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.

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!

Complexity, Pattern & Process

Species are biologically complex. The Merriam-Webster Online Dictionary define Complex as "a whole made up of complicated or interrelated parts", that is 'interrelated parts' that are "consisting of parts intricately combined". Species on the other hand are harder to define.

I will not define a species here. There are enough species concepts to go around and adding another one will not aid the growing problem of understanding species. The difficulty that many have with species is that they do not classify well. This presents us with a problem: if classification makes sense of complexity, then why can't we classify species? Why, for instance, do some claim species are never monophyletic? If species are presented by genealogical and therefore reticulated lineages that include ancestors and descendants, it will be impossible for us to classify them - to divided up related individuals into separate groups. The same argument can be made of genera and families too, but we are able to classify them. Why do species present us with this problem. The answer lies in what we mean by pattern and process.

A pattern is a repeating relationship. The character-states 0(11) for instance represent a relationship or homolog that relate the taxa A, B and C. If A = 0, B= 1 and C = 1, the relationship can be expressed as A(BC). If this taxic relationship occurs many times in different characters, it forms a pattern or homology. Process however is harder to define.

Returning to the Merriam-Webster dictionary we find the process means "a natural phenomenon marked by gradual changes that lead toward a particular result". For example, ontogeny is a process. What of the processes we are unable to see or measure? These processes can be discovered through patterns. The homology A(BC) is a discovery of evolution. That is a common and shared history. A 'hidden' process, such as the sexual behavioral traits of hadrosaurs is completely unknown to us (if they had any at all). We are able to model these traits based on assumptions, wild guesses or on the behavior of related living taxa such as birds. What ever result is generated (artificially produced) will never represent a discovery. We will never see such behavioral traits, so our models are merely speculations. The same is true for genealogical relationships. We only know who we are related to simply by observation, written documentation or by word-of-mouth. Through our DNA we are able to discover how similar we are to other people, either dead or alive, but we will never know if they are our direct descendants. Genealogy, as an unobserved process, is therefore often hypothesized. In order to make that process consistent we assign a rational hypothesis or explanatory mechanism. Genealogical relationships that move beyond our understanding (i.e., observation, recorded history etc.) rely on this hypothesized explanatory mechanism.

Explanatory mechanisms (unobserved processes) do not discover patterns. They generate artificial and ad hoc hypotheses. Observed processes however do. They provide a more robust explanation, but offer little in the way of a direct or trivial narrative (e.g., who begot whom).

Let us return to species. We assume that they are interbreeding classificatory 'units' real or otherwise. Species that are defined on an unobserved 'process' are mechanical. For some this helps conceptualize a species, for others it has little to do with classification.

Biological classification is based on patterns and the observed processes that help to uncover them. We may infer explanatory mechanism from patterns, but we will never be able to discover patterns from explanatory mechanisms. Species, as defined by explanatory mechanisms, have no place in classification. As arbitrary taxa (like genera or families), however, they make perfect sense.

The Evolution Slogan

The term "evolution" can be used recklessly in a variety of ways: "If evolution was outlawed, only outlaws will evolve", "Paraphyly is evolution all the way" (Brummitt, 2002:40) and most recently, "Because we understand how evolution happens, we can also guess where it will go next" (Jones, 2008; see also John Wilkins's post). The two main points of contention, highlighted in the latter statement by Steve Jones, are our "understanding" of evolution and our ability to "guess".

The late Colin Patterson, ichthyologist at the then British Museum, Natural History in London, gave a presentation that questioned the term. The talk, titled "Systematics and Creationism", was given at American Museum of Natural History (Patterson, 2002) in November 1981. There Patterson noted:

"...the theory is evolutionary theory, descent with modification" (Patterson, 2002:23; see also Martin Brazeau's post)

Combined with the above slogans we may suggest that 'evolution' is: a process of descent with modification that results in paraphyly problem arises. How do we see this process?

In order to know we need to be able to observe or measure. Paraphyly, for instance, cannot be observed. It exists only when an artificially delineated taxonomic group is discovered to be monophyletic (homologous) - like 'invertebrates' or 'aliens'. Descent with modification is also difficult to see in action. Although we can see genealogy and ontogeny, they do not constitute 'descent with modification', at least not in the way Jones uses the term.

What systematists and biogeographers know is that evidence for evolution is based on retrodictions - that is past 'predictions' or patterns. These patterns are homologies or relationships - evidence for evolution. Our task as systematists is to discover whether our groups are a result of evolution, rather than poor taxonomy. Evolution should not be taken for granted - just because we know it exists doesn't mean we should stop looking. Reptiles, for example, are not an evolutionary group. They are a poorly defined taxonomic group like 'insectivores' and 'creepy, crawling things'. Discovering that taxa within the reptilia share closer relationships with taxa in mammalian than with any other taxon does not validate reptiles as an evolutionary group. The task of herpetologists is find those evolutionary groups and, not to defend existing names that have no evolutionary significance. Patterns, homologies, relationship and monophyletic groups are all the same thing: evidence for evolution.

