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.

References
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]

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.

RELATIONSHIP / INTRINSIC & EXTRINSIC THINKING

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

Relationship
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.

Intuition
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
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.

Knowledge
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.

References

"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.

Whiggish Historians of Science

Recently we came across Richard A. Richards chapter on 'Species and Taxonomy', in the edited volume The Oxford Handbook of Philosophy of Biology by Michael Ruse. Reading it, we discovered the following:

"Pattern cladists, like pheneticists, typically claim their method is superior because it is theory-free and relies only on pure observation (Sober 2000, 185-86). Pattern cladistics has remained on the fringe because of, first, its implausible assumption that there can be pure observation untainted by theory; and second, its rejection of the evolution assumption" (Richards, 2008 :171).

How could anyone be so wrong?

We guess it is because Richards has not actually read the pattern cladistic literature [also known as transformed cladism]. Instead he relies on Elliott Sober's work (see below) - one that contains many misinterpretations, especially when referring to cladistics. What fascinates us, however, is why historians and philosophers of science refer to his work when there is ample primary literature and, real live pattern cladists available for comment? Shouldn't philosophers and historians of science refer to or cite primary sources, especially when making claims such as Richards has above? Many don't, and doing so has created a whiggish history and philosophy of the science of cladistics promoted by several extremist views. Let's dissect Richards's argument in context of this whiggish history:

"Pattern cladists, like pheneticists, typically claim their method is superior because it is theory-free and relies only on pure observation".

Pattern cladists have never claimed 'superiority' or used the term in above context. Pattern cladists have long argued that their method finds homologies based on proximal relationship - i.e., 0(11) - rather than assumptions of character-state transformations - i.e., 0 => 1. The argument centers around transformation and its use at the character-state level rather than at any other level. Pattern cladists reject the notion of any hypothetical transformations (taxa, character-state or otherwise) in order to find the most parsimonious, compatible or most likely cladogram. Instead they believe that characters and their states be treated like taxa, in that they are related by proximity rather than by hypothetical transformation. This does not mean that the method is phenetic or theory-free (the differences between cladistics and phenetics has been argued on another post). Pattern cladistic theory assumes that character-states can be related prior to analysis (as hypotheses of homology) and tested (i.e., contra to phenetics). Incongruent hypothetical character-state relationships are rejected in favour of congruent relationships. The question is not about superiority or theory-free methods, but about treating characters and their states as taxa. Richards's point merely romanticizes the apparent 'anti-Darwinian' nature of pattern cladistics and it's conflict with mainstream cladistics.

Where does Richards's get these ideas? Most likely from Elliott Sober:

"The [pattern cladistic] idea is that evolutionary ideas are dispensable " (Sober, 2000, Box 6.3 on p. 186)

And quite possibly from the anti-pattern cladistic literature advocated by Hull (1988):

"Sara Fink (in Hull, 1988:257) in her report noted that the "tug of war between the pattern viewpoint and the phylogenetic viewpoint in cladistics is leading on the one hand to an attempt to divorce hierarchical pattern from evolution and create a nearly assumption-free methodology, and on the other to new approaches to the study of the transformation of form".

Richards, like Hull, has made the same error - to choose sides in a conflict rather than to report both equally and without prejudice. This creates a whiggish history one that, ironically, historians of science have warned us about (Hull, 2000). It is strange to see it endemic within the works of historians and philosophers of science. Richards's whiggish history continues:

"Pattern cladistics has remained on the fringe because of, first, its implausible assumption that there can be pure observation untainted by theory ..."

Richards's 'implausible assumption' is clearly another example of fiction. No pattern cladists has ever endorsed or even entertained the idea of 'pure observation untainted by theory'. Again this is the work of reading anti-pattern cladistic literature rather than primary sources:

"Because this work [Sober (1988)Reconstructing the Past, Parsimony, Evolution & Inference] is about phylogenetic inference, not classification, nothing will be said about the current controversy concerning so-called "pattern" cladism ... See Ridley [1986] for references to the primary literature" (Sober, 1988, footnote 7, p. 8).

