Burning library books - loss of information = loss of context?

Richard Pyle deepreef at BISHOPMUSEUM.ORG
Thu Aug 22 11:44:42 CDT 2002


> So the analogy is that the books are species. The language they
> are written
> in is their 'context' representing the species' habitat and all of the
> ecological (biotic and abiotic) interactions that involves.

As I said previously, the analogy as posted to this list was but a brief
summary of the original, which included more language about the importance
of documenting the ecological context of the specimens as they are captured.
Without a good understanding of that context, future efforts to reconstitute
lost biodiversity might end up representing little more than highly divers
"zoos", that don't quite "work" as an ecological community.

However, the language of the "books", as I originally conceived the analogy,
consists of only four letters: A, G, T, C ("and sometimes U").  The value of
the vault contents, in my opinion, is not so much the flesh-and-blood
specimens, but rather the vast diversity of DNA sequences they contain.  The
content of those "texts" was written by evolution over the course of
billions of years (or at least a quarter of a billion years, in terms of
most of the more visible critters & weeds that are most in peril). The
"fire" may destroy it all over the course of a mere few decades or
centuries -- a virtual instant in Earth's history.  When I imagine myself as
an extraterrestrial outside observer, I can't help but characterize modern
human society (in general) as reckless, irresponsible teenagers, naively
squandering perhaps their most precious asset, without even an inkling of
the potential consequences down the road.

Yes, we need to capture information about how the living things interact
with each other, etc.  But a lot of that has the potential of reconstituting
itself over time.  There are many examples of obliterated habitat that
undergoes a series of natural successions of communities, perhaps over many
decades or centuries, to re-create "old growth" wilderness.  It certainly
won't happen magically, and historically it has happened only in the context
of adjacent or surrounding "old growth" that has remained intact to serve as
the source of colonizers.  So certainly if future human societies ever are
to have hope of reconstituting biodiversity and natural habitat, they will
need a robust knowledge of ecology.

But still, the goldmine of information, in my view, is the *genetic*
diversity.  Within those whole genomes lie the bulk of information not just
about development and morphology, but behavior and inter- and intra-species
interactions.  The blueprints are the most important thing to preserve, if
the building cannot be saved.  The letters and words in the books are the
base pairs and codons of the genomes; and at this point in human history
(for how much longer, I don't know), it's still easier to preserve a
specimen with intact genomes, than it is to acquire a complete genomic
sequence from a specimen.  That threshold may eventually be crossed; but I
imagine there will still be value in preserving the "flesh & blood" (wood &
leaf) specimens along with their whole genomes.

> The death of
> this language does not necessarily imply the loss of the habitat, but
> represents the removal of the book (a.k.a. species) from its context
> (a.k.a. habitat); effetively the extinction of the species. The vault is
> still the museum collections. The 'linguistics expert' is your friendly
> neighbourhood gene-jockey with his DNA sequencing widget in his back
> pocket. Letters, words and sentences are nucleotides, genes and gene
> complexes. Meanwhile the vernacular language and nuances are more plastic
> responses (morphological or behavioural) manifested in response to every
> day life.

Yes, now I see we are more in agreement than I had previously thought.  And
this is why I think that some (50? 75?) of the volunteers need to remain on
the task of carrying buckets, so your concept of the "language" can be
preserved in as many places as possible, allowing a future society that
takes on the task of reconstituting nature will have as many and varied
templates to learn the language from.  The problem as I see it now, though,
is that a great amount of attention is devoted to putting out the fire, and
a fair amount is placed on trying to understand how the library is
structured (i.e., using only the larger, more obvious books to extrapolate
the value of the entire collection; and understanding how different books
relate to each other from the general subject level down to the "Edition"
and "Printing Run" level) -- but appallingly little effort is placed on
filling up the contents of the vault -- not for real-time, current analysis,
but as an important snapshot, or insurance policy to protect against what is
in very real peril of disappearing FOREVER.

> The bottom line is that once that book has been separated from
> its language
> it is a hell of a job to understand just what it is all about. Similarly,
> once a species has been removed from its niche (effectively extinct in the
> wild; either locally or globally) we loose important, even vital,
> information.

Agreed, but there is a huge difference between "hell of a job" and
"impossible".  The former is *infinitely* (literally) more achievable than
the latter.  Once a species has gone extinct before it has been preserved in
a Museum (or in exceedingly rare cases, via long-term natural mummification
of some sort, with the hope of some day being re-discovered), it will be
IMPOSSIBLE to reconstitute the eons of information contained within its
genome.

> Sequencing the genome of an extinct species won't tell us how
> it interacted with other individuals of it own species or what it ate,
> where it lived etc.