Now we return to Jones. He, like many other evolutionary biologists, has committed a classic error - assuming that life progresses from an incomplete to complete phase: also known as 'primitive to derived'. A typical example is the 'primitiveness' or 'plesiomomorphy' of Archaeopteryx lithographica. The half bird-half reptile is always considered to be transition - fossilized in the middle of evolving. Like all living things dead or alive, Archaeopteryx is perfect in its own right. It has no hidden agenda, no purpose other than to be Archaeopteryx. If we were to assume, unwittingly and in hindsight, that it was primitive, then we are advocating some purpose or teleology, namely that Archaeopteryx was aiming to become a bird. This sort of thinking gives evolution a bad reputation and opens it up to attack from protagonists of anti-science. The logic behind it does not work. Let us assume for the moment that we could go back in time, back when Archaeopteryx was alive. We would assume, that this is a highly evolved 'reptile', a derived form. See the problem? Archaeopteryx is both derived and primitive at the same time in form and space but not in geological time. The whole 'primitive – derived' argument is based stratigraphic sequence and not evolution (homology).

To counter Jones's argument - we are complete, so is Archaeopteryx and all other life that has ever existed and will ever exist on this planet. What does this completeness say about evolution? Absolutely nothing at all. Instead it tells us of a desire for explanation.

We may think 'nothing in biology makes sense except in the light of evolution' (Dobzhansky, 1973), but without a doubt, evolution only makes sense in the light of homology. Biological classification provides us with the tools to discover relationships and a way to understand the evolution of life. Without it we are just telling never-ending stories. I am sure that in 200 millions years time, an octopod biologist, will wonder how something as incomplete and primitive as Homo sapiens lived for as long as it did.

References

Brummitt, R. K. 2002. How to chop up a tree. Taxon 51: 1-41.
Dobzhansky, T. 1973. Nothing in Biology Makes Sense. Except in the Light of Evolution. The American Biology. Teacher, 35:125-129.
Jones, S. 2008. Evolution is complete: so where do we go from here? Daily Telegraph Online, http://www.telegraph.co.uk/earth/main.jhtml?xml=/earth/2008/10/07/scievolution107.xml
Patterson, C. 2002. Evolutionism and creationism. The Linnean 18: 15-33.

Naef and Cephalopod Awareness Day

Cephlapodcast has announced the Second Annual Unofficial International Cephalopod Appreciation and Awareness Day. I wonder what Adolf Naef would have said?

Naef said a lot about cephalopods and their relationships. As a respected world authority on octopuses and their relatives, Naef has produced several texts that have until now only interested David and I in parts (mostly the systematic theory and methodology). Our only foray into the fascinating world of calamari occurred recently when were contacted by Jan Strugnell - a cephalopodist from the University of Cambridge and admirer of Naef's work. Jan had an interesting question - why did Naef's phylogeny and classification of Argonautoidea differ?

The Argonautoidea Lamarck, 1809 (paper nautiluses and their relatives) are divided into two subfamilies: Tremoctopodinae and Argonautinae. The former includes Alloposidae and Tremoctopodidae and, the latter Argonautidae and Ocythoidae. Naef produced the following diagram (Figure 1a) with the following accompanying text:

"The typical relationship between the 4 genera which form the family are shown in the following graph: i.e., the genera developed by secondary specialization from forms I-IV in a direct series.
The ideal or hypothetical form I corresponds to the type of the family; form II corresponds to the type of the 3 genera, form II to the type of the 2 highest genera. Form IV is the ancestral form of Argonauta. The forms derived from II and III are clearly natural groups which can be defined, despite the specialization of their recent representatives. The important morphological relationships, however, call for a division into 2 subfamiles by drawing a line between II and II, i.e. a distinction between lower (I) and a higher (II) stage of variation. This is, of course, arbitrary ... and is only intended to introduce order for practical purposes by stressing the essential and omit characters of less importance. This division stresses the distance between forms II and III and creates the two natural subfamiles: Tremoctopodinae and Argonautinae (Naef 1972: 732).

These two conflicting statements (one pictorial and one as text) pose an interesting problem. What does the diagram represent and what was Naef thinking?

Naef believed both subfamilies to be monophyletic (natural groups). What Naef did diagrammatically shows a transition from the Haeckelian tree-thinking to modern systematics.

In order to understand what Naef did we go to the introduction of his work on the Fauna and Flora of the Bay of Naples. Firstly the graph is a phylogenetic tree as we understand it today. Back in Naef's day (prior to molecular systematics) the graph was termed a 'genealogical' tree. Phylogenetic trees were considered to be true depictions of ancestor-descendant relationships, an idea rarely entertained today. In Naef's phylogenetic tree, we see that forms are placed at the nodes. Naef's forms are types, namely "an abstract but naturally possible form from which a multitude of actually existing forms may have developed ..." (Naef, 1972: 15). Forms are not ancestor-descendant relationships but rather abstract transitional series between basic and specialized forms based on the concept of metamorphosis. Incorporate theses points together and you have a tree depicting the transition of forms that relate directly to the relationships of the taxa on the branches.

Confused?

Naef is depicting a back-to-front cladogram. In Naef's diagram the forms are being shown to be transitional within a dichotomous framework (Figure 1b); very much like showing a character tree within a consensus tree at the same time. A modern representation of Naef's tree would place the forms at the nodes (Figure 1c). What at first appears to be a rooted phylogentic tree, turns out to be a poorly drawn cladogram that places too much emphasis on transitional forms than it does on taxic relationships.

Naef's tree represents a transitional period between Haeckel and Hennig. Naef attempted to save us from the Haeckel's 'oak' trees that later inspired the neoDarwinian Modern Synthesis by emphasizing the importance of natural (monophyletic) groups. Naef's methodological and theoretical work should also be celebrated on Cephalopod Awareness Day.

References

Naef, A. (1972). Cephalopoda (systematics). Fauna and Flora of the Bay of Naples (Fauna e Flora del Golfo di Napoli), Monograph 35, Part I, [Vol. I], Fascicle II. Washington, Smithsonian Institute Libraries.