Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Tuesday, 23 December 2008

More Whiggish Historians

The recently published book, Real Essentialism by David S. Oderberg, is another example of Whiggish History and Philosophy of Science.

I refer to Oderberg's use of Elliott Sober's and Mark Ridley's work to make statements about cladistics:
    "See also Sober 1993:Ch. 6 for a defense of cladism and criticism of competing methods" (Oderberg 2008: 214).
    Ridley is a little less sanguine about the implications of cladistics ..." (Oderberg, 2008:222).
    "Ridley notes briefly that [t]here is no orthodoxy among evolutionary biologists [I take him to mean mainly cladists] ..." (Oderberg, 2008:222).
The problem of using the work of non- or even anti-cladists to defend cladistics is remarkable - especially when making outlandish claims:
    "So it looks like the cladist has to believe in the existence of inorganic evolutionary descent at every stage in the past history of the universe" (Oderberg, 2008:220).
    "Common sense - which is not, as I will argue, the same as cladistic sense ..." (Oderberg, 2008:215).
Yet the only cladists Oderberg cites are:
    Another bizarre consequence of cladism is the following (LaPorte 2004: 50-62; Okasha 2002: 205-7)" (Oderberg, 2008:220).
    "Yet this absurd result of cladistics is accepted by LaPorte with equanimity, and taken by Okasha (2002: 205-7) at face value since he upbraids essentialists ..." (Oderberg, 2008:221).
LaPorte and Okasha may 'upbraid essentialists', but they are not representative of cladistic theory nor do they represent the views of all cladists - in the same way that not all historians and philosophers of science are Whiggish in their views.

LaPorte, J. (2004). Natural Kinds and Conceptual Change. Cambridge University Press, Cambridge, UK.
Oderberg, D.S. (2007). Real essentialism. Routledge, London.
Okasha, S. (2002). Darwinian metaphysics: species and the question of essentialism. Synthese 131:191–213.
Sober, E. (1993). Philosophy of Biology. Westview Press, Boulder.

Publications for 2008

Below is our list of publications for 2008. For those with no access to the links, will be happy to provide pdf copies on request.

    Ebach, M.C., Williams, D.M., & Gill, A.C. (2008). O Cladistics, Where Art Thou? Cladistics, 24: 851–852. [pdf]
    Ebach, M.C., Gill, A.C. & Williams, D.M. (2008). Ebach et al. reply: A Future for Astrobiogeography. Astrophysics and Space Science, 317: 147. [pdf]
    Ebach, M.C., Gill, A.C. & Williams, D.M. (2008). The Pitfalls of Astrobiogeography. Astrophysics and Space Science, 317: 143-144. [pdf]
    Ebach, M.C., Morrone, J.J. Parenti, L.R. & Viloria Á.L. (2008). International Code of Area Nomenclature. Journal of Biogeography, 35: 1153–1157. [pdf]
    Ebach, M.C., Morrone, J.J. & Williams, D.M. (2008). A new cladistics of cladists. Biology and Philosophy, 23: 153-156. [pdf]
    Reid, G. & Williams, DM. The diatom slide collection and bibliography of the Reverend Richard Fraser Bastow (c. 1888-1 October 1960). Diatom Research 23: 117-128.
    Reid, G. & Williams, DM. Some commentary on molecules and morphology, species and higher taxa in diatoms, with a note on the relationships of the genus Cistula Cleve. Proceedings of the 1st Central European Diatom Meeting 2007, Kusber, W.-H. & Jahn, R. (ed.), Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, pp. 135-138.
    Toyoda, K, Williams, DM, Tanaka, J., & Nagumo, T. 2008. Nomenclatural problem[s] on [in] Conferva armillaris Müller (Bacillariophyta). Bulletin of the Nippon Dental University 37: 65-70.
    Williams, DM. New names for three fossil species in the genus Tetracyclus Ralfs from Shangu County, Inner Mongolia, P.R. China. Diatom Research 23: 249-253
    Williams, DM. Studies on species of the genus Tetracyclus (Bacillariophyta, Diatomaceae), with recognition of a 'cruciform' sub-group, and comments on their paleogeography. Micropaleontology 53: 1-9.
    Williams D.M. & Ebach, M.C. (2008). Evolutionary theory: don't skimp on teaching its history. Nature 453: 719. [pdf]
    Williams, D.M. & Ebach, M.C. (2008). Foundations of Systematics and Biogeography. Springer, New York. [Flyer]

