University of Glasgow

Roderic Page

In an earlier post ([Are names really the key to the big new
biology?](http://iphylo.blogspot.com/2010/10/are-names-really-key-to-big-new-biology.html),
I questioned Patterson et al.\'s assertion in a recent TREE article
([doi:10.1016/j.tree.2010.09.004](http://dx.doi.org/10.1016/j.tree.2010.09.004))
that names are key to the new biology.  
  
In this post I\'m going to revisit this idea by doing a quick analysis
of how many species in GenBank have \"proper\" scientific names, and
whether the number of named species has changed over time. My definition
of \"proper\" name is a little loose: anything that had two words,
second one starting with a lower case letter, was treated as a proper
name. hence, a name like [Eptesicus sp. A
JLE-2010\"](http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=867837)
is not a proper name, but *Eptesicus andersoni* is.  
  
**Mammals**  
  
Since GenBank started, every year has seen some 100-200 mammal species
added to the database.  
![](https://spreadsheets.google.com/oimg?key=0AuPC5KKdhYCQdEFuaWJ3LW96TUM3QXQ3RnpObEp2T1E&oid=12&zx=tkb6ncmtkrum){width="425"}  
  
Until around 2003 almost all of these species had proper binomial names,
but since then an increasing percentage of species-level taxa haven\'t
been identified to species. In 2010 three-quarters of new tax_ids for
mammals weren\'t identified.  
  
![](https://spreadsheets.google.com/oimg?key=0AuPC5KKdhYCQdEFuaWJ3LW96TUM3QXQ3RnpObEp2T1E&oid=11&zx=twmn209jqqky){width="425"}**Invertebrates**  
  
For \"invertebrates\" 2010 saw an explosive growth in the number of new
taxa sequenced, with nearly 71,000 new taxa added to GenBank.  
  
![](https://spreadsheets.google.com/oimg?key=0AuPC5KKdhYCQdEFuaWJ3LW96TUM3QXQ3RnpObEp2T1E&oid=6&zx=yli94apaylpb)  
  
This coincides with a spectacular drop in the number of properly-named
taxa, but even before 2010 the proportion of named invertebrate species
in GenBank was in decline: in 2009 just over a half of the species added
had binomials.  
  
![](https://spreadsheets.google.com/oimg?key=0AuPC5KKdhYCQdEFuaWJ3LW96TUM3QXQ3RnpObEp2T1E&oid=5&zx=7hm3uo18odsj)**Bacteria**  
  
To put this in perspective, here are the equivalent graphs for
bacteria.  
Although at the outset most of the bacteria in GenBank had binomial
names, pretty quickly the bulk of sequenced bacteria had informal names.
In 2010 less than 1% of newly sequenced bacteria had been formerly
described.  
  
![](https://spreadsheets.google.com/oimg?key=0AuPC5KKdhYCQdEFuaWJ3LW96TUM3QXQ3RnpObEp2T1E&oid=8&zx=lopfb2yyqhoq)![](https://spreadsheets.google.com/oimg?key=0AuPC5KKdhYCQdEFuaWJ3LW96TUM3QXQ3RnpObEp2T1E&oid=7&zx=3mstujfg79vp)**Dark
taxa**  
  
For bacteria the graphs are hardly surprising. To get a proper name a
bacterium must be cultured, and the vast majority of bacteria haven\'t
been (or can\'t be) cultured. Hence, microbiologists can gloat at the
nomenclatural mess plant and animal taxonomists have to deal with only
because microbiologists have a tiny number of names to deal with.  
  
For mammals and invertebrates there\'s clear a decline in the use of
proper names.It would be tempting to suggest that this reflects a
decline in the number of taxonomists - there might simply not be enough
of them in enough groups to be able to identify and/or describe the taxa
being sequenced.  
  