Just as Richards refers to Sober to make his assumptions about pattern cladism, Sober refers to Ridley (1986). Finally we arrive at the source of Richards's misunderstandings:

"... transformed cladism has no justification, and is nakedly subjective" (Ridley, 1986:91)"

"If cladism transforms into phenetic classification it will make itself subjective too. It will lose its justification, and become quite arbitrary. And despite the arguments we are about to examine ... transformed cladism does admit that its position is arbitrary and unjustifiable"(Ridley, 1986:92)"

"In a similar style they [transformed cladists] assert that it is perfectly possible to classify species without any help from any theories ..." (Ridley, 1986:14).

"There, what matters is the rejection of evolution (Ridley, 1986:10)

Just how many cladists are extreme transformed cladists, in the sense of rejecting (or finding 'unnecessary') the theory of evolution from cladism, is not clear" (Ridley, 1986:88)

"... the rejection of evolution from classification is the most far-reaching ambition of transformed cladism ..." (Ridley, 1986:125)

"The transformed cladistic argument thus fails"(Ridley, 1986:156)

Ridley, a zoologist, is clearly not a friend of pattern [transformed] cladism*. Why then refer to Ridley?

Sober has already made up his mind. Pattern cladistics does not fall into his world view and referring to primary sources serves no purpose. The purpose, it seems, is to write a history of classification and phylogenetics from an extreme 'process' viewpoint. Hull should heed his own advice:

"Science is important, scientists use a wide variety of strategies to get their views accepted, including the publication of Whiggish histories of science, but historians must be firm" (Hull, 2000: 70).

That same warning extends to Richards and Sober.

The final and most common critique of pattern cladism is:

"... its rejection of the evolution assumption."

This is perhaps one of the most incredulous assumptions made about pattern cladism. The most commonly cited reference is to Colin Patterson (2002), British paleoichthyologist and the author of the text Evolution. This is where some historians and philosophers of science share commonality with creationists - confusing Darwinism with evolution. Patterson was a critic of using evolutionary narratives to build classifications. A narrative is a hypothetical explanation or story that is immune to testing or pattern. We may say that A is the ancestor of B, which is the ancestor of C, or; A is the ancestor of C, which is the ancestor of B or; A is the ancestor of B and C. Either way, the relationship A(BC), namely B and C are more closely related to each than they are to A, is true in each case. The narratives add little to the relationship other than scenarios that are impossible to validate. Whether B or A are the ancestors of C will not affect the relationship in anyway. Rather than obsess with which narrative is the best one, Patterson, like many other pattern cladists is interested to see whether these taxonomic groups are related or not. Evolution, for Patterson, was simply whether a taxon is monophyletic or not - whereas superficial narratives can be discarded without affecting the result. The equation Evolution = Darwinism has caused this misinterpretation (i.e., the process of evolution being equated to a particular theoretical explanatory mechanism, in this case Natural Selection). Similar ridiculous associations include: Cladistics = Parsimony (e.g., cladistic analysis can be done using compatibility); "Similarity = Homology" and; Arabs = Terrorists.

Referring to the secondary literature and, in the case of Richards and Sober, tertiary literature has caused philosophers and historians to create a Whiggish history - one that consists of grave misinterpretations based on hearsay.


*In fact, Ridley (1986) thanks Richard Dawkins, Joseph Felsenstein and David Hull for commenting on previous manuscripts in the acknowledgments of his book. This again emphasizes the extreme subjectivity and bias of the work.


References

Hull, D.L. 1988. Science as Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago: University of Chicago Press.
Hull, D.L. 2000. The Professionalization of Science Studies: Cutting Some Slack. Biology and Philosophy 15: 61–91.
Patterson, C. 2002. Evolutionism and creationism. The Linnean 18: 15-33.
Richards, R.A. 2008. Species & Taxonomy. In: M. Ruse (ed.) The Oxford Handbook of Philosophy of Biology. Oxford University Press, New York.
Ridley, M. 1986. Evolution and Classification: The Reformation of Cladism, Longman, London.
Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference, Bradford Books/MIT Press.
Sober, E. 2000. The Philosophy of Biology. Second Edition. Boulder: Westview.

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!