nameless taxonomy/barcoding life

Doug Yanega dyanega at POP.UCR.EDU
Tue Feb 4 17:13:37 CST 2003


David Orlovich wrote:

>Let's use the other half of the brain for a moment ... apart
>from salary (which I'll assume for this argument is paid for by your
>institution), what is the most expensive aspect of non-molecular
>systematics research?  I'd say field work.  So, if you're going to
>write a grant application to carry out traditional systematics
>research, how will you get the most amount of money?

Hmm. I think a better case could be made that the major expense in
traditional systematics is traveling to see type specimens at
institutions that will not or cannot loan them out.

>So, if some people don't like the provocative comments from a "DNA is
>the only things that exists"-type of scientist, then I reckon the idea
>is to add value to the DNA with whatever means you have, be it
>traditional or otherwise, and look for holistic approaches to
>systematics, and not get into an "us and them" argument about it.

You can't add "DNA value" to a project that involves only
decades-to-centuries-old museum specimens any more than you can add
DNA to a paleontology project. We may not all work on fossils, but
for most practical purposes, there is little difference - most of
what we do involves material that cannot be sequenced (and it will
continue to be this way as long as mega-diverse countries maintain
Byzantine permitting regulations, enforce draconic limitations on
exchange of specimens, and/or encourage their citizenry to obliterate
the natural environment; note that even countries like the US fall
under this umbrella, not just "developing" countries). Even if we
*were* to accept the premise that only taxonomy based on
freshly-collected, sequenceable specimens was worthwhile, there
aren't enough cubic space of freezer space on the *planet* to hold
the 50,000,000 liters of arthropod samples alone that would
accumulate in backlog awaiting sequencing in just the first year.
After all, even if every institution in the world had an entire
building full of sequencers, there is still an incredible amount of
human labor required to extract and amplify DNA for sequencing, a
bottleneck Dr. Hebert ignores in his 20-year estimate.

Andrew Mitchell tried to support this approach, saying:

>  >Note the figure mentioned of 1 billion dollars.
>Do you think the cost is excessive? The human genome project is
>estimated to have cost $3 billion over 15 years. Why not $1 billion over
>20 years as suggested.

Because that doesn't even come close to being realistic. Just
consider the labor alone, as I mentioned above:
In a real-world molecular lab, it requires (with all time-consuming
steps taken into account, bearing in mind the ability to perform
multiple extractions at one time, and averaged) between 1 and 2 hours
of technician labor to take each preserved specimen and extract a DNA
sample that is ready to sequence. Let's be EXCEEDINGLY generous and
cut it to one hour of labor per specimen, ignoring the many months of
trial and error needed to find primers and gene regions to sequence
for each different taxon. A work year is approximately 2000 hours of
labor (50 weeks times 40 hours per week). That means each technician
can process 2000 specimens per year. If I'm doing an insect survey, I
can easily collect 2000 specimens in two hours at a black light in
Honduras, or do the same with a malaise trap in one day. Therefore,
just one locality's samples for a year (easily 200K specimens) will
require a minimum of 100 technicians to keep ahead of the backlog.
This is even assuming that one or more technicians with morphological
training have gone through the samples and pulled out only
*exemplars* of each morphotaxon, so maybe only 5% of the collected
material actually gets sequenced; the total number of specimens from
which those 200K samples were culled could easily exceed 5 million
(this is from first-hand experience with just such a project, so
these are realistic figures - and that's JUST for insects!). If we
give the technicians a modest yearly salary of, say, US$40K, then
we're at $4 million to process just ONE year's set of samples as fast
as they're collected.

With me so far? So, we have 100 technicans processing 200K specimens
from a single collecting locality per year, then we sample each
locality for 2 years, to help account for annual variation and
sampling error. Are 400K specimens enough to detect and document
every species of organism that occurs in a single locality? Doubtful,
but let's assume it is. That means each team of 100 can cover 10
localities in 20 years, at a cost of $80 million per team. Now, how
many different localities will we need to sample to cover just the
*terrestrial* life forms? That $1 billion projection would, if labor
to process specimens were the ONLY expense (i.e., ZERO costs for
field work, preservatives, shipping, equipment, and storage, ZERO for
photographic records of specimens destroyed by sequencing, ZERO for
the actual extraction and sequencing, ZERO for lab and office space
to house the personnel involved, etc.), only allow for roughly 1000
different localities to be sampled thoroughly in those 20 years -
requiring 10,000 technicians. Does anyone here believe that we could
find and sequence every species of terrestrial life just by
intensively sampling 1000 different localities for 2 years each?

