[Taxacom] New species of the future

Wed Oct 30 13:36:57 CDT 2013

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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