tag:blogger.com,1999:blog-86976165609777195862024-02-20T22:03:13.762-08:00Systematics and BiogeographyDelving into the Science of ClassificationMalte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.comBlogger86125tag:blogger.com,1999:blog-8697616560977719586.post-12870797897858775532012-11-05T20:58:00.000-08:002012-11-05T20:58:52.642-08:00Squirrels, Eels, Algae and Ardi: A ClarificationThe "First human ancestor", which the <a href="http://www.abc.net.au/science/articles/2012/10/23/3616932.htm" target="_blank">ABC</a> reports looked "like a squirrel" is of course not to be mixed up with the "Human Family's Earliest ancestor", namely<i> Ardipithecus ramidu</i>s or “Ardi”, which <a href="http://www.smithsonianmag.com/science-nature/The-Human-Familys-Earliest-Ancestors.html" target="_blank">Smithsonian.com</a> tells us is a "... a female who lived 4.4 million years ago”. Not that this is to be confused with the <a href="http://www.telegraph.co.uk/science/evolution/9123601/Eel-like-creature-identified-as-earliest-human-ancestor.html" target="_blank">Telegraph’s</a> 'earliest human ancestor', a “prehistoric eel-like creature discovered in a Canadian shale bed has been identified as the earliest known ancestor of man", or indeed the <a href="http://www.abc.net.au/science/articles/2012/04/27/3490291.htm" target="_blank">ABC's</a> "Oldest Human ancestor", an "elusive, single-cell creature evolved about a billion years ago and did not fit in any of the known categories of living organisms - it was not an animal, plant, parasite, fungus or alga, they say."<br />
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I hope this clarifies who our first, oldest and earliest ancestors really were.Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-38829729999303866692012-09-06T17:16:00.000-07:002012-09-06T17:16:16.819-07:00 Birds are Fish<blockquote>
<i>Birds really are dinosaurs, and a sparrow or a blackbird is every bit as much a dinosaur as Tyrannosaurus or Stegosaurus (Dr. Dave Hone, <a href="http://www.guardian.co.uk/science/lost-worlds/2012/sep/06/dinosaurs-garden-birds/print" target="_self" title="">Guaridian online</a> 6 September, 2012)</i></blockquote>
birds r relly fish cause i askd my cous and he sed so. fish are animals with 4 legs, scales & a hed. everifin wif 4 legs, scales & a hed is a fish, like cats, sparros and Barry. dinasaurs r fish wif fevhvers so a bird iz relly a fish-dinasaur coz dinasaurs r like small fish in a klassafikayin like vis:<br />
<ul>
<li>animals (birds & shit)</li>
<li>fish (animals wif scales)</li>
<li>dinasaurs (fish wif fevhers)</li>
<li>birds (dunno)</li>
</ul>
vat klassafikayin tellz u vat birds r fish wif fevhers.<br />
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uno other animals r spinless like worms & bugs & shit. so r plankton & trees i guess so va klassafikayin of bugs r:<br />
<ul>
<li>animals (uva stuff)</li>
<li>spinless (like trees)</li>
<li>worms (veges wif eyes)</li>
<li>bugs (worms wif legs)</li>
</ul>
vis klassafikayin tells ya vat bugs r wormies wif legs.<br />
<br />
sum idiots fink vis is rong, but all my mates rekon its right. i ave a lot of mates & in a democracy the majority rules: <b>bugs r worms & birds r fish!</b>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com1tag:blogger.com,1999:blog-8697616560977719586.post-70290202080325167142012-01-09T14:49:00.000-08:002012-01-09T14:51:14.574-08:00Publications for 2011Below is our list of publications for 2011. For those with no access to the links, will be happy to provide pdf copies on request. <br />
<ol>Cecca, F., Morrone, J.J. and Ebach, M.C. (2011). Biogeographical convergence and time-slicing in cladistic biogeography: Concepts and methods. In P. Upchurch; A. McGowan & C. Slater (eds.), Palaeogeography and Palaeobiogeography: Biodiversity in Space and Time. Taylor & Francis (CRC Press), Boca Raton, Florida, pp. 1-12. </ol><ol>Ebach, M.C. (2011). Taxonomy and the DNA Barcoding Enterprise. Zootaxa, 2742: 67–68. </ol><ol>Ebach, M.C. (2011). Biogeógrafos del mundo... ¡uníos!: un camino hacia la unificación. Revista de Geografía Norte Grande, 48: 5-10. </ol><ol>Ebach, M.C., de Carvalho M.R. and Nihei, S.S. (2011). Saving Our Science from Ourselves: The Plight of Biological Classification. Revista Brasileira de Entomologia, 55: 149–153. </ol><ol>Ebach, M.C., de Carvalho, M.R. and Williams, D.M. (2011). Opening Pandora’s Molecular Box. Zootaxa, 2946: 60—64. </ol><ol>Ebach, M.C. and Williams, D.M. (2011). A Devil's Glossary for Biological Systematics. History and Philosophy of the Life Science,s 33: 251—258. </ol><ol>Ebach, M.C., Valdecasas, A.G. and Wheeler, Q.D. (2011). Impediments to Taxonomy and Users of Taxonomy: Accessibility and Impact Evaluation. Cladistics, 27: 550–557. Levkov, Z. and </ol><ol>Williams, D.M. (2011). Fifteen new diatom (Bacillariophyta) species from Lake Ohrid, Macedonia. Phytotaxa, 30: 1—41. </ol><ol>Mooi, R.D., Williams, D.M., and Gill, A.C. (2011). Numerical cladistics, an unintentional refuge for phenetics – a reply to Wiley et al. Zootaxa, 2946: 17—28. </ol><ol>Williams, D.M. (2011). Synedra, Ulnaria: definitions and descriptions – a partial resolution. Diatom Research, http://dx.doi.org/10.1080/0269249X.2011.587646 </ol><ol>Williams, D.M. and Gill, A.C. (2011). ‘Adventures in the fish trade’ by Colin Patterson, edited and with an introduction by David M. Williams & Anthony C. Gill. Zootaxa, 2946: 118—136. </ol><ol>Williams, D.M. and Kociolek, J.P. (2011). An overview of diatom classification with some prospects for the future. The Diatom World (Sebach, J & Kociolek, JP, eds), pp. 47—91. </ol><br />
<ol> </ol>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com1tag:blogger.com,1999:blog-8697616560977719586.post-21712115090511566312011-12-15T13:29:00.000-08:002011-12-15T13:30:21.214-08:00Agnosticism in Comparative Biology<i>Gnostic adj. of or relating to knowledge (from gnōstos meaning 'known') <br />
<br />
Agnostic adj. a person who believes that nothing is known on some topic, either at the present, or in principle</i> <br />
<br />
In the philosophy of religion and recent public debates over atheism, a distinction is made of the difference between believing in God (theism) and not believing in God (atheism), but a third option, agnosticism is often regarded as the equivocation or uncertainty about whether or not there is a God. In fact, agnosticism is the denial that the existence of a God can be known one way or the other, and that we should stick to the facts we do know. Agnostics reject gnosticism of either kind. In biology, there are similar matters to consider. <br />
<a name='more'></a>Comparative biology is a now relatively unpopular (and often thought to be outmoded, replaced by unqualified reliance upon molecular data) approach to the nature and relationships of living things. So, what is knowledge in comparative biology? We are able to observe and therefore know organisms and their parts from fossil and living specimens to some degree through direct acquaintance, under microscopes, or as gels and know something of their behaviour, genetics and ontogeny. We can even see fertilization, cell growth, life cycles and environmental conditions in modern organisms. Knowledge, in comparative biology, is inextricably linked to what we can observe. It is empiricism of the highest order, and relies upon actual observations as the basis for knowledge claims. However, it is what we can predict (rather than observe), which makes comparative biology 'interesting' to the majority of contemporary biologists. <br />
<br />
Given the hypothesis-driven emphasis in of 21st century comparative biology, many systematists and biogeographers have made their careers on predictions and modelling. We believe we can, for instance, predict divergence times based on molecular clocks. We attempt to predict which taxa and areas are ancestral based on models of evolution and geography. However none of these predictions are knowledge to the comparative biologist, as proponents of these models can never prove their predictions beyond a hypothesis, best guess or hunch. At best, they have tested, and to that extent warranted, theories. Warranted theories are far less reliable and certain than observations, and they hitchhike on data. <br />
<br />
Call this "experimental envy" if you wish, but comparative biology is simply that - comparative. Knowledge for the comparative biologist lies in the ability to recognise organisms and their parts (as described above). If, for instance, a prediction proves to be true at some point in time, it was the comparative biologists' observation and knowledge of the organism, rather than a knowledge of a particular evolutionary process, that grounded that prediction. Theories and hypothesis are dependent on evidence (e.g., observation). <br />
<br />
But knowledge of an organism is not enough. In their quest to predict and model, the contemporary comparative biologist is insisting a certain 'knowledge' of processes that extend beyond known and observable material phenomena. They claim to know what they cannot: that their hypotheses are true. Using their prior hypotheses, they ground their later ones on probabilities and likelihoods that are no better founded than the strength of the priors. Hypotheses build on hypotheses. This is inference, but it is not knowledge. <br />
<br />
It appears that some comparative biologists appear to exhibit a certain form of non-religious and secular gnosticism - analogous to the gnosticism of atheists and theists described by Huxley when he coined the term "agnostic". That is, they claim to know more than what the evidence (i.e., data) can possibly claim. One example is ancestors. Having found the oldest known specimen of trilobite does not mean one has found the ancestor of all trilobites. What is known is that it is the oldest at the time of discovery - an older one may still exist. A trilobite's relations are inferred and always defeasible by new data. Data are not defeasible, however. <br />
<br />
This phylogenetic agnosticism does not deny the existence of ancestors or centres of origin, only of our ability to recognise them with much certainty based on what we know (as opposed to what we merely think). <br />
<br />
We recognise that a form of gnosticism has arisen in comparative biology since the 19th century due to the blurring of what we know for sure and what we believe we know. What we know is limited and restricted to what we can observe. What we believe to be happening, however, is not knowledge, but a best guess or informed opinion. Confusing it with actual knowledge creates a gnosticism that is already quite widespread in biology. <br />
<br />
We appeal for warranted agnosticism, one that recognises the distinct difference between what we do know and what we believe we know. For instance, we may say that "I know this is a mammal" based on the diagnosis of mammals. We may also confidentially state that "I believe this to be the centre of origin for all palms" based our conviction of the truth of a theory of dispersal and speciation. For example we may be convinced that method <i>x</i> is better than say method <i>y</i>. On this basis we can determine which method is better. However, knowing which method is better does not guarantee that method will extend our knowledge of other unobservable processes. <br />
<br />
