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.

Three tales of Systematics and Biogeography

Would it be wrong to write fables of systematics and biogeography? A fable may be defined as conveying a moral concerned with accepted rules and standards of human behavior. Is this the stuff of science? Science purports to eliminate human 'bias' in its findings. However, there are many journals and institutions that suppress the publication of alternative or contradictory methods and theories in the name of scientific culture or 'morals'. One method may be favored not because of its logic or aims, but because it represents the scientist’s or editor’s own personal views. We evidently cannot write human bias out of the process of science. Nevertheless, we must endeavor to reveal where human judgment is impeding scientific rigor, if science is to progress.

Below we have done this in the form of tales that covey scientific concepts and catalog common mistaken processes. Most 'new' scientific methods are independent discoveries of old methods or theories that have already been proven as failures or successes, were recorded in scientific literature and promptly forgotten by the majority of active researchers. Many scientists see their methods as being wholly new, or as exceptions to existing scientific rules and laws. The same 'logic' is used by speeding drivers. They accept the endless warnings that 'speed kills', but most believe that they are an exception.

There are no exceptions in comparative biology. Unlike general biology, comparative biology has no laws or rules. In systematics and biogeography however many have taken it upon themselves since the Modern Synthesis to apply a synthesis (or a series of laws) in order to unify of field of science under a common goal. These so called 'laws' are:

1. There is a fundamental difference between the type of data one uses (i.e., morphological data = macroevolutionary/plylogenetic and, molecular = mircoevolutionary/genealogical).
2.Ancestor-descendant relationships can be either 'seen' or measured.
3.Centres of origin are known quantities that are supported by evidence.

The scientific literature of this field is full of these three 'rules'. We however dismiss these three 'rules' as irrelevant to systematics and biogeography. We have done so frequently, adding even more publications to the vast literature dedicated to warning biologists of the three troublesome 'rules'. For the first time, we will express the moral dilemma that one enters when adhering to these 'rules' in the form of three short allegorical tales that convey 'a moral concerned with accepted rules'.

Form

Once a tailor stood on a hill admiring an immense tree and an old philosopher perched beneath. The tree blossomed the most beautiful flowers that the tailor had ever seen. The blossoms grew off branches that twisted and joined a haggard trunk that has grown strong with the passing of time. The tailor noticed that the etched face of the philosopher also bore the traces of time.

“I have lived in the village below for many years and yet I had never before seen nor heard of the large magnificent tree.” Remarked the tailor.
The old philosopher maintained his silent mediation.
“Each branch” contemplated the tailor, “reminds me of the links I have with my fathers, fathers and mothers, mothers.’
The philosopher stirred.
“So you know of your fathers, fathers and your mothers, mothers?” Replied the philosopher.
“Yes, I do.”
The philosopher smiled and remembered a long forgotten thought. “I once knew a mason who claimed the same.”
“Did he have evidence?” Enquired the tailor.
“Oh yes, he showed me heirlooms, trinkets, precious and rare.”
The tailor reached for his large pocket. “I have no trinkets, but proof. Pictures. Each member of my clan, as far back as my grandmothers’ mother, her sisters and brothers.” The tailor displayed several cameos before the philosophers’ wizened eyes.
“Just heirlooms. No more, no less.” The philosopher replied.
“No, they are evidence of my mother and of my kin.”
“The mason claimed to have those.”
The tailor dismissively flicked his hand. “You say those are heirlooms and not real proof. The pictures show in detail their faces and features, not mere possessions like heirlooms, but actual parts passed down our bloodline”.
“Did you paint these pictures yourself?” Asked the philosopher.
“No. I have never met my relatives for I am adopted. This is why I seek my clan among the many that walk in this world. All I possess of my family are these pictures to help me find them in the many lands through which I will pass.”
“Then how do you know that these are true depictions? How do you know who is who and when they lived?”
“I have been told on good authority that the artists all painted the portraits from live sittings. The age does not matter, I know by their features who is who.” The tailor seemed proud to have achieved this understanding.
The old philosopher sighed. “Like you, the mason said the same. He knew his bloodline by the name of the owner inscribed on each heirloom that was passed to an ambitious orphan like you.”
The tailor winced as the philosopher continued.
“The features on these pictures may show parts of your clan. They are heirlooms, precious and rare but not real proof.”
“No!” cried the tailor. “They reveal my past, my bloodline and who begat whom.”
The philosopher shook his head. “You imagine you see your past and your bloodline, but all I see are members of your family, related somehow and in some fashion. Perhaps that man you see is not your father, but your uncle, and this woman a cousin, not an aunt.”
The tailor retorted. “I share their features. I see them pass from mother to mother. They tell the truth about me and about by mothers, mothers.”
A deep weariness flooded the philosopher. “Your pictures are the heirlooms of forgotten and lost relatives. They only speak of features of a thing. The mason orphaned in birth thought the same as you. Those heirlooms, these pictures, are artefacts of the past. You cannot tell who is your mother, any more than she could recognize you.”

