Cladistics
Cladistics (2019) 1–15
Background knowledge: the assumptions of pattern cladistics
Andrew V. Z. Brower*
USDA-APHIS National Identification Service, Riverdale, MD 20737, USA
Accepted 26 February 2019
Abstract
This paper reviews the ontogeny of pattern cladistics from the 1970s and 1980s, rebuts criticisms by contemporary
anti-cladists, and endeavours to clarify persistent misunderstandings about the philosophical foundations of the approach.
© The Willi Hennig Society 2019.
Empiricism alone is not enough; a healthy advance in taxon-
omy depends on a sound theoretical foundation. E. Mayr
(1968:548)
There is no such thing as philosophy-free science, just science
that has been conducted without any consideration of its
underlying philosophical assumptions. D. Dennett (2014:20)
Indeed, the phenomena we call ‘things’ are in fact form-
mediated syntheses of knowledge and matter, or knowledge
networks with an object-like appearance. U. Raulff
(2017:350)
Introduction
Several recent articles by philosophers and/or histo-
rians of science (Pearson, 2010; Quinn, 2017; Sterner
and Lidgard, 2018) give the impression that there may
still be a lack of clarity as to the origins and major
tenets of a school of systematic biology known as pat-
tern (or transformed) cladistics. Pattern cladistics may
be distinguished from “process cladistics” (Brower,
2000; also referred to as traditional or phylogenetic
cladistics, cf. Carpenter, 1987) by the efforts of its pro-
ponents to eliminate a priori evolutionary background
assumptions from the inference of patterns of relation-
ship among taxa. Despite this difference of opinion
regarding critical background knowledge, there is no
*Corresponding author.
E-mail address: andrew.v.brower@aphis.usda.gov
© The Willi Hennig Society 2019
10.1111/cla.12379
practical distinction between pattern and process cla-
dists’ evidence, analyses or results. From a method-
ological perspective, all cladists group by
synapomorphy alone (Kluge and Farris, 1999).
The eschewal of a priori evolutionary theory and the
rejection of “theory” in general are clearly not the
same thing, yet the notion that “pattern cladists main-
tain cladism can and should remain ‘theory-neutral’
or, more modestly, ‘theory-minimal’” (Pearson,
2010:476) is a frequently voiced criticism of the
approach (see also Ereshefsky, 2001; Kluge, 2001;
Quinn, 2017). This is despite the fact that, from the
outset, advocates of pattern cladistics have clearly sta-
ted the opposite. For example, Platnick and Gaffney
(1978:387) said,
A typical revisionary study may assert that there are, for
example, ten species in a given group, and the assertion will
be presented as the truth, as a true fact. It is not a true fact,
of course, but only a theory, a set of hypotheses that have
already been tested by each specimen that the taxonomist
examined, and that can (and will) be tested in the future by
every additional specimen of the group that is found and
studied. Numerous lower-level hypotheses about characters
and their distributions are involved, and frequently these
hypotheses are refuted by additional specimens, resulting in
the falsification of the original theory, and its replacement by
another (by the synonymy of named species or the naming of
new ones).
Although Williams and Ebach (2008, 2014); see also
Vergara-Silva, 2009) have provided a thorough and
articulate historical discussion of these matters, in
order “that the record be set straight with respect to
2 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
Cladistics, or at the very least it be rendered a little
more accurate” (Williams and Ebach, 2008:82), it is
apparent that further myth-busting is needed. The
object of this essay is to revisit the theoretical under-
pinnings of cladistics, addressing the perspectives of
both advocates and critics of the pattern cladistic view,
in order to correct misunderstandings and counter
false accusations.
The prime movers who conceived pattern cladistics
in the late 1970s and 1980s, as subjectively measured
by the number of their publications advocating some
aspect of that approach and/or their bearing the brunt
of criticism or calumny for their actual or imputed
views by others, include American Museum of Natural
History ichthyologists Gareth Nelson and Donn
Rosen, and arachnologist Norman Platnick, British
Museum (Natural History) ichthyologist Colin Patter-
son, and philosopher of science Ronald Brady, from
Ramapo College, New Jersey. My own involvement in
this imbroglio began in 1997, with discussion at the
George Washington University Hennig meeting, which
provoked me to defend pattern cladistic philosophical
ideas in a review that eventually appeared as Brower
(2000).
The current essay is structured in two parts: first, a
historical commentary on the origins of pattern cladis-
tics and a critical review of misconceived attacks on
the approach, and second, a discussion of philosophi-
cal questions emerging from that dialogue. The aim is
to dispel the notion that “theory-freedom” is a philo-
sophical desideratum of cladistics, and to sort theories
that are necessary as background knowledge from
those that are not.
Part 1. History
Roots
Pattern cladistics took form as a distinct epistemo-
logical perspective within the cladistic paradigm about
a decade after the publication of Willi Hennig’s (1966)
book in English, and Lars Brundin’s (1966) mono-
graph, the two works that triggered the cladistic revo-
lution at the British Museum (Natural History)
(BMNH) in London and the American Museum of
Natural History (AMNH) in New York. Throughout
the early 1970s, there were two groups of systematists
with somewhat antithetical views, both claiming phylo-
genetic classifications as their aim (a third group, the
pheneticists, thought phylogeny to be irrelevant, and
so are irrelevant to this narrative). The older, institu-
tionally established group, evolutionary taxonomists,
believed that taxonomy should be informed by
detailed evolutionary considerations, and recognized
groups based both on inferred evolutionary branching
patterns and on degree of difference – thus, for exam-
ple, reptiles were recognized as a class separate from
birds due to their many shared ancestral character
states, such as scales and cold-bloodedness. The newer
group, dubbed “cladists” by members of the other
groups (Camin and Sokal, 1965; Mayr, 1965), followed
the precepts laid out by Hennig and Brundin: only
shared, derived characters provide evidence of group-
ing, and classifications based upon such features reflect
inferred recency of common ancestry alone. In the cla-
dists’ view, birds are a specialized clade of dinosaurs,
and “reptiles” not including birds are a paraphyletic
assemblage.
Willi Hennig encumbered his Phylogenetic Systemat-
ics (1966) with a fairly detailed microevolutionary pro-
cess model: “we will call ‘phylogenetic relationships’
the genetic (genealogical) relations between different
sections. . . each bounded by two cleavage processes in
the sequence of individuals that are connected by
tokogenetic relations.” (p.20), and a metaphysical met-
ric of affinity: “the measure of phylogenetic relation-
ship is the ‘relative recency of common ancestry’”
(p.74). Both of these are ontological claims about his-
tory that need to be supported by evidence from other
sources to gain empirical legitimacy. To provide this,
Hennig clearly indicated that the epistemological basis
for inference of phylogenetic relationships relies upon
observed patterns of character distribution: “only
synapomorphy justifies the presumption of monophyly
in a group of species” (p.93). See Brower (2016a) for
further discussion of Hennig’s empirical1 approach.
Even as early as 1970, the cracks between pattern
and process in the application of Hennig’s methodol-
ogy were beginning to show, particularly as applied to
palaeontology. Hennig and Brundin were entomolo-
gists, and their work focused mainly on extant taxa,
but traditional phylogenetic hypotheses for vertebrates
were dominated by narratives from the fossil record
about ancestral groups. Rejecting that tradition, Gar-
eth Nelson (1970:378) said, “operationally, common
ancestors are at best only hypothetical constructs.
Thus, ‘tracing homologous features back to some com-
mon ancestor’ amounts only to erecting an hypothesis
of ancestral conditions.” In a similar vein, Schaeffer
et al. (1972:38) said, “the notion of ancestry and des-
cent is, of course, implicit in the concept of phylogeny
and is a logical concomitant to the entire idea of
1
Note that when I refer to an “empirical approach”, I mean an
approach that is based on the observation and interpretation of evi-
dence, not an approach that denies a theoretical component underly-
ing the successful performance of those activities. “It is quite true
that any particular hypothesis we choose will have been preceded by
observations - the observations, for example, which it is designed to
explain. But these observations, in their turn, presupposed the adop-
tion of a frame of reference: a frame of expectations: a frame of the-
ories.” (Popper, 1965:47).
 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
organic evolution. But there exists a large information
gap between what we know must have happened and
knowledge of what actually did happen. . .. an actual
phylogeny is not capable of outright discovery; it is a
system of relationships that needs to be analyzed.”
And, modifying his earlier (Brundin, 1968) perspective
considerably, Lars Brundin (1972:107) said, “investiga-
tions of character distribution among the species
groups of nature’s own system are a prerequisite for
clear understanding of the factors that have deter-
mined the course of evolution.”
At conferences in the mid-1970s, cladists began to
emphasize a distinction between phylogenetic patterns
and the processes invoked to explain them. For exam-
ple, Niels Bonde (1977: 793) said that cladistics “can
proceed quite comfortably without a too detailed
knowledge of the basal processes behind the recog-
nized patterns.” Eugene Gaffney (1979:86) observed of
the cladistic approach, “There is no reliance upon the
‘synthetic theory’ of evolution or any other particular
hypothesis of evolutionary mechanism, and there is no
reliance on any particular model or hypothesis of spe-
ciation or the nature of species.” Patterson (1977:631)
and Farris (1979a): 489) both referred to cladograms
as “synapomorphy schemes” and argued that they
represent direct descriptions of the history of charac-
ter change (as opposed to evolution of lineages).
And, echoing Brundin (1972), Platnick and Nelson
(1978:126) said, “(t)he investigation of patterns in the
distribution of characters (taxonomy) is both indepen-
dent of, and a necessary prerequisite to, any investiga-
tion of evolutionary processes.”