What agnosticism in comparative biology is <b>not</b>, is banning, denigrating or rejecting certain hypotheses because they are not based on knowledge. Every comparative biologist has the right to express their convictions and opinions. They do not, however, have the right to confuse knowledge with a hypothesis. Doing so illicitly validates a hypothesis (i.e., a conjecture or best guess) as a discovery or known fact. A good comparative biologist is agnostic to all hypotheses and theories, until they are demonstrated to be true. <br />
<br />
<i>The highest happiness of man is to have probed what is knowable and quietly to revere what is unknowable</i> (Goethe). <br />
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<i>John S. Wilkins contributed a portion of this post. Please cite as Ebach, M.C., Wilkins, J.S. and Williams, D.M. (2011). Knowledge and Agnosticism in Comparative Biology. Systematics and; Biogeography Blog, http://urhomology.blogspot.com/2011/12/agnosticism-in-comparative-biology.html</i>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com2tag:blogger.com,1999:blog-8697616560977719586.post-50701347460190831542011-11-09T12:58:00.000-08:002011-11-09T13:05:41.809-08:00Tweeted Histories I #Homology<b><span style="color: blue;">@Goethe1824</span></b> I can relate a worm and a man via a third thing! I'll write a poem about it!<br />
<b style="color: blue;">@sexy_Blumnbch</b> What?<br />
<b style="color: blue;">@henrich.B</b> if you hang a human skeleton next to that of bird, you can compare their structures <a href="http://books.google.com.au/books?id=b_gTAAAAQAAJ&printsec=frontcover&dq=Untersuchungen+u%CC%88ber+die+Entwickelungs-Gesetze+der+organischen+Welt&hl=en&ei=lOi6TvvwHMKviQfvuaWmBw&sa=X&oi=book_result&ct=result&resnum=1&ved=0CC8Q6AEwAA#v=onepage&q&f=false">#Bronn1858</a> <br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbvTBE1egozJahN6TA0U3XkbM9jF6T3IFdFQG2WuZtlijEkMjxvVzFLuWtx2aSIWmHuUoRYt8IDT1erf2LrDN5KPBucyDTuPeyEvIqz4MNTtSslKRytD-8qLZFfNfmH3UEkXhoilJmxNg/s1600/twitter-bird-logo.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="172" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjbvTBE1egozJahN6TA0U3XkbM9jF6T3IFdFQG2WuZtlijEkMjxvVzFLuWtx2aSIWmHuUoRYt8IDT1erf2LrDN5KPBucyDTuPeyEvIqz4MNTtSslKRytD-8qLZFfNfmH3UEkXhoilJmxNg/s200/twitter-bird-logo.jpg" width="200" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">@Darwinathome's birdy</td></tr>
</tbody></table><div style="text-align: right;"></div><b style="color: blue;">@sexy_Blumnbch</b> Eww!<br />
<b style="color: blue;">@MonsterMoa</b> nah! what you want is a bauplan. <a href="http://books.google.com.au/books/about/On_the_archetype_and_homologies_of_the_v.html?id=IYqb_btyzS0C&redir_esc=y">#Owen1849</a><br />
<b style="color: blue;">@Swiss_Pride</b> What evidence have you got? You need space, time as well as form!<a href="http://books.google.com.au/books?id=yyYxVoClJacC&printsec=frontcover&dq=An+Essay+on+Classification.&hl=en&ei=Hee6TtnKBYasiAeFkemfBw&sa=X&oi=book_result&ct=result&resnum=1&ved=0CDYQ6AEwAA#v=onepage&q&f=false"> #Agassiz1859</a><br />
<b style="color: blue;">@Embryo.boy</b> I think he means comparing embryos and how they develop <a href="http://books.google.com.au/books?id=NA4_AAAAcAAJ&printsec=frontcover&dq=Grundzu%CC%88ge+der+vergleichenden+Anatomie&hl=en&ei=1ea6TqfHAqqYiAekqfDuBA&sa=X&oi=book_result&ct=result&resnum=1&ved=0CC8Q6AEwAA#v=onepage&q&f=false">#Gegenbaur1859</a><br />
<b style="color: blue;">@Swiss_Pride</b> no I don't!<br />
<b style="color: blue;">@Darwinathome</b> I found a birdy!<br />
<b style="color: blue;">@MonsterMoa</b> just compare the forearms of bats, humans and whales. See? Analogy!<br />
<b style="color: blue;">@RayL</b> Don’t just compare: find the origin of things. Homology? Bah! Homogeny!<br />
<b style="color: blue;">@asagray</b> I like @Darwinathome's birdy. Can u send photo?<br />
<b style="color: blue;">@Stammbaum</b><span style="color: blue;"> </span>Origins, we need origins! My own Stammbaum gives origins; now all is homogeny<br />
<b style="color: blue;">@Darwinathome</b> can someone tell @Stammbaum to leave me alone?<br />
<b style="color: blue;">@RayL</b> Not all is homogeny, some comparisons are not true: homoplasy!<br />
<b style="color: blue;">@Stammbaum</b> Who cares. I have lots of stammbaume, one for every creature. All with homogeny, homoplasy and homology<br />
<b style="color: blue;">@naefnotnaf</b> @Stammbaum got it wrong. You can't mix phylogeny and systematics <a href="http://books.google.com.au/books?id=kz5UAAAAMAAJ&q=Idealistische+Morphologie+und+Phylogenetik+%28zur+Methodik+der+systematischen%29.&dq=Idealistische+Morphologie+und+Phylogenetik+%28zur+Methodik+der+systematischen%29.&hl=en&ei=e-a6TsqaDoqtiAeew7mzBw&sa=X&oi=book_result&ct=result&resnum=3&ved=0CDsQ6AEwAg">#Naef1919</a><br />
<b style="color: blue;">@naefnotnaf</b> homology is a systematic relationship separate from phylogeny<br />
<b style="color: blue;">@angry_mayr</b> Typologist!<br />
<b style="color: blue;">@Zimmermann</b> no it's not! homology is a transformational relationship.<br />
<b style="color: blue;">@a.remane</b> or a process <a href="http://books.google.com.au/books?ei=5OW6To2KJKuyiQe2xtCfBw&ct=result&id=kOxKAQAAIAAJ&dq=Die+Grundlagen+des+natu%CC%88rlichen+Systems%2C+der+vergleichenden+Anatomie+und+der+Phylogenetik%2C+Theoretische+Morphologie+und+Systematik+I.+Akademische+Verlagsgesellschaft%2C+Geest+and+Portig&q=Remane#search_anchor">#Remane1952</a><br />
<b style="color: blue;">@willi</b> Why not compromise? Use @naefnotnaf's systematics for taxa and @Zimmermann for their characters!<a href="http://books.google.com.au/books?id=qJ0KAAAAMAAJ&q=Grundzu%CC%88ge+einer+Theorie+der+phylogenetischen+Systematik.&dq=Grundzu%CC%88ge+einer+Theorie+der+phylogenetischen+Systematik.&hl=en&ei=T-a6TtiEJ-mPiAf3-YScBw&sa=X&oi=book_result&ct=result&resnum=1&ved=0CC8Q6AEwAA"> #Hennig1950</a><br />
<b style="color: blue;">@ggsimp</b> what about ancestors? Homology is similarity between the bits of us and ancestors<br />
<b style="color: blue;">@sokal_123</b> you mean overall similarity at a node?<a href="http://books.google.com.au/books?id=3Y4aAAAAMAAJ&dq=numerical%20taxonomy&source=gbs_similarbooks"> #SokalSneath63</a><br />
<b style="color: blue;">@willi</b> no, special similarity, that is synapomorphy <a href="http://books.google.com.au/books?id=xsi6QcQPJGkC&printsec=frontcover&dq=phylogenetic+systematics&hl=en&ei=Z-W6TqWIM-iXiQf2rOzCBw&sa=X&oi=book_result&ct=result&resnum=1&ved=0CC4Q6AEwAA#v=onepage&q&f=false">#Hennig66</a><br />
<b style="color: blue;">@angry_mayr</b> Cladist!<br />
<b style="color: blue;">@nelson_usa</b> perhaps it's a non-transformational relationship?<a href="http://www.ucpress.edu/series.php?ser=spsy"> #NelsonPlat81</a><br />
<b style="color: blue;">@beaty.boy</b> Pattern Cladist!<br />
<b style="color: blue;">@Colin82</b> non-transformational but based on similarity <a href="http://books.google.com.au/books?ei=5-S6TtLSK4GZiAesy7yvBw&ct=result&id=bawNoVwsSMkC&dq=Problems+of+Phylogenetic+Reconstruction&q=Morphological+characters+and+homology#search_anchor">#Patterson82 </a><br />
<b><span style="color: blue;">@ron.brady</span></b> forget similarity, homology is simply an affinity. See @Goethe1824<br />
<b style="color: blue;">@normlovesspiders</b> homology is a three-item relationship regardless what is based on<br />
<b style="color: blue;">@hennig_superstar</b> %$#%! Homology is synapomorphy?<br />
<b style="color: blue;">@k.nixon</b> homology = synapomorphy + symplesiomorphy <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2011.00371.x/abstract">#NixonCarp11</a>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com1tag:blogger.com,1999:blog-8697616560977719586.post-90370100246283356752011-11-06T15:48:00.000-08:002011-11-06T15:48:05.040-08:00The Autonomous Algorithm: Malpractice in Theory<div class="separator" style="clear: both; text-align: center;">
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In our last post we introduced the topic of the <a href="http://urhomology.blogspot.com/2011/08/autonomous-algorithm.html">Autonomous Algorithm</a>, a black box that acts as the foundation for a theory and method. In this post we explain what we mean by theory and method and why we believe that no tool can function as a logical foundation. Doing so is a form of malpractice.<br /><br />For all the non-philosophers reading this post, we define theory as a set of mathematical principles on which an activity is based. The set of principles that underlie the study of geophysics is that radio waves and sound waves for instance have different levels of penetration. When a sound wave is reflected it can tell us the density and depth of an object, like a rock. These principles are based on physics, and not on the actual program that models the depth and density of rock. Doing that would be putting the cart before the horse. If we change the way we model the results of our acoustic test, we do not change the underlying principles of physics.<br /><br />A method is a procedure to accomplish something. Methods are generally activities that can be done by pen and paper (although sometimes they are easier when automated) in which we determine the steps, for instance, to find out how to tell what is beneath a particular surface. The implementation is the tool that is used to do implement the method. This is usually as a computer algorithm. So, an algorithm is a tool that is based on a method that is underpinned by a theory. Seems simple enough, but this is often misinterpreted.<br />
<a name='more'></a>Take parsimony for example (and by parsimony we mean Wagner parsimony). It is a method that has several implementations. It is not a theory. The theory is phylogenetic systematics. In recent times, however, many have unwittingly chosen to treat the implementation as a tool for testing a method that in turn decides what the theory should be. Not only is this non-empirical and non-scientific, it is also a form of malpractice within systematics. <br /><br />Algorithms are simply tools. The algorithm/s in parsimony programs, for example, are not capable of recognising reversals, parsimony, evolution, plesiomorphy, homology and synapomorphy. They are tools that manipulate binary digits to do certain things. When character-state 0 in character 1 of Taxon A is forced to be basal (because of a 0 present in the outgroup), its appearance further up the branching diagram is interpreted as a reversal by the operator (us), not by the algorithm. Parsimony programs have no concept of transformation. That concept lives with the operator (us).<br /><br />So what are these programs doing? In one sense they are mimicking concepts that would remain incomprehensible to any machine (naturally). To use one of Douglas Adams' analogies, an algorithm doesn't know what transformation is as much as a "tea-leaf knows the history of the East India Company".<br /><br />Transformations, reversals, plesiomorphies are all concepts interpreted by us. What is a reversal to one user is homoplasy to another. The current crop of algorithms act upon and manipulate 'similarities' not homologies. They are phenetic methods. While this is not a bad thing (providing we do not interpret our cladograms to be the real thing), phenetics does have its limitations: it cannot identify homology. This is left to us, the observer and user of a program.<br /><br />Malpractice in phylogenetics is due to interpreting a quantitative result as qualitative reality. For example, representation is a relationship interpreted by similarity only. Algorithms represent real objects (e.g., think of two binary characters depicting the presence of wings). Representation however is often confused with replication, namely a copy of a real object. Algorithms cannot replicate evolution, reversal, transformation, homology and so on. Assuming that it does and presenting results in this way is a form of malpractice.<br /><br />Where this type of thinking has lead us is to the incorrect notion that a homolog (the part of any organism) is actually a homology (that organism's relationships). But more of this in the next post.<br /><br />Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com2tag:blogger.com,1999:blog-8697616560977719586.post-46070398008225192612011-08-24T13:46:00.000-07:002011-08-24T13:46:26.368-07:00The Autonomous AlgorithmThe S&B Blog will be running a series of posts dealing with the rise of the black box and the fall of the foundations of systematics.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjt3n0rMxneBrdwzfqo-dM252CfaDk0J-secYhvhgjUIAn8OMsGPGB4QkF0BfMY30xtRC0UdaY5keghRIL456IP4Mi3Xm92ZwrOkhvtBf3RxeDw0Vkp_-m1MNakRAsq_PQTkSgt7HmVNMY/s1600/timetree_lg.jpg.jpg" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="200" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjt3n0rMxneBrdwzfqo-dM252CfaDk0J-secYhvhgjUIAn8OMsGPGB4QkF0BfMY30xtRC0UdaY5keghRIL456IP4Mi3Xm92ZwrOkhvtBf3RxeDw0Vkp_-m1MNakRAsq_PQTkSgt7HmVNMY/s200/timetree_lg.jpg.jpg" width="188" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The Timetree of Life: A product <br />