Time

A collector of heirlooms trudged along a narrow, winding mountain path. The air was cold and the collectors’ mule stumbled over the uneven gravel surface, tiring of its heavy burden. Night fell and the collector decided to find a camp in a cleft that dominated the rocky terrain. Before him he saw a fire and a white robed philosopher crouched before it in deep mediation. The mule and its owner drew near.
“A fine beast you have there.” The philosopher was looking at the tired mule. “A fair creature, but laden with a great burden. Are you a merchant?” The philosopher asked.
“No. I am a collector of fine antiques.”
“Come sit beside me and relate your tale”. The philosopher beckoned to the collector.
“I have been sitting here by my fire admiring the great folds in the mountains yonder.”
The collector sat and gazed out into the great valley below.
“You say you collect antiques. For pleasure, or for business?”
“For the sake of my heritage” answered the collector.
“Heritage, that is a fine thing. The antiques you carry must be old and valuable?”
The collector’s eyes brightened. “These are exceptional antiques. They not only show the skills and the tools that were used in our long lost heritage, but they also identify the makers style and craftsmanship.”
“What do you gain from collecting these articles of old?” the philosopher enquired.
“I can tell the lives of their makers, their dates of their very first works and the dates of their very last. I admire the antiques, yet I wonder at the minds and hands that created them.”
“So, you too study the art of craftsmanship?”
“With these works I can recreate the clays, glasses and fires that were used. See here!” The collector sprang up and retrieved an object wrapped in silk from a leather pack strapped to the mules side. “Behold, this object from the second period!” The collector held a beautifully crafted trinket before the philosopher. “This work of art betrays its maker. See the fine textures in the glass and the way the iron is gently wrought?” The philosopher nodded. “Those are the trade marks of the great fire welder of the second period and this is his last piece,” said the collector.
“Oh dear, did the artist die once he had created it?” The philosopher looked saddened.
“Yes. All craftsmen tinker to their last day. It is these great works of mature masters and the first brave attempts by the artist as a naive youngster are what I seek. Like my father before me, I have scaled the many mountain paths that divide these vast lands and scoured every corner to retrieve every last piece that was created by these artisans!”
“How do you know that these are their last works? There have been many wars and restorations since the second period, not much survives, only memories and myths.”
“I am certain that I have found the last works of these great creators. Alas, now their secrets are gone. They all perished in the Great War at the end of the second period. Since then, no others have been able to create the artefacts in the form that you see before you.”
The philosopher returned his attention to the fire. “Perhaps they gave up their craft to join the war and perished much later.”
“No, never! These artists tinkered till their final breath. None would have left his toil for the fortunes of war!” The collector laughed.
“How do you know that these artists did not return to their craft after the wars and made more precious trinkets?”
The collector was amazed at the naivety of the question. “Because I, and my fathers before me, have never found such antiques after the second period. It is obvious that the disappearance of these works marks their demise.”
“Is it?” the philosopher mused. “But you can never know. These trinkets that you hold could be the oldest, but there could be many more made by the great fire welder lying shattered in the rubble of ruins or in the crypts of proud and jealous owners.”
“I and my forebears have considered these notions, but there may be a few that still lie hidden. However, there will be none that is any older than the one I hold. The great fire welder did not live beyond the second period and here is evidence of that.” The collector held the antique out in one hand.
The philosopher remarked; “What you hold in that hand is an antique made by someone that lived during the second period. What you hold in the other is all you know of the great fire welder’s demise.”
The collector stared at his second, empty hand. The philosopher continued. “You cannot assume that what you do not have is evidence of the demise of great artists, any more than I can conclude that those who rule these lands are dead because they do not sit by my side.”

Space

One fair morning an orphan lay in an open meadow enjoying the spring sunshine and contemplating his journey and the direction he should take.
The orphan lay thinking of a family that he never met and of the many parchments that he had collected in the town halls on his travels. The youth had wanted to find his roots. There had been no family to show him the way, no uncle or cousin to guide him, and he had been alone except for his meagre inheritance, a certificate of birth. No place, no date, just a name, his name.

It was now a long time ago since the boy had set off on his long journey. He thought hard and counted the seasons. He thought it must now be ten or maybe more. The long northern winters seemed to last forever, yet he still moved on.

When he was just old enough to read he thought that his long deceased relations would have the same parchment, with a similar name. Curiosity got the better of him, and after enquiring with the local town cryer of the whereabouts of such parchments he was guided to the local town hall. There he found that other town halls have such records and he reasoned perhaps that in those he would find the same seal of his fore fathers. The orphan enquired about the seal on his parchment. The officer was not certain of its origin and suggested that the boy head north. “Town seals such as that belong to the wealthier lands in the north”.

His journey had been marred by sickness, and only a few villages could offer a state official who all too often knew little of such documents. Success came one summers’ day when he found a parchment in the archives of a small town. There he had evidence at last. Someone did share his name. Finally the journey became worthwhile. The parchment had a little more information to offer him. A woman who had been born in the village of the seal had moved to this place with her kin. That woman came from his village, with his name. The seal in the bottom left corner resembled the one on his own parchment. The officer that tended the archive knew little of the seal and of the towns and great cities of the north. He too suggested that the seal may have originated there, and that the boy seek his luck even further north.

The boy lay still in the long grass. He rolled over and began to unroll his parchment and study the seal. Only one other person had found his journey interesting, a wizened, old philosopher that he had met last winter.

The boy had told the philosopher his story and his ambition to seek his fore fathers’ home. The philosopher asked why he wanted to go there?
“To seek my fore fathers, those whom I had not known. I want to be close to them and their home. My home.”
“But your home is your ambition, your wit and desire to seek” Replied the old philosopher. “Once you reach that goal you will be alone in a foreign land without further ambition and wit that kept you company on you long journey.”
The young boy was stirred by the philosopher’s remark.
“But reaching those lands of my kin is all that I desire.” The boy could not find any other answer.
“Surely by finding your ancestral home, you will not be content. Are there not other mysteries you seek?”
“I have one mystery,” said the boy. “Why do all the lands have different seals?”
“It is the lands that claim you. It is you that belongs to them. A wanderer like yourself can not claim to belong to all that he sees.”
The boy was confused. “But I know I was not born in the town in which I was brought up. The seal proves this. But others I know were born there and they have never seen a seal like the one my parchment bore.”
The philosopher explained. “Everyone is born in a town or a village. The officials of that town stamp your parchment and claim you as its citizen. The towns lie in the valleys that are separated by the high mountains in the east and the wide deep seas in the east. Every person whether they are born there or not can only live in one town at a time. Your seal states that you are different, but yet you are part of at least one town and one family.”
“But my family lives in one town. This seal proves my case.” The boys’ confidence was waning.
“Some of your relatives may have been born there but yet grew up elsewhere like yourself.” The boy remembered the woman’s parchment that bore his seal as the philosopher spoke. “People move and what remains of their home towns are no more than memories and parchments stamped with seals.”
“Then my time is wasted seeking the origin of this seal?” The boy sulked.
“Perhaps there is fairer game in seeking why each town has a seal and why some seals resemble others. Your ambition is your life. You aim to seek and to discover. Once you see the impossibility of finding the origin of that seal, you will be lost. You will have no aim, your ambition like your seal, will then become a mystery.”
The saddened eyes of the orphan brightened slightly.
The philosopher smiled. “There are many lands, more with seals of this kind. There are kingdoms and cities in the north that even I, in my old age, have never seen. Perhaps they may tell the story of the significance of your seal and the others that you have encountered.”