In a contemporaneous book review, Niles Eldredge
(1978:130) neatly summarized the differences of per-
spective:
Some systematists feel a need to adopt an a priori set of beliefs
about the nature of evolutionary process as a rationale for
adopting a particular methodology of phylogenetic reconstruc-
tion. Others prefer to view the connection between evolution-
ary process and phylogenetic history the other way around -
that hypotheses of process can only be tested when predicted
patterns are compared with “actual” (albeit hypothesized) phy-
logenetic patterns. In this latter view, phylogenetic reconstruc-
tion precedes investigation into evolutionary process.
The terms “transformed cladistics” and also “pattern
cladistics” apparently stem from Norman Platnick’s
(1979) paper, “Philosophy and the transformation of
cladistics”. On p.538, Platnick articulated what he con-
sidered to be the three main principles of contempo-
rary cladistics (italics added):
First, that nature is ordered in a single specifiable pattern
which can be represented by a branching diagram or hierar-
chical classification; second, that the pattern can be estimated
by sampling characters and finding replicated, internesting
sets of synapomorphies; and third, that our knowledge of
evolutionary history, like our classifications, is derived from
the hierarchic pattern thus hypothesized.
3
Here, Platnick concisely summarized the views of
colleagues at the AMNH, BMNH and elsewhere
regarding their solution to the inconsistency between
Hennig’s (1966) metaphysics and his methods. Platnick
also provided a logical argument to support that solu-
tion: “if classifications (that is, our knowledge of pat-
terns) are ever to produce an adequate test of theories
of evolutionary process, their construction must be
independent of any particular theory of process”
(p.539). He concluded (p.546) with the following
emphasis on patterns in Hennig’s (1966) “Phylogenetic
Systematics”:
So what Hennig may well have done in general (and may per-
haps even have set out to do) is to demonstrate the inade-
quacy of the syntheticist paradigm, by showing us that we are
hardly likely to achieve any understanding of the evolutionary
process until we have achieved an understanding of the pat-
terns produced by that process, and that even today we have
hardly begun to understand the patterns.
David Hull, individualist
The metaphysically-minded philosopher David Hull
was an early disciple of Ernst Mayr’s campaign against
typological thinking (Mayr, 1959), advocating (as did
Willi Hennig, 1966:83) that species and other mono-
phyletic taxa are individuals and not classes (Hull,
1965, 1978).2 According to this perspective, because
species and other taxa are limited spatiotemporally
and can change through time, they have no essential
characteristics and thus cannot be defined by such
attributes. The attribute that holds them together is
monophyly. But monophyly divorced from its empiri-
cal basis is an empty metaphysical belief, which has
led some authors to refer to the individuality hypothe-
sis as “origin essentialism” (Griffiths, 1999; Rieppel,
2010).
2
Credit (or blame) for the individuality hypothesis also is due to
Michael Ghiselin (1966, 1975, 1997) for his magisterial insistence
regarding the metaphysical status of taxa. Ponder three quotes from
Ghiselin (1997): “the natural groups of systematic biology are indi-
viduals” (p.45), “there are no laws ‘for’ or ‘about’ or ‘making neces-
sary reference to’ an individual” (p.222), and “with respect to the
place of laws of nature in working out the history of the earth and
its inhabitants, we may confidently draw the conclusion that such
laws do indeed exist, and also that they may indeed be used to infer
the truth of historical hypotheses” (p.243). Or two more from Ghis-
elin (1986): “The transformed cladists’ philosophy is a throwback to
pre-Darwinian idealistic morphology, combined with a naive induc-
tionism that rejects modern hypothetico-deductive method out of
hand. According to this ideal of science, we are supposed to wait
until the ‘patterns’ have been worked out before we begin to study
the ‘process’. . .” (p. 652). But, “Once the basic phylogenetic tree has
been worked out, biologists will then find it much easier to place the
whole range of their findings in an evolutionary context” (p.653).
There is no need to argue with someone who disagrees so fundamen-
tally with himself.
4 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
Regardless of whether or not the point of view that
species and monophyletic taxa are individuals is
semantically or ontologically “correct”, it is not how
systematists and other biologists recognize, diagnose
or talk about groups of organisms. Specimens exhibit
characters, and those characters bear information that
is at least heuristically reliable about the identities, life-
styles and relationships of their bearers (Rieppel,
2006). An indigo bunting is blue, a canary is yellow;
both of them have feathers, a pygostyle and a beak. If
characters such as these were not reliable indicators of
the identities of their taxa, the field guide industry
would not exist, nor would philosophers be able to
contemplate the existence of white or nonwhite swans.
Likewise, if every individual human were an histori-
cally unique “chunk of the genealogical nexus” (Ghis-
elin, 1969, is the source of that trope) with no
predictable physiological responses to treatment, how
would medicine function? Nobody has ever seen my
appendix, but I bet I have one, and I bet that a sur-
geon would know where to make the cut if I had
appendicitis. Going a step further, from predictable
similarities among conspecific individuals to similari-
ties among species, if the biological constitutions of
model organisms such as Drosophila or mice did not
resemble ours in an orderly manner, how would medi-
cal research on those species pertain to human health?
These are all class-like attributes, yet nobody frets
about medical clinicians’ and researchers’ essentialist
perspectives on anatomy and physiology.
Clearly, in such circumstances, science treats species
as though their members/parts exhibit and share char-
acteristics––homologues–-even if species are not “de-
fined” by those homologous features (Williams and
Ebach, 2008). These are the same kinds of regularities
of nature that allow scientists to discover oil and pre-
dict the weather (both of these examples also are spa-
tiotemporally restricted phenomena). Such discovery
and explanation of order in nature is the aim of
science, and the individuality perspective (which can
be viewed as an equally sceptical corollary to Hume’s
problem of induction) is corrosive to that aim. Under
a strict interpretation of the individuality hypothesis,
in which attributes are entirely contingent, we cannot
be any surer that Aedes aegypti is a vector of yellow
fever, than we can that those particular wings will not
fall off of this particular airplane. Although the indi-
viduality thesis may mesh well with Mayrian “popula-
tion thinking”, it is antithetical to the epistemology of
empirical systematics, not to mention physiology, med-
icine and molecular biology, that all rely on the regu-
larity of characters. Before his book, Science as a
Process (1988, see below), Hull’s main contribution to
the philosophy of systematics thus seems to have been
the undermining of the scientific character of phylo-
genetic inference by promoting these metaphysical
conundrums. As he said (Hull, 1978:147), “thus far,
the interplay between professional philosophers and
practicing biologists has been a mixed blessing.”
The Halstead kerfuffle
In September 1978, the Palaeontological Association
held its 26th Symposium of Vertebrate Palaeontology
and Comparative Anatomy at the University of Read-
ing (UK), home to the eccentric and opinionated pale-
ontologist L. Beverly Halstead. At a special session
devoted to cladistic approaches towards fossil fishes
(attended by, among others, Peter Forey, Brian Gar-
diner, Philippe Janvier and Colin Patterson), Halstead
was appalled by the cladists’ toppling of fossils from
their pre-eminent role in the inference of ancestry. He
fired off a three-column letter to Nature (Halstead,
1978), ending with the dire pronouncement that “cla-
dists adhere to the tenets of Hennigism with religious
fervour and are already entrenched in some of the
major museums of the world.”
Initially, the cladists were happy for the press: “The
debate on cladism has smouldered in specialist jour-
nals for over a decade, and we are glad that Halstead
has brought it to Nature.” (Gardiner et al., 1979).
Enthusiasm soon faded, however, as Halstead (1980a,
b) labelled the BMNH curators and other cladists as
creationists (for denying the applicability of empirical
evidence to inference of direct ancestor–descendant
relationships) and Marxists (for advocating punctuated
equilibrium––oddly enough, a process theory!). Unfor-
tunately, Halstead’s tirades coincided in the news with
political acrimony over evolution in Arkansas school-
books, as well as a controversial conference on
macroevolution at the Field Museum (Lewin, 1980),
resulting in the spread of titillating headlines from
Nature (Anonymous, 1981a,b,c) to Science (Wade,
1981), and a miasma of guilt-by-association between
pattern cladistics and creationism.
Colin Patterson chums up the creationists
There was already blood in the water when Colin
Patterson gave his notorious talk, “Evolutionism and
Creationism” at the AMNH’s Systematics Discussion
Group in November 1981. He had been goaded by
creationists who noticed the absence of illustrations
of transitional forms in his evolution textbook (Pat-
terson, 1978a)––a decision he explained by observing
that “statements about ancestry and descent are not
applicable in the fossil record” (Patterson, 1979––the
same iconoclastic tenet that triggered the Halstead
episode). Patterson generally read his presentations
from prepared notes, and the text of this talk has
been published posthumously (Patterson, 2002). It is
clear from the transcript that he wanted to provoke
 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
his audience, but he believed that audience to be a
collegial group of fellow professional systematists.
The main substance of the talk was a criticism of
Ernst Mayr’s “genes in common” defence of para-
phyletic groups, and a consideration of the problem
of inferring homology and synapomorphy from
molecular data (Patterson was a strong advocate of
the ontogenetic rooting criterion, which is inapplica-
ble to DNA). Both of these were rather esoteric, spe-
cialized topics that required a command of the
relevant literature to fully appreciate. As he said, “if
any militant creationists have come here looking for
political ammunition, I hope they will be disap-
pointed.” Unfortunately, it didn’t work out like that:
there were several creationists in the audience, one of
them surreptitiously recorded the talk, and soon,
salacious excerpted sound bites were widely circulat-
ing in the anti-evolutionary literature. Patterson was
relentlessly quoted out of context for years as
expressing “agnosticism” about evolution, or worse.
Alan Charig asks, are “pattern cladists” cladists?