of the Autonomous Algorithm?<br />
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</td><td class="tr-caption" style="text-align: center;"><br />
</td></tr>
</tbody></table>Presently, the majority of systematic analyses are constructed in the same way - a matrix is assembled and fed into a computer that then produces a branching diagram. Students of systematics are taught how to produce this branching diagram, using the algorithm, without context to the foundations of systematics. The result is a whole new generation of computer users ignorant of the basic fundamentals of systematics, such as theory (i.e., homology, monophyly), history (i.e., why we do what we do) and methodology (i.e., how to find homologs and construct a cladogram by hand). This also results in an increased dependency on algorithms, which in turn creates a new systematic history and theory that revolves around algorithms rather than concepts. The former black box, which implemented basic algorithms to find approximations of cladograms, is now totally autonomous to the theory, method and history that had gone into its creation. We call this the Autonomous Algorithm.<br />
<a name='more'></a><br />
<br />
The Autonomous Algorithm is a self perpetuating phenomenon. Many users of phylogenetic software are unaware of the foundations of systematics and are totally reliant on algorithms to do their work. They are also dependent on the developers and programmers, who themselves are dimly aware of the foundations and their relevance to each new published algorithm. The Autonomous Algorithm has created a number of problems which we will attempt to address, namely:<br />
<ol><li>Malpractice in Theory: Homologs as Homology</li>
<li>Misaligned Methodology: Cladistics as Phenetics</li>
<li>A Misconstrued History: Systematics as Phylogenetics</li>
</ol>Before we begin, we wish to reemphasise our terminology to avoid any confusion.<br />
<br />
<b>Rationale of Terms</b><br />
<br />
Theory herein are the basic fundamental principles underlying what we do. This means defining what we do and its associated logical procedures.<br />
<br />
Methodology herein is the practice of what we do. Creating cladograms by hand, finding homologs, understanding the anatomy of an organism etc. are all part of what a systematist does.<br />
<br />
Implementation herein refers to the numerical tools we use. These are generally black boxes (i.e., software that uses numerous algorithms that process our data). Most systematists are generally unaware of how these work exactly, but use them by proxy. An implementation is not equivalent to a methodology.<br />
<br />
History herein is the history of an idea. This is sometimes referred to as an ‘internalist history’, since we are concerned with the theory and methodology of systematics over time. Whatever external history has occurred generally is irrelevant to how a systematic method works. <br />
<br />
A natural classification herein is a hierarchical ordering of organisms based on systematic relationship.<br />
<br />
A systematic relationship equivalent to kinship, that is, when two taxa are more closely related to each other than they are to any other taxon (herein <i>systematic Monophyly</i> or <i>sMonophyly</i>). Relationship here means a shared history. In hindsight this shared history is a result of some known or unknown evolutionary process/es. This relationship is only true if the relationship is based on two homologs that are more closely related to each other than they are to any other homolog (<i>sHomology</i>). <br />
<br />
The Cladistic Parameter (herein CP) is a hierarchical representation all manifestations of a systematic relationship. Homology, for instance is a systematic relationship of homologs, or the parts of an organism, while monophyly is a relationship of taxa based on homologies. This can be expressed diagrammatically (as branching diagrams) to highlight the dependancy of one relationship within another, that is to say monophyly cannot exist without homology and homology cannot exist without a relationship between homologs, or:<br />
<br />
<div style="text-align: center;">The Cladistic Parameter = Relationship : sHomology : sMonophyly : sTaxon</div><br />
<i>sTaxa</i> herein are deemed to be relationships between organisms (e.g., their parts, individuals, populations, etc.). We recognize that there are many artificial taxa that share closer relationships to other taxa than they do to themselves (e.g., reptiles, fish etc.). These taxa are not informative and add little to our knowledge of natural classifications. When we refer to sTaxa we refer to natural classifications.<br />
<br />
In the next post we will tackle Malpractice in Theory, namely the widespread phenomenon of confusing homologs with homology.Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com3tag:blogger.com,1999:blog-8697616560977719586.post-40471340930774317372011-04-20T02:30:00.000-07:002011-04-20T02:33:55.347-07:00Willi Hennig (1913 - 1976)<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSRjUgyydRc21vFILryScduzO0HXVymX2p45TMgn_OqOeBHn7s5Hd39uWbZZ-BLVx-O4m7Vo1gyYoco9wByrTBzphBMCS29xsMNoKmSA04ttK7XFsbvAJU8rhRnAQvmGlpzhOL-Wh-7Kke/s1600/Willi_Hennig2.jpg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 246px; height: 320px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSRjUgyydRc21vFILryScduzO0HXVymX2p45TMgn_OqOeBHn7s5Hd39uWbZZ-BLVx-O4m7Vo1gyYoco9wByrTBzphBMCS29xsMNoKmSA04ttK7XFsbvAJU8rhRnAQvmGlpzhOL-Wh-7Kke/s320/Willi_Hennig2.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5597574994126464050" /></a> <br />
The great entomologist <a href="http://zoo.bio.ufpr.br/diptera/bz023/willi_hennig.htm">Willi Hennig</a> (1913—1976), founder of ‘Phylogenetic Systematics’, was born on this day. Had he lived, he’d be 98.David Williamshttp://www.blogger.com/profile/09011818890918076960noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-64987043888675293332011-02-04T01:08:00.000-08:002011-02-04T01:21:44.358-08:00So Long, and Thanks for All the FishIt’s time to say goodbye to Paraphyly Watch, paraphyly, holophyly and all who sailed in them. It was fun while it lasted but all good things must come to an end and, alas, as you can see, we are moving on, redesigning, removing and rolling on. The year 2010 witnessed a spate of relevant papers to the Watch but time and inclination prevent us from devoting ourselves to their contents and absorbing their message. Save one last remark.<br /><br />For us, organisms and taxa, taxa and areas call our attention, and our time might be more usefully spent elsewhere, doing these other things. It is these other things our blog will now be chiefly devoted, such that we might find subjects worthy of study, particularly classification and all its implications. Evolution is one such implication. Evolution, too, is a subject we find of interest. Hennig devoted many pages to the subject of classification – and evolution, as it happens. Our view contrasts with that of Cavalier-Smith: <br /><br />“Real evolution often ignores Germanic cladistic logic; its messiness and lack of rules makes classification an art where compromise is necessary and rigid formalism harmful” (Cavalier-Smith 2010, p. 115). <br /><br />German logic? ‘Real’ evolution? Classification as ‘art’? Cavalier-Smith continues:<br /><br />“I agree with Mayr (1974), Halstead (1978) and others that the Hennigian perspective impedes realistic scientific discussion of phylogenetic history, because of its evolutionarily unrealistic formalism based on an intellectually impoverished view of the complexities of actual phylogenies, especially its failure to come to grips with evolutionary transformation, the reality of ancestors, and not least its dogmatism” (Cavalier-Smith 2010, p. 116).<br /><br />“Realistic scientific discussion of phylogenetic history”? Cavalier-Smith embraces paraphyly; it looms large in his many works, they are sprinkled liberally among his various, ever-changing classifications, his artworks(Cavalier-Smith 2010, p. 115, fig. 1). An aversion to paraphyletic groups is, of course, anti-evolutionary:<br /><br />“Cladistic aversion to paraphyletic groups, and lumping of paraphyly and polyphyly as ‘non-monophyly’, are logically flawed and anti-evolutionary” (Cavalier-Smith 2010, p. 117, legend to fig. 2).<br /><br />János Podani (2010) echoes the sentiment:<br /><br />“For pattern cladists, paraphyly is a less useful concept, because paraphyly together with polyphyly are “explanations for non-groupings, or more accurately, excuses for the absence of monophyly” (Williams, 2007). Paraphyletic and polyphyletic groups are therefore referred to “non-monophyletic groups” (Williams & Ebach, 2007; definition P4). For pattern cladists, non-monophyletic groups do not exist, being unnatural (“nongroups”). The approach is an evidently non-evolutionary one, paraphyly and polyphyly having very different evolutionary implications (Cavalier-Smith, 2010)” (Podani 2010, 1014). <br /><br />Non-evolutionary? Anti-evolutionary? <br /><br />Hörandl & Stuessy, when summarising the various concepts of paraphyly, understood it as a tool for classification – and evolution. For them “Cladistics put considerations of evolution, i.e., phylogeny, back into classification” – but left a bit out. They cite, with approval, Podani. With respect to monophyletic classification they suggest it “neglects important evolutionary processes” – which must be ‘Real’ evolution (Hörandl & Stuessy 2010, p. 1646)<br /><br />The statements above, from Cavalier-Smith, Podani, Hörandl & Stuessy: Are any true, or even any part of them true? <br /><br />It is time to say goodbye to Paraphyly Watch and paraphyly. It is time to devote our attention to classification, what we see is the saviour of comparative biology, maybe even all of biology.<br /><br /><a href="http://rstb.royalsocietypublishing.org/content/365/1537/111.full.pdf+html">Cavalier-Smith, T. 2010. Deep phylogeny, ancestral groups and the four ages of life. Phil. Trans. R. Soc. B 365: 111—132, doi: 10.1098/rstb.2009.0161</a><a href="http://www.ingentaconnect.com/content/iapt/tax/2010/00000059/00000006/art00001"><br /><br />Hörandl, E. & Stuessy, T.F. 2010. Paraphyletic groups as natural units of biological classification. Taxon 59: 1641—1653</a>.<br /><a href="http://www.ingentaconnect.com/content/iapt/tax/2010/00000059/00000004/art00002"><br /><br />Podani, J. 2010. Monophyly and paraphyly: A discourse without end? Taxon 59: 1011—1015.</a>David Williamshttp://www.blogger.com/profile/09011818890918076960noreply@blogger.com2tag:blogger.com,1999:blog-8697616560977719586.post-23514774362528771902011-02-02T00:53:00.000-08:002011-02-02T00:53:53.545-08:00A MakeoverYou like it? The <i>Blogger Template Designer</i> calls it "Simple". We like it and hope that it is easier on the eye.<br />