The crickets sang sweetly and the thick scent of spring flowers perfumed the air. He knew that he had set off on a journey that he would never complete. Now he realized, it was why his seal differed not how it came to be there, that sent him on his journey. The philosopher was right. If he did find the origin of the seal his life would change from ambition to old memories of where he had been. He did not want to live on memories, or to find the home of his fore bears. It is the seals that hold the key to the histories of the lands between the vast mountains of the east and the wide deep seas of the west. That was his ambition. He now realized he had never been alone. Now his journey could begin.

The Culture of Molecular Systematics

The longer one reads papers on molecular systematics, and speaks to molecular systematists, the more one is convinced that there is a prevalent molecular systematic culture. What makes it so convincing is the consistency of language, attitude and ignorance that is standard worldwide. What then is this molecular systematic culture?

Consider this response to a recently rejected manuscript:

"This manuscript seems inappropriate for [journal name removed]. Its purpose is to question the foundation of molecular phylogenetics, a well-established field. Moreover, the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated. I doubt that the readership of [journal name removed] would find the arguments presented particularly compelling. It is well known that DNA is the material of inheritance, and that morphological homoplasy is common. Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods. No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".

The response is an exemplary in its language, attitude and ignorance of comparative biology, that is taxonomy, systematics and biogeography.

Let us start with the first point, namely, attitude:

"Its purpose is to question the foundation of molecular phylogenetics, a well-established field".

Molecular Systematics, like any other field in science, is open to questioning. It is not immune like faith or religion as some, I suspect, believe. Moreover, it is not "well established", that is based on a sound foundation. There is little discussion about the foundations of molecular systematics, which the next comment reveals, namely:

"the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated".

These "non-standard" definitions are presented below:

Homologies are the only evidence for relationship; A molecular tree based on the relationships of taxa at the terminal branches is not a genealogy, but a cladogram. A cladogram however can be tested and represents all possible relationships in a taxon

One might ask, "Where is homology in molecular systematics?" The question of homology has been raging in morphological systematics for almost 300 years. In molecular systematics it is simply ignored. I ask what are the foundations of molecular systematics? What makes it so well established? Why is it one of the few fields in science where its foundations are rarely discussed? These questions make sense in the light of molecular systematic culture.

Molecular systematics also uses a convincing language. Stating that "DNA is the material of inheritance" creates an air of reverence that defies questioning. In fact it is a diversion. We are the material of inheritance. DNA is just part of it. The above statement is reductive, that is to say, it says that only our smallest 'bits' are relevant. We may take that statement further and say that 'Morphology is simply an expression of DNA', or take it one step further and state 'DNA tells us everything about genealogy and phylogentics, morphology is irrelevant, after all morphological homoplasy is common'. Language can be used in a deceptive way as the above example demonstrates.

Ignorance is another part of the molecular systematic culture. Consider for instance this statement:

"Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods".

This conflates a few important points. Firstly homoplasy, that is, the "correspondence between parts or organs acquired as the result of parallel evolution or convergence" (Merriam-Webster's Dictionary Online), is not exactly 'detectable' in cladistic analysis. It causes characters to conflict resulting in polytomies, that is the absence of pattern, and therefore, of information. Cladistic analysis is there to find patterns, not uncover homoplasy.

Ignorance of history is another vital part of the molecular systematic culture, for instance:

"No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".

We have addressed this point in an earlier post. No matter how old an argument or discussion is, the points made may still be relevant today. In the case of the above comment, the discussions of yesteryear still have not concluded. The discussions were replaced by a thirst for technology. Molecular systematics is enslaved in a technological culture. The algorithms or black boxes determine which phylogeny is best. The question of whether it is really homologous is never discussed. The foundations of molecular systematics lies in its applications, literally the programs made to run molecular sequences. We ask, is this a science that is based on solid foundations - a "well established field"?

The Dispersal Myth

Organisms disperse. We do it, birds do it, plants do it. Dispersal is a fact of life. As an unobserved mechanism that explains distribution and evolution, dispersal fails. The evidence that 'supports' hypotheses of dispersal is the same 'evidence' that discredits the same mechanism. Like any explanatory mechanism, evidence that apparently 'supports' it is the same that also supports a competing and conflicting hypothesis and so forth. Dispersal in its descriptive form (i.e., iguanas disperse within their area of distribution) can be shown empirically. Dispersal as an explanatory mechanism (i.e., iguanas dispersed to an oceanic island and subsequently evolved into a new species) is merely hearsay.

Despite its non-empirical and highly subjective nature, many still feel that dispersal is the best or unifying theory for organic distribution and subsequent evolution. However, the less evidence there is it seems, the greater validity the hypothesis gains. In the case of pan-Pacific distributions, for instance, there is little or no geological evidence to suggest what the Pacific Plate looked like 200 million years ago. Without such geological evidence, dispersalism gains greater validity as being the only possible mechanism to explain distribution. The option of not knowing how things got to where they are, or using phylogenetic patterns to retrodict former area relationships, are rarely considered. For the most part a trivial answer will suffice - How else do things get to where they are?

The introduction of the molecular clock has only increased our obsession with dispersal (see de Querioz, 2005). These 'clocks' are based on geological (i.e., palaeontological) data (i.e., the age of fossils) in order to measure divergence times. Since we will never know if we have the oldest fossil, the chance that a single fossil will tell us any more is highly unlikely. But yet proponents of the molecular clock believe it does. This reinforces what I herein term the Dispersal Myth, namely, the less data there is, the more likely things are to disperse (Figure 1).

But what if we lack data altogether, that is, we have no information regarding the organism and its distribution? Do we still speculate in a highly subjective and non-empirical manner, or do we give up this flight of fancy altogether?

This week in Astrophysics and Space Science: An International Journal of Astronomy, Astrophysics and Space Science Wickramasinghe & Wickramasinghe (2008) push the limits of the Dispersal Myth. In short they propose the hypothesis that life may have dispersed from Venus to Earth.

The thinking behind this incredulous theory (first proposed by Barber in 1963) links three ideas together:

1. The discovery of complex "molecular structures" in Martian meteorite ALH84001.
2. Possible "transfer pathways" between Venus and Earth via solar winds and;
3. The possibility that extremophilic "Venusian microbes" may form within the atmosphere of Venus.

So why resurrect something endemic to the psychedelic 60s? Namely "at the time a mechanism for aerosol transfer between the planets was not identified ...", that is, there was no satisfactory explanatory mechanism proposed at the time. In other words, the mechanism makes the theory appear real, even if evidence, in this case extremophilic "Venusian microbes, are completely missing or unknown. What is more, the theory gains acceptance because the explanatory power of the mechanism now makes the eventuality of life on Venus more likely or predictable.