The Systematics Association held a symposium,
“Problems of Phylogenetic Reconstruction”, in April
1980. The proceedings (Joysey and Friday, 1982) con-
tain a spectrum of views on cladistics, ranging from
Patterson’s (1982a) classic paper on homology, to an
essay by Halstead (1982) on phylogeny of Agnatha, a
Trojan horse he employed to revisit his calumnies
against Karl Popper, cladistics and punctuated equilib-
rium. Another of the participants, Alan Charig, a
dinosaur palaeontologist from the BMNH, published a
77-page long diatribe (Charig et al., 1982, excerpted as
Charig, 1980), claiming that, “‘transformed cladistics’
is neither Hennigian nor phylogenetic - nor even
cladistic in the proper sense of the word”(p.366), and
remarking, “how absurd that natural order systematics
[his neologism for pattern cladistics] and Hennigian
systematics should be bracketed together as ‘cladis-
tics’!” (p.436). The paper unloaded a blunderbuss of
criticisms, some of which appear self-contradictory:
. . . the philosophy of natural order systematics does not rec-
ognize evolution as a proven fact and permits neither evolu-
tionary theory nor the time dimension to play any essential
part in its procedures. Yet every natural order systematist
whose works I have read or to whom I have spoken obvi-
ously believes, as strongly as I do, that evolution has
occurred; they believe this, despite the lack of proof of evolu-
tion and its possible unprovability. Although I cannot object
to this slightly paradoxical conjunction, I do find myself
bewildered by the curious inconsistency which those same
people display in their resulting approach to systematics.
(p.374)
So, if, as Charig admitted, evolution lacks proof
and might be unprovable, is it more sensible or
5
“consistent” to freight up your systematic approach
with a priori evolutionary assumptions, or not? “Prov-
ability” aside (few contemporary scientists are in the
business of confirming the veracity of their theories),
pattern cladists have never asserted that evolution is
not a well-supported empirical theory, but we think
that the evidence (if not proof) for macroevolutionary
narratives of adaptation, convergence and other phe-
nomena is made accessible by hypotheses of character-
state transformation and relationship independently
derived from systematics (Brady, 1985). To me, read-
ing this essay in 2019 mainly serves to corroborate
Charig’s own admission (p.364) that “It seemed to me,
an ordinary working palaeontologist, that many of the
issues were becoming unnecessarily complex, so
extraordinarily complex in some instances that they
were quite beyond my comprehension.”
John Beatty makes a category error
In 1982, Hull’s colleague John Beatty picked up on
the individuals vs. classes discussion to argue that the
views of “pattern cladists” (Beatty is considered to be
the first to apply that moniker in print) are not merely
“theory neutral”, but in fact antagonistic to evolution-
ary theory. He suggested that cladists were led astray
by a desire to fit phylogenetic hypotheses within the
Popperian demarcation of science as strictly universal
statements. Popper (e.g. 1957) labelled evolutionary
biology as a metaphysical research programme,
because of its spatiotemporally restricted domain (his-
tory of life on earth). As noted above, a demarcation
of science that applies only to atemporal, “universal”
laws is not a very useful demarcation of science (even
atoms undergo decay, and even the universe itself,
apparently, had a beginning at some point). Indeed,
Popper (1957:33) noted that, “science or knowledge
presupposes something that does not change but
remains identical with itself - an essence.” What he
wanted to criticize in “The Poverty of Historicism”
was not the idea it is possible to study the pattern of
history (of course, statements about singular events, or
conjunctions of them, are falsifiable), but that the pat-
tern of history cannot be used to predict the future
because it is contingent and offers no general laws.
That is a straightforward Humean sceptical complaint
about the uniformity of nature. But of course, system-
atists, and most particularly cladists, are not in the
business of prognostication.
Beatty’s main argument (1982:31) is as follows:
“evolutionary theorists do not recognize any traits
with respect to which species cannot evolve, but
pattern cladists insist that there are such traits -
namely, the defining traits.” When Beatty wrote the
paper, he had recently heard a talk by Colin Patterson,
and also read Nelson and Platnick (1981), who, in
6 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
addressing just this concern, made the bold claim that
“systematists always have been, are, will be, and
should be, typologists” (p.328). To Beatty, this per-
spective represented na€ıve falsificationism, but I think
that is a misinterpretation of pattern cladists’ views,
and suggest that the na€ıvete may have been Beatty’s
own (Platnick, 1982; Patterson, 1982b, and Ronald
Brady, 1982, each responded to Beatty’s critique, and
Nelson, 1985, added some pertinent observations
about “the excluded middle”).
The issue is that whereas Beatty is worried about
what might have happened, Nelson, Platnick and other
cladists are interested in what we can infer did happen
(see, e.g., Schaeffer et al., 1972, quoted above). The
latter approach is epistemological and empirical; the
former is metaphysical and, I suppose “philosophical”:
of course, evolution might cause radical changes to
some taxon resulting in characteristics that belie its
true genealogy, but as Darwin said (1859:435), “(w)e
have no written pedigrees; we have to make out com-
munity of descent by resemblances of any kind. There-
fore, we choose those characters which, as far as we
can judge, are the least likely to have been modified
in relation to the conditions of life to which each
species may have been recently exposed.” Thus, even
the Ur-“evolutionary theorist” recognized that, as a
practical matter, taxa are semaphoronts that reveal
through their characters the pattern we interpret as
evolutionary history. From this epistemological per-
spective, characters, taxa and relationships are neither
individuals nor classes, but theories: as Nelson and
Platnick (1981:14) said, “cladograms represent struc-
tural elements of knowledge”––not pictures of “phy-
logeny” (see also Brower, 2016b). The evidentiary
basis of systematics, with or without evolutionary spin,
needs to be epistemologically static for the same
ancient reason that Popper (1957:33) attributed to
Heraclitus: “changing things defy rational descrip-
tion”––or as Hennig (1966:65) put it, “we cannot work
with elements that change with time.” Beatty’s stance
thus rejected not only pattern cladistics, but the empir-
ical foundations of all scientific knowledge.
Mark Ridley and “justification”
In 1986, Mark Ridley, an animal behaviorist, fol-
lowed up an anticladistic screed in New Scientist (Rid-
ley, 1983) with a book-length treatment, claiming
(Ridley, 1986:14) to “oppose and destroy” the philo-
sophical basis of transformed cladism. It appears that
he absorbed a rather partisan version of systematics at
the knee of his erstwhile advisor, Richard Dawkins
(who was evidently even more confused about cladis-
tics than Ridley; cf. Dawkins, 1987). Ridley (1986)
argued that although cladistics underlain by evolution-
ary assumptions is, in his view, superior to phenetics
or evolutionary taxonomy, pattern cladists’ jettisoning
of a priori evolutionary background knowledge leaves
the method without its Hennigian “justification” (Rid-
ley is most fond of this word––I counted 230 “justify”,
“unjustified”, “justifications”, etc. in the 166 pages of
his polemic).
Ridley did not grasp that the critical differences
among phenetics, evolutionary taxonomy and cladis-
tics are methodological rather than metaphysical (cla-
dists count character-state transformations, others
count character state identities––see Brower, 2000,
2016a), and his argument is erected upon on the
sophomoric foundationalist notion that cladistics suc-
ceeds because evolution is true. In Ridley’s view,
cladistic classifications are “objective” because they
correspond to actual phylogenetic history better than
other sorts of classifications do. Of course, there is no
way to know that such is the case, even if advocates of
other methods concede that their methods do not
reflect phylogenetic patterns as well as cladistics is pur-
ported to do. The success of cladistics stems not from
its accuracy, but from its methodological coherence.
Nor does an evolutionary gloss provide any corrobo-
rative support or grounding for any particular phylo-
genetic hypothesis: “The clades we choose to explain
as products of phylogenesis are simply those groups
supported by the empirical evidence as interpreted
within our particular methodological world view. As
contradictory evidence accrues or our world view
changes, lo and behold! the phylogenetic narrative fol-
lows the cladogram like a shadow.” (Brower,
2002:223).
The epistemological fact is, that our understanding
of the history of life and most of the support for the
theory of evolution, at least above the level of spe-
cies, arose from comparative morphology (including
fossils), and continues to be corroborated by the pat-
terns revealed from DNA sequences. As Platnick
(1982:283) said, “without the overwhelming evidence
for the existence of a natural hierarchic system of
real groups, compiled by a motley assortment of sys-
tematists - of all shades of opinion with regard to
causal theories - over three centuries, there is abso-
lutely nothing in evolutionary biology for any causal
theory to explain.”
One wonders what kind of theory Ridley thought
“evolution” might be, that it offers an all-encompass-
ing vera causa for the justification of homology, hierar-
chical phylogenetic patterns, the fossil record, and so
on. Popper (1979:265) said, “A scientific result cannot
be justified. It can only be criticized, and tested.” He
also said (p.266), “Whenever a theory appears to you
as the only possible one, take this as a sign that you
have neither understood the theory, nor the problem
which it was intended to solve.” An explanation that
can explain everything and anything explains nothing,
 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
and resorting to casuistic foundationalist arguments
simply swaps out one prime mover for another. That’s
not science.