<br />
Above you will see our new design, a '<i>Chtenopteryx</i> ontogeny motif', and below that, an additional quote that will change from time-to-time (this month it's Darwin).<br />
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We hope to hear from you, dear <i>Systematics & Biogeography</i> reader, especially those can enlighten us on the ontogeny in the header above. You will be hearing from us.Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com2tag:blogger.com,1999:blog-8697616560977719586.post-73422168045002904982011-01-23T13:35:00.000-08:002011-01-23T13:35:49.036-08:00Adventures with my DNA Barcoder<blockquote>"<i>But humanity is bioilliterate. Yes, there is a high priest for the name and natural history of some species. That person, however, is almost never standing by your side. But with Google, can you get it? No, there is no hole in your computer or handheld into which to insert the biobit to link through Google. Who is going to give you that name in the dark, the rain, the backyard, or the rain forest? True bioliteracy is being able to link what humanity knows to the biodiversity in hand, eye, or mouth, and build on it. What is the cost to let all seven billion of us read wild biodiversity, now? The barcorder in the back pocket</i>" (Janzen, 2010, <i>Biotropica</i>, 42:540-542).</blockquote><br />
<b>Thursday, 25th</b><br />
I am so excited! Today I bought my DNA Barcoder from the gift shop at my local natural history museum. It comes with a two page booklet that tells me I need 6 AAA batteries and something to barcode.<br />
<br />
<b>Friday, 26th</b><br />
I went down to the university to show my new barcoder to my sister. She needs lots of fresh tissue to do her molecular work and always complains that her specimens are either too old or contaminated. "Not with this!" I told her. She looked at me and my barcoder and started laughing. Stuck-up cow.<br />
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<b>Saturday, 27th</b><br />
Today is my first barcoding day (it rained all week, so there was nothing to barcode). I barcoded my cat, which it turns out, is 'human'. Perhaps it's because humans and cats are closely related? Perhaps I need something more distantly related?<br />
<br />
<b>Sunday, 28th</b><br />
I barcoded an ant that I found crawling behind the sofa. The barcoder tells me it's a fungus. I see no other ants. Later on I find a honey bee trapped in my kitchen window. It comes up as a 'geranium'. The barcoder really needs to be calibrated or something.<br />
<br />
<b>Wednesday, 1st</b><br />
Finally, a hot and sunny day! I tried to entice a bird with bread crumbs. No luck. <br />
<br />
<b>Thursday, 2nd</b><br />
Couldn't get close enough to the house sparrows in my park to barcode them. I barcoded various trees in the arboretum. Amazing! The barcoder gets it right <i>every</i> time. There was only one plant sign in the whole park that was wrong!<br />
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<b>Sunday, 5th</b><br />
What a day! Yesterday morning I found a whip snake sunning itself on my porch. I managed to barcode it before it bit me in self defense. Luckily the hospital knew which anti-venom to use because my trusty barcoder got it right again!<br />
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<b>Tuesday, 7th</b><br />
I’m going to be famous! I barcoded a cicada and found that it was 7 different species! I rushed down to the local natural history museum to tell them of the news. Perhaps they can name a news species after me? Apparently the museum barcodes species from all over world and no longer employs taxonomists (the ones who describe new species). A barcoding technician pointed out several local amateur entomological groups I could join. "That's where you find taxonomists now" he said. Perhaps I’ll try Google.Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-45831999709592932032011-01-09T14:42:00.000-08:002012-01-09T14:42:52.005-08:00Publications for 2010Below is our list of publications for 2010. For those with no access to the links, will be happy to provide pdf copies on request. <br />
<ul><ol>Christenhusz, MJM., Baker, W., Chase, MW., Fay, MF., Lehtonen, S., Van Ee, B., Von Konrat, M., Lumbsch, T., Renzaglia, KS., Shaw, J., Williams, DM and Zhang, Z-Q. (2010). The first anniversary of Phytotaxa in the International Year of Biodiversity. Phytotaxa, 15: 1–8. </ol><ol> </ol><ol>Ebach, M.C. (2010). Paleobiological Revolution: Essays on the Growth of Modern Paleontology. Systematic Biology, 59: 753-755.</ol><ol> </ol><ol>Ebach, M.C. (2010). A new book on biogeography. Cladistics, 26: 560-562.</ol><ol> </ol><ol>Ebach, M.C. and de Carvalho M.R. (2010). Anti-intellectualism and the DNA Barcoding Enterprise. Zoologia, 27: 165-178 [<a href="http://www.google.com.au/url?sa=t&rct=j&q=anti-intellectualism%20and%20the%20dna%20barcoding%20enterprise&source=web&cd=1&ved=0CCMQFjAA&url=http%3A%2F%2Fwww.scielo.br%2Fpdf%2Fzool%2Fv27n2%2F03.pdf&ei=d2vHTr6QMeGZiQevzZgO&usg=AFQjCNET5hjHxqEsQGWFrxglTuI41XeOSw&sig2=5iFO8iUV3ABhiCMP_Btlpg&cad=rja">access free pdf here</a>]. </ol><ol> </ol><ol>Ebach, M.C. and Williams D.M. (2010). Aphyly: A Systematic Designation for a Taxonomic Problem. Evolutionary Biology, 37: 123-127.</ol><ol> </ol><ol>Ebach, M.C. and Williams D.M. (2010). Systematics and Biogeography: Cladistics and Vicariance. Systematic Biology, 59: 612-614.</ol><ol> </ol><ol>Parenti, L.R. and Ebach, M.C. (2010). Wallacea Deconstructed. In D.M. Williams & S. Knapp (eds.), Beyond Cladistics: The Branching of a Paradigm. University of California Press, Berkeley, pp. 303-318.</ol><ol> </ol><ol>Reid, G. and Williams, D.M. (2010). Notes on the genus Semiorbis Patrick with a description of a new species. Diatom Research, 25: 355—365. </ol><ol> </ol><ol>Toyoda, K, Nagumo, T. and Williams, DM. (2010). A new marine monoraphid species, Achnanthes pseudolongipes sp. nov. From Miyagi, Japan. Diatom Research, 25: 185—193.</ol><ol> </ol><ol>Tuji, A, Williams, D.M, Sims, P.A, and Tanimura, Y. (2009) [2010] An Illustrated Catalogue of Type Specimens from the H.M.S. Challenger Voyage in Castracane’s Slide Collection in the Natural History Museum, London. In: Joint Haeckel and Ehrenberg project: Re-examination of the Haeckel and Ehrenberg Microfossil Collections as a Historical and Scientific Legacy Y. Tanimura and Y. Aita, eds). National Museum of Nature and Science Monographs, No. 40, pp. 7—11.</ol><ol></ol><ol>Williams, D.M. (2010). Historical biogeography, microbial endemism and the role of classification: everything is endemic. In Biogeography of microorganisms. Is everything small everywhere? (Fontaneto, D, ed.), Cambridge University Press, Cambridge, pp. 11—31. </ol><ol></ol><ol></ol><ol> </ol><ol>Williams, D.M, Chudaev, D.A, Lomonosov, M.V and Gololobova, MA.. (2010). Punctastriata glubokoensis spec. nov., a new species of ‘Fragilarioid’ diatom from lake Glubokoe, Russia. Diatom Research, 24: 479—485. </ol><ol>Williams D.M. and Ebach, M.C. (2010). Molecular Systematics and the Blender of Optimization: Is There a Crisis in Systematics? Systematics and Biodiversity, 4:481-484. </ol><ol> </ol><ol>Williams, D.M, Ebach, M.C. and Wheeler, Q.D (2010). Beyond belief: the steady resurrection of phenetics. In D.M. Williams & S. Knapp (eds.), Beyond Cladistics: The Branching of a Paradigm. University of California Press, Berkeley, pp. 169-197.</ol><ol> </ol><ol>Williams, DM and Kociolek, JP. (2010). Classifications of Convenience: The Meaning of Names. Diatom Research 25: 213—216. Williams, DM and Morales, EM. (2010). Pseudostaurosira medliniae, a new name for Pseudostaurosira elliptica (Gasse) Jung et Medlin. Diatom Research 25: 225—226.</ol><ol></ol><ol> </ol><ol>Yanling Li, Williams, D.M, Metzeltin, D., Kociolek, J.P. and Zhijun Gong (2010). Tibetiella pulchra gen. nov. et sp. nov., a new freshwater epilithic diatom (Bacillariophyta) from River Nujiang in Tibet, China. Journal of Phycology, 46: 325—330. </ol></ul>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-72151803234903713502010-07-17T16:22:00.000-07:002010-07-17T16:22:01.564-07:00New Book: Beyond Cladistics<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1Bb-9N-DcdVyKYMste5f482QoalczOwo4vOlw7qhDvxSrYrcVlZZTlUO4q4MWT8O90OeC6XBLJEtIrEhkIdskNhTTVqJt9CcdtkDy8H-ksrd0c_8rRWTBCpvMAmVhdax-mF15APz1CaOG/s1600/9780520267725.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 212px; height: 320px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1Bb-9N-DcdVyKYMste5f482QoalczOwo4vOlw7qhDvxSrYrcVlZZTlUO4q4MWT8O90OeC6XBLJEtIrEhkIdskNhTTVqJt9CcdtkDy8H-ksrd0c_8rRWTBCpvMAmVhdax-mF15APz1CaOG/s320/9780520267725.jpg" alt="" id="BLOGGER_PHOTO_ID_5494831290041417298" border="0"></a><br />
<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSg_K3Vcrx7fJKj10Jxnd3JsMjKhu2PmDyQHvuYq51Y2373QGfGsOv5IGcjuJRd0UKQfwLrBE-2Kw3H_yOKmyZ64rammTooieFfFWXNI-haMkkR_HlKltt3wppYYA7EetLMRdiUR8ZLdPy/s1600/11396.110.jpg"><img src="file:///C:/DOCUME%7E1/David/LOCALS%7E1/Temp/moz-screenshot.png" alt=""><br />
</a><br />
<div style="text-align: center;"><a href="http://www.ucpress.edu/book.php?isbn=9780520267725">Beyond Cladistics: The Branching of a Paradigm</a><br />
<br />
Edited by David M. Williams and Sandra Knapp<br />
<br />
Available worldwide<br />
<br />
Third title in the <a href="http://www.ucpress.edu/series.php?ser=spsy">Species and Systematics</a> Book Series, published by the University of California Press<br />
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Pre-publication Sale! Save 20% if you order <a href="http://www.ucpress.edu/book.php?isbn=9780520267725">directly</a> from UC Press!<br />
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Click here to see other titles in the <a href="http://www.ucpress.edu/series.php?ser=spsy">Species & Systematics</a> Book series.<br />
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</div>David Williamshttp://www.blogger.com/profile/09011818890918076960noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-70441123740475392242010-04-06T21:55:00.000-07:002010-04-06T21:55:39.901-07:00Awareness in Classification 2<em>In response to <a href="https://www.blogger.com/comment.g?blogID=8697616560977719586&postID=5727840210226099137">Michael</a> from last 'Awareness in Classification' post</em><br />
<br />
Several relationships are proposed, some conflict with others:<ol>1. Bird - dinosaur</ol><ol>2. Humans - Apes</ol>or:<ol>3. Bird - non-avian dinosaur</ol><ol>4. Human - non-human ape</ol>In examples 1 and 2 above dinosaur implies some distinct group of animals, as does apes. In examples 3 and 4 above 'non-avian' stands for 'not-bird', and 'non-human' stand for 'not human'. Thus,<ol>5. Bird - not bird</ol><ol>6. Human - not human</ol>It is tempting to explore the idea of what a 'not bird' might be (resisting exploring what a 'not-human' might be): a flower, a rabbit, a house...<br />