The hypothesis proposed by Wickramasinghe & Wickramasinghe (2008) is extremely subjective. It puts the cart in front of the horse. It proposes a mechanism to explain data before the data even exists. Even if life was discovered on Venus, it does not make the explanatory mechanism more likely. In fact, the reverse is true. If we, for arguments sake, we investigated Venusian microbes, we would know more about their physiological limits to disperse via solar winds than if they did not exist. Therefore the possibility of microbial dispersal from one planet to another is far more likely if the evidence was non-existent.

The message in figure 1 rings loud and clear - the less data there is, more "relevant" or "likely" dispersal appears. Dispersal, as an explanatory mechanism, is highly subjective, non-empirical and is nothing more than a myth.

References
Barber, D. (1963) Perspective 5: 201–208.
de Queiroz A. (2005). The resurrection of oceanic dispersal in historical biogeography. TREE 20: 68-73.
Wickramasinghe, N.C. & Wickramasinghe, J.T. (2008) On the possibility of microbiota transfer from Venus to Earth. Astrophys Space Sci. DOI 10.1007/s10509-008-9851-2

Goethe's Philistines

The Sturm und Drang movement of the 18th and 19th centuries not only produced Romantic literature and Naturphilosophie but also a nemesis - the philistine.

The typical materialistic bourgeois, content with all the pleasures without delving in or appreciating culture, art and nature, was labeled a philistine. They had no interest in nature, no compassion or pity. The philistine also favored a life dedicated to industry, profit and security, rather than a life devoted to following ones dreams. Where those of the Strum und Drang movement, for instance, would applaud a devoted artist, whose self sacrifice has led to a life of hardship in order to follow the pursuit of happiness, the philistine would dismiss it as thoughtless and naive. Imagine the reaction of Mr. Potter of a Wonderful Life, to the self sacrifice of van Gogh.

Goethe also made the philistine his nemesis. Those who considered Goethe the greatest living poet and dramatist did not appreciate him for his obsession and devotion to natural history. During his life time he was criticized for his work on the Theory of Colours. A living legend, one that presents all things German, was, it seems, forbidden to make any contribution outside his own area of 'expertise'. These were the philistines speaking.

Today they still exist, each with their own copy of Werther, gathering dust, prominently in their book cases. The German middle class, obsessed with success and measuring history, culture, art and nature as expendable commodities, dismiss Goethe's scientific contributions. Goethe is unsellable to future generations as a natural historian. Leave that to the English who had Newton, Darwin and Wallace. Germany had the poets, composers and philosophers. These are the philistines speaking.

The philistines have the power and industry to rewrite or edit history. Goethe's work on color was misguided and his ideas on morphology naive. Darwin discovered evolution and provided the means to do biogeography. French are all Gallic and the Germans are all Huns. Non-Greeks are barbarians and people in the middle ages thought the Earth was flat. These are the philistines speaking.

No wonder Goethe thought that:

It is laughable when Philistines praise themselves for possessing the greatest knowledge and enlightenment of their age and call those of the past barbarians. Reason is as old as the world! (Goethe to Riemer May 10, 1806).

The philistines have there point of reference in history, theory, culture, art and natural history. These are simply markers, to give unappreciated things meaning in the form of measurement, value and commodity. Before Darwin there was no evolutionary biology; before Aristotle, no science and before Adam, no people. These are the philistines speaking.

FSB Online

The Foundations of Systematics and Biogeography can be viewed online at Google Books. Although it only offers a limited preview, it does list the table of contents and a few chapters.

International Code of Area Nomenclature (ICAN)

The International Code of Area Nomenclature (ICAN) is available in a printed format from the Journal of Biogeography.

The project is a long term initiative of the Systematic & Evolutionary Biogeographical Association (SEBA), which seeks to introduce a naming standard in biogeography. The ICAN is also available online from the SEBA site (for those that do not have access to Blackwell Online). If you would like a reprint please send us an email.

The abstract of the printed version is given below:

"Biogeography needs a standard, coherent nomenclature. Currently, in biogeography, the same name is used for different areas of biological endemism, and one area of endemism is known by more than one name, which leads to conflict and confusion. The name ‘Mediterranean’, for example, may mean different things to different people – all or part of the sea, or the land in and around it. This results in ambiguity concerning the meaning of names and, more importantly, may lead to conflicts between inferences based on different aspects of a given name. We propose the International Code of Area Nomenclature (ICAN), a naming system that can be used to classify newly coined or existing names based on a standard. When fully implemented, the ICAN will improve communication among biogeographers, systematists, ecologists and conservation biologists" (Ebach et al. 2008).

References
Ebach, M.C., Morrone, J.J., Parenti, L.R. & Viloria, Á.L. (2008) International Code of Area Nomenclature Journal of Biogeography. 35 (7) , 1153–1157.

Investigative Science Journalism: Who Guards the Guards?

Plato’s reaction was simple: they will guard themselves. Distaste for power and a desire for righteousness will prevent them from taking advantage of their position. This is Plato’s Noble Lie – a valiant failure at best.

The media, journalists, editors and reporters, are also the guardians or watchmen of science. Not only do they report news and events, but they also keep politicians or spheres of power in check by questioning their actions and reasoning. Such is the power of the media in Britain that is can (almost) topple politicians and governments.

The same media also cover scientific discoveries and events, but there is a catch. Unlike politicians and government officials, scientists are not subject to critical questioning by the media. Whereas politicians acquire their positions through elections, scientists are assumed get to where they are through expertise and merit.

Any form of expertise may separate one field or profession from another. Take chamber music for example. It takes a typical violinist many years to reach a level of expertise required to perform in a chamber ensemble or symphony orchestra. In addition to other than the extracurricular training they receive as children, their university degrees and auditions, musicians are always open to scrutiny and also in their performances by the media. Newspapers dedicate columns to either praise or rubbish performances. Medical doctors and dentists are also open to scrutiny. Malpractice is often exposed first in a newspaper before it is reported elsewhere. The media also seem to find space to criticize new alternative medicines, the forms of chemicals used in chemotherapy, which diet is best, which isn’t and so on. This aside, scientists appear to be all but immune from critical scrutiny any from of questioning by journalists.