However, if we look at the recent peaks of unnamed animal species, we
discover that many have names like [Lepidoptera sp.
BOLD:AAD7075](http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=736493),
indicating that they are DNA Barcodes from the [Barcode of Life Data
Systems](http://www.boldsystems.org/). Of the 62,365 unnamed
invertebrates added last year, 54,546 are BOLD sequences that haven\'t
been assigned to a known species. Of the 277 unnamed mammals, 218 are
BOLD taxa. Hence, DNA bnacording is flooding Genbank with taxa that lack
proper names (and typically are represented by a single DNA bnacode
sequence).  
  
There are various ways to interpret these graphs, but for me the message
is clear. The bulk of newly added taxa in GenBank are what we might term
\"dark taxa\", that is, taxa that aren\'t identified to a known species.
This doesn\'t necessarily mean that they are species new to science, we
may already have encountered these species before, they may be sitting
in museum collections, and have descriptions already published. We
simply don\'t know. As the output from DNA barcoding grows, the number
of dark taxa will only increase, and macroscopic biology starts to look
a lot like microbiology.  
  
  
**A post-taxonomic world**  
If we look at the graphs for bacteria, we see that taxonomic names are
virtually irrelevant, and yet microbiology seems to be doing fine as a
discipline. So, perhaps it\'s time to think about a post-taxonomic world
where taxonomic names, *contra* Patterson et al., are not that
important. We can discover a good deal about organismal biology from
GenBank alone (see my post [Visualising the symbiome: hosts, parasites,
and the Tree of
Life](http://iphylo.blogspot.com/2011/03/visualising-symbiome-hosts-parasites.html)
for some examples, as well as Rougerie et al. 2010
[doi:10.1111/j.1365-294X.2010.04918.x](http://dx.doi.org/10.1111/j.1365-294X.2010.04918.x)).  
  
This leaves us with two questions:  

1.  How much biology can we do without taxonomic names?
2.  If the lack of taxonomic names limits what we can do (and, playing
    devil\'s advocate, this is an open question) how can we speed up
    linking GenBank sequences to names?

  
  
I suspect that the answer to (1) is \"quite a lot\" (especially if we
think like microbiologists). Question (2) is ultimately a question about
how fast we can link literature, museum collections, sequences, and
phylogenies. If progress to date is any indication, we need to rethink
how we do this, and in a hurry, because dark taxa are accumulating at an
accelerating rate.  
  
**How the analyses were done**  
  
Although the NCBI makes a dump of its taxonomic database available via
FTP (at <ftp://ftp.ncbi.nih.gov/pub/taxonomy/>), this dump doesn\'t have
dates for when the taxa were added to the database. However, using the
[Entrez EUtilities](http://eutils.ncbi.nlm.nih.gov/) we can get the
tax_ids that were published within a given date range. For example, to
retrieve all the tax_ids added to the database in December 2010, we set
the URL parameters `&mindate=2010/12/01` and `&maxdate=2010-12-31` to
form this URL:  
  
<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&mindate=2010/12/01&maxdate=2010/12/31&retmax=1000000>.  
  
I\'ve set `&retmax` to a big number to ensure I get all the tax_ids for
that month (in this case 23511). I then made a local copy of the NCBI
database in MySQL ( [instructions
here](http://linnaeus.zoology.gla.ac.uk/~rpage/tbmap/downloads/ncbi/))
and queried for all species-level taxa in GenBank. I used a rather crude
regular expression `REGEXP '^[A-Z][a-z]+ [a-z][a-z]+$'` to find just
those species names that were likely to be proper scientific names
(i.e., no \"sp.\", \"aff.\", museum or voucher codes, etc.). To group
the species into major taxonomic groups I used the `division_id`.  
  
Results are available in a [Google
Spreadsheet](https://spreadsheets.google.com/ccc?key=0AuPC5KKdhYCQdEFuaWJ3LW96TUM3QXQ3RnpObEp2T1E&hl=en&authkey=COz7oqsC).


