> of the conductor, but the conductor is a role of some system
> >> (maybe comprising of a single entity).
>
> PG> No you mean conductance is a property of an entity which has the
> PG> role of being a conductor in certain circumstances.
>
> Yeah, that might be clearer. Either works I think. I tend to prefer
> mine, I think, but yours might be more straightforward.

ok, let's take what might be clearer then.

>
> PG> OK, let me anticipate on where I wanted to go. Seeing
> PG> conductance as a disposition of the conductor would also mean
> PG> that this disposition is realized when the conductor actually
> PG> has its role, i.e. when it conducts. I am not particularly
> PG> confortable with this, but this is the intuition.
>
> Yeah, that would cover it. I guess with your representation any entity
> which was capable of becoming a conductor would have a conductance,
> where as in mine, it doesn't, unless it actually is conducting. Mine
> representation makes more sense to me, but is counter to the way that
> most electricians and scientists would think of it.

well...

>
> Hmmm. I hoped that my weekend brain wave would simplify the
> situation. Perhaps, it has not.

what with all this Newcastle Brown having modified your brain's brain
wave-conductance...

pierre

> Phil
>
> >
>

Phillip Lord

unread,
Apr 25, 2007, 10:14:02 AM4/25/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

MS> I just saw that the rdfs:comment for the dispostion class gives
MS> several examples for dispositions, one of them is "the
MS> disposition of metal to conduct electricity." (quote). So I
MS> guess it has already been decided?
>>

>> As I think the discussion has shown, this isn't generalisable to
>> a membrane.

PG> tut tut tut

PG> not generalizable perhaps, but possibly similar...

Sorry, I didn't mean to appear abrupt. Yes, there is similarity
here, but a lot of discussion focused on what the conductor was. So
while there may still be a disposition to conduct electricity, it's
not clear that this relates to the membrane.

With metal, we have all we need -- a matrix (the atomic structure) and
charged entity (the electron probabilities) and away we go.

>> It's also worth mentioning that conductance is NOT the
>> disposition to conduct electricity. It's the ratio between
>> voltage and current, when passed over a conductor. Metal might
>> have a disposition to conduct electricity but this is not the
>> same thing as a numerical value associated with this tendency.

PG> right, though the disposition is the anchor in the ontology for
PG> such a value

I'd suggest that you need an layer of indirection in there. The
tendency to conduct electricity is one thing, the numerical measure of
this tendency another and the value of this numerical measure in a
particular case another still.

Phil

Pierre Grenon

unread,
Apr 25, 2007, 10:41:10 AM4/25/07
to bfo-d...@googlegroups.com
> PG> right, though the disposition is the anchor in the ontology for
> PG> such a value
>
> I'd suggest that you need an layer of indirection in there.

This must be geordie talk...

> The
> tendency to conduct electricity is one thing,

yes, and this is in the ontology of membranes, this is what we worry
about for the moment, we can plug any treatment of measurement later
on

> the numerical measure of
> this tendency another

here it is going to be another disambiguation routine:

the measurement or call it measuring as a laboratory procedure say?

ok then, and this belongs to an ontology of measurement

or is this data produced by such a process? If your worry is that
measures are approximative and so on, this can be embedded in the
suitable relation between the tendency and the measure...

> and the value of this numerical measure in a
> particular case another still.

i realize people who worry about measurement have various sort of
anguish, i'm not too sure what yours are with this

i think that sort of thing has been discussed in the past already
either on this list or the OBI's, i wouldn't know where to direct you
though

pierre

> Phil
>
> >
>

Phillip Lord

unread,
Apr 25, 2007, 10:51:26 AM4/25/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

>> I had to look "condensator" up on wikipedia! I would normally use
>> "capacitor".

PG> sorry, 'condensateur' in French, I tend to put -or wherever I
PG> can,

I thought it was the a translation thing. We have "condensor" in
English which means the same as "capacitor" but is generally
considered archaic usage.

>> Yes, this is the setup. Obviously, with this set up, the current
>> would jump up and down a bit, so the conductance would not be
>> entirely smooth over time. If you put say 10 balls however it
>> would smooth a lot. Inside a black box, you wouldn't be able to
>> tell (well, except for the noise).

PG> this doesn't mean anything to me. Where does the current jump up
PG> and down? Is it the balls moving in the field that you are
PG> calling the current?

Yes, the balls are charge entities moving in a field and so are
current. By current "jumping up and down" I was being imprecise. The
value of the current would change quite a lot. When the ball hits the
plate, you'd get a current spike


PG> Yes, but then again, maybe you are shooting at something so
PG> general -- e.g. movement -- that we are not talking of
PG> conduction either.
>>
>> *shrugs*. Well, you can measure the conductance of such a system.

PG> really you can? oh wait I think I see what you mean with the
PG> balck box.

Yes, very easily.

PG> Suppose there is something which produces a beam of elctrons A
PG> and it's directed toward the plate B, the electrons start from A
PG> and arrive in B. We have:

PG> A-Vacuum-B

A is an electron gun (a hot filament with a -ve potential), otherwise,
yes.

PG> This is you black box, right? You plug something in A and you
PG> get some detection device linked to B, or something along those
PG> lines. Then you are saying we can measure the conductance of the
PG> blackbox based on waht gets in at A and what gets out at B.

Yes.


PG> Really, you are making things complicated, we have to start with
PG> an homogeneous system, for lack of better word, better some
PG> simple, non composite, 'conductor' (where this will mean a
PG> medium in which something can move).