David Hull, Lord of the Flies
Hull’s, 1988 book, Science as a Process, is with little
doubt the main source of many of the persistent myths
about pattern cladistics. The book represents a
denouement of Hull’s 15 years as a fly-on-the-wall,
studying the interplay between professional and per-
sonal interactions in the Society for Systematic Zool-
ogy, and from 1981, in the Willi Hennig Society. The
book’s focus in particular is on the rise of cladistics as
both a scientific and sociological phenomenon, and
Hull’s reporting and interpretation is based as much
on personal communication and imputation of peo-
ple’s sentiments as it is on published documentary evi-
dence. Chapter 7 focuses on the origins of pattern
cladistics, and here are a few of Hull’s claims:
““pattern cladists” or “transformed cladists” insist that cladis-
tic classifications should be as theory-free as possible”
(pp.235–236)
“cladists insist on perfectly nested characters” (p.249)
“The reaction of those who have been labeled as ‘pattern cla-
dists’ has been surprisingly impassioned. Knuckles whiten;
lips curl back from incisors. One explanation for such strong
emotions is that pattern cladism is a myth, and cladists are
simply expressing their exasperation at being told that some-
thing which they know to be patently false is nevertheless
true.” (p.238)
Hull said (pp.252–253), “According to Popper, Dar-
winism is best construed as a metaphysical research
program. As such it is not falsifiable.” Two paragraphs
later, he said, “(b)y excluding process theories from
cladistics in the generic sense, Nelson and Platnick
have defined cladistics so that it, like Darwinism, is
outside the realm of Popperian science.” Or maybe,
because the process theory Nelson and Platnick
endeavoured to exclude WAS Darwinism, they were
trying to frame cladistics in a manner that is NOT
outside the realm of Popperian science? If Hull
believed that Popper’s philosophy is irrelevant to biol-
ogy because life on Earth is spatiotemporally
restricted, then the gist of Hull’s criticism seems to be
that Nelson and Platnick’s version of cladistics lacks
Popperian scientific character in the same way that the
rest of biology does. Like Beatty’s, Hull’s complaint is
no criticism of pattern cladistics.
Farris and Platnick (1989) wrote a long review/re-
buttal of Hull’s book, the source of the header of this
section. Farris (2014) continued to find fault with
Hull’s characterizations of cladistic history. In the end,
Hull (1988) admitted that he did not want pattern
cladistics to succeed, because he thought its success
7
threatened his “general philosophy” (p.491), presum-
ably referring to the individuality thesis. His paradigm,
like Ridley’s, is one of cause (evolution) and effect
(phylogenetic trees), rather than explanans (evident
biological hierarchy) and explanandum (evolution)––a
realist rather than an empiricist perspective (Brady,
1985).
Scott-Ram and his attitudes
In 1990, another book about pattern cladistics
appeared, this time stemming from a Cambridge Ph.D.
thesis. Its author (N.R. Scott-Ram, indicated on the fly
leaf as a biotechnology consultant) apparently never
published anything else related to systematics, but the
acknowledgments reveal the tutelage of, among others,
our old friend Beverly Halstead. Scott-Ram framed a
classification of schools of taxonomy, with process
cladistics and evolutionary taxonomy occupying the
“theoretical attitude”, which he claimed views classifi-
cations as theories. Contrasted to this is the “descrip-
tive attitude”, populated by pattern cladistics and
phenetics, which Scott-Ram (1990:15) said, “abandons
the search for hidden or underlying causes.” He goes
on: “All aspects concerning the explanation of a system
are rejected in favor of a description which does not
entail a model process.” This characterization seems to
me to conflate explanation and cause, which in my
view are separable: an explanation is an a posteriori
epistemological claim, whereas a cause is an a priori
ontological claim. Oddly, although Scott-Ram cited
several other papers by Ronald Brady, he did not cite
Brady (1985), which specifically addresses this issue.
Perhaps because critique of “the rejection of explana-
tion” is a central pillar of Scott-Ram’s thesis, that
omission was not an accident.
The book is critical of both the theoretical and the
descriptive attitudes: “Given that pattern recognition is
procedurally prior to an assessment of common ances-
try, the view (in the theoretical attitude) that homolo-
gies are first calculated, and then linked to a
phylogenetic tree is clearly spurious” (p.29), and the
reader gets a sense that Scott-Ram did not think much
of systematics, period. On the other hand, he did rec-
ognize that pattern cladists do not claim their
approach to be theory neutral, and said that the sug-
gestions by Charig et al. (1982), Beatty (1982) and
Ridley (1986) that they do were “misguided” (p.141).
Nevertheless, as in those other works, pattern cladis-
tics is Scott-Ram’s ultimate whipping boy, too: “if the
transformed cladist wants to avoid the charges of
either Platonism or unintelligibility, then it can only be
argued that his methods are rendered intelligible by
evolutionary theory” (p.161). This also was Beatty’s
(1982) argument, as noted by Patterson (1982b:286):
“I can appeal to evolutionary process (assume
8 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
common ancestry) or not (discard that assumption) at
will. According to Beatty, when I make the assump-
tion, my groups are real, all is well and I can make
sense of the world, but when I discard it, my groups
are classes, my attitude is ‘antagonistic. . . to,. . . under-
mines and is undermined by evolutionary theory’
[Beatty, 1982:30], and I am beset by philosophical rid-
dles.”
Of course, Scott-Ram’s criticism depends upon the
meaning of “intelligible”, and, for that matter, in what
context “intelligibility” matters. I don’t speak Urdu,
but that does not mean it is “unintelligible” to the mil-
lions of people who do. A synapomorphy scheme is a
synapomorphy scheme, and what it “means” or
implies about one’s metaphysical stance regarding evo-
lution or Platonism, or whatever, is a matter separate
from the empirical fact of its existence. A detective
who went to a crime scene to gather evidence with an
a priori “theory of the case” would not make a very
objective witness in the eyes of the law: the evidence
makes the case; the case does not make the evidence.
As noted above, I think that if we can keep clear in
our minds the philosophical difference between a cause
and an explanation, and remember that the explanans
(an explanation) requires an independent explanandum
(a phenomenon to be explained), then, Patterson’s rid-
dles are solved. As noted by Brady (1985:125) “if we
lose the distinction between pattern and its explanation
by a process hypothesis, we lose the reason for our
inquiry, not merely historically, but logically.”
Desperate ground
This narrative has described the rise of, and reaction
to pattern cladistics in the period from 1970 to the
mid-1980s. There were parallel theoretical struggles
during the same timeframe, such as Steve Farris’
development of quantitative cladistics and systematic
demolition of competing schools of numerical taxon-
omy (e.g. Farris, 1977, 1979a,b, 1980, 1982), and a lit-
tle bit later an effort to overthrow Linnean
nomenclature with a “phylogenetic” alternative, that
time with the cladists trying to preserve the status quo
(e.g. Nixon and Carpenter, 2000; Schuh, 2003) There
also have been, of course, subsequent squabbles and
schisms over tangentially related methodological issues
that have divided cladists into more rarified camps,
with concomitant name-calling and imputation of
motives. Those controversies are not discussed here,
because, as they relate to the focus of this essay, they
merely reiterate the venerable but persistent criticisms
of pattern cladistics that have been discussed in the
preceding sections. Most or all of those criticisms
were naive and/or deliberately hostile misinterpreta-
tions, apparently motivated more often by politics
and personal animus than by reason. In Part 2, I
endeavour to provide a coherent summary of the epis-
temological framework that supports the pattern cladistic
approach.
Part 2: Philosophy
Having argued in Part 1 that the principal historical
criticisms of pattern cladistics consist of misrepresenta-
tions or misunderstandings, I now discuss a few fur-
ther issues that may help more fully explain the
theoretical underpinnings of cladistics. This discussion
is not intended to provide a comprehensive synopsis of
the cladistic philosophical perspective, but merely to
highlight a few nuances that even some cladists seem
not to fully appreciate. For complementary discussion,
see Rieppel (1988), Brower (2000, 2016a), Williams
and Ebach (2008), and Schuh and Brower (2009).
The Razor of Denial and the Razor of Silence
Elliott Sober has written a good deal about the rela-
tionship between the principle of parsimony and
cladistics, including two books (Sober, 1988, 2015). I
do not agree with everything Sober has said, particu-
larly in regard to his “likelihood justification of parsi-
mony” (see Brower, 2017). Nevertheless, he does
present thoughtful ways to parse the parsimony princi-
ple. Sober (2015) described two different interpreta-
tions of the principle of parsimony. The stricter of
these is what he called the “razor of denial”, under
which certain phenomena or processes are actively
asserted not to occur or play a role in an explanation.
The “razor of silence” is a milder assertion of parsi-
mony, in which the phenomenon or process in ques-
tion might or might not be pertinent to an
explanation, but the evidence supporting it is absent
or insufficient to warrant its invocation. By analogy,
we might contrast the views of atheists, who deny the
existence of gods, to those of agnostics, who do not
see compelling evidence to convince them of either the
existence or nonexistence of gods. The former make a
metaphysical assertion, the latter consider the question
to be outside the scope of available evidence and
therefore uninteresting, and carry on with their busi-
ness (I suppose an empirical-minded agnostic’s null
hypothesis on this question might depend upon
whether she considered it more parsimonious for a
god to exist, or not). At any rate, the razor of denial/
razor of silence distinction provides a useful frame-
work to contrast some of the differing applications of
the parsimony principle in the methods and assump-
tions of cladistics vs. those of evolutionary taxonomy,
and also between pattern and process cladistics.
Hennig’s methodological rule that only synapomor-
phies indicate patterns of grouping is the fundamental
 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
differentia that separates cladistics from phenetics and
evolutionary taxonomy, and represents a razor of
denial. Symplesiomorphies, autapomorphies and
“branch length” are components of state similarity
employed by pheneticists and evolutionary tax-
onomists. A corollary of grouping by synapomorphy
alone is that paraphyletic groups, past or present, are
invalid in cladists’ estimation, because those groups
can be recognized only on the basis of a combination
of synapomorphies and symplesiomorphies. Also fol-
lowing from this rule is the claim that there are no
groups (i.e. taxa above the species level) that are ances-
tors of extant taxa, because ancestral groups by defini-
tion do not include their descendants and so must be
paraphyletic. This was the original source of disputes
among fish palaeontologists in the 1970s, and the rea-
son that authors have characterized the early cladistic
revolution as a reformation of palaeontology (Nelson,
1998).