One reason maybe that much scientific expertise differs from other forms in that it does not seem to directly affect our day-to-day lives. While many people have a favorite recording of Beethoven’s 9th symphony, their own opinions on dieting and whether smoking or drinking too much is harmful. However, the average person’s opinion on evolutionary biology for example, is often no more than received wisdom, given little personal reflection. In fact the science press, that is the popular media who report on science, struggle to correctly interpret the scientists message and to attract the attention of the average reader. The recent debate in Framing Science (Nesbit & Mooney, 2007) addresses how scientists and the media can work together to express a scientific idea or discovery in such a way that it informs the public in a clear and engaging manner. The article draws much needed attention to the still burning question: who watches the watchmen?

Recently the popular press reported the discovery of a new fossil 'amphibian' nicknamed the 'frogamander' (Gerobatrachus hottoni). The article went on to state:

"The discovery of a "frogamander," a 290 million-year-old fossil that links modern frogs and salamanders, may resolve a longstanding debate about amphibian ancestry … Modern amphibians -- frogs, salamanders and earthworm-like caecilians -- have been a bit slippery about divulging their evolutionary ancestry. Gaps in the fossil record showing the transformation of one form into another have led to a lot of scientific debate." (Reuters)

The press, keen to promote science, clearly do not question what they are being told. In this case the "showing the transformation of one form into another" is impossible without the aid of a time machine. The media did not concoct the story, they simply translated what the scientists said:

"It's a missing link that falls right between where the fossil record of the extinct form and the fossil record for the modern form begins,' said Jason Anderson of the University of Calgary, who led the study" (Reuters).

This is not a problem of framing, but that of the media blindly accepting a "story".

The science media rarely question the scientist. The level of expertise that separates the scientist and the reporter is the same between that of the violin soloist, general practitioner, attorney general, civil service account and engineer. If a politician clearly fabricates a story in order to win favor with voters prior to an election or, a police commissioner justifying the arrest of a member of a suspects family under dubious terrorism charges, the media wouldn't think twice of questioning their reasoning. If a geneticist however states that the platypus is "...the semi-aquatic animal is a genetic potpourri - part bird, part reptile and part lactating mammal" (ABC News), no one questions their poor reasoning or understanding. Clearly the platypus is a mammal (along with the fish-like dolphin and bird-like bat). This distinction was made in the 19th century and every school child would be able to pick this out at once (except perhaps science journalists).

The problem is not one of not understanding the technical nature of science or the way scientist "frame" their arguments. Scientists can be just as uninformed as the rest of us. The media do question the expertise of professionals from other fields excepting that of science. What is needed is investigative science journalism, not glossy parroting. By investigative science journalism, I do not mean exposing practices outside of mainstream science such as anti-science (e.g., creationism), pseudo-science (e.g., homeopathy) or malpractice (e.g., evangelical healing). Neither do I mean exposing scientific fraud (e.g., cloning) or moral issues (e.g., stem cell research) (see Knight Fellowships). Investigative scientific journal would be far more effective in keeping science in check if it uncovers its inner workings, including the politics behind certain ideas and the funding supporting one method or theory over another as well as simple misinterpretations or downright untruths that scientists make which enter the mainstream media as "facts". Through exposing the malpractice of scientists, investigative science journalism can inform the public where their money goes and how it is at times misused. So far there is no such caliber of journalism in science has not been equal to the challenge. Presently, many biologists, geologists, geneticists and astronomers have no representation in the media and no voice. To let them suffer in silence seems unjust when experts in most other fields enjoy the guardianship of investigative journalism and the attention of the public.

Reference

Nesbit, M.C. & Mooney, C. 2007. Framing Science. Science 316: 56.

Defining Phenetics ... one last time

The term phenetic is defined in the Oxford English Dictionary (OED) (online version) as:

"Designating or relating to the classification of organisms on the basis of their observed similarities and differences (often assessed in numerical terms), without reference to functional significance or evolutionary relationships".

The term was first used by Cain and Harrison (1960) "[f]ollowing a suggestion made by Mr. H. K. Pusey, we shall refer to the arrangement by overall similarity, based on all available characters without any weighting as phenetic, since it employs all observable characters (including of course genetic data when available)" (Cain and Harrison, 1960: 3).

The OED defines the term phenetics as "phenetic taxonomy or the systematics of phenotypes". It was first used by Ehrlich & Holm (1963) to refer to "[t]he study of relationships of individuals [which] may permit the creation of a 'population phenetics' which will add new dimensions to the study of microevolution" (Ehrlich & Holm, 1963: 240-2).

If the first definition of phenetic is true, then phenetics by definition cannot find evolutionary or phylogenetic relationships, only similarities.

References
Cain A.J. & Harrison G.A. (1960) Phyletic Weighting. Proceedings of the Zoological Society of London 135: 1–31.
Ehrlich P. & Holm R.W. (1963) Letter to the Editor. Science 139: 240 – 242.

The Enduring Legacy of Misinterpreting Darwin

Kevin Padian's (2008) claim that Charles Darwin founded the main principles of biogeography and ecology is clearly incorrect. Biogeography was alive and well long before Darwin's birth, in fact Augustin Pyramus de Candolle and Alexander von Humboldt produced the founding works of biogeography four years before Darwin was born, while the younger Alphonse Candolle and Ernst Haeckel erected the foundations for chorology and ecology in 1855 and 1861 respectively.

Prior to the publication of Origin of Species in 1859, Darwin would have had access to an extensive array of literature, including biogeographical concepts espoused by Charles Lyell, Louis Agassiz, Joseph Dalton Hooker and Phillip Lutely Sclater. Furthermore, Padain's claim that in "Darwin's day, dispersal through migration was the only mechanism thought possible for species to move among continents" (p. 633) is also erroneous as concepts such as vicariance were already in existence. Darwin's contribution to biogeography and ecology was to provide a synthesis or unifying mechanism that explains why organisms are distributed the way they are today, namely natural selection.

References
Padian, K. 2008. Darwin's enduring legacy. Nature 451: 632-634.
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The Problem of Similarity

Systematics and Biogeography has a problem: similarity. Ever since Goethe, naturalists and biologists have been rejecting similarity. It is the foundation of artificial classifications, non-evolutionary groupings and the basis for many arguments against evolution (i.e., homology).