Is my point, I think. A metal wire is NOT a conductor through which
electrons can move. The electrons are (part of) the metal. Take away
the electrons, you no longer have a metal. This is not a merelogical
essentialist (I think you called it) argument here. No electrons, you
have a pile of protons.


>> >> with ions moving through it. This whole thing is the
>> >> conductor.

PG> no this is just not analogous, maybe we should not speak about
PG> conductance in the electrical circuit sense and try to adapt it
PG> to other things, such as objects moving in sites or matrixes (is
PG> that the plural?) of sort

"matrix" in this sense is not pluralisable I think.

Well, conductance is measureable in either circumstance, and in an
identical way (think black box).


>> >> You can't lose any aspect of it, without it ceasing to be a
>> >> conductor (in this example, not in general). Hence my
>> >> conclusion that a membrane is not a conductor -- it's part of
>> >> one.

PG> But we have just lost the use of a notion of conductor here,
PG> replaced with one of matrix.

My idea is that the matrix (the membrane, the solvent) is part of the
conductor.


PG> In both cases, the question arises of whether the specific
PG> objects moving are what the feature of the thing in which they
PG> move depend on

I'm still not sure I can answer this.

>> >> We have also reached the conclusion that in general, the
>> >> matrix is not required. We can move a charged entity across a
>> >> vacuum quite happily.

PG> wouldn't you say that vacuum is a medium of sort with some
PG> correlated feature then? all of this seems circular

Well a vacuum, an 4D volume of spacetime, whatever, isn't a medium, in
that sense of the word.


>> With an electron gun, and a positive plate. You need the whole
>> system. A bunch of electrons sitting there in space minding their
>> own business would not be, I think.

PG> yeah, but the case is not analogous, you want to deal with too
PG> many things at once

Sorry!

>> If you have a capacitor connecting to an AC current, then it will
>> transmit this current continuously. Nothing is flowing across the
>> dielectric (the vacuum in this case) in the middle, except an
>> electrical field (or some kind of photon if you want to go
>> quantum). But it will move around the rest of the circuit.

PG> Right, no conduction between the plates of the capacitor,
PG> conduction in the rest of the circuit:

PG> capacitor: not conductor rest of the circuit: conductor

No. A capacitor conducts electricity with a conductance that changes
over time. So

I = C dV/dt (eqn 1)

which means that for a given t, we can calculate I/V or
conductance.

>> In this case, incidentally, you would be able to tell inside a
>> black box, because the capacitor pushes the current out of phase
>> wrt to the voltage, and the apparent conductance varies with the
>> frequency of the current.

PG> the apparent conductance varies? this is getting, well, strange

Well, my apologies for using "apparent", but yes the conductance
varies. After sometime, given eqn 1, a DC current over a capacitor will
have no current (therefore a conductance of 0). If you use an AC
current, then you can have a constant current flowing (well,
alternating but still constant in that sense) and a conduntance of
some non-zero value.

Now, a DC current is just an AC current with an frequency of zero, so
it's clear that the frequency is important.

>> You can conduct current without a charged entity moving, is what
>> I am saying, at least for the over the full loop within space
>> that the current appears to be moving.

PG> I still don't understand

PG> there is an electrical field, are you speaking about a field ?
PG> are you being non strict again in speaking of current then?

Again, I don't think so. We could argue whether the current is flowing
over the gap or not, till we are blue in the face. I *think* that the
physicist would say that there is a flux in the system, as you can't
measure the current without changing the system.



>> Yeah, that might be clearer. Either works I think. I tend to
>> prefer mine, I think, but yours might be more straightforward.

PG> ok, let's take what might be clearer then.

Ok.


>> Yeah, that would cover it. I guess with your representation any
>> entity which was capable of becoming a conductor would have a
>> conductance, where as in mine, it doesn't, unless it actually is
>> conducting. Mine representation makes more sense to me, but is
>> counter to the way that most electricians and scientists would
>> think of it.

PG> well...

I should qualify this and say, it's counter to the way I THINK most
electricians and scientists would think of it. Does a conductor have
conductance when it's not conducting is a sound-of-one-hand-clapping
kind of argument.


>> Hmmm. I hoped that my weekend brain wave would simplify the
>> situation. Perhaps, it has not.

PG> what with all this Newcastle Brown having modified your brain's
PG> brain wave-conductance...

Think it was Marstons pedigree actually, but yeah, it's possible.

Phil

Phillip Lord

unread,
Apr 25, 2007, 11:34:38 AM4/25/07
to bfo-d...@googlegroups.com
>>>>> "PG" == Pierre Grenon <pierre...@gmail.com> writes:

PG> right, though the disposition is the anchor in the ontology for
PG> such a value
>>
>> I'd suggest that you need an layer of indirection in there.

PG> This must be geordie talk...

>> The tendency to conduct electricity is one thing,

PG> yes, and this is in the ontology of membranes, this is what we
PG> worry about for the moment, we can plug any treatment of
PG> measurement later on

>> the numerical measure of this tendency another


PG> i realize people who worry about measurement have various sort
PG> of anguish, i'm not too sure what yours are with this

PG> i think that sort of thing has been discussed in the past
PG> already either on this list or the OBI's, i wouldn't know where
PG> to direct you though


Well, I have a height, and height can be measured, so there is some
measurement of height (and all spatial dimensions share this) and then
the measurement of my specific height.

Conductance is the middle of these three, I think.

I agree that this will have been discussed within OBI. I shall ask my
chums.

Phil

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