However, given the Hennigian convention that a
parental species goes extinct when it undergoes specia-
tion, it is de facto necessary that cladists acknowledge
the existence of ancestral species. The trouble is, these
are only diagnosable by symplesiomorphies, and so are
difficult or impossible to identify unambiguously. Cla-
dists’ rejection of ancestral species thus represents a
razor of silence––we do not deny that they existed, but
we cannot empirically discover them, so we omit them
from our hypotheses of relationship. This also is the
reason why fossils and extant taxa are treated as
equivalent terminals in cladistic analyses. This razor of
silence was criticized as “epistemic vagueness” by Reif
(2005), but I think that Reif’s complaint has more to
do with his own lack of clarity regarding pattern cla-
dists’ views, rather than any ambiguity in our position:
there is no equivocation in the statement that some-
thing is unknowable.
The assumption of dichotomous branching also has
long been a source of criticism of the cladistic approach.
But as Hennig (1966:210) said, “If phylogenetic system-
atics starts out from a dichotomous differentiation of
the phylogenetic tree, this is primarily no more than a
methodological principle.” This also is a razor of
silence: “the impossibility of determining with certainty
the sequence of dichotomous cleavages in a group never
means that all the species arose simultaneously (by
radiation) from one stem species” (p.211). A “soft poly-
tomy” is an epistemological claim (we have no evi-
dence), whereas a “hard polytomy” is an ontological
claim (there was a radiation). Lack of resolution is
explained more parsimoniously by lack of evidence than
by invoking ad hoc evolutionary processes.
As we have seen, cladists’ employment of characters
to differentiate taxa and infer phylogenetic relation-
ships has led to accusations of essentialism, and even
the assertion by Nelson and Platnick (1981:328) that
9
“systematists always have been, are, will be, and
should be, typologists”. This is not a metaphysical
claim that species have Aristotelian essences (a razor
of denial regarding individuality and change through
time), but rather a razor of silence about the nature of
taxa, and an epistemological assumption about the
nature of evidence and the calculus of relationship in
systematics, which require that taxa exhibit fixed dif-
ferences in character states in order for them to be dis-
tinguished from one another in practice. Likewise,
cladists do not deny that intraspecific polymorphism
might exist, and various microevolutionary mecha-
nisms might be at work at the tokogenetic level, as in
Hennig’s (1966) famous fig. 4. However, in most
groups of organisms, the specifics of those processes
are not known well enough to provide relevant infor-
mation to the systematist, and the epistemological view
of the speciation process is sublimated to the simple,
monistic diagram of a single ancestor with two descen-
dants seen above the tokogenetic network in Hennig’s
diagram.
Some critics of cladistics have suggested that cladists
refuse to recognize homoplasy (e.g. Hull, 1988:236):
“If putative characters do not fall into perfectly nested
transformation series, then they are not actually ‘char-
acters’.” That would be a razor of denial. As far as I
am aware, that is an attribute of cliques, not clades
(Farris, 1983), and even Hennig (1966:116) said, “The
fact that almost any organ that once appeared in a
transformation series as a new apomorphous character
may later be reduced to the point of complete disap-
pearance shows that retrograde evolution can take
place. However, the possibility that characters that
have disappeared may reappear again is probably
often underestimated.” (Of course, in DNA data,
homoplasy is ubiquitous.) So the claim that cladists do
not admit homoplasy is false. However, the minimiza-
tion of homoplasy, which cladists endorse, is an invo-
cation of the razor of silence:
I have therefore called it an “auxiliary principle” that the
presence of apomorphous characters in different species “is
always reason for suspecting kinship [i.e., that the species
belong to a monophyletic group], and their origin by conver-
gence should not be assumed a priori” [Hennig 1953]. This
was based on the conviction that “phylogenetic systematics
would lose all the ground on which it stands” if the presence
of apomorphous characters in different species were consid-
ered first of all as convergences (or parallelisms), with proof
to the contrary required in each case. (Hennig, 1966:121).
Note that the minimization of homoplasy is not the
same thing as a claim that homoplasy is minimal (or
conversely, that evolution must proceed parsimo-
niously in order for the cladistics approach to be legiti-
mate). The latter argument was dismissed long ago by
Cavalli-Sforza and Edwards (1967) and dissected with
greater clarity by Farris (1983).
10 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
Another flashpoint for criticism is the notion that
pattern cladists view cladograms as “atemporal
synapomorphy schemes”, with the accompanying
insinuation that this represents a denial of ancestry
and descent, and an adoption of Platonism (e.g. Scott-
Ram, 1990). Once again, the cladistic position is a
razor of silence. Nobody denies that time is a real
dimension, or believes that the objects of systematic
study reside on a supernatural plane populated by
atemporal Platonic forms (except, perhaps, those who
believe phylogenetic relationships can be described
with statistical models). Even Richard Owen consid-
ered his vertebrate archetype to represent a conceptual
ground plan, rather than an idealized perfect form
(Rupke, 1994). The cladists’ empiricist perspective
leads them to treat fossils as remnants of organisms,
with features that can be compared as homologues
with those of other organisms, rather than as potential
ancestors, by virtue of the fact that they are old. Thus,
fossils appear as terminals on cladograms like any
other taxon, and the vertical axis represents a simple
empirical scale of relative degree of relationship or
branching order that is implied by the evidence from
the specimens themselves, rather than a chronogram’s
theory-laden absolute time axis.
When we consider the supposed differences of phi-
losophy between pattern and process cladistics, we find
that all of these also represent razors of silence on the
part of pattern cladistics, rather than razors of denial.
No cladist I am aware of has ever denied that evolu-
tion occurred. There may be some differences of opin-
ion about particular mechanisms, but the general
propositions of change through time and descent with
modification are consistent with observable microevo-
lutionary phenomena and with more inclusive patterns
that systematists have discovered (Darwin, 1859). Even
at his most dismissive, Colin Patterson (1982a:55) said
only that “belief in, or knowledge of, evolution is
clearly unnecessary for the analysis of homology”,3
and Nelson and Platnick (1981:159), “that, synapo-
morphy has the same empirical basis as homology,
that both concepts are interdependent, that both may
be considered without reference to evolutionism, and
that an evolutionary element of interpretation may be
added to them without necessarily changing their
empirical basis.” These are plainly not denials that
evolution is a good explanation of phylogenetic pat-
terns, but merely statements that one does not need
3
Note that Patterson’s rejection of Popperian falsificationism was
a consequence of his view that species and monophyletic taxa are
individuals, sensu Hull, whereas paraphyletic grades are classes (Pat-
terson, 1978b). This implies greater commitment to an evolutionary
metaphysics than many of the other pattern cladists embrace, and
belies claims that Patterson was a “creationist”.
evolutionary theory to draw systematic inferences (cf.
Brower, 2000).
Thus, the fundamental question is not whether pat-
tern cladists believe that evolutionary theory is legiti-
mate or warranted, but whether we consider that
evolutionary theory provides necessary background
knowledge for conducting phylogenetic analyses, as
asserted, for example, by Wiley (1981), Kluge (1997,
2001) and Fitzhugh (2006). If evolutionary assumptions
are not necessary, then it is methodologically parsimo-
nious to not assume them (razor of silence). Further, if
the explanatory power of a hypothesis is reduced by
unnecessary auxiliary assumptions, then a cladistic
hypothesis without unnecessary evolutionary assump-
tions would seem to be a stronger source of evidence
than one that includes them. As Sober (1988:11) said,
the “less we need to know about the evolutionary pro-
cess to make an inference about pattern, the more con-
fidence we can have in our conclusions.”
The theories of pattern cladistics
Process cladists and phylogeneticists have pro-
claimed that the assumption of “descent, with modifi-
cation” (DWM) provides a (or “the”) justification for
believing that taxa exhibit characters inherited from a
common ancestor, that shared, derived character
states––synapomorphies––reveal relative recency of
common ancestry, and that the history of life takes the
form of an irregularly bifurcating hierarchy (de
Queiroz, 1988; Kluge, 2001; Wiley and Lieberman,
2011; Baum and Smith, 2013). DWM is a process
model that could produce those patterns, or lots of
other patterns. DWM also could result in reversals,
parallelism, convergence or anastomosis of lineages, all
of which are pattern-obscuring mechanisms. Therefore,
it is clear that the assumption of DWM is not suffi-
cient background knowledge for the success of cladis-
tic inference. Is it necessary?
For pattern cladists, DWM is an explanation for the
phenomena of synapomorphy and hierarchy, but we
think that the phenomena are intelligible with or with-
out the explanation. There is a rich theoretical basis
supporting that intelligibility, encompassing recogni-
tion of characters and their states, character polarity,
and the tree-like structure of phylogenetic hypotheses.
As noted, because DWM does not preclude alternative
patterns, whatever other theories underlie the empirical
basis of pattern cladistics are implicitly necessary for
process cladistics, too.
Brower (2000) reviewed many of the epistemological
issues surrounding the pattern cladistic approach to
character coding, hierarchy and rooting. The famous
Belon (1555) illustration of bird and human skeletons
anchors in history the fact that it is epistemologically
possible to recognize transformational homologues
 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
(anatomical parts of different organisms that are “the
same”) without an evolutionary mindset, and indeed,
this is precisely what pre-Darwinian systematists such
as Linnaeus, Cuvier and Owen did. Whatever these
systematists’ conception of the “meaning” of these
phenomena might have been is immaterial to the fact
that they were able to conduct successful research on
comparative morphology, and to develop both critical
theoretical concepts such as homology (Brower and de
Pinna, 2012, 2014) and hypotheses of relationship that
are still viewed as largely correct today. Homology is
indisputably “intelligible” without reference to evolu-
tion.
