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La Busqueda del Metodo Natural.

Article  in  Systematic Biology · June 1992

DOI: 10.2307/2992530

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Mario de pinna Patricia Escalante

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268 SYSTEMATIC BIOLOGY VOL. 4 1

Sys/. Biol. 41(2):268, 1992 with insightful quotations from classical literature.
Together with names familiar to the systematic metier
(Linnaeus, Simpson, Hennig, Mayr), one finds allu-
La Busqueda del Metodo Natural.—J. Llorente B. 1990. sion also to other thinkers such as Foucault, Koestler,
La Ciencia desde Mexico, Fondo de Cultura Econo- Feyerabend, and Lucrecius. The combination results
mica, Mexico, D.F. 155 pp. Available from Fondo in an original style that lends the book a delightfully
de Cultura Economica, S.A. de C.V., Av. de la Uni- humanistic flavor. These characteristics will make its
versidad 975,03100 Mexico, D.F., Mexico. US $5.00. reading enjoyable even for those who already have
Perhaps a paradigm can be considered established expertise in systematics (and reading knowledge of
in society when its precepts are incorporated into the Spanish), even if their high-school days are long past.
We expect the book to be quite stimulating to stu-
basic school system. If so, Llorente's book may be the dents in the process of determining how to view the
first clear indication that cladistics is moving from world and deciding what to pursue for a future career.
the status of a controversial scientific subject to that Coupling philosophical sophistication and digestible
of an "established" component of formal education. scholarship, the book is an effective popularization
La Busqueda is a book intended mainly for high school of systematics. One may regret only that the function

Downloaded from http://sysbio.oxfordjournals.org/ at University of Melbourne on August 3, 2015

