[Taxacom] New species of the future

Wed Oct 30 18:10:20 CDT 2013

Van Valen's conjecture was that if two organisms are "doing the same thing"
(think multidimensional niche), then, for the purposes of understanding
their role in a system, they are the same thing.  If they are allopatric,
they can't be doing the same thing - they must, by definition, be in
different environments.

I'm not suggesting that we should use this as an operational species
concept.  What I was trying to point out was that until we understand
exactly what an organism is doing, we can't answer van Valen's question.
Besides, according to the posts here, this new species is different in
substantive ways and my guess is that it is doing something that no other
species is doing.

Dick J

On Wed, Oct 30, 2013 at 3:51 PM, Stephen Thorpe
<stephen_thorpe at yahoo.co.nz>wrote:

> That's a controversial claim! For a start, different species could be
> doing the same thing in different places (i.e. allopatry), and if they are
> sympatric, a morphological difference in genitalia might be keeping them
> separated, even if they are "doing the same thing". I'm not convinced that
> competitive exclusion really would eliminate all but one of them. At least
> it might take some time (millions of years?)
>
>   *From:* Richard Jensen <rjensen at saintmarys.edu>
> *To:* JF Mate <aphodiinaemate at gmail.com>
> *Cc:* Taxacom <taxacom at mailman.nhm.ku.edu>
> *Sent:* Thursday, 31 October 2013 8:39 AM
> *Subject:* Re: [Taxacom] New species of the future
>
> An observation on this quote:
>
> "People, reasonably, want to know what this new taxon is doing differently
> from other things.  If nothing, then why do we need to name it?"
>
> If it's not doing anything differently from other things, then it must
> belong to an existing species, a la van Valen's ecological species
> concept.  Thus, it already has a name and we just haven't recognized it as
> belonging to an existing species.  But, the rather detailed description
> would lead us to a different conclusion (it is a species in its own right)
> and we simply don't know enough to fully evaluate what it is doing!
>
> Dick J
>
>
> On Wed, Oct 30, 2013 at 2:36 PM, JF Mate <aphodiinaemate at gmail.com> wrote:
>
> > Dear Lyubomir,
> >
> > the quote you are replying to is in reponse to this statement from Dave:
> >
> > "People, reasonably, want to know what this new taxon is doing
> differently
> > from other things.  If nothing, then why do we need to name it?"
> >
> > I am not sure what you interpreted but I think that should at least
> clarify
> > what I meant.
> >
> > In regards to:
> > "Now a transcriptomic profile, although still not trivial as barcoding
> is,
> > is definitely affordable. Even a full genome sequencing is now affordable
> > for a middle-size institution."
> >
> > In spite of continuously decreasing cost of X-omics, it is still outside
> > the reach of most taxonomists or even countries. As such, it is more
> > valuable and cost-effective to extract and preserve the DNA of new
> species
> > for future full genome sequencing, than doing a transcriptome now.
> Further,
> > although one transcriptome was not a bank-breaker for this institute, I
> am
> > convinced that a monograph including a few tens of species (not unusual
> in
> > invertebrates) would have raised some alarm in the treasury.
> >
> > Having said that, I admit that for taxonomists like Dan, there is no
> option
> > but going molecular now regardless of the cost. But his is a special
> case:
> >
> > Microscopic size
> > Few morphological characters
> > Broadly overlapping techniques
> > More generous funding due to obvious economic applications
> >
> > And that is why I was clear to stress "in this particular case". In
> > hindsight maybe I should have said "in the case of this particular
> > organism" and saved myself some grief.
> >
> >
> > Best
> >
> > Jason
> >
> >
> >
> > On 30 October 2013 18:08, Lyubomir Penev <lyubo.penev at gmail.com> wrote:
> >
> > > "Chalara fraxinea or Agrilus planipennis were probably not very
> > interesting
> > > when first described. You cannot determine a priori the value of a
> > species,
> > > and often it requires decades to build a basic picture of the biology
> and
> > > ecology of each one. So how exactly is this model going to accelerate
> the
> > > output?"
> > >
> > > Jason, how one could know "a priori the value of a species description"
> > > for this centipede species?
> > >
> > > It won't take decades, it will take few more years to see the true
> value
> > > of this kind of pilots. Just a few years ago, it was impossible even to
> > > dream for a full transcriptome sequencing and micro CT simply did not
> > exist
> > > (at least for the purposes of taxonomic research). Now a transcriptomic
> > > profile, although still not trivial as barcoding is, is definitely
> > > affordable. Even a full genome sequencing is now affordable for a
> > > middle-size institution.
> > >
> > > Is, for example,  producing phylogenies that may change with adding a
> > > single new taxon, of more value or more cost-efficient than a
> fundamental
> > > description of species, even of "unknown value" at the point of
> > > description?
> > >