As noted, cladists count character-state transforma-
tions, which means that characters and states need to
be formalized as hypotheses of identity among parts.
Platnick (1979:542) said, “(a) character is. . . a theory
that two attributes which appear different in some way
are nonetheless the same (or homologous)” (see also
de Pinna, 1991; Brower and Schawaroch, 1996). Align-
ment of DNA sequence data is the same process for a
different kind of evidence. Initial hypotheses of charac-
ter-state identity (primary homology) are tested by
congruence, which is a corollary of the parsimony cri-
terion. The phylogenetic tree with the smallest amount
of homoplasy for a given dataset is preferred. At the
same time, homoplasy is neither ignored nor dis-
counted, although cladists do not feel the need to
explain or accommodate it with ad hoc mechanistic
hypotheses.
To “group by synapomorphy” is the distinguishing
feature of cladistics vs. other phylogenetic approaches,
shown to be the most natural and efficient means to
classify taxa by Farris (1979a,b, 1982). Sorting synapo-
morphies from symplesiomorphies, once performed by
inferring polarities for individual characters, is usually
accomplished nowadays by providing a “root” for the
group we are interested in after an unrooted most-par-
simonious network has been inferred. By “root” is
meant, “connection to the rest of the tree of life”,
which for any monophyletic group occurs at a single
branch point. In the 1970s, vertebrate biologists in
particular felt that ontogenetic rooting was the only
“direct” method to polarize characters, following von
Baer’s law. But as DNA has become the most abun-
dant source of evidence for phylogenetic inference,
outgroup rooting has predominated.
Determining the position of the root for a given
taxon is an aspect of phylogenetic inference where
reciprocal illumination comes into play. If we adopt
an irregularly bifurcating hierarchy as a useful frame-
work for summarizing apparent patterns of relation-
ship, as systematists since Aristotle have implicitly
done via logical division classifications, then it is evi-
dent that there are many unique and striking features
found only in particular groups of organisms,
11
including nuclei in eukaryotes, feathers on birds, hair
on mammals and spinnerets on spiders. These are
characters recognized centuries or millennia ago that
pick out groups we consider even today to be mono-
phyletic. Sereno (2007) called such characters “neo-
morphic,” and what is interesting about them is that
their complementary symplesiomorphies unite no
group (unlike other symplesiomorphies, which are
synapomorphies for a more inclusive taxon, such as
fins vs. limbs in vertebrates). I consider characters such
as these to provide an existential criterion of character
polarity that precedes either ontogenetic or outgroup
polarization, and I think these sorts of features offer
epistemological anchors for testing and refining
hypotheses of character polarity in other cases, such as
DNA sequences. Because a given clade connects to the
remainder of the tree of life by a single branch, these
existential anchors imply, at least as an initial hypothe-
sis, the polarity of character states and relationships of
taxa within the clade in question. And so hypotheses
are tested and refined. This perspective reveals the
false premise of Sober’s (1993:182) claim, “If the
methodology of cladistic parsimony is inextricably
connected to the idea of descent with modification in a
branching process, the goal of pattern cladism cannot
be achieved.” Instead, if we are willing to accept the
straightforward phenomenological proposition that the
presence of some character is more compelling evi-
dence that the taxa which possess it form a group,
than the absence of that character unites the group’s
complement, then pattern cladistics provides an empir-
ical solution to the problem of character polarity that
is more general than either the ontogenetic or out-
group criterion. That approach, in turn, provides con-
crete and independent evidentiary support for the
theory of evolution.
In the heat of the fray, Olivier Rieppel argued nor-
matively for the pattern cladistic view: “Pattern recon-
struction retains logical priority over process
explanations, and the best evidence for evolution
remains a highly corroborated pattern of order in nat-
ure which is itself based on the empirical analysis of
character distribution.” (Rieppel, 1993:217; see also
Rieppel, 1988). The “mature” Rieppel (2007, 2014) has
adopted a more neutral-descriptive stance, suggesting
that “philosophy” such as I have endeavoured to artic-
ulate here, is mere instrumentalism: “the methodology
used to arrive at the phylogenetic system. . . is an atem-
poral calculus, and it is this calculus that pattern cla-
dists uprooted from its ontological grounding,
separating the epistemology of systematics from the
ontology implied by evolutionary theory” (Rieppel,
2014:130–131). I agree, and respond, so what? Why
does the phenomenology of characters as evidence for
taxa require ontological grounding from evolutionary
theory, if the explanandum is independent of the
12 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
explanans, as Brady (1985) argued it ought to be? By
analogy, I might ask, can I be an ethical person only
if I have an external morality imposed upon me
through a system of supernatural metaphysical beliefs,
or can one choose to be ethical in the absence of those
beliefs? Did God really hand those tablets to Moses,
or were the Commandments just helpful socially nor-
mative guidelines that Moses thought might keep the
Israelites in line? Colin Patterson (in litt., 16 August
1994) wrote, “I still maintain that scepticism is the sci-
entist’s duty, however much the stance may expose us
to ridicule.” Although critics are fond of imputing pat-
tern cladists’ eschewal of evolutionary assumptions to
be blinkered operationalism, in many ways, scientists
who are interested in discovering independent evidence
that provides support for a theory would seem to be
engaged in more genuine and substantial research than
scientists who invoke the theory as an a priori govern-
ing metaphysical premise in their quest for corroborat-
ing instances. Systematics under the latter paradigm
seems to me to be “puzzle solving” (Kuhn, 1970).
Here is a dead rat
Arnold Kluge (1997, 1999, 2001, 2009) has repeat-
edly asserted that “descent, with modification” is the
required background knowledge for phylogenetic infer-
ence, as framed in a formal Popperian hypothetico-
deductive, or Hempel–Oppenheim nomothetic-deduc-
tive scheme (Hempel and Oppenheim, 1948; Popper,
1959). In self-contradiction, Kluge has elsewhere
argued that species and other taxa are individuals and
that systematics is an idiographic science (Frost and
Kluge, 1994; Grant and Kluge, 2004; Kluge, 2005,
2007). As discussed earlier in this essay, these two real-
ist positions are fundamentally incompatible: if the lat-
ter conception is valid, then the former cannot be.
Thus, if taxa are individuals then they are not subject
to universal laws or the logic pertaining thereto (Ghis-
elin, 1997), they fall outside Popper’s demarcation of
science, and only metaphysical statements regarding
them may be asserted.
As we have seen, individuality is not an especially
productive philosophical stance for systematics, and is
not how systematics or other biological sciences pro-
ceed, from a practical perspective. Therefore, let us
assume, for the sake of argument, that the nomothetic
perspective is more appropriate and the idiographic
view is less so. In the nomothetic view, species and
other taxa are treated as theories rather than concrete
physical entities, and so explanatory hypotheses may
be proposed regarding their characters and implied
patterns of relationship.
Karl Popper (1979) distinguished explanatory deduc-
tion from the more typical and widely discussed pre-
dictive deduction. In Popper’s explanatory deductive
scheme, the explicandum––the phenomenon or obser-
vation to be explained (equivalent to Brady’s
explanandum)––is the conclusion of a deductive syllo-
gism, whereas the explicans (equivalent to Brady’s
explanans) constitutes two premises: a statement of ini-
tial conditions, and a universal law. In the “dead rat”
situation, according to Popper (1979:350–351), “the
explicandum is definitely known to us - the fact lies
before us in stark reality. If we want to explain it, we
must try out some conjectural hypothetical explana-
tions (as the authors of detective stories do); that is to
say, explanations which introduce something unknown,
or at any rate much less known to us.” Under such
circumstances, “descent, with modification” takes the
form of the universal law in the premise. As Popper
(1983:132) observed, “The explicans, on the one hand,
which is the object of our search, will as a rule not be
known: it will have to be discovered. Thus, scientific
explanation, whenever it is a discovery, will be the
explanation of the known by the unknown.”
Applying this explanatory syllogistic scheme to a phy-
logenetic context, we might observe that some group of
organisms shares a feature––say feathers, or abdominal
spinnerets–that no other taxon possesses. That repre-
sents the explicandum––the observation to be explained.
The specific initial condition might be a hypothesis of
monophyly of that taxon, and the universal law would
be “descent, with modification.” Note again, in this
application of Popper’s explanatory syllogism model,
that what is “known” is the distribution of the charac-
ter, and what is “unknown” is the explanation. Nelson
and Platnick’s characterization (1981:141) of cladistics
fits this scheme rather well: “The concept of ‘patterns
within patterns’ seems, therefore, an empirical general-
ization largely independent of evolutionary theory, but,
of course, compatible with, and interpretable with refer-
ence to, evolutionary theory.”
According to Popper (1983:132–133), two additional
criteria must be met for the explicans to be satisfactory:
“it must logically entail the explicandum” and “it must
be independently testable; and it will be the more satis-
factory the greater the severity of the independent tests
it has survived.” If the explicandum is a test of the expli-
cans, then in the systematic context, independent tests
would be additional characters that might or might not
support the group in question (congruence test), or
other characters that support other monophyletic groups.
The “independence” of the tests seems very much in
agreement with Brady’s (1985) argument regarding the
“independence of systematics”, which offers a strong
endorsement of the pattern cladistic approach.