Similarity implies that organisms are similar and not the same, that is it remains silent about sameness. The difference between being similar and the same is astronomical. Any two things in the universe can be similar. It is not a discovery. It demands no explanation. It is a means unto itself. However, when two things are discovered to be the same, they require explanation. This is when the study of evolution begins. By denying sameness -- or ignoring it -- we remain in the realm of artificial classification.

So why, then, is similarity so popular? All methods in molecular systematics use "similarity methods", herein phenetics, in order to measure nothing more than similarity. No evolution is (or can be) discovered, nor even touched upon. Molecular trees are simply meaningless in the context of evolution. They tell us nothing about sameness and therefore demand no explanation whatsoever. Regardless of this fact, all molecular systematists seem to explain similarity as if it means sameness. A molecular tree is generated and not discovered. They are means unto themselves. The gargantuan task of sequencing, aligning and building trees to find similarity ends with nothing at all. We are by no means poo-pooing similarity methods (phenetics).

Similarity methods are vital for understanding in non-evolutionary fields, such as geology. The chemical composition of rock is important for classification and identification. The same is true for biological keys and other artificial classifications. They helps us identify organisms based on their characteristics. The key will still work if the characters are homologous, not homologous or a mixture of both. Similarity will never be able to show which is which. Phenetics is useful outside of systematics and biogeography and evolutionary biology as its popularity shows. But popularity alone will not validate phenetics, or any similarity, in evolutionary biology.

What do we do with all the data, the matrices and the trees, produced by phenetics? We hope that their owners have fluked it - actually found a meaningful evolutionary, that is a monophyletic group. The sad news is that they'll never know.

Of course, molecular data have meaning and we should not be understood as attempting to trash molecular systematics. We simply feel they have been sold short. Maximum likelihood, parsimony optimization, and so on, are all kinds of phenetics: they are similarity methods. They are useless in the pursuit of evolutionary patterns, namely homology and monophyly. Molecular systematists need to stand up and shake loose the shackles of similarity, realize that their data and their methods are two separate issues and question those that wrongly promote similarity methods as "evolutionary".

Didn't we discuss this before?

I once walked into my colleague's room and pointed out that his sink was leaking and getting some boxes full of reprints wet. I suggested he should get it fixed or move the boxes. We discussed it a little and after a short while it was forgotten. A year later I noticed that the problem had not been fixed. The reprints were all moldy and the leak had spread staining his carpet. I pointed it out to him again. He simply dismissed it with the line "Didn't we discuss this before?"

That same line is used throughout systematics and biogeography to dismiss lengthy heated debates that never were resolved. Who, for instance, were the victors in the following debates?

Cladistics versus Phenetics

Pattern Cladistics versus Numerical cladistics

Modern Synthesis versus Cladistic Revolution

Dispersal versus vicariance

It is said that history is written by the victors. Looking at the above examples we assume that cladistics triumphed over phenetics (overall similarity); Pattern cladistics simply lost a pointless debate; The Modern Synthesis was expelled from numerical revolution and that the dispersalist have finally won in their campaign against the dusty old vicariance biogeographers. In every case above, a heated debate occurred, the problems were addressed and everyone went home feeling like something was resolved. If this is the case why is vicariance still the most prominent theory in systematic biogeography? Why does everyone use phenetic methods? Where have all the cladists gone?

None of the above debates were resolved. Phenetists kept doing phenetics. The idea of overall similarity (a non-cladistic idea) swept over all of numerical phylogenetics. The pattern cladistics never left, the Modern Synthesis never died and vicariance was never abandoned. If we are to complain that this was all discussed before, then isn't it because the debate never really ended?

In a recent paper all opposition to DNA Barcoding was dismissed has “... having been controversial” (Lahaye et al. 2008). The paper suggests that by doing DNA Barcoding regardless of its flaws, immunizes it from any criticism. I am sure if another paper is published criticizing barcoding it would be dismissed with that one line "Didn't we discuss this before?" This is the same tactic used by phenetists (overall similarity), Modern Synthesists and Dispersal Biogeographers. It seems that history is not written by the victors, but by those with leaky sinks, a stained carpet and no ambition to do anything about it. But surely "we have discussed this before?"

References

Lahaye, R., van der Bank, M. Bogarin, D., Warner, J, Pupulin, F., Gigot, G., Maurin, O.,Duthoit, S., Barraclough, T.G., Savolainen, V. 2008. DNA barcoding the floras of
biodiversity hotspots. PNAS.10.1073/pnas.070993610395.

Biogeography & Systematics: Call for Papers

Biogeography is a complex discipline, in the sense that it deals with complex processes — of evolution of life in space through time — not directly observable, occurred in the geological past. Biogeographical reconstructions demand precise and complex data — systematic and distributional information — and intricate methods. It should be no surprise to learn that evolutionary biogeography is a relatively recent area of research within the history of comparative biology.

The late 1970s and early 1980s faced an especially rich period of development of biogeographical theory and methodology, with the inclusion of the concept of vicariance in the mainstream of biological literature. The journal Systematic Zoology played a major role in the publication of papers in this area during that period. The intricacies of the subject, however, along with decisions concerning the policies of the primary main journals of the subject — Systematic Biology, Cladistics and Journal of Biogeography — resulted in problems publishing large papers with analytical studies of historical biogeography. Typically large papers with biogeographical studies also contain analyzes of the relationships of a group of organisms, often requiring new taxa to be named, to properly identify the nodes on a cladogram.

To fill this publishing void, the Systematic and Evolutionary Biogeography Association (SEBA) has decided to launch a new, open-access online journal, Biogeography and Systematics, to occupy such niche in the primary literature.

Biogeography & Systematics will publish original papers on historical biogeography and phylogenetic systematics. The journal will have the following sections:

Invited Papers — for topics of major interest in biogeography and systematics under invitation from the editor-in-chief;
Original articles – on analytical, historical, epistemological, and methodological aspects of biogeography and systematics, without page limit;
Forum – opinion pieces on any topic of biogeography or systematics (maximum, 3000 words).
Book Reviews – usually under invitation, but submitted reviews (including classical works) may be considered (max. limit 1000 words).

The editorial policy of Biogeography & Systematics is to ensure that articles published are of the highest quality and relevant to the interests of our readers. The journal is peer-reviewed. The journal is not biased towards any biogeographic region, in terms of taxa studied or author affiliation, nor any method of analysis. All papers shall be written in English (US spelling).

The first number of the journal is scheduled for August, 2008.