> > > Taxonomy is not a low cost science at all, at least until we think that
> > > publishing of a name and diagnosis, or sharing a PDF description with
> 5-6
> > > fellow taxonomists, is all what the "people" want.
> > >
> > > Cheers,
> > > Lyubomir
> > >
> > >
> > >
> > >
> > >
> > > On Wed, Oct 30, 2013 at 5:06 PM, JF Mate <aphodiinaemate at gmail.com>
> > wrote:
> > >
> > >> To Dave Kirk and Lyubomir:
> > >>
> > >> We are discussing two separate things here. On the one hand we have
> the
> > >> rise of digital, media-rich publications. To me multiple sources of
> > >> information added to a description or any other paper for that matter
> > is a
> > >> plus. As an exercise or proof of concept I see the angle of the paper.
> > But
> > >> deep down it is a PR exercise, which no doubt is necessary in these
> days
> > >> of
> > >> shrinking budgets. But if this is the case, expensive descriptions are
> > not
> > >> going to enhance biodiversity inventorying.
> > >>
> > >> My argument is that a big portion of the cost is down to the cybertype
> > >> and the transcriptome. I can see the applications of the CT scans,
> > though
> > >> I
> > >> would argue that a cyber-type can also take other forms. The
> > transcriptome
> > >> though is superfluous. I understand that BGI wants to do its 1000
> > >> transcriptome project but really, not useful in this specific case.
> Its
> > >> use
> > >> is more like a placeholder for a genome or as another bit of data
> added
> > >> for
> > >> sales purposes. Nothing wrong, simply rather pointless. Maybe if the
> > paper
> > >> had included several stages and both genders or done a comparison
> across
> > >> several close species, then I could understand its inclusion.
> > >>
> > >> This brings me to the issue of expectations by "people" (not sure who
> > you
> > >> are referring to). People have multiple expectations but surely a
> common
> > >> one should be the ability to successfully discriminate species X from
> > all
> > >> other previously described species. At its most basic, people just
> want
> > a
> > >> name. After that come the questions: what does it do; is it dangerous;
> > >> rare, etc. But the first step is establishing that this group of
> > organisms
> > >> is different from the other groups we have previously defined, and it
> is
> > >> identified for human purposes with this label.
> > >>
> > >> In this respect taxonomy is very economical, probably  the most
> > economical
> > >> aspect of biology, yet the argument here is that before spending a
> small
> > >> amount of resources describing organisms we should spend a bunch to
> > >> determine if they are worthy of description in the first place.
> Ignoring
> > >> the problems with this economic model, who determines what is worthy?
> > >> Chalara fraxinea or Agrilus planipennis were probably not very
> > interesting
> > >> when first described. You cannot determine a priori the value of a
> > >> species,
> > >> and often it requires decades to build a basic picture of the biology
> > and
> > >> ecology of each one. So how exactly is this model going to accelerate
> > the
> > >> output?
> > >>
> > >> When it comes to cost "(5) The effort was huge, the costs are there,
> but
> > >> the project is not that
> > >> expensive as one might think. It is surely cheaper if compared to the
> > >> costs of
> > >> an expedition to a tropical country to collect new species that will
> > >> (probably)
> > >> be never described." Yes, an expedition to the tropics to collect
> > material
> > >> is costly, probably more than a single description, but that is
> > comparing
> > >> apples and oranges. I am sure that spelunking for critters is costly
> as
> > >> well, more so if we work out the cost per new species uncovered, but
> > what
> > >> we are discussing here is taxonomy. How Laputan taxonomy would improve
> > >> access to funds is an open question, unless things have changed a lot
> > >> lately and resources are infinite.
> > >>
> > >> So to me point 3 in Lyubomir´s list is the paper the aim of the paper,
> > and
> > >> there is nothing wrong with it, but the rest, including taxonomy, is
> at
> > >> best incidental.
> > >>
> > >> Best
> > >>
> > >> Jason
> > >>
> > >> P.S. "tight adherence to the Old Ways is not going to ensure the
> > survival
> > >> of taxonomy" not the best sales pitch
> > >> _______________________________________________
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> > >>
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> > >>
> > >> Celebrating 26 years of Taxacom in 2013.
> > >>
> > >
> > >
> > >
> > > --
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> >
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>
> --
> Richard Jensen, Professor
> Department of Biology
> Saint Mary's College
> Notre Dame, IN 46556
>
> _______________________________________________
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>
> The Taxacom Archive back to 1992 may be searched with either of these
> methods:
>
> (1) by visiting http://taxacom.markmail.org/
>
> (2) a Google search specified as:  site:
> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>
> Celebrating 26 years of Taxacom in 2013.
>
>
>

-- 
Richard Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556