But does “descent, with modification” logically
entail the distribution of any particular character or
the existence of any particular taxon? I don’t believe it
does: “descent, with modification” entails neither a
hierarchical pattern of relationships, nor any particular
 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
relationship between evidence and the true history of
diversification (Brower, 2002). As Sober (1988) pointed
out, evolution is both an information-creating and an
information-destroying process. Thus, the assumption
that there has been descent with modification offers no
guarantee that there is accessible evidence of the
course of that descent. Perhaps a more appropriate
covering law would be “there is an irregularly bifurcat-
ing hierarchy of groups nested within groups that exhi-
bit homologues parsimoniously explained by their
ancestry.” This is still not a universal law, but it states
a hypothesis that is falsifiable, that has survived many
severe and independent tests, and that, together with
the specific initial condition, does entail the explanan-
dum. And, in fact, a statement akin to this is just what
Platnick (1979:538) said right back at the start.
Conclusion
Historical criticisms of pattern cladistics have
imputed metaphysical beliefs upon its practitioners that
we do not hold. The echoes of these aspersions may still
be heard today. The main substance of these critiques
was off the mark, suffering from a failure to distinguish
between the razor of denial and the razor of silence. Pat-
tern cladists are neither creationists nor Platonists. Nor
are we operationalists who deny a theoretical frame-
work for our work. However, “descent, with modifica-
tion” is neither necessary nor sufficient to provide a
“justification”, or foundational background knowledge,
for systematics. DWM merely serves as a quasi-religious
metaphysical security blanket, too general to provide
specific predictions, and largely devoid of empirical sub-
stance without the evidentiary basis that systematics
provides. The actual background assumptions of the
pattern cladistic perspective, including the empirical
basis, hierarchy and character polarity, also underlie
other contemporary phylogenetic approaches. Because
it minimizes these ad hoc hypotheses, pattern cladistics
represents the most parsimonious philosophical
approach to the problem of phylogenetic inference.
Because it makes no a priori assumptions about mecha-
nisms of evolution, pattern cladistics provides indepen-
dent evidence supporting the theory of evolution, which
legitimates and frees from circularity the explanation
for the patterns systematists observe. Rather than being
hostile to evolutionary theory, pattern cladistics pro-
vides perhaps the clearest and most compelling material
basis for it to exist.
Acknowledgements
I thank Gareth Nelson, Norman Platnick and three
anonymous reviewers for reading and commenting on
13
drafts of the manuscript. Support for this work was
provided through a collaborative grant, Dimensions
US-Biota-S~ao Paulo: Assembly and evolution of the
Amazon biota and its environment: an integrated
approach, supported by the US National Science
Foundation (NSF DEB 1241056), National Aeronau-
tics and Space Administration (NASA), and the
Fundacß~ao de Amparo a Pesquisa do Estado de S~ ao
Paulo (FAPESP Grant 2012/50260-6). The opinions
expressed in this essay do not necessarily represent the
policies of the U.S. Department of Agriculture.
References
Anonymous, 1981a. Darwin’s death in South Kensington. Nature
289, 735.
Anonymous, 1981b. How true is the theory of evolution? Nature
290, 75–76.
Anonymous, 1981c. Does creation deserve equal time? Nature 291,
271–272.
Baum, D.A., Smith, S.D. 2013. Tree Thinking: An Introduction to
Phylogenetic Biology. Roberts & Co., Greenwood Village, CO.
Beatty, J., 1982. Classes and cladists. Syst. Zool. 31, 25–34.
Belon, P. 1555. L’Histoire de la Nature des Oyseaux. Guillaume
Cavellat, Paris.
Bonde, N. 1977. Cladistic classification as applied to vertebrates.
In: Hecht, M.K., Goody, P.C., Hecht, B.M. (Eds.), Major
Patterns in Vertebrate Evolution. Plenum, New York, NY,
pp. 741–804.
Brady, R.H., 1982. Theoretical issues and “pattern cladistics”. Syst.
Zool. 31, 286–291.
Brady, R.H., 1985. On the independence of systematics. Cladistics 1,
113–126.
Brower, A.V.Z., 2000. Evolution is not an assumption of cladistics.
Cladistics 16, 143–154.
Brower, A.V.Z., 2002. Cladistics, phylogeny, evidence and
explanation - a reply to Lee. Zool. Scripta 31, 221–223.
Brower, A.V.Z. 2016a. Are we all cladists? In: Williams, D.M.,
Schmitt, M., Wheeler, Q.D. (Eds.), The Future of Phylogenetic
Systematics: the Legacy of Willi Hennig. Cambridge University
Press, Cambridge, pp. 88–114.
Brower, A.V.Z., 2016b. What is a cladogram and what is not?
Cladistics 32, 573–576.
Brower, A.V.Z., 2017. “Parsimony be damned!”. Cladistics 33, 667–
670.
Brower, A.V.Z., de Pinna, M.C.C., 2012. Homology and errors.
Cladistics 28, 529–538.
Brower, A.V.Z., de Pinna, M.C.C.., 2014. About nothing. Cladistics
30, 330–336.
Brower, A.V.Z., Schawaroch, V., 1996. Three steps of homology
assessment. Cladistics 12, 265–272.
Brundin, L., 1966. Transantarctic relationships and their
significance, as evidenced by chironomid midges. Kungl. Svenska
Vetenskapsakad. Handl. Fj€arde Ser. 11, 1–472. 30 plates.
Brundin, L. 1968. Application of phylogenetic principles in
systematics and evolutionary theory. In Ørvig, T. (Ed.), Current
Problems of Lower Vertebrate Phylogeny. Wiley Interscience,
London, pp. 473–495.
Brundin, L., 1972. Evolution, causal biology, and classification.
Zoolog. Scr. 1, 107–120.
Camin, J.H., Sokal, R.R., 1965. A method for deducing branching
sequences in phylogeny. Evolution 19, 311–326.
Carpenter, J.M., 1987. Cladistics of cladists. Cladistics 3, 363–375.
Cavalli-Sforza, L.L., Edwards, A.W.F., 1967. Phylogenetic analysis:
models and estimation procedures. Evolution 21, 550–570.
Charig, A.J., 1980. Cladistics: a different point of view. Biologist 28,
19–20.
14 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
Charig, A.J. 1982. Systematics in biology: a fundamental
comparison of some major schools of thought. In: Joysey, K.A.,
Friday, A.E. (Eds.), Problems of Phylogenetic Reconstruction.
Academic Press, London, pp. 363–440.
Darwin, C. 1859. On the Origin of Species by Means of Natural
Selection. John Murray, London.
Dawkins, R. 1987. The Blind Watchmaker: Why the Evidence of
Evolution Reveals a Universe Without Design. W. W. Norton,
New York, NY.
Dennett, D. 2014. Intuition Pumps and Other Tools for Thinking.
W.W. Norton, New York, NY.
Eldredge, N., 1978. Evolution: taxic or transformational? Syst. Zool.
27, 130–132.
Ereshefsky, M., 2001. The Poverty of the Linnean Hierarchy.
Cambridge University Press, Cambridge.
Farris, J.S. 1977. On the phenetic approach to vertebrate
classification. In: Hecht, M.K., Goody, P.C., Hecht, B.M.(Eds.),
Major Patterns in Vertebrate Evolution. Plenum, New York,
NY, pp. 823–850.
Farris, J.S., 1979a. The information content of the phylogenetic
system. Syst. Zool. 28, 483–519.
Farris, J.S., 1979b. On the naturalness of phylogenetic classification.
Syst. Zool. 28, 200–214.
Farris, J.S., 1980. The efficient diagnoses of the phylogenetic system.
Syst. Zool. 29, 386–401.
Farris, J.S., 1982. Simplicity and informativeness in systematics and
phylogeny. Syst. Zool. 31, 413–444.
Farris, J.S. 1983. The logical basis of phylogenetic analysis. In:
Platnick, N.I., Funk, V.A. (Eds.), Advances in Cladistics.
Columbia University Press, New York, NY, pp. 7–36.
Farris, J.S., 2014. Pattern poses. Cladistics 30, 116–119.
Farris, J.S., Platnick, N.I., 1989. Lord of the flies: the systematist as
study animal. Cladistics 5, 295–310.
Fitzhugh, K., 2006. The abduction of phylogenetic hypotheses.
Zootaxa 1145, 1–110.
Frost, D.R., Kluge, A.G., 1994. A consideration of epistemology in
systematic biology, with special reference to species. Cladistics
10, 259–294.
Gaffney, E.S. 1979. An introduction to the logic of phylogeny
reconstruction. In: Cracraft, J., Eldredge, N. (Eds.), Phylogenetic
Analysis and Paleontology. Columbia University Press, New
York, NY, pp. 79–111.
Gardiner, B.G., Janvier, P., Patterson, C., Forey, P.L., Greenwood,
P.H., Miles, R.S., Jefferies, R.P.S., 1979. The salmon, the
lungfish and the cow: a reply. Nature 277, 175–176.
Ghiselin, M.T., 1966. On psychologism in the logic of taxonomic
controversies. Syst. Zool. 15, 207–215.
Ghiselin, M.T., 1969. The Triumph of the Darwinian Method.
University of California Press, Berkeley, CA.
Ghiselin, M.T., 1975. A radical solution to the species problem.
Syst. Zool. 23, 536–544.
Ghiselin, M.T., 1986. Ordered thoughts on taxonomy. Nature 320,
652–653.
Ghiselin, M.T., 1997. Metaphysics and the Origin of Species. State
University of New York Press, Albany, NY.
Grant, T., Kluge, A.G., 2004. Transformation series as an
ideographic character concept. Cladistics 20, 23–31.
Griffiths, P.E. 1999. Squaring the circle: natural kinds with historical
essences. In: Wilson, R.A. (Ed.), Species. MIT Press, Cambridge,
MA, pp. 209–228.
Halstead, L.B., 1978. The cladistic revolution - can it make the
grade? Nature 276, 759–760.