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Another relationship might be:<ol>7. Vertebrate-invertebrate</ol>or<ol>8. Vertebrate-not vertebrate</ol>It is tempting to explore the idea of what a 'not vertebrate' might be: a flower, a rabbit, a house...<br />
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One might argue that context is all important. Of course, a 'not vertebrate' doesn't mean a flower. Well, once again, what does it mean? 'Not vertebrates' are paraphyletic. One might re-classify all 'not vertebrates' as vertebrates, thus making 'not vertebrates' monophyletic (One might re-classify birds as dinosaurs making them monophyletic). Does this mean, now, that birds are invertebrates? Prokaryotes are paraphyletic. One might re-classify all 'prokaryotes' as eukaryotes, thus making 'prokaryotes' monophyletic. Does this mean, now, that birds are prokaryotes?<br />
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Words do indeed have multiple meanings. A taxon name is best associated with a relationship. Then the meaning can be empirically explored.Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-57278402102260991372010-03-28T18:19:00.000-07:002010-03-28T18:19:47.636-07:00Awareness in Classification 1<div>Our recent post reveals a few things we believe are simply misunderstandings: <br />
<ol>1) Paraphyletic groups and their reality</ol><ol>2) Taxa descending from other taxa</ol><ol>3) Phylocode adjustements to make taxa monophyletic.</ol>Let's change to a more general issue, that of invertebrates. Are invertebrates real? No. <a href="http://en.wikipedia.org/wiki/Invertebrate">Wikipedia</a> begins: <br />
<ol>"An invertebrate is an animal without a backbone. The group includes 95% of all animal species - all animals except those in the Chordate subphylum Vertebrata..."</ol>Can invertebrates be defined? Yes. We could list all taxa that are included within and then list as absent all the characters vertebrates have: "An invertebrate is an animal without a backbone" -- but anything can be so defined. Are invertebrates monophyletic? No. They are paraphyletic, they exclude vertebrates. But if we include vertebrates within them, then do they become monophyletic? Yes, but then that is chordates. Are vertebrates descended from invertebrates? It's a nonsense question as invertebrates do not exist in any meaningful way - from nothing comes something?<br />
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Now, replace the terms 'invertebrate' for 'dinosaur' and 'vertebrate' for 'bird'.<br />
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To say dinosaurs are amniotes is like saying invertebrates are animals. Both true but neither telling us what dinosaurs actually are (lots of thing are amniotes). Are dinosaurs monophyletic? Are inverterbrates monophyletic?</div>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com1tag:blogger.com,1999:blog-8697616560977719586.post-20587752685993641042010-03-26T04:01:00.000-07:002010-03-26T04:02:13.035-07:00The Mystery of the Siberian Pinkie: When Classification goes Wrong<span style="float: right; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;"/></a></span>Biological classification is often misunderstood and misused in the scientific literature and especially in the media:<ol>“... birds are dinosaurs” (<a href="http://www.nytimes.com/2010/02/05/science/05dino.html">New York Times</a>, 2010).</ol><ol>“Humans are apes” (Dawkins, 2010 in <a href="http://www.theaustralian.com.au/news/nation/science-education-failing-richard-dawkins/story-e6frg6nf-1225835818671">The Australian</a>).</ol><ol>“Scientists have identified a previously unknown type of ancient human through analysis of DNA from a finger bone unearthed in a Siberian cave” (BBC News Online).</ol>These slogans, popular with the public, are completely misinformed and provide inaccurate information about biological classification. Let’s start with <em>birds are dinosaurs</em>.<span class="fullpost"><br />
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The slogan assumes we know something about the classification of dinosaurs, namely that they include birds. This assumption derives from a cladogram that shows that some dinosaurs (feathered therapods) are more closely related to birds than they are to other dinosaurs (see Gauither et al., 1998). <br />
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Moreover, birds are diagnosed as any amniote that possesses feathers, meaning that therapods are birds. The slogan then should instead read “some dinosaurs are birds”. This then begs the question “what are dinosaurs?” <br />
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The phrase “Humans are apes” has been used quite often as a slogan, most notably by Richard Dawkins. Like the dinosaur bird example, it assumes that we know something about human classification. In fact, the term ‘ape’ refers to:<ol>“... any of two families (Pongidae and Hylobatidae) of large tailless semi-erect primates (as the chimpanzee, gorilla, orangutan, or gibbon) ...” (Merriam-Webster Online Dictionary, 2010).</ol>Humans on the other hand belong to the Hominidae. In classification and in common usage, we are hominids and not apes. So why the confusion?<br />
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Many scientists misuse existing terms in classification to make assumptions about evolution. Since evolution and classification are two separate issues, there is a degree of confusion. The slogan “humans are apes” is supposed to infer that humans evolved from apes or both apes and humans evolved from something else. In classification, this slogan is meaningless, unless it is meant to say that humans are members of either pongidae and hylobatidae. The same misuse of classification can be seen in a recent report of a newly discovered hominid from Siberia. The report by Krause et al (2010) states:<ol>“DNA sequence retrieved from a bone [the distal manual phalanx of the fifth digit, or the 'pinkie'] excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago (Krause et al., 2010).</ol>mtDNA is not used in taxonomy to diagnose new species. Moreover the variability in mtDNA has been found to be high between individuals (see <a href="http://www.nature.com/nature/journal/v464/n7288/full/nature08802.html">He et al., 2010</a>). So what is this hullabaloo about? It appears it concerns itself over a newly discovered pinkie and there isn't much it can tell. You need more evidence than a pinkie to determine and describe a new species into an existing taxonomy. What Krause et al (2010) have found is a reconfirmation that hominid mtDNA is highly diverse. But yet, reading both Krause et al (2010) and the media, we are led to believe that a new species of hominid has been discovered. This is clearly not the case. Until further evidence is found (e.g., bones or bone fragments) and a diagnosis made can we be sure that “scientists have identified a previously unknown type of ancient human”.<br />
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<strong>References</strong><br />
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Gauthier, J. A., Estes, R and de Queiroz, K 1988. A phylogenetic analysis of Lepidosauromorpha. In: R. Estes and G. Pregili (eds), Phylogenetic relationships of the lizard families. Stanford University Press, Stanford, CA, pp. 15-98.<br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Nature&rft_id=info%3Adoi%2F10.1038%2Fnature08802&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Heteroplasmic+mitochondrial+DNA+mutations+in+normal+and+tumour+cells&rft.issn=0028-0836&rft.date=2010&rft.volume=464&rft.issue=7288&rft.spage=610&rft.epage=614&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fnature08802&rft.au=He%2C+Y.&rft.au=Wu%2C+J.&rft.au=Dressman%2C+D.&rft.au=Iacobuzio-Donahue%2C+C.&rft.au=Markowitz%2C+S.&rft.au=Velculescu%2C+V.&rft.au=Diaz+Jr%2C+L.&rft.au=Kinzler%2C+K.&rft.au=Vogelstein%2C+B.&rft.au=Papadopoulos%2C+N.&rfe_dat=bpr3.included=1;bpr3.tags=Biology">He, Y., Wu, J., Dressman, D., Iacobuzio-Donahue, C., Markowitz, S., Velculescu, V., Diaz Jr, L., Kinzler, K., Vogelstein, B., & Papadopoulos, N. (2010). Heteroplasmic mitochondrial DNA mutations in normal and tumour cells <span style="font-style: italic;">Nature, 464</span> (7288), 610-614 DOI: <a rev="review" href="http://dx.doi.org/10.1038/nature08802">10.1038/nature08802</a></span><br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Nature&rft_id=info%3Adoi%2F10.1038%2Fnature08976&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=The+complete+mitochondrial+DNA+genome+of+an+unknown+hominin+from+southern+Siberia&rft.issn=0028-0836&rft.date=2010&rft.volume=&rft.issue=&rft.spage=&rft.epage=&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fnature08976&rft.au=Krause%2C+J.&rft.au=Fu%2C+Q.&rft.au=Good%2C+J.&rft.au=Viola%2C+B.&rft.au=Shunkov%2C+M.&rft.au=Derevianko%2C+A.&rft.au=P%C3%A4%C3%A4bo%2C+S.&rfe_dat=bpr3.included=1;bpr3.tags=Biology">Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia <span style="font-style: italic;">Nature</span> DOI: <a rev="review" href="http://dx.doi.org/10.1038/nature08976">10.1038/nature08976</a></span></span>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com10tag:blogger.com,1999:blog-8697616560977719586.post-88219063144617917452010-03-22T03:44:00.000-07:002010-03-22T03:44:33.429-07:00Publications for 2009Below is our list of publications for 2009. For those with no access to the links, will be happy to provide pdf copies on request.<ol>de Carvalho M.R. & M.C. Ebach 2009. Dearth of the specialist, rise of the machinist. History and Philosophy of the Life Sciences 31:467-470.</ol><ol>Ebach, M.C. 2009. Goethe to Linneaus. In (eds. Wheeler, Q.D. & Knapp, S.) Letters to Linnaeus. Linnean Society, London, pp. 81-83.</ol><ol>Ebach, M.C. & Williams, D.M. 2009. How objective is a definition in the subspecies debate? Nature 457:785.</ol><ol>Ebach, M.C. 2009. Phylogeny. In: Brix J.H. (ed.) Encyclopedia of Time. Sage Publications Inc., Thousand Oaks, CA.</ol><ol>Ebach, M.C. & Wheeler, Q.D. 2009. Cybertaxonomy. In: Brix J.H. (ed.) Encyclopedia of Time. Sage Publications Inc., Thousand Oaks, CA, pp. 252-260.</ol><ol>Karthick B., Toyoda, K., Ramachandra, TV., & Williams, DM. 2009. A note on the identity of Ceratoneis iyengarii Gonzalves & Gandhi (Fragilariophyceae, Bacillariophyta). Diatom Research 24: 233-236.</ol><ol>Li, Y., Williams, DM., Metzeltin, D., Kociolek, J.P., & Gong, Z. 2010. Tibetiella pulchra gen. nov. et sp. nov., a new freshwater epilithic diatom (Bacillariophyta) from River Nujiang in Tibet, China. Journal of Phycology Published Online: Dec 11 2009; DOI: 10.1111/j.1529-8817.2009.00776.x</ol><ol>McNamara, K.J., Feist, R. & Ebach, M.C. 2009. Patterns of evolution and extinction in the last harpetid trilobites during the Late Devonian (Frasnian). Palaeontology, 52:11-33.</ol><ol>Parenti, L.R. & Ebach, M.C. 2009. Comparative Biogeography: Discovering and Classifying Biogeographical Patterns of a Dynamic Earth. University of California Press, Berkeley. </ol><ol>Parenti, L.R., Viloria, Á.L., Ebach, M.C. & Morrone, J.J. 2009. On the International Code of Area Nomenclature (ICAN): a Reply. Journal of Biogeography, 36:1619-1621.</ol><ol>Stachura-Suchoples. K& Williams, DM. 2009. Description of Conticribra tricircularis, a new genus and species of Thalassiosirales, with a discussion on its relationship to other continuous cribra species of Thalassiosira Cleve (Bacillariophyta) and its freshwater origin. European Journal of Phycology 44: 477-486.