and beginning undergraduate students whose native of Llorente's book is unavoidably restricted to a Span-
language is Spanish. It also targets the educated lay- ish-language audience. Perhaps this restriction in-
person who is interested in the literature for popu- dicates that a work of similar scope for the English-
larization of science. Its subject is systematics in a language world is timely.
broad sense, and its approach is eminently historical.
There are also sections devoted to the importance and Mario de Pinna, Patricia Escalante, and Careth Nelson,
aim of systematics and the role of museum collections American Museum of Natural History, Central Park West
in systematic research. Particularly surprising and in- at 79th Street, New York, New York 10024, USA.
formative to those more restricted to the strictly sys-
tematic literature will be the accounts about folk tax-
onomies among the Maya and Purepecha peoples.
Llorente's historical scope extends from Aristotle to
the present, with accounts of Linnaeus, Adanson, Cu- Syst. Biol. 41(2):268-269, 1992
vier, Lamarck, Darwin, and other great names in the
history of comparative biology.
The unifying thread of the book is the duality be- ACCESSING THE LITERATURE AND DATA
tween natural and artificial classifications. Llorente BASES OF MOLECULAR BIOLOGY
emphasizes that the meaning of a "natural" system Entrez: Sequences on CD-ROM.—National Center
changes throughout history, but it is always the object for Biotechnology Information. 1992. U.S. Depart-
of an intellectual quest, even in those periods when ment of Health and Human Services, National In-
artificial systems were regarded as indispensable. The stitutes of Health, Bethesda, Maryland. $57.00 per
notion of a natural system is as old as systematics year (6 releases).
itself, and adoption of artificial classification for the
most part reflects an admitted inability to recover the Technological development in the areas of molec-
natural system rather than a denial of its existence. ular sequence distribution, manipulation, and man-
To Llorente, the meaning of a natural system is at agement are finally beginning to catch up to the de-
present adequately accounted for by the evolutionary velopments in sequence acquisition. The appearance
paradigm. However, he recognizes that the evolu- of Entrez: Sequences on CD-ROM is striking evidence
tionary paradigm did not provide a method for the of this trend. For a very reasonable annual fee, sub-
retrieval of the natural system and that there is a scribers receive bimonthly updates of a compact disk
historical mismatch between the "explanation" for its that contains complete nucleotide and protein data
existence (genealogy) and the means for its objective bases and the literature in which they were reported,
study. Tools for retrieval of the natural system came as well as the software to conduct simple and effective
with the development of cladistics, which Llorente searches of the data bases.
presents as the culmination of the systematic method. For several years, the sequence data base GenBank
Nowhere, however, does he forget to stress that any has been available on CD-ROM, which is the most
method or theory is necessarily provisional and tem- cost-effective and convenient distribution medium for
porary. users who need local and continuous access to exist-
The text is illustrated with humorous cartoons re- ing sequence information. Searches of GenBank for
lated to themes treated in each section. Readers may sequences relevant to comparative evolutionary stud-
remember that high-school books do not usually in- ies are part of the daily routine in many labs. Like-
clude citations for their statements, which therefore wise, data bases such as MEDLINE provide an im-
must be taken at face value. However, two lists of portant source for literature searches for topics in
further readings at the end of the book provide a molecular biology. The Entrez: Sequences CD includes
reasonable compilation of recent general works on the complete nucleotide and protein data bases from
systematics and evolutionary biology. GenBank, PIR, and Swiss-Prot, as well as all the MED-
Llorente's account is permeated throughout with LINE references and abstracts that concern sequence
references to philosophy and sociology of science and data. One can search any of three summary data bases
 1992 REVIEWS
(nucleotide, protein, or MEDLINE) through Boolean
queries and then immediately ask for all similar pa-
pers or sequences. Entrez includes a built-in table of
closest neighbors for all sequences and references,
therefore finding related papers or sequences takes
minutes rather than hours or days. There are also
direct connections among the data bases, so that one
can match a sequence with the relevant MEDLINE
abstract immediately (or vice versa). Searches of the
MEDLINE data base can include text in the abstract
or title, key words, authors, journals, gene names,
Enzyme Commission numbers, MEDLINE identifi-
cation numbers, or any combination of the above.
Likewise, the nucleotide data base can be searched
by any combination of text terms, key words, authors,
journals, organisms, accession numbers, or gene
names. Creating Boolean combinations of search terms
is easily accomplished by dragging the appropriate
terms into groups.
The table of sequence neighbors in Entrez was con-
structed with the BLAST algorithm of Altschul et al.
(1990); the neighbors of articles were determined with
an as yet unpublished algorithm that weights and
matches key terms from the titles and abstracts. In-
clusion of neighbor calculations effectively elimi-
nates most of the search time one would normally
need to find similar sequences or papers (at the ex-
pense of sacrificing any control over the details of
the search). For instance, imagine you are interested
in the evolution of globin genes. You might start by
searching the titles and abstracts of the MEDLINE
data base for the key words "evolution" (1,336 titles
and 3,195 abstracts) and "globin" (420 titles and 967
abstracts) and then asking for the intersection of these
two searches (that is, papers with both terms in the
titles a n d / o r abstracts). This would yield 82 relevant
papers. You might want to expand the search to in-
clude papers that mention "evolution" and any of the
terms "globin, hemoglobin, or myoglobin." This
would yield 117 papers. Adding the requirement that
the papers also mention "vertebrates" in the title or
abstract reduces the 117 to 5. You could then retrieve
and skim through the five abstracts and mark those
you find particularly interesting. It is then a simple
task to ask for related papers and sequences and quickly
retrieve and save the relevant sequences for further
analysis and print out copies of the relevant abstracts.
Obviously, little of this is really new; existing soft-
ware can perform most of these functions. What is
View publication stats
269
new is the combination of these tasks into a single,
highly affordable package that performs extremely
quickly. For example, I conducted all of the functions
outlined above from starting the software to printing
the abstracts in under 6 min using Entrez on a Mac-
intosh Quadra. Previously, conducting the MEDLINE
searches, finding the related papers, searching
GenBank for similar sequences, and extracting or sav-
ing all of the above would have taken many hours
with the best software I have seen.
Entrez requires only a CD-ROM driver and a per-
sonal computer running under either the Macintosh
or Windows operating systems (I have not tested it
with Windows). It is scheduled for final release in
October 1992. I have worked with two prereleases
(October 1991 and April 1992), and the latest prere-
Downloaded from http://sysbio.oxfordjournals.org/ at University of Melbourne on August 3, 2015
lease eliminates virtually all of my complaints. The
user's guide is simple and easy to follow, the menus
are intuitive, and I have not detected any compati-
bility problems. The main problems that remain are
not really the fault of the software; they are related
to limitations of the existing data bases. For instance,
searching any of the data bases by organism can be
a terribly frustrating experience. There has been no
attempt to standardize the format for listing organ-
isms, and whatever the original authors reported is
repeated verbatim. This means that if you are inter-
ested in sequences of Zea mays you will have to search
at least "corn," "maize," "Zea mays," and "Zea mays
L." in the nucleotide data base.
This program does not replace software that search-
es GenBank (or other data bases) with a user-entered
sequence; it is limited to comparisons among sequenc-
es that are already in the data bases. It also does not
replace software that conducts thorough searches of
the entire data base for all similar sequences or any
software used for alignment or analysis. However,
for rapid scans and comparisons of nucleotide, pro-
tein, and publication data bases, Entrez is the perfect
solution. I expect it to become an integral part of most
molecular systematics labs.
REFERENCES
ALTSCHUL, S. F., W. GISH, W. MILLER, E. W. MYERS,
AND D. J. LIPMAN. 1990. Basic local alignment
search tool. J. Mol. Biol. 215:403-410.
David M. Hillis, Department of Zoology, The University
of Texas, Austin, Texas 78712, USA.