In an earlier post (Are names really the key to the big new biology?, I questioned Patterson et al.'s assertion in a recent TREE article (doi:10.1016/j.tree.2010.09.004) that names are key to the new biology.In this post I'm going to revisit this idea by doing a quick analysis of how many species in GenBank have "proper" scientific names, and whether the number of named species has changed over time.

Dark taxa: GenBank in a post-taxonomic world

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgioHPzg6OSWxmmEToo_h2KhqTcLtjRCetrTSf6X3aVnOEmjNcZ4wKxzQ5itYGo1ffQ1nkUCCnhooBT7l4LtIoGFN0gXXB-6UUuIbzncjDVo83s-IphQfv_pPVblgLtMq7A41XK/s320/ff_barcodeoflife6_f.jpg){#BLOGGER_PHOTO_ID_5255069016578675362
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgioHPzg6OSWxmmEToo_h2KhqTcLtjRCetrTSf6X3aVnOEmjNcZ4wKxzQ5itYGo1ffQ1nkUCCnhooBT7l4LtIoGFN0gXXB-6UUuIbzncjDVo83s-IphQfv_pPVblgLtMq7A41XK/s1600-h/ff_barcodeoflife6_f.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
The latest issue of Wired has an [article on DNA
barcoding](http://www.wired.com/science/discoveries/magazine/16-10/ff_barcode),
entitled \"A Simple Plan to ID Every Creature on Earth\". The article
doesn\'t say much that will be new to biologists, but it\'s a nice intro
to the topic, and some of the personalities involved.


The latest issue of Wired has an article on DNA barcoding, entitled "A Simple Plan to ID Every Creature on Earth". The article doesn't say much that will be new to biologists, but it's a nice intro to the topic, and some of the personalities involved.

Wired barcoding

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2IGLPGOKPdHa-B6ujqp4h_jyJfWJxD1LljWh7X6xV8NQ2Hp1NXQURffqrzEgpjaDrwHShGeABpLCsQ_G61k8mCunPJOzkWmIl2vMDnlCQ0kJiueM2Mf_rMByN3u6aCP0IVckJ/s200/1607_home.jpg){#BLOGGER_PHOTO_ID_5218457523568191394
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2IGLPGOKPdHa-B6ujqp4h_jyJfWJxD1LljWh7X6xV8NQ2Hp1NXQURffqrzEgpjaDrwHShGeABpLCsQ_G61k8mCunPJOzkWmIl2vMDnlCQ0kJiueM2Mf_rMByN3u6aCP0IVckJ/s1600-h/1607_home.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Mauro Cavalcanti brought Chris Anderson\'s [The End of
Theory](http://www.wired.com/science/discoveries/magazine/16-07/pb_theory/)
article in Wired to my attention, part of the July issue on \"The End of
Science\".  
  
Of course, the end of science is hyperbole of the highest order (as,
indeed, is the \"end of theory\"). It is also ironic that in the same
issue Wired confess to [having gotten 5 predictions of the death of
something hopelessly
wrong](http://www.wired.com/techbiz/media/magazine/16-07/st_15deadthings)
(including web browsers and online music swapping, no less). However, I
guess the reason Mauro sent me the link is this section:  
  

> The best practical example of this is the shotgun gene sequencing by
> J. Craig Venter. Enabled by high-speed sequencers and supercomputers
> that statistically analyze the data they produce, Venter went from
> sequencing individual organisms to sequencing entire ecosystems. In
> 2003, he started sequencing much of the ocean, retracing the voyage of
> Captain Cook. And in 2005 he started sequencing the air. In the
> process, he discovered thousands of previously unknown species of
> bacteria and other life-forms.  
>   
> If the words \"discover a new species\" call to mind Darwin and
> drawings of finches, you may be stuck in the old way of doing science.
> Venter can tell you almost nothing about the species he found. He
> doesn\'t know what they look like, how they live, or much of anything
> else about their morphology. He doesn\'t even have their entire
> genome. All he has is a statistical blip --- a unique sequence that,
> being unlike any other sequence in the database, must represent a new
> species.  
>   
> This sequence may correlate with other sequences that resemble those
> of species we do know more about. In that case, Venter can make some
> guesses about the animals --- that they convert sunlight into energy
> in a particular way, or that they descended from a common ancestor.
> But besides that, he has no better model of this species than Google
> has of your MySpace page. It\'s just data. By analyzing it with
> Google-quality computing resources, though, Venter has advanced
> biology more than anyone else of his generation.