</ol><ol>Stachura-Suchoples, K., Williams, DM. & Jahn, R. 2009. On extinct, freshwater taxa in the genus Thalassiosira with observations on Thalassiosira species from Pliocene deposit in Oregon, U.S.A. Diatomededelingen 33: 111-113.</ol><ol>Toyoda, K., Tanaka, J. & Williams, DM. 2009. A new brackish water diatom, Achnanthes secretitaeniata sp. nov. from Japan. Journal of Japanese Botany 84: 19-26.</ol><ol>Tuji, A., Williams, DM., Sims, P.A. & Tanimura, Y. 2009. An Illustrated Catalogue of Type Specimens from the H.M.S. Challenger Voyage in Castracane's Slide Collection in the Natural History Museum, London. JOINT HAECKEL and EHRENBERG PROJECT: Reexamination of the Haeckel and Ehrenberg Microfossil Collectionsas a Historical and Scientific Legacy, edited by Y. Tanimura and Y. Aita, pp. 7-11. National Museum of Nature and Science Monographs, No. 40, Tokyo 2009.</ol><ol>Williams, D.M. 2009. 'Araphid' Diatom Classification and The 'Absolute Standard'. Acta Botanica Croatica 68: 455-463.</ol><ol>Williams, DM, Chudaev, DA, Lomonosov, MV, & Gololobova, MA. 2009. Punctastriata glubokoensis spec. nov., a new species of 'Fragilarioid' diatom from lake Glubokoe, Russia. Diatom Research 24: 479-485.</ol><ol>Williams D.M. & Ebach, M.C. 2009. What, exactly, is cladistics? Re-writing the history of systematics and biogeography. Acta Biotheoretica, 57:249–268.</ol><ol>Williams, DM. & Reid, G. 2009. New Species in the Genus Colliculoamphora. Williams & Reid with Commentary on Species Concepts in Diatom Taxonomy.Beihefte zur Nova Hedwigia (Eugene Stoermer Festschrift) 135: 185-200. </ol>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-38748357460214678032010-02-12T04:34:00.000-08:002010-02-12T04:39:08.080-08:00Australian Postgraduate Award in Biogeography Available at UNSW<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoNcCpoVRWASKKFKhqwPE158x_hxQY6dWgFDaNv-uUD9pnih5nbZSEAyamOq5Gr-zkH80baSEOQ-gueznWOEwhK5dbyWUuJ8fnYmXu9ER1TOCl7gco0D0o3PcVSvOLfXd1VFIGb19Oyno/s1600-h/UNSW_logo.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="104" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjoNcCpoVRWASKKFKhqwPE158x_hxQY6dWgFDaNv-uUD9pnih5nbZSEAyamOq5Gr-zkH80baSEOQ-gueznWOEwhK5dbyWUuJ8fnYmXu9ER1TOCl7gco0D0o3PcVSvOLfXd1VFIGb19Oyno/s400/UNSW_logo.jpg" width="400" /></a></div><br />
<div style="text-align: left;">An Australian Postgraduate Award (APA) is available for a PhD in the Biogeography Lab of Dr Malte Ebach at the School of Biological, Earth and Environmental Sciences, University of New South Wales. The Biogeography Lab investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification over time. We seek a highly motivated student with a good honours or Masters degree in biology/ evolutionary biology or geology/palaeontology to choose from two projects:</div><div style="text-align: left;"><br />
</div><div style="text-align: left;"><b>1. Evolution and biogeography of water-bugs of Eastern Australasia</b><br />
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This project, in collaboration with Professor Gerry Cassis (UNSW), examines the morphological and molecular systematic relationships of selected endemic taxa of water-bugs (Gerromorpha and Nepomorpha) in Australasia and the relationships between the biotic areas they inhabit. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification. Requirements: Interest in evolutionary biology, taxonomy, biogeography, field work and natural history. Experience in either systematics, biogeography and molecular techniques would be an advantage.</div><div style="text-align: left;"><br />
</div><div style="text-align: left;"><b>2. Palaeozoic biogeography and trilobite evolution</b></div><div style="text-align: left;"><br />
</div><div style="text-align: left;">This project, in collaboration with Dr John Paterson (UNE), investigates the systematic biology of Carboniferous trilobites (Proetida) and their evolutionary relationships in order to infer palaeogeographic and tectonic reconstructions. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification.</div><div style="text-align: left;"><br />
</div><div style="text-align: left;">Requirements: Interest in palaeobiology, palaeobiogeography, field work and natural history. Experience in either sedimentology, biostratigraphy and taxonomy would be desirable.</div><div style="text-align: left;"><br />
</div><div style="text-align: left;">Please note that applicants must be a citizen or permanent resident of Australia.</div><div style="text-align: left;"><i><br />
</i></div><div style="text-align: left;"><i>Please direct all enquiries and applications to Dr Malte Ebach (mcebach@gmail.com).</i></div>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-88863369418085345792010-02-09T13:01:00.000-08:002010-02-09T13:01:50.313-08:00Darwin came from Essex (via Peru) says cat's DNA<em>From the Wollongong Herald</em><br />
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<em>The DNA recovered from Charles Darwin's cat has proven that the 19th century naturalist was descended from South American Indians.</em><br />
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The aspirant <em>Find-an-Ancestor Project</em> uses the DNA from celebrity pets to map human origins. Tiddles, Charles Darwin's first tabby, is one of 30 exhumed ex-pets. "We'd never thought we'd find Tiddles, or any of the 10 cats Darwin owned during his life" says Prof. Trevor Bruce of the University of Ulladulla". <br />
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Research funded by the <em>Geelong Anti-ageing Centre</em> tested Tiddle's preserved DNA and discovered that Darwin's ancestors came from a small village in present-day Peru. From there they travelled directly to Essex, possibly via a land bridge made of ice, or by small raft, from France. "The evidence is astounding" says Prof. Bruce, "it is amazing how much information one can extrapolate from DNA".<br />
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Tests have led scientists to propose the 'Out of Anywhere hypothesis'. Prof. Bruce explains: "Look, it doesn't matter whose DNA you have, people just seem to originate anywhere. We had the late Liberace's budgie examined and found out that 'The Glitter Man' was descended from Eskimos". <br />
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Further research hopes to discover the centre of origin for all humans. Dr. Karen Hall hopes that this will herald a new hypothesis. "Palaeoanthropologists say that humans and apes originated in Africa. Show me one celebrity with a pet gorilla!"<br />
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You can participate in the <em>Find-an-Ancestor Project</em> by sending $120.00 for a 'detection kit'. The kit includes a swab and a shovel for extracting pet DNA.<br />
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<em>Related Post: <a href="http://www.telegraph.co.uk/news/worldnews/australiaandthepacific/australia/7158271/Charles-Darwins-genetic-history-unlocked-by-DNA-project.html">Charles Darwin's genetic history unlocked by DNA project</a></em>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com1tag:blogger.com,1999:blog-8697616560977719586.post-63032135498260580242009-12-14T15:34:00.000-08:002009-12-15T03:18:16.727-08:00Paraphyly Watch 2009: Pewter Leprechaun Awards Ceremony<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0F_UQhBj2zz6ma9CQUXxoXJ0E5ESgkwAhdBmDEJwGnnX3OVaAmxE_IPNtGFliEIj1apG34-AKwxNvKnSrgm6FHjIcMgd9pooVKfS5ICGDQ-l5pr9YnXb2aMC4YDqkHI1gczFHvMEgwsQ/s1600-h/Haeckel.jpg"><img style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 267px; height: 303px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi0F_UQhBj2zz6ma9CQUXxoXJ0E5ESgkwAhdBmDEJwGnnX3OVaAmxE_IPNtGFliEIj1apG34-AKwxNvKnSrgm6FHjIcMgd9pooVKfS5ICGDQ-l5pr9YnXb2aMC4YDqkHI1gczFHvMEgwsQ/s400/Haeckel.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5415253652592312050" /></a>Albert Hall, London. <br /><br /><em>Thousands of people gather outside in the snow, lining up and waiting to get in to what is tipped to be a star-studded awards ceremony. Inside, we see seats slowly being filled, hear the humdrum of excited voices and the clink of champagne glasses. The air is electric with excitement.<br /><br />[Announcer] Welcome to the most awaited event of the year! Thousands of people are lining up outside to see the winner of the 2009 Pewter Leprechaun. The Hall is sold out and rumors have it that hawkers are selling tickets for over £1000. The air is tense and the crowds excited by the news that this year nominations are a close tie. Walking up to the booth I saw several of the judges looking tired and worn from the week-long debate as to who will be this year’s winner. We also have several famous scientists in the crowd. There I see ... I think ... is it Aristotle? Possibly. Since the introduction of the <em>Simpson-Darlington Time Machine</em> many international and temporal guests are able for the first time to visit on a whim. I guess it could be Plato ... err ... not to sure. Yes, there is the guest of honor Aristotle, carrying the ceremonial <em>Great Chain of Being</em> ladder - the <em>Scala Naturae</em> itself. He will of course be chairing the session from the right of the stage.</em><span class = "fullpost"> <br /><br />This year’s nominees are:<ol><a href="http://urhomology.blogspot.com/2009/01/paraphyly-watch-1-fossil-fish-missing.html">Martin D. Brazeau</a> on ‘The braincase and jaws of a Devonian ‘acanthodian’ and modern gnathostome origins’ published in <em>Nature</em> (2009, 457:305-308)</ol><ol><a href="http://urhomology.blogspot.com/2009/05/paraphyly-watch-2-paraphyly-catalogue.html">Dennis P. Gordon</a> on ‘Towards a management hierarchy (classification) for the Catalogue of Life’ a Draft Discussion Document published in <em>Species 2000 & ITIS Catalogue of Life Annual Checklist</em> (2009, on CD-ROM)</ol><ol><a href="http://urhomology.blogspot.com/2009/06/paraphyly-watch-3-transitional-fossils.html">Donald R. Prothero</a> on the ‘Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals’ published in <em>Evolution, Education and Outreach</em> (2009, 2:289-302)</ol><ol><a href="http://urhomology.blogspot.com/2009/06/paraphyly-watch-3-transitional-fossils.html">Todd F. Stuessy and Christiane Konig</a> on the ‘Classification should not be constrained solely by branching topology in a cladistic context’ published in <em>Taxon</em> (2009, 58:347-348)</ol><ol> <a href="http://urhomology.blogspot.com/2009/12/paraphyly-watch-4-monoclady-and.html">János Podani</a> on the ‘Taxonomy versus evolution’ by also published in <em>Taxon</em> (2009, 58:1049-1053)</ol><br /><em>The audience is seated and the lights dim</em><br /><br />[Announcer] I see that the lights are dimming and...<br /><br /><em>Applause</em> <br /><br />[Announcer] ... rapturous applause for the man himself - the father of paraphyly and host for tonight - Ernst Haeckel! He is walking onto stage, completely out-fitted in tweeds and ... is that a duck hanging from his belt....?<br /><br /><em>Applause ends</em><br /><br />[Ernst Haeckel] Danke Schoen! Meine Damen und Herren! Tonight ve vill avard zi Pewter Leprechaun for 2009 to zi most admirable abuse and misuse of paraphyly. It iz my pleasu ...<br /><br /><em>Applause. Haeckel gets annoyed</em><br /><br />[Ernst Haeckel] Aufhalten! Ve applaud at zi end! AT ZI END!<br /><br /><em>Applause ends abruptly</em><br /><br />[Ernst Haeckel] Zat ist better. Ver vos I. Ach ja ... my pleasure to announce the vinner. Bevor I do, may vi present and bless die Pewter Leprechaun?