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.

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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.

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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".

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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.

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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.

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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.

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