Monday, 22 December 2008

QOR: Relationship / Intrinsic & Extrinsic thinking [Part 1]

The serialization of our forthcoming book A Question of Relationship (QOR) investigates relationship as an active way of thinking and interacting with the world in contrast to providing epistemological, metaphysical, transcendental or structural explanations. By adopting this way of thinking we are able to identify problematic trends in systematics and biogeography without having to resort to comparing methods, theories or epistemologies. The way systematists and biogeographers do their science is based on the way they perceive and interact with the world, rather than on philosophical stand points. Understanding how we think about day to day concepts will help us identify problems and ways to resolve them without having to rely on philosophical arguments outside our own field.

We are not philosophers or historians of science and will not use current philosophical arguments to justify our arguments. Our experiences lie in practicing systematics and biogeography; therefore we prefer to present our case from this position as it will provide a clearer discussion without adding any confusion to a field that rarely uses philosophical jargon.


In this chapter we will define the terms used in this book and how they are used in comparative biology. We aim to provide a simple example for each term and how each can be interpreted differently. Moreover, these definitions will be revisited in each of the following chapters in order to show how they are used in systematics and biogeography to represent different ways of thinking.

Defining Relationship, Intuition, Anschauung & Knowledge

A relationship is an aspect or quality that binds or connects two or more things as being the same kind, that is, a fundamental quality or nature (Merriam – Webster, 2008). In other words, a relationship is a qualitative expression of different manifestations of a single form. In the strictest sense, form is the shape and structure as distinguished from its material nature (Merriam – Webster, 2008). Within comparative biology however, form is restricted to the shape and structure of what we study. For instance, a DNA molecule is no different from a shoulder blade considering they are all parts of an organism, which have shape and structure and, are studied by comparative biologists (see discussion below). The material nature of form therefore is purely at the atomic level, where shape and structure are subject to different laws (i.e., quantum mechanics).

The way we recognize form is by comparing its parts to other forms we have experienced. The act of recognition occurs in two fundamentally different ways, either by seeking similarities or by intuiting manifestations. The former can be done quantitatively and the latter through direct experience. For example, Sam is on a blind date in a cafe. The woman Sam is meeting is wearing a purple blouse. He found her by comparing the color of the clothes of other people in the café who look like women. The act of seeking similarities simulates recognition artificially because Sam has never seen the woman and therefore has gained no experience of her appearance. A list of quantitative characteristics acts as an artificial system for identification.

The process of intuiting manifestations occurs in a completely different way. Charlotte has five cats. On her visit to her sister she sees and instantly recognizes a cat ambling across the street. Charlotte does not need a list of characteristics or even a language to identify a cat. Her experiences are sufficient.

These two ways in which a person recognizes form are fundamentally different, as we will demonstrate later on. The first uses an artificial system of recognition, such as a list of characteristics, a key (e.g., as a card catalog) or a pictorial map. The latter uses our own intuition or active participation.

The difference between artificial and natural recognition is not one between a false reality and a true reality. Rather it denotes a mechanical operation from a natural occurrence. We encourage readers to challenge the notion of truth, namely the notion of a hidden mechanism, which can only be revealed by rational explanation. Intuition, as immediate cognition, presents an entirely different way of thinking.