<br /><br /><em>Haeckel looks around slightly confused. The main doors open and a procession starts at the back of the Hall</em><br /><br />[Announcer] And we see the procession of the Pewter Leprechaun held aloft by George Gaylord Simpson. Following behind him is the Holy Order of the Lineage, Ernst Mayr, P.J. Darlington, Peter Ashlock all holding candles ... and ... there is some commotion at the back ... some shouting ... oh dear ... is that Adolf Naef? My word! Naef is attacking Simpson - he must just have read <em>Principles of animal taxonomy</em> during his brief visit here. He is <em>not</em> happy ... some more shouting ... OH! Simpson has punched Naef! The American has swiped the Swiss in a spectacular left-hook! Naef has recovered and is grabbing the Pewter Leprechaun.. has he got it? He HAS GOT IT! Mayr tackles Naef, Naef passes it on to ... Zangerl! My God, see that man run! Dodges Remane and Zimmermann ... who are discussing functional homology and ... knocks over Hennig, who was admiring Remane ... a crash-tackle by Ashlock and Zangerl looses the Leprechaun! They have lost the Leprechaun! .. It’s ... Ashlock ... picks up the leprechaun and passes it onto .... Darlington .... pushes over Hennig who just got up again ... passes it onto Mayr, back to Darlington who ... misses the catch! He has <em>missed</em> the catch! There is a scramble for the Leprechaun and Haeckel, yes Haeckel, joins in and ... punches out Hennig who just got up again ... and runs and leaps onto stage. What a performance from the German!<br /><br />This has been a most remarkable entry for the <em>Holy Order of the Lineage</em>! The audience is wild with excitement. Aristotle stands up to bless the Leprechaun .. and ... it’s blessed! The Leprechaun has been blessed by the <em>Great chain of being</em> ladder! Haeckel struts back to the podium and puts his hand in his top pocket ... yes ... it’s a golden envelope!<br /><br />[Ernst Haeckel] Meine Damen und Herren! Zi vinner of zi 2009 Pewter Leprechaun is ...<br /><br /><em>Haeckel slowly opens the envelope and pulls out a card</em><br /><br />[Ernst Haeckel] Mein Gott! <br /><br /><em>Haeckel appears startled and looks to Aristotle holding out the card. Aristotle strains to see what is written on it. The audience titters</em><br /><br />[Ernst Haeckel to Aristotle] Iz dis ein f*cking joke?<br /><br /><em>Aristotle shrugs. Haeckel composes himself</em><br /><br />[Ernst Haeckel] Well ... zi judges ... have decided that the award should go to zi most prolific <em>publisher</em> of zi use and abuse of paraphyly. The vinner iz ... Taxon, zi journal of the International Association for Plant Taxonomy!<br /><br /><em>Audience applauds insanely</em><br /><br />[Announcer] This <em>is</em> a surprise! The Pewter Leprechaun has never been awarded to a journal, in fact, it has never been awarded to anyone. I hope the nominees aren’t too disappointed. But aren’t the audience just loving it! Ernest Haeckel bows and leaves the stage. Aristotle leads the procession of the Holy Order out the Hall as the audience slowly rises in respect. Simpson and Darlington looking a bit bruised but enjoying the moment. Do I see a smile from Mayr? Err ... no, but I am sure he is loving every minute of it! <br /><br /><em>So ends the Pewter Leprechaun Awards Ceremony for 2009. We hope that 2010 brings forth a startling array of nominations. All entries can be submitted to the </em>Systematics & Biogeography Blog<em> via next year’s 2010 Paraphyly Watch post.</em> <br /><br />Have a Merry Christmas and a Happy New Year!</span>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com0tag:blogger.com,1999:blog-8697616560977719586.post-88199721011921303242009-12-07T13:40:00.000-08:002009-12-07T14:08:22.951-08:00Paraphyly Watch 4: Monoclady and Paraclady<span style="float: right; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;"/></a></span>Just when you thought all possible abuses and misuses of paraphyly have been thoroughly exhausted, one totally mind-boggling and confused piece of writing appears in the <del>Journal of Paraphyly</del> <a href="http://www.botanik.univie.ac.at/iapt/s_taxon.php">Taxon</a>. We refer to <em>Taxonomy versus evolution</em> by János Podani, a dainty ditty that transcends all boundaries of comprehension and ventures into the field of evolutionary science fiction. <br /><br />The story so far...<span class="fullpost"><br /><ol><em>On the planet Zog, the Mayrian Monks enforce rigid elections that decide the fate of the foundations of science. One day new heretical “discoveries” of what are called ‘natural groups’ questions the validity of Reptiles - rulers of the land. The heretics have called them a group of ‘unrelated animals’ - nothing more than systematic bastards! The Mayr-Monks are never wrong and, science never gets in their way. A snap election is called, the ballot counted and science-democracy enforced. The vote was unanimous: 130 in favour - zero against. “Good to see science done” says one Monk to another. That night they all sleep peacefully with a clear conscious, awaiting morning when their sun will rotate around their flat earth once again.</em></ol>The Mayrian Monks will do anything to protect paraphyletic groups. Rather than revise a taxonomic group, evolutionary taxonomists will dabble in systematics in order to change the foundations of classification. This is akin to the alcohol fueled idea of trying the change the laws of gravity in order to balance this year’s Christmas tree in the front sitting room. It doesn’t work. Neither does <em>monoclady</em> and <em>paraclady</em>. Oh dear, where <em>does</em> one start?<br />Let’s kick off with Podani’s arguement, namely:<br /><ol>“... that there are four major aspects of taxonomic systems in which achievements of evolutionary biology are not recognized fully and properly, if evolution is considered at all” (Podani, 2009: 1049).</ol>Podani does this by distinguishing diachronous and synchronous classifications (not to be confused with similar terms used in Ebach & Williams [2004] as Podani does). In Podani’s view a diachronous classification includes fossil organisms, which he equates with ‘ancestors’ and synchronous taxa that he describes as extant. Apparently, classifying fossils with extant taxa poses problems hence the need for both classifications. He goes on...<br /><ol>“If we use a synchronous classification for extant organisms, we are concerned with the result of evolution, history is only relevant as long as common ancestry is to be detected, and an inclusive hierarchy is suitable to summarize diversity of life” (Podani, 2009: 1050).</ol>and...<br /><ol>“On the other hand, a diachronous classification cannot be Linnaean for two reasons: (1) units of classification and the groups change in time and, more importantly, (2) wide gaps necessary for separating supraspecific taxa are evolutionary absurdities in the spatio-temporal continuum of populations” (Podani, 2009: 1050).</ol>Got it? Now, onto the next bit...<br /><ol>“The only tool for representing the diachronous pattern of life adequately is the Darwinian phylogenetic tree, showing ancestor–descendant relationships between extinct and extant populations” (Podani, 2009: 1050-1051; original emphasis).</ol>...so [drum roll]...<br /><ol>“I suggest restricting the original definition of monophyly to phylogenetic trees, so that it is a diachronous phenomenon and can only be examined in a diachronous classification. For cladograms, I introduced the new term monoclady: a group is monocladistic if it includes all terminals of a given clade. This condition has to do with extant taxa and is particularly meaningful for a synchronous classification” (Podani, 2009: 1051; original emphasis).</ol>...therefore...<br /><ol>“Reptiles are most certainly para- phyletic because extinct ones include the ancestors of birds and mammals as well. Extant reptiles are paracladistic, since crocodiles are sister to birds rather than to other reptiles” (Podani, 2009: 1051).</ol>...and to sum it all up...<br /><ol>“If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic. Paraclady means that the group cannot be embedded into a monophyletic taxon, and it is therefore indication of paraphyly or even polyphyly in the corresponding diachronous classification. A Linnaean taxon, which is preferably synchronous as the above logic dictates, can only be monocladistic, paracladistic or polycladistic and the monophyly/paraphyly problem vanishes. Paraphyly, as understood earlier, may often be reflection of the disagreement of a diachronous classification with a synchronous analysis. Therefore, the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications” (Podani, 2009: 1052).</ol>In order to keep this argument short we will not discuss Podani’s bogus adventure into nomenclature, but start with his first and last points, namely, “... the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications”. Is it? Taxonomy has always remained considerably neutral about how one groups extant and extinct taxa together, why then should there be two classifications? Because extinct taxa are more likely to be ‘ancestors’ and, genealogical relationships (as Podani correctly points out) make poor classification systems. So where does this leave taxonomy? Well, where it has always been - as a neutral way to classify taxa without needing to know who is ancestor to whom. The same is true for cladograms - extinct and extant taxa are placed at the terminals because there are related in some way. It appears that Podani has missed something here, such as the whole cladistic revolution from the 1960s to the 1980s. Cladograms remove the need for phylogenetic trees as all relationship can be shown equally. So both the diachronous and synchronous classification systems are utterly pointless as taxonomy remains neutral about ancestors and fossil taxa (they classify along with extant groups) and equally useless in systematics, as all taxa are treated equally. Podani’s <em>rasion d'être</em> for two classification systems is a vain attempt to preserve paraphyletic groups (number 2 for this year after Stuessy and Koenig [2009]).<br /><br />Here is how it works. First debunk monophyly as irrelevant to classification by assigning them as problems found in phylogenetic trees. Since phylogenetic trees are diachronous and diachronous classifications “cannot be Linnaean” and, are therefore invalid. Clever. Now he introduces a new term <em>monoclady</em> and <em>monocladistic</em>, which means, “If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic” (Podani, 2009: 1052). There we have it. Monocladistic groups can be paraphyletic seen from a phylogenetic perspective. Get it?<br /><br />Let’s put it another way. Take an existing term like monophyly and replace it with a similar term like monoclady (“includes all terminals of a given clade”), which of course does not change its overall meaning. Now dismiss monophyly as irrelevant to classification, but relevant to 19th century Haeckelian phylogenetics, hence radically changing not only its meaning but also its usage. Here comes the best bit - <em>do the same to paraphyly</em>. Replace its overall meaning with another term, like paraclady, and then dismiss paraphyly as irrelevant to classification. No problems here (as it is not relevant to classification). The <em>coupe de grace</em> is defining some forms of monoclady (formerly monophyly) as paraphyly! Wow, the sheer audacity! <br /><br />Yes folks, I think we have a clear forerunner in the 2009 Pewter Leprechaun for the <strong>misuse</strong> and <strong>abuse</strong> of paraphyly.