Leaving aside whether Venter has indeed \"advanced biology more than
anyone else of his generation\" (how, exactly, can one measure that?),
it started me thinking about the yawning chasm between efforts such as
the [Encyclopedia of Life](http://www.eol.org) and the Catalogue of Life
on one hand, and, say metagenomics on the other. EoL and CoL have a view
of life that is taxon, indeed, species-centric, that appeals to our
sense of what matters (basically those organisms we can see comfortably
with the naked eye, and interact with). But if you browse the NCBI
taxonomy, not only do you see an attempt to classify organisms
phylogenetically, you will also encounter \"taxa\" that are
[metagenomes](http://en.wikipedia.org/wiki/Metagenome) (e.g., NCBI
Taxonomy ID [408169](http://view.ncbi.nlm.nih.gov/taxonomy/408169)).
These metagenomes are the result of shotgun sequencing environmental
samples, they comprise multiple taxa. In this way, they resemble
large-scale sampling events such as plankton netting, or tree fogging,
which results in masses of material, much of it unidentified. One
difference is that the metagenomes are digitised (i.e., sequenced), and
hence can be analysed further (as opposed to a mass of specimens in
jars). Indeed, this is one motivation behind DNA barcoding \-- the
ability to digitise massive samples of organisms.  
  
So, perhaps if we overlook the \"end of theory\" bit (although this is
appealing given that some critiques of DNA barcoding have made overblown
claims for taxonomy as hypothesis-driven science), the key here is that
much of what in an earlier age might have been provisional knowledge
unfit for public consumption (e.g., a bunch of unidentified samples) is
now very public. In the past, taxonomists wouldn\'t describe new taxa
without sufficient information for a decent description, now the most
actively growing taxonomic database (NCBI) has \"taxa\" that are
aggregates of unidentified, unknown (and possibly, unknowable)
organisms.


Mauro Cavalcanti brought Chris Anderson's The End of Theory article in Wired to my attention, part of the July issue on "The End of Science".Of course, the end of science is hyperbole of the highest order (as, indeed, is the "end of theory"). It is also ironic that in the same issue Wired confess to having gotten 5 predictions of the death of something hopelessly wrong (including  web browsers and online music swapping, no less). However, I

The end of science, and the end of taxonomy

Continuing on this theme of [embedded
metadata](http://iphylo.blogspot.com/2007/05/itunes-and-citation-metadata.html),
this is one reason why [DNA
barcoding](http://phe.rockefeller.edu/barcode/blog/)is so appealing. A
DNA barcode is rather like embedded metadata \-- once we extract it we
can look up the sequence and determine the organism\'s identity (or, at
least whether we\'ve seen it before). It\'s very like identifying a CD
based on a hash computed from the track lengths. Traditional
identification is more complicated, involves more nebulous data (lets
see, my frog has two bumps on the head, gee, are those things in that
picture of a frog bumps?), much of which is not online.


Continuing on this theme of embedded metadata, this is one reason why DNA barcodingis so appealing. A DNA barcode is rather like embedded metadata -- once we extract it we can look up the sequence and determine the organism's identity (or, at least whether we've seen it before). It's very like identifying a CD based on a hash computed from the track lengths.

Publicaciones de Rogue Scholar

Dark taxa: GenBank in a post-taxonomic world

Wired barcoding

The end of science, and the end of taxonomy

iTunes, embedded metadata, and DNA barcoding