It might not tell *us*....but the information for all of this may very well
be buried within the genome.  How many behavioral interactions, and foraging
behaviors, are actually passed on from generation to generation via "memes"
(sensu Dawkins)?  I'd wager not a lot -- certainly not in the biological
world outside of vertebrates (i.e., the vast majority of biodiversity).  The
point is, the genome includes a *lot* more information than just what we as
humans tend to read from it in the present day & age.  If you can clone a
milkweed, it will be able to photosynthesize and grow.  If you can clone a
Monarch Butterfly, its larva will not hesitate to eat the milkweed.  The
trick, of course, is knowing that you need to put the newly cloned monarch
egg on the milkweed plant.

This is why the unabridged version of my analogy included a more robust
defense of the importance of gathering not only the information about where
a specimen was collected in a geographic sense (addressing your "where it
lived" point), but also the micro-scale species associations taking place.
Not necessarily the behavioral interactions (most of which are probably
contained within the genomes), but the physical proximity & placement at all
scales. This is *vitally* important for dealing with the as-yet under
appreciated vast diversity of parasites/symbionts; but also for examples
like the Monarch life cycle.  Obviously, we can't work out the complete
life-cycles of every species on Earth before the fire does its damage.  But
we can be a bit more careful about how we do our collections -- such as
whenever collecting a milkweed leaf specimen, we are always very careful to
simultaneously note that it has eggs laid upon it.

> Consider that the 100 bucket carriers, once they have thrown their water
> into the inferno they now have empty buckets, and they are stood next to
> the very shelves on which our books are sat. Why not get them to grab a
> few books, put them in there bucket and hand them over to be taken to the
> vault?

VERY good point -- I would like to add that to the full analogy, if you
don't mind.  Perhaps best represented as the buckets being filled with books
as the firefighters run back for more water.  Not a perfect analog to how it
works in biodiversity, but the basic point is that the people on the "Front
Lines" are in a tremendous position to address both fronts simultaneously.
Several examples of this approach already exist -- Dan Janzen comes
immediately to mind. (Dan and I have already discussed this analogy before.)

> I find it very difficult to see the value of a collection
> made up of specimens of extinct species IN CONSERVATION TERMS (of course
> there is useful information for phylogenetic, evolutionary and
> morphological studies, as well as the historical value). To my mind the
> philosophy of conservation efforts should focus on efforts retain the
> 'context' of the species; without this our knowledge becomes severely
> curtailed.

This gets to the very crux of my point in making the analogy.  Another part
of the analogy that I glossed over in the Taxacom summary post was the point
about what happens to the books in the vault after the fire goes out.  At
first, they wouldn't be of much use to people, because they'd be protected
in the vault.  But eventually, the monks (the full analogy took place in
ancient Rome) would laboriously begin to make copies by hand (somewhat
representative of cloning technology today).  As technology progressed, the
printing press would be invented, followed by the computer and laser
printer, and then the internet and then...?  The books could be duplicated
as quickly as I can now copy a PDF file from one disk drive to another.
Armed with that technology, the library could be rebuilt.  But it could
NEVER be rebuilt if we never had the foresight to populate the vault.

It doesn't take much imagination to envision a world a few decades hence
where cloning organisms (thousands of them) would be as easy as sending an
email today (imagine how hard *that* would have been to pull off a few
decades ago).  It seems impossible to us that we could ever "rebuild" an
entire ecosystem from scratch -- but no more impossible than sending an
instant message, complete with color images, to dozens of people all over
the planet simultaneously, would have seemed at the dawn of the previous
century. I think most of the reason we see it as impossible now, is because
our grasp on biodiversity is so appallingly anemic. Why? Because we're not
filling up the vault -- we're just hoping we can save the Library, regarding
the inventory process as a mere luxury to be undertaken when the crisis has
passed. But from my read, a *lot* of genetic diversity will be PERMANENTLY
lost before the crisis eventually does pass.

Sure, maybe it will be impossible for future generations to reconstitute
natural habitat from a collection of whole genomes and basic information
about how the ecosystems once functioned.  But it will DEFINITELY be
impossible if 80% of the species-level genomic diversity is utterly gone --
as happens when a species goes extinct before it has been properly preserved
in a Museum.  I'll take "maybe" over "definitely" any day -- especially when
the stakes are so high.

No, the true subtle nuances of an environment can probably never be
reconstituted, no matter what technology lies ahead.  But I think we can do
a pretty good job.  About a month ago, I whipped up a web page with another
analogy relevant to this -- in terms of thinking of the vault contents as a
"backup" file in the sense that a JPEG image file serves as a backup to a
Bitmap image file.  Check out:
http://www2.bishopmuseum.org/HBS/allspecies/biodiversitybackup.html. The
vault contents are the JPEG file, and the information about ecology,
distribution, etc. is the JPEG decompression algorithm.

Aloha,
Rich

Richard L. Pyle
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://www.bishopmuseum.org/bishop/HBS/pylerichard.html
"The opinions expressed are those of the sender, and not necessarily those
of Bishop Museum."




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