Halstead, L.B., 1980a. Museum of errors. Nature 288, 208.
Halstead, L.B., 1980b. Popper: good philosophy, bad science? New
Scientist 87, 215–217.
Halstead, L.B. 1982. Evolutionary trends and the phylogeny of the
Agnatha. In: Joysey, K.A., Friday, A.E. (Eds.), Problems of
Phylogenetic Reconstruction. Academic Press, London, pp. 159–196.
Hempel, C.G., Oppenheim, P., 1948. Studies in the logic of
explanation. Philos. Sci. 15, 135–175.
Hennig, W., 1966. Phylogenetic Systematics. University of Illinois
Press, Urbana, IL.
Hull, D.L., 1965. The effect of essentialism on taxonomy: two
thousand years of stasis. Brit. J. Philos. Sci. 15, 314–326; 16, 1–18.
Hull, D.L., 1978. The principles of biological classification: the use
and abuse of philosophy. Proc. Biennial Meeting Philos. Sci.
Assoc., 2, 130–153.
Hull, D.L. 1988. Science as a Process. University of Chicago Press,
Chicago, IL.
Joysey, K.A., Friday, A.E. (Eds.), 1982. Problems of Phylogenetic
Reconstruction. Academic Press, London.
Kluge, A.G., 1997. Testability and the refutation and corroboration
of cladistic hypotheses. Cladistics 13, 81–96.
Kluge, A.G., 1999. The science of phylogenetic systematics:
explanation, prediction, and test. Cladistics 15, 429–436.
Kluge, A.G., 2001. Parsimony with and without scientific
justification. Cladistics 17, 199–210.
Kluge, A.G. 2005. What is the rationale for ‘Ockham’s razor’ (a.k.a.
parsimony) in phylogenetic inference? In: Albert, V.A. (Ed.),
Parsimony, Phylogeny, and Genomics. Oxford University Press,
Oxford, pp. 15–42.
Kluge, A.G., 2007. Completing the neo-Darwinian synthesis with an
event criterion. Cladistics 23, 613–633.
Kluge, A.G., 2009. Explanation and falsification in phylogenetic
inference: exercises in Popperian philosophy. Acta Biotheoret 57,
171–186.
Kluge, A.G., Farris, J.S., 1999. Taxic homology = overall similarity.
Cladistics 15, 205–212.
Kuhn, T.S., 1970. The Structure of Scientific Revolutions. University
of Chicago Press, Chicago, IL.
Lewin, R., 1980. Evolutionary theory under fire. Science 210, 883–
887.
Mayr, E. 1959. Typological versus population thinking. In: Meggers,
B.J. (Ed.), Evolution and Anthropology: a Centennial Appraisal.
Anthropological Society of Washington, Washington, DC, pp.
409–412.
Mayr, E., 1965. Numerical phenetics and taxonomic theory. Syst.
Zool. 14, 73–97.
Mayr, E., 1968. Theory of biological classification. Nature 220, 545–
548.
Nelson, G.J., 1970. Outline of a theory of comparative biology. Syst.
Zool. 19, 373–384.
Nelson, G.J., 1985. Class and individual: a reply to M. Ghiselin.
Cladistics 1, 386–389.
Nelson, G.J., 1998. Colin Patterson (1933-1998) palaeontologist -
reformer of the fossil record. Nature 394, 626.
Nelson, G.J., Platnick, N.I., 1981. Systematics and Biogeography:
Cladistics and Vicariance. Columbia University Press, New York,
NY.
Nixon, K.C., Carpenter, J.M., 2000. On the other “phylogenetic
systematics”. Cladistics 16, 298–318.
Patterson, C. 1977. The contribution of paleontology to teleostean
phylogeny. In: Hecht, M.K., Goody, P.C., Hecht, B.M. (Eds.),
Major Patterns in Vertebrate Evolution. Plenum, New York,
NY, pp. 579–643.
Patterson, C. 1978a. Evolution. British Museum (Natural History),
London.
Patterson, C., 1978b. Verifiability in systematics. Syst. Zool. 27, 218–
222.
Patterson, C. 1979. (letter to Luther Sunderland, 10 April, 1979)
Patterson, C. 1982a. Morphological characters and homology. In:
Joysey, K.A., Friday, A.E. (Eds.), Problems of Phylogenetic
Reconstruction.Academic Press, London, pp. 21–74.
Patterson, C., 1982b. Classes and cladists or individuals and evolution.
Syst. Zool. 31, 284–286.
Patterson, C., 2002. Systematics and creationism. Linnean 18 , 15–37.
Pearson, C.H., 2010. Pattern cladism, homology and theory-neutrality.
Hist. Philos. Life Sci. 32, 475–492.
de Pinna, M.C.C., 1991. Concepts and tests of homology in the
cladistic paradigm. Cladistics 7, 367–394.
 Andrew V. Z. Brower / Cladistics 0 (2019) 1–15
Platnick, N.I., 1979. (1980). Philosophy and the transformation of
cladistics. Syst. Zool. 28, 537–546.
Platnick, N.I., 1982. Defining characters and evolutionary groups.
Syst. Zool. 31, 282–284.
Platnick, N.I., Gaffney, E.S., 1978. Systematics and the Popperian
paradigm. Syst. Zool. 27, 381–388.
Platnick, N.I., Nelson, G., 1978. The purposes of biological
classification. Proc. Biennial Meeting Philos. Sci. Assoc. 1978 ,
117–129.
Popper, K.R., 1957. The Poverty of Historicism. Beacon Press,
Boston, MA.
Popper, K.R., 1959. The Logic of Scientific Discovery. Basic Books,
New York, NY.
Popper, K.R., 1965. Conjectures and Refutations: the Growth of
Scientific Knowledge. Harper Torchbooks, New York, NY.
Popper, K.R. 1979. Objective Knowledge – An Evolutionary
Approach. Clarendon Press, Oxford.
Popper, K.R. 1983. Realism and the Aim of Science. Routledge,
New York, NY.
de Queiroz, K., 1988. Systematics and the Darwinian revolution.
Philos. Sci. 55, 238–259.
Quinn, A., 2017. When is a cladist not a cladist? Biol. Philos. 32,
581–598.
Raulff, U. 2017. Farewell to the Horse: a Cultural History. (Kemp,
R.A. Transl.). Liveright, New York, NY.
Reif, W.-E., 2005. Problematic issues of cladistics 8: philosophical
vagueness and the reality of ancestors. N. Jb. Geol. Pal€aont.
Abh. 235, 137–173.
Ridley, M., 1983. Can classification do without evolution? New Sci.
100, 647–651.
Ridley, M. 1986. Evolution and Classification: the Reformation of
Cladism. Longman, London.
Rieppel, O.C., 1988. Fundamentals of Comparative Biology.
Birkh€ auser, Basel.
Rieppel, O.C., 1993. Patterns and processes. Nature 362, 216–217.
Rieppel, O.C., 2006. On concept formation in systematics. Cladistics
22, 474–492.
Rieppel, O.C., 2007. The nature of parsimony and instrumentalism
in systematics. J. Zool. Syst. Evol. Res. 45, 177–183.
Rieppel, O.C., 2010. New essentialism in biology. Philos. Sci. 77,
662–673.
15
Rieppel, O.C. 2014. The early cladogenesis of cladistics. In:
Hamilton, A. (Ed.), The Evolution of Phylogenetic Systematics.
University of California Press, Berkeley, CA, pp. 117–137.
Rupke, N.A., 1994. Richard Owen: Victorian Naturalist. Yale
University Press, New Haven, CT.
Schaeffer, B., Hecht, M.K., Eldredge, N., 1972. Phylogeny and
paleontology. Evol. Biol. 6, 31–46.
Schuh, R.T., 2003. The Linnean system and its 250-year persistence.
Bot. Rev. 69, 59–78.
Schuh, R.T., Brower, A.V.Z. 2009. Biological Systematics: Principles
and Applications (2nd Edn.), Cornell University Press, Ithaca,
NY.
Scott-Ram, N.R., 1990. Transformed Cladistics, Taxonomy and
Evolution. Cambridge University Press, Cambridge.
Sereno, P.C., 2007. Logical basis for morphological characters in
phylogenetics. Cladistics 23, 565–587.
Sober, E., 1988. Reconstructing the Past: Parsimony, Evolution and
Inference. MIT Press, Cambridge, MA.
Sober, E., 1993. Philosophy of Biology. Westview Press, Boulder,
CO.
Sober, E., 2015. Ockham’s Razors: a User’s Manual. Cambridge
University Press, Cambridge, UK.
Sterner, B., Lidgard, S., 2018. Moving past the systematics wars. J.
Hist. Biol. 51, 31–67.
Vergara-Silva, F., 2009. Pattern cladistics and the ‘realism-
antirealism debate’ in the philosophy of biology. Acta
Biotheoret. 57, 269–294.
Wade, N., 1981. Dinosaur battle erupts in British Museum. Science
211, 35–36.
Wiley, E.O., 1981. Phylogenetics: Theory and Practice of
Phylogenetic Systematics. John Wiley & Sons, Hoboken, NJ.
Wiley, E.O., Lieberman, B.S., 2011. Phylogenetics: Theory and
Practice of Phylogenetic Systematics (2nd Edn.) . John Wiley &
Sons, Hoboken, NJ, .
Williams, D.M., Ebach, M.C., 2008. Foundations of Systematics and
Biogeography. Springer Science+Business Media, New York,
NY.
Williams, D.M., Ebach, M.C. 2014. Patterson’s curse, molecular
homology, and the data matrix. In: Hamilton, A. (Ed.), The
Evolution of Phylogenetic Systematics. University of California
Press, Berkeley, CA, pp. 151–187.