The concept of intuition is commonly associated with 'subjectivity', however it is rarely defined in this way. The Oxford English Dictionary for instance defines intuition as "direct or immediate insight", "Immediate apprehension by the intellect alone", "The action of mentally looking at; contemplation, consideration; perception, recognition; mental view" and "The action of looking upon or into; contemplation; inspection; a sight or view". These definitions, in our view, are expressed best as '“knowledge without recourse to inference” (Ornstein, 1996, p. 24). We will also use the term Anschauung (a.k.a. intuitive perception) to refer to the act of 'mentally looking' or 'knowing without recourse to inference'.

Anschauung is one way in which we can view the world and understand without referring to explanatory mechanisms or purpose. Inferences, such as explanatory mechanisms, are tools we use to make sense of phenomena. At times, they provide a reason or purpose for a phenomena coming into existence. For example, seeing a bird sing on the bough of a tree may be expressed into two different ways - either as a sexual/territorial behavioural mechanism, or as a bird and a flower

The explanatory mechanisms provide us with an explanation and/or purpose. The bird for instance may be attracting a mate or warding off potential suitors or competitors for food. The purpose could be genetic survival, Divine will, or mere joy. Since we are in this case referring to inference, the best rational argument will suffice. This would mean that the same bird behaviour has equal valid meanings in three different rational worlds. Within a modern western 21st century society, survival is the best rational explanation whereas in 11th century Gaul divine causation would be the best explanation. Inference is linked to what we know and what rational arguments are accepted within our society at any given time. The bird behaviour symbolizes an explanatory mechanism, rather than representing two observable forms.

Seeing the bird as a form in time and space does not require any explanation or purpose. The bird is an explanation in itself, regardless of what purposes or rational explanations are acceptable or not. The bird and flower are forms that can be understood by intensive observation or anschauung. The rational explanations for their interaction may vary or not be correct at all. Explanations, no matter how absurd or rational, are considered to add to our wealth of 'knowledge', even if they ignore the phenomena themselves. Observing the world through anschauung, we come to appreciate that knowledge, based on inference, is no more than abstract observation and rationalization.

Defining knowledge is difficult. It is used in different ways to express what we know. The example Oxford English Dictionary has several contradictory definitions, including "intuition" and "perception gained through information or facts about it rather than by direct experience" . Herein we use these two definitions to distinguish between intuitive and abstract knowledge. Each is obtained via a different facility. Intuitive knowledge is gained via experience and abstract knowledge is gained via reasoning. The division highlights the difference between acquiring knowing naturally and artificially as described above. identifying an object through recognition is based on intuitive knowledge, whereas using a list or key to identify a phenomenon is artificial. The distinction between artificial and natural, intuitive and abstract become apparent when we investigate the type of thinking we do.

A Question of Relationship: The Role of Homology in Systematics and Biogeography is a forthcoming book by David M. Williams & Malte C. Ebach. The book will be published by Forrest Text.


"form" Merriam-Webster Online Dictionary. 2008.
"kind" Merriam-Webster Online Dictionary. 2008.
"relation" Merriam-Webster Online Dictionary. 2008.
Ornstein, R (1996). The mind field. Cambridge: Malor Books ISHK.

Monday, 8 December 2008

Serializing our New Book: A Question of Relationship

David Williams and I have signed our contract for a new book to be published by Forrest Text. The book A Question of Relationship: the role of homology in systematics and biogeography (our working title) will be serialized on this blog over next few months (or until we get it written).

We hope that our book addresses some of the more important issues in systematics and biogeography, as well as getting your feedback. The task will be an arduous one as we hope to cover the following topics recently discussed in the literature and on this blog:
    Defining Relationship
    Bortoft's Intrinsic & Extrinsic Thinking in systematics and biogeography
    Complexity and Classification
    Homology versus Similarity
    Paraphyly and Monophyly
    Phenetics versus Natural Classifications
    Phylocode and Artificial Classifications
    Molecules and Morphology
    DNA Follies and the Thin Blue Line
We hope that this interactive experiment in science writing ends in a well rounded and balanced text. Let the writing commence!