<br /><br />As you read, judges are conferring in what is to be some pretty stiff competition. The results for the Winner of the 2009 Pewter Leprechaun will be announced very soon. Stay tuned!<br /><br /><strong>References</strong><br />Ebach, M.C. & Williams, D.M. (2004). Classification. Taxon 53: 791–794.<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Taxon&rft_id=info%3A%2F&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Taxonomy+versus+evolution&rft.issn=&rft.date=2009&rft.volume=&rft.issue=58&rft.spage=1049&rft.epage=1053&rft.artnum=http%3A%2F%2Fwww.ingentaconnect.com%2Fcontent%2Fiapt%2Ftax%2F2009%2F00000058%2F00000004%2Fart00001&rft.au=Podani%2C+J.&rfe_dat=bpr3.included=1;bpr3.tags=Biology">Podani, J. (2009). Taxonomy versus evolution <span style="font-style: italic;">Taxon</span> (58), 1049-1053</span>.<br />Stuessy, T.F. & König, C. (2009). Classification should not be constrained solely by branching topology in a cladistic context Taxon, 58, 347-348.</span>Malte C. Ebachhttp://www.blogger.com/profile/11901602320985626811noreply@blogger.com3tag:blogger.com,1999:blog-8697616560977719586.post-11739322890976760632009-09-30T04:50:00.000-07:002009-09-30T05:03:39.028-07:00The Aquatic ApeMore fossil news: <br /><br /><a href="http://www.guardian.co.uk/science/2009/sep/23/darwin-country-fossil-hunters-meet"><em>Fossil hunters arrive in Darwin country, but will they find a pub?</em></a><br /><br />The story ends with this snippet:<br /><br /><em>In the corridors and coffee areas, some students were angling for jobs – the recession hits fossil hunting too – while others were hijacking experts to help them with their work. Such as Bristol student, Brian Machin, whose thesis is on the theory that a type of monkey found in South America got there by floating from Africa on a raft. "It's nonsense of course," he said, "But it's hard to prove it's nonsense."</em><br /><br />Who is Brian Machin? We need to know.David Williamshttp://www.blogger.com/profile/09011818890918076960noreply@blogger.com2tag:blogger.com,1999:blog-8697616560977719586.post-60541714855322695792009-09-19T12:54:00.000-07:002009-09-19T13:00:02.052-07:00(Not) Lars (Brundin)Nestling, possibly unread by many, in the first comment on the announcement of the downloadable copy of Systematics and Biogeography, is an offering from Professor Lars (of whom about we know absolutely nothing). At first we thought it a jape, one of our friends or colleagues trying to tease us. But no! (“Blimey!!”, that was Williams [he’s British]; “Cricky”, that was Ebach [he’s Australian]). We read the text closely and could see that the well thought out and reasoned commentary was, indeed, real – a series of penetrating observations on the state of systematics today – and, of course, the follies of the past. We were humbled in its presence – but unwilling to let it pass and, because we are both very humble people, have decided to bring it to wider attention. Read on and enjoy, and consider what might be the follies of present day systematics and systematists.<br /><br /><em>Lars said... <br />I can't see why cladists (remember this term was first used by Ernst Mayr to distinguish them from other schools) consider themselves "revolutionaries". Cladistics is only efficient when one is dealing with morphology, and this kind of information is so terribly biased by subjectivity, that it should never be used as phylogenetic inferential data.<br /><br />Molecular data, on the other hand, is much less biased (bias comes from sequencing errors, lateral gene transfers and poorly chosen alignment parameters) and should reflect the correct evolutionary relationships if correctly analyzed. With the advance of genetic barcoding, the Cladistic methods has become obsolete.<br /><br />Morphology can be interpreted in many ways by different authors, and given the infinity of manners the same information can be scored, it becomes not much more than an exercise of subjectivity.<br /><br />Cladistics is traditionally viewed by serious molecular biologists as a sectarian (almost a religious cult / secret society!) branch of evolutionary research that claims to possess the most efficient and and best logic to propose hypotheses on organismal relationships. <br /><br />Unfortunately, this is not true. Cladists are often narrow-minded and do not accept their "parsimony" method is much more prone to LBA artifact than those usually referred to as "Phenetics", such as Neighbor-Joining and Maximum-Likelihood. This last is the pinnacle of evolutionary inference, since it uses both raw nucleotide data AND genetic distance in its calculations, thus using all data explanatory power.<br /><br />Hence, considering the high subjectivity implied in morphologic matrices, the risk of LBA bias, and the suboptimal use of data explanatory power, Cladistics should be avoided.<br /><br />This makes Phenetics, and not Cladistics, the actual revolution!</em><br /><em></em><em></em>David Williamshttp://www.blogger.com/profile/09011818890918076960noreply@blogger.com4tag:blogger.com,1999:blog-8697616560977719586.post-42712784282800506212009-09-15T03:46:00.000-07:002009-09-15T08:21:47.656-07:00Systematics and Biogeography: Cladistics and Vicariance Online!<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBxAoJPNDtdVhMdnIQxfBlXhUHX0p4oPefebkxGqLTJDU7B7loK4pkkOOhYpoEddAVdQSmXZBChUjVUY122ntIwO5QM-P3NydlA-erV1-ZEm12gX9fdJX_CqHzFOHe_7oKSx1flMdk-vo/s1600-h/Blue+Book"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 140px; height: 201px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBxAoJPNDtdVhMdnIQxfBlXhUHX0p4oPefebkxGqLTJDU7B7loK4pkkOOhYpoEddAVdQSmXZBChUjVUY122ntIwO5QM-P3NydlA-erV1-ZEm12gX9fdJX_CqHzFOHe_7oKSx1flMdk-vo/s400/Blue+Book" border="0" alt=""id="BLOGGER_PHOTO_ID_5381708921777629762" /></a> Every now and then a scientific discipline undergoes a revolution, an episode that changes the way a subject is perceived, the way it is understood and undertaken – a new vision emerges that prevents a return to the subject matter as it was before, a paradigm change, some genuine progress. In the last century, there was a revolution in phylogenetics and systematics that began with the work of entomologist Willi Hennig (1950, 1966) and its interpretation by Lars Brundin (1966), a chironomid specialist. The need for revolution was succinctly put by palaeontologist Colin Patterson, some years later<ol>“By about 1960 palaeontology had achieved such a hold on phylogeny reconstruction that there was a commonplace belief that if a group had no fossil record its phylogeny was totally unknown and unknowable” (Patterson 1987:8).</ol>That ‘commonplace belief’ was eventually rejected in favour of determining relationship from evidence (characters, homologies) provided by organisms (living or extinct), a shift from the preoccupation of discovering ancestry directly from the fossil record to determining common ancestry. As Brundin later noted, “little by little some palaeontologists have perceived that Hennig’s principles of phylogenetic systematics meant a revolution to their science.” Hennig called his approach Phylogenetic Systematics, the title of his 1966 book (Hennig 1966), an approach that eventually became known as cladistics, hence the cladistic revolution: the cladistic revolution overturned the central position of palaeontology in determining phylogenetic relationships: turning Ernst Haeckel’s Systematische Phylogenie into Hennig’s Phylogenetic Systematics.<br /><br />By the early 1980s three books were published, all dealing with cladistics. Each approached its topic from a different perspective: <em>Phylogenetic Analysis and Paleontology</em> by Joel Cracraft & Niles Eldredge (Columbia University Press, New York, 1981), <em>Phylogenetics: The Theory and Practice of Phylogenetic Systematics</em> by Ed Wiley (New York: Wiley Interscience, 1981) and <em>Systematics and Biogeography: Cladistics and Vicariance</em> by Gary Nelson and Norman Platnick (Columbia University Press, New York, 1981).<br /><br />While all three books have their merits, it is the last, <em>Systematics and Biogeography: Cladistics and Vicariance</em> that broke into new ground; and it is the last that, some 28 years after its first appearance and almost impossible to get a copy, is being made available by the University of California Press at <a> http://www.ucpress.edu/books/series/spsy.php</a><br /><br />Cladistics, as outlined in <em>Systematics and Biogeography: Cladistics and Vicariance</em>, might be understood as a reaction to phylogeny reconstruction, or more specifically, Haeckel’s paleontological version of it, developed by Matthews and Simpson. <em>Systematics and Biogeography</em> is a detailed critique of Haeckel’s legacy and an outline of what can be understood as natural classification, as first sketched by Candolle in his <em>Théorie élémentaire de la Botanique</em> – the question addressed being: How do ancestor—descendant relationships relate to natural classification?<br /><br />Since <em>Systematics and Biogeography</em> there have been discourses on ‘tree-thinking’, ‘group-thinking’ and ‘population-thinking’, none seemingly appropriate for classification: Classification (and phylogeny, and systematics) are all best referred to as relationship-thinking, of which <em>Systematics and Biogeography</em> is a meditation on.<br /><br />Download this book now from the University of California Press <a href="http://www.ucpress.edu/books/series/spsy.php">website</a> – and see if you can start another revolution.David Williamshttp://www.blogger.com/profile/09011818890918076960noreply@blogger.com1tag:blogger.com,1999:blog-8697616560977719586.post-43612761233295347052009-08-06T03:02:00.000-07:002011-02-02T00:16:02.224-08:00Chris Humphries – Natural History Museum, London (1947—2009)Chris Humphries, botanist and biogeographer, died on Friday 31st July. Chris was a leading figure in the cladistic revolution in systematics and biogeography. He worked in the Botany Department of the Natural History Museum from 1972 until his retirement in 2007. <br />
Chris was one of the first to explore, develop and promote cladistics in botany, examining classification and biogeography from its novel perspective. Chris produced a classic in biogeography, <em>Cladistic Biogeography</em> (1986) (with Lynne Parenti, of the Smithsonian; a revised 2nd edition appeared in 1999) and produced a widely read and used manual for cladistic systematics, <em>Cladistics: A practical course in systematics (1992)</em> (with staff of the Natural History Museum; a revised 2nd edition appeared in 1998 as <em>Cladistics: the theory and practice of parsimony analysis</em>). <br />
Chris’s research extended from organizing and annotating the first complete full-colour edition of Banks’ <em>Florilegium</em> to addressing conservation issues with <em>WorldMap</em> (with Dick Vane-Wright and Paul Williams, both of the Entomology Department, NHM). <br />
Chris received the Linnean Society’s Bicentenary Medal in 1980 and their Gold Medal in 2001. He was President of the Systematics Association (2001—2003) as well as its Treasurer (1996—1999), and President of the Willi Hennig Society (1989—1991), being elected a Fellow <em>honoris causa</em> in 1998. Chris was also Vice-President and Botanical Secretary of the Linnean Society (1994—1998).<br />
<br />
<strong>David M. Williams & Charlie Jarvis</strong><br />
Botany Department<br />
The Natural History Museum<br />
Cromwell Road<br />
London SW7 5BD<br />
UKDavid Williamshttp://www.blogger.com/profile/09011818890918076960noreply@blogger.com1