Then add in all the things this hypothetical scheme excludes, and
we're probably talking about more like 10 billion dollars JUST TO GET
THE SEQUENCES for those 1000 localities. Then add in doing sequence
alignments, working out relationships, data entry and storage, and
other post-sequencing expenses. Then add in the aquatic habitats. You
get the idea. The human genome project was NOTHING compared to what
Hebert is proposing. Sure, even the traditional approach to this task
would be expensive, but it would almost certainly be much cheaper
than Hebert's plan. The real bottleneck with that is having enough
taxonomists to cover all the different taxa; I doubt that even 10,000
taxonomists working for 20 years would be enough if there are really
50 million species left to describe. Either way, $1 billion isn't
nearly enough - we'd be lucky if that much money even got us a list
of all the mite species of the world. Even if we had $1 billion a
year, I think expecting the task to be done in 20 years would be
unrealistic. To pick up an analogy used here before, the library is
burning, while we're arguing about whether a robot could pull all the
books out cheaper and faster than a team of firemen. Me, I don't
trust robots; give me more firemen and screw trying to automate the
process.

>  >This is not for sequencing
>>all the genes of all taxa, but for sampling.
>Sequencing all the genes of all the taxa? THAT would indeed be a waste
>of time and money. Why determine a few billion nucleotides from each
>species when a few thousand will do the job? We *sample* taxa not only
>because of limits of time and money but because of the law of
diminishing returns.

Even if that was what Hebert was implying, the excerpts didn't convey
the impression that this was supposed to be in conjunction with
conventional morphological analyses - he said they only come "later",
after the MANDATORY sequencing has been done (and, presumably, not
included in the $1 billion budget). What a load of
cart-before-the-horse rubbish, especially when so many of the world's
extant species are (and only ever will be) known from unsequenceable
museum specimens, just due to sampling error alone. Ultimately,
traditional taxonomists cannot be limited solely to studying that
which can be sequenced. That would be a completely different sort of
science, and molecules can only be subservient to traditional
systematics if the two fields are to co-exist at all.

Why? If the world came to be dominated by molecular biology, we and
everything we do would be rendered superfluous, since the foundation
of traditional systematics is type specimens - for which we will
*never* have the DNA sequences. This is apparently the intrinsic
appeal (to non-taxonomists, at least) of the logical endpoint of
Hebert's unquestionably myopic vision: a world where there are no
taxonomists to impede progress, no excruciating delays in getting
specimens identified, no reliance upon any outside authority's
opinion, no revisions or keys to consult, and no disorienting changes
in classification. Just submit your sequence, see if it turns up a
match, and if not, it's automatically registered as a new taxon, and
the "master cladogram of life" database is updated to insert it at
the appropriate point. The fact that this vision is absolutely
*impossible* to attain evidently has no bearing on the ability or
willingness of people like Hebert to blithely dismiss an entire field
of science that they clearly don't appreciate, and apparently don't
truly understand. That we've had 250 years and only done 10% of the
job cannot be blamed on the morphological approach, but rather on how
pitifully our science is supported relative to what it actually needs
to *do* the job! To condemn several generations of scientists' best
efforts (while claiming you can do better) over lunch with colleagues
is one thing, but to do so in such a high-profile public forum -
under a pretense of authority - is irresponsible and unforgivable
(and yes, I do realize the irony of condemning HIM in public, but
he's just so fundamentally, baldfacedly *wrong* I can't help
returning fire).

For that matter, I can think of a least a few Guelph alumni
systematists who would not look kindly on being relegated to the
dustheap by some grandstander from their alma mater. Maybe they
should write a few scathing letters. Then again, I believe Hebert is
a tenured department chairman, and so feels safe to say anything he
darn well pleases, however wrong it may be. ;-)

Sincerely,
--

Doug Yanega        Dept. of Entomology         Entomology Research Museum
Univ. of California - Riverside, Riverside, CA 92521
phone: (909) 787-4315 (standard disclaimer: opinions are mine, not UCR's)
            http://entmuseum9.ucr.edu/staff/yanega.html
   "There are some enterprises in which a careful disorderliness
         is the true method" - Herman Melville, Moby Dick, Chap. 82




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