Please click here to see the Guide for Authors.

Editorial Policy
Biogeography & Systematics has an editorial policy in order to ensure that the articles we receive are of high quality and relevant to the interests of our readers.

• Biogeography & Systematics publishes in English (US spelling) only.


• Biogeography & Systematics publishes original research papers in biogeography and systematics.


• Biogeography & Systematics is a peer-reviewed journal.


• Biogeography & Systematics publishes monographic taxonomic, systematic and biogeographical treatments.


• Articles may cover any aspect of biogeography, systematics or taxonomy.

Types of Articles
Biogeography & Systematics publishes the following types of articles:

• Biogeographical anaylses, revision of methods or epistomological reviews.


• Systematic revisions that may include biogeographical analyzes.


• Taxonomic treatments that include systematic analyzes.


• Historical revisions in biogeography, systematics and taxonomy, including biographies.

If you have been invited to contribute an article please submit your manuscript as an .odt, .rtf or .doc. We ask authors to only use Primary (bold) headings.

Citations
All citations are to be made without using commas between author and year (Wallace 1855) and commas between multiple authors (e.g. Nelson and Platnick 1981, Brandon-Jones 1998). Quotes should be cited as (Willis 1922, p. 100). Please refer to this issue for further usage of figures (see figure 1 or Fig. 1), tables and numerals.

References
Please include the full titles of journals and books. Do not use abbreviations! Please keep your references in the styles listed below.

Brandon-Jones D. 1998. Pre-glacial Bornean primate impoverishment and Wallace’s line. In Hall R, Holloway JD eds. Biogeography and geological evolution of SE Asia. Leiden: Backhuys Publishers, pp. 393-404.

Heads M. 2006. Panbiogeography of Nothofagus (Nothofagaceae): Analysis of the main species massings. Journal of Biogeography 33: 1066-1075. Merriam CH. 1898. Life zones and crop zones of the United States. U.S. Department of Agriculture Division Biological Survey Bulletin 10: 1-79.

Nelson G, Platnick NI. 1981. Systematics and biogeography: Cladistics and vicariance. New York: Columbia University Press.

Wallace AR. 1855. On the law which has regulated the introduction of new species. Annals and Magazine of Natural History 16 (2nd series): 184-196. [http://www.victorianweb.org/science/science_texts/wallace_law.html; http://www.wku.edu/~smithch/wallace/S020.htm; http://www.zoo.uib.no/classics/new_species.txt].

Proofs
Authors will be given a chance to proof their paper prior to publication. The final proof will be published on the SEBA website simultaneously as the journal is printed.

Copyright Form
Authors will be asked to complete a copyright form upon acceptance of their manuscript.

Submissions
Please submit your articles in electronic format to the Editor-in-Chief, Dalton de Sousa Amorim

Biogeography & Systematics is printed by the Instituto Venezolano de Investigaciones Científicas, Venezuela.

Defining Phenetics, Intentions and Mimics

Many reading this blog are probably wondering why we seem to call everything phenetics. Phenetics is a term used, incorrectly, to only describe a certain type of methodology, namely clustering based on similarity (i.e., neighbor-joining etc.). In fact phenetics is nothing more than Numerical Taxonomy (Sneath & Sokal, 1973), a topic that we have discussed in a previous blog (Phenetic "Natural" Classifications).

Phenetics attempts to classify organisms based on over-all similarity. An excellent definition of phenetics, which can be found at Wikipedia, goes one step further:

"In biology, phenetics, also known as numerical taxonomy, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation".

Where phenetics becomes problematic is when these classifications are considered to be natural, that is monophyletic. A monophyletic taxon is based on relationship, namely homology. Homology is not a measurement of similarity but an expression of relationship. Phenetically grouped organisms may not necessarily be more closely related to each other than they are to another group. In other words, phenetics cannot distinguish paraphyly from monophyly. An analogous problem exists in biogeography.

Parsimony Anaylsis of Endemicity (PAE) is a method developed in order find similarities between areas (see Rosen 1988). The method simply requires a data matrix of presence and absences of taxic distributions. In contrast, cladistic biogeography demands that taxa used in analysis are monophyletic, however many fossil groups have no relations that coexisted in the same period. This means that some paleontologists are forced to deal with higher taxon biogeography (i.e. at family or ordinal level) or abandon cladistic biogeography altogether. The idea behind PAE is to use any group within a phenetic context. Monophyly is not a requirement of PAE therefore absences can be used to cluster organisms into areas since no notion of homology or relationship is assumed. As with phenetic findings in systematics, some users have made the mistake of assuming that PAE can find phylogenetic signals based on non-evolutionary data, that is, non-homologous information, in the data matrix.

On closer examination we find that many systematists and biogeographers intent on discovering homology, monophyly and endemism are nevertheless using phenetic methods. Perhaps this is due to a lack of readily available methods in the literature. After all, cladistics and cladistic biogeography started off as "pen and paper" methods whereas phenetics was always a numerical method (hence numerical taxonomy). The issue at stake is whether using phenetic methods jeopardizes our intent, namely to search for homologies, monophyly and endemic areas. We argue that it does.

The problems lie in transposing data into a data matrix using neighbor-joining, clustering, parsimony or compatibility as are all phenetic - that is, methods that use overall similarity in order to find classifications. These methods can not distinguish natural (monophyletic) from artificial (non-monophyletic) classifications.

Our favorite programs are rightly pointed out as black-boxes yet we shrug this off and cite Farris (1983) or recite some algorithm. In some extreme cases we justify our intentions by making sure that our data is compatible to our methods (sensu Patterson 1982). But we cannot continue skirting this issue. Similarity is an anathema that our forebears, Goethe, Vic D'Azyr, Saint Hilaire, Owen, the founders of homology had quickly disposed. Similarity is the foundation of phenetics, not cladistics. Our intent to find homology, monophlyly and endemicity (rather than the superficial cousin, similarity) must be held when selecting methods and programs that we use, ne c'est pas?

Assumptions held so dearly by some cladists, such as Patterson's test for homology and similarity as a requisite for monophyly, are all phony. Cladists should not use phenetic methods in order to make sense of classification, instead they should use homology and relationships. The only way (if any) which we are able to use phenetics meaningfully is to treat it as a mimic of the real thing (cladistic pen and paper methods). After all that is what phenetics is about, mimicking reality.

