Inflorescence - Peduncle

Mon Dec 6 18:22:04 CST 2004

I agree with all you say.....but the problem still remains: words/terms can have various definitions and meanings according to context and usage - but unless an attempt is made to formalize and relate these definitions and usages we cannot progress knowledge integration.

One possible route to achieve this is to define extents/domains of usage where a defined terminology might apply - and to create a well-defined terminology for this domain. Initially this might be just one small user group - but in order to share data with other user groups an agreed shared terminology - or a mapping between separate terminologies  is required.

The technique of capturing a terminology as a set of defined terms with (possibly multiple) relationships between terms can be used to create an 'ontology', which formalizes a terminology even further and allows one to reason about the relationships between terms. For example  the term  'leaf'  can have a textual definition, and  in addition can have  defined relationships to other terms - these could include developmental, homology, compositional, etc relationships. Different users could reason over this knowledge according to their needs: some users may not wish to know/consider that leaves, petals and bracts are all homologous structures, for other work it would be critical. 

The ontology that we built in our work is relatively simplistic in that it reflects the terminolgy used in the classical morphological description of angiosperm specimens,  and olly captures a few relationships between terms (specifically not developmental homologies). It is however extensible, and new terms and definitions can be added. We realize that there are enormous biological  not to mention sociological difficulties in creating more useful inter-taxon terminologies, but the development of semi-formal ontologies is one route that could be followed because it allows users to explore term relationships according to different viewpoints (and is being widely developed in other domains of biological knowledge description).

I used the phrase 'old chestnut' to imply  'a well known story'

a better idiom would be 'can of worms' - ;-)

>-----Original Message-----
>From: Richard Jensen [mailto:rjensen at saintmarys.edu]
>Sent: 06 December 2004 17:42
>To: Paterson, Trevor
>Cc: TAXACOM at LISTSERV.NHM.KU.EDU
>Subject: Re: Inflorescence - Peduncle
>
.>......  In my quick reading of your discussion of 
>Descriptive  Elements, I noticed that there was no reference 
>to the problem of homology.  In fact. you use
>two of my favorite examples of the problem of homology: leaves 
>and berries.  Many plants have what appear to be simple 
>leaves, but not all simple leaves are homologous structures.  
>And, every fruit that is called a berry (as you say in your 
>paper "fruit is of the type berry") is not the same.
>
>I see nothing in your model that answers the question posed: 
>what is a peduncle?  If we have an inflorescence, is the 
>peduncle part of the inflorescence or is it part of the shoot 
>supporting the inflorescence?  Is there some biological 
>reality that would allow me to refere to one shoot as a 
>peduncle and another as a stem (or branch, twig,
>etc.) and know that I am referring to two different 
>structures?  Agreeing on terminology is not the same as 
>agreeing on homology and proper comparisons of taxa require 
>that the comparisons be based on perceived homologies.
>
>Cheers.
>
>Dick
>
>"Paterson, Trevor" wrote:
>
>> This issue is a very old chestnut:
>>
>> Unless people suscribe to a shared terminology (i.e. agree 
>shared  definitions of  structures, states, measurement units 
>etc.) they will never be able to share  and compare data meaningfully.
>>
>> We have a paper coming out in Taxon soon about this, and a 
>rather more technical/computer modelling paper available online:
>>
>> Paterson, T., Kennedy, J.B., Pullan, M.R., Cannon, A., 
>Armstrong, K., Watson, M.F., Raguenaud, C., McDonald, S.M., 
>Russell, G.: A Universal Character Model and Ontology of 
>Defined Terms for Taxonomic Description. Proc. Data 
>Integration in the Life Sciences (DILS 2004) (ed. E. Rahm) in: 
>Lecture Notes in Bioinformatics 2994 (2004) pp63-78
>>
>> 
>http://www.dcs.napier.ac.uk/~prometheus/prometheus_2/publicatio
ns/Paterson_etal_DILS.pdf
>>
>>
>> Trevor Paterson PhD
>> t.paterson at napier.ac.uk <mailto:t.paterson at napier.ac.uk>
>>
>> School of Computing
>> Napier University
>> Merchiston Campus
>> EDINBURGH
>> EH10 5DT
>> Scotland UK
>>
>> tel:          +44 (0)131 455-2752
>>
>> www.dcs.napier.ac.uk/~cs175
>> <http://www.dcs.napier.ac.uk/~cs175> www.prometheusdb.org 
><http://www.prometheusdb.org>
>>
>> >-----Original Message-----
>
>> >From: Taxacom Discussion List [mailto:TAXACOM at LISTSERV.NHM.KU.EDU]On
>> >Behalf Of Richard Jensen
>> >Sent: 06 December 2004 16:06
>> >To: TAXACOM at LISTSERV.NHM.KU.EDU
>> >Subject: Re: [TAXACOM] Inflorescence - Peduncle
>> >
>> >
>> >Curtis Clark wrote:My general tendency is to call everything
>> >basal to the
>> >pedicels and
>> >
>> >> terminal to the first foliage-leaf-bearing node the
>> >peduncle, but it's
>> >> worth noting that the stalk of a grass spikelet, tecnically
>> >a peduncle,
>> >> is usually called a pedicel.
>> >
>> >If the stalk of the individual spikelet is a pedicel, then
>> >what is the stalk
>> >of the entire inflorescence?  And, what about grasses that have
>> >single-flowered spikelets, e.g., Zizania?  Is the stalk of the
>> >spikelet then
>> >a pedicle and the stalk of the inflorescence a peduncle?
>> >
>> >A grain of wisdom would come in handy about now.
>> >
>> >Dick
>> >
>> >Dick
>> >--
>> >Richard J. Jensen              | tel: 574-284-4674
>> >Department of Biology      | fax: 574-284-4716
>> >Saint Mary's College         | e-mail: rjensen at saintmarys.edu
>> >Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen
>> >
>
>--
>Richard J. Jensen              | tel: 574-284-4674
>Department of Biology      | fax: 574-284-4716
>Saint Mary's College         | e-mail: rjensen at saintmarys.edu
>Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen
>
>
>