Philosophy of Biology

HOMOLOGY AND HOMOPLASY

Brian K. Hall

“In [the various] kinds of animals and plants [we see] simply the parts of

one great genealogical tree, which have become detached and separated

from one another in a thousand different degrees, through the operation

of the great destroyer Time...” [Lankester,1870a, 34].

1 INTRODUCTION

Homology, from the GreekHomologia, agreement, has been foundational for any

comparisons of biological objects for millennia. Homology normally is contrasted

with analogy (similarity of function) and/or with homoplasy (similarityarising

through independent descent).^1

Clasically, homology and analogy both referred to similar parts (features) of

organisms.^2 Because homology applies across the entire biological hierarchy from

genes to individuals — perhaps even to populations and communities ([Hall,

1994a,b; 2004; 2007a]; [Hallet al., 2004]) — and even though thedefinitionof

homology is invariant across the hierarchy, theapplicationof homology must spec-

ify the level of the biological hierarchy to which the term and concept is applied,

and so we must speak of ‘homologous as an appendage’, ‘homologous as a gene

network’, and so forth. Homology at the level of the phenotype (phenotypic or

structural homology) is the continuous occurrence of the same feature (be it gene,

gene network, cell type, tissue, organ, structure or behaviour) in two organisms

whose common ancestor possessed the feature. The same definition applies to

synapomorphy, which is a derived character, shared by two or more different or-

ganisms.^3 Operationally, knowledge of a homologue precedes use of that knowledge

to identity a feature as a synapomorphy.

(^1) See Hall [1994a] and Bock and Cardew [1999] for homology, Sanderson and Hufford [1996]
for homoplasy, and Cohen [1994] and Panchen [1999] for analogy. My entry draws on material
from Hall [1994a; 2003a] which may be consulted for fuller development and illustration of the
arguments.
(^2) See Moment [1945], Smith [1967], Bock and von Wahlert [1965], Gans [1985], Rieppel [1988],
Bock [1991] and Hall [2003a; 2007a] for discussions and analyses of similarity and of features in
extant and extinct organisms.
(^3) A character is any trait or feature of the phenotype, for which see Patterson [1982], M. H.
Wake [1996], Matthen [2000], P. J. Wagner [2000], McShea [2000], and the chapters in Wagner
[2001] and in Hall and Olson [2003].
General editors: Dov M. Gabbay,
©c2007 Elsevier B.V. All rights reserved.
Handbook of the Philosophy of Science. Philosophy of Biology
Volume editors:
Paul Thagard and John Woods
Mohan Matthen and Christopher Stephens