A mimic in cladistics is any phenetic method that attempts to implement a genuine theory or intention. Any phenetic implementation needs to be considered carefully since they were originally not intended for cladistic for biogeographical analysis. Many of the methods and implementations we use today have existed in statistical and mathematical classifications (i.e., data matrix, parsimony, compatibility, clustering, subtrees etc.). Rather than accepting these methods wholeheartedly as being "cladistic", cladists should fool the mimics. This has been successfully done by a program called TAX (Nelson & Ladiges, 1991). TAX fools the program into treating areas of no relationships as questions marks, without treating absences as evidence.

If cladistics is to survive as an evolutionary field intent on finding homologies and monophyly, it needs to re-examine the phenetic methods that it uses. A field that is becoming dependent on phenetic methdology can easily become phenetic.

The image above was made by David Maddison in 1981 when "... Cladistics versus Phenetics debates were still fresh in people's minds". We hope that the same image may re-spark some of that debate. The image may be found on his website.

References

Farris, J. S. 1983. The logical basis of phylogenetic analysis. pp. 1-47 in Advances in Cladistics, Volume 2, Proceedings of the Second Meeting of the Willi Hennig Society. ed. Norman I. Platnick and V. A. Funk. Columbia University Press, New York.
Nelson, G., & Ladgies, P.Y. 1992. TAS and TAX: MSDOS programs for cladistics, version 3.0. Pub- lished by the authors, New York and Melbourne.
Patterson, C. 1982. Morphology characters and homology. In: K. A. Joysey and A. E. Friday (eds.), Problems of Phylogenetic Reconstruction. Systematics Association Special Volume, 21: 21-74.
Rosen, B.R. (1988) From fossils to Earth history: applied historical biogeography. Analytical biogeography: an integrated approach to the study of animal and plant distributions (ed. by A.A. Myers and P.S. Giller), pp. 437–481. Chapman & Hall,
London
Sneath, P.H.A. & Sokal, R.R. 1973. Numerical taxonomy — The principles and practice of numerical classification. W. H. Freeman, San Francisco.

Evidence and Motive: Anna's Hummingbird and Loretta's knife

As comparative biologists we are limited in our knowledge of the natural world. We know for instance that some groups are natural and that they share closer relationships with each other than they do to other groups. We also know that some taxa belong to certain groups while others do not. Take the case of Anna's hummingbird (Calypte anna). It is a taxa that belongs to a monophyletic group called birds. We discover that Anna's hummingbird shares closer relationships with other birds than it does to say mammals. As a systematist relationships are all we know of the phylogeny of Anna's hummingbird.

Knowing a relationship doesn't seem to grab the attention of the general public, students or granting bodies as much as evolutionary mechanisms do. What if we proposed that Anna's hummingbird originated in Madagascar and generated a plausible rational argument to support that hypothesis? Suddenly we stir some interest within the biogeographic and marco-ecology communities. When we propose that hummingbirds and birds as a whole are not only related to therapods, but are also their descendants, do we really get everyone excited. But what happens when we reverse the situation - swap our knowledge of hummingbird relationships as explanatory hypotheses and explanatory hypotheses as knowledge? Ebach & Williams (2004) proposed a thinking exercise that is analogous to the suggested proposition above.

Loretta the Murderess

A hypothetical group of detectives kick down a locked door. Behind it stands a woman who answers to the name of Loretta. Next to her on the floor lies a man with a knife in his back. All three objects are covered in blood, which upon further investigation turns out to belong to the deceased. For added effect, the knife has the word "Loretta" inscribed on it in black ink. How do we interpret the scene?

As the title suggests we may call it a "murder", and "a horrible accident", or even "an act of self defense". Whatever the motive is, what is unmistakable is that the locked room contains a woman (Loretta), a man (deceased) and a knife (inscribed with the name "Loretta"). Since no one outside the room witness any action or event, all motives are suspended. All we know are the existence of these three objects.

Let us say that, for some unexplainable reason, the scene is no longer investigated and, for the sake of this argument, all information relating to the Man, the knife and Loretta vanishes. We are left are a series of conflicting motives (i.e., vengeance vs. victimization) and morals (i.e., justice vs. injustice) that all are supported by that same evidence. Now for the analogy - what would happen if we were to swap the evidence for motive and the motive for evidence?

Depending on which way you argue the "evidence" (read "motive") Loretta's innocence is based on the best argument based on the "motive" (read "evidence"). We may propose two explanations to defend or accuse Loretta, namely the "extremely vengeful person" hypothesis and the "victimized person" theory. Each of these totally conflicting theories however based on the same "motive" (read "evidence") - a knife, a dead man and Loretta covered in blood all located in a single locked room. Given that this is all that there is in terms of real evidence, any hypothesis can be made to fit based on nothing more than rhetoric.

Thankfully we no longer live in a society where motives are considered to be evidence (e.g., witch-hunts and other heresies). We do however live in a society that does treat its subjective mechanisms as evidence and its evidence as explanation.

There would be many people who would support the following argument below:

"Birds have evolved from Dinosaurs"

or

"The center of origin for hominids is Africa"

Let us take the first argument. The motive or explanation has been replaced as "evidence". Birds have not evolved from Dinosaurs because "Dinosuars" do not exist as an evolutionary group, that is a monophyletic or natural group. The Dinosauria as a non-monophyletic group is real evidence. The argument that Dinosaurs evolved into birds is by far a more exciting prospect. In doing so however we disregard the evidence to hand - namely that Dinosaurs are a non-evolutionary grouping. The second argument is similar.

We as outside observers have never seen Loretta place the knife into the man, we assume she did because it is her knife and the room was locked. Guilt by association is a terrible tragedy when it occurs in our legal system, but the practice is encouraged in systematics and biogeography. The oldest hominid remains are found in Africa, therefore it is assumed that this is where the group originated from. Guilt by association is not empirical or scientific in anyway as it is based mere speculation, namely what may or may not be there. Additionally no one has seen hominids originate in Africa, so the whole argument is superfluous and speculative, every much like the motive (if any) in the Loretta example. If an older hominid bone is found elsewhere, say Antarctica, the hypothesis will change, but be based on motive rather than on evidence. Systematics and biogeography may appear to become more interesting the more non-empirical hypotheses we spout, but by no means do we become more knowledgeable.

References
Ebach, M.C. & Williams, D.M. (2004). Classification. Taxon 53: 791-794.