Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Monday 5 November 2012

Squirrels, Eels, Algae and Ardi: A Clarification

The "First human ancestor", which the ABC reports looked "like a squirrel" is of course not to be mixed up with the "Human Family's Earliest ancestor", namely Ardipithecus ramidus or “Ardi”, which tells us is a "... a female who lived 4.4 million years ago”. Not that this is to be confused with the Telegraph’s '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 ABC's "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."

I hope this clarifies who our first, oldest and earliest ancestors really were.

Thursday 6 September 2012

Birds are Fish

Birds really are dinosaurs, and a sparrow or a blackbird is every bit as much a dinosaur as Tyrannosaurus or Stegosaurus (Dr. Dave Hone, Guaridian online 6 September, 2012)
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:
  • animals (birds & shit)
  • fish (animals wif scales)
  • dinasaurs (fish wif fevhers)
  • birds (dunno)
vat klassafikayin tellz u vat birds r fish wif fevhers.

uno other animals r spinless like worms & bugs & shit. so r plankton & trees i guess so va klassafikayin of bugs r:
  • animals (uva stuff)
  • spinless (like trees)
  • worms (veges wif eyes)
  • bugs (worms wif legs)
vis klassafikayin tells ya vat bugs r wormies wif legs.

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: bugs r worms & birds r fish!

Monday 9 January 2012

Publications for 2011

Below is our list of publications for 2011. For those with no access to the links, will be happy to provide pdf copies on request.
    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. 
    Ebach, M.C. (2011). Taxonomy and the DNA Barcoding Enterprise. Zootaxa, 2742: 67–68. 
    Ebach, M.C. (2011). Biogeógrafos del mundo... ¡uníos!: un camino hacia la unificación. Revista de Geografía Norte Grande, 48: 5-10. 
    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. 
    Ebach, M.C., de Carvalho, M.R. and Williams, D.M. (2011). Opening Pandora’s Molecular Box. Zootaxa, 2946: 60—64. 
    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. 
    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 
    Williams, D.M. (2011). Fifteen new diatom (Bacillariophyta) species from Lake Ohrid, Macedonia. Phytotaxa, 30: 1—41. 
    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. 
    Williams, D.M. (2011). Synedra, Ulnaria: definitions and descriptions – a partial resolution. Diatom Research, 
    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. 
    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.


Thursday 15 December 2011

Agnosticism in Comparative Biology

Gnostic adj. of or relating to knowledge (from gnōstos meaning 'known')

Agnostic adj. a person who believes that nothing is known on some topic, either at the present, or in principle

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.

Wednesday 9 November 2011

Tweeted Histories I #Homology

@Goethe1824 I can relate a worm and a man via a third thing! I'll write a poem about it!
@sexy_Blumnbch What?
@henrich.B if you hang a human skeleton next to that of bird, you can compare their structures #Bronn1858
@Darwinathome's birdy
@sexy_Blumnbch Eww!
@MonsterMoa nah! what you want is a bauplan. #Owen1849
@Swiss_Pride What evidence have you got? You need space, time as well as form! #Agassiz1859
@Embryo.boy I think he means comparing embryos and how they develop #Gegenbaur1859
@Swiss_Pride no I don't!
@Darwinathome I found a birdy!
@MonsterMoa just compare the forearms of bats, humans and whales. See? Analogy!
@RayL Don’t just compare: find the origin of things. Homology? Bah! Homogeny!
@asagray I like @Darwinathome's birdy. Can u send photo?
@Stammbaum Origins, we need origins! My own Stammbaum gives origins; now all is homogeny
@Darwinathome can someone tell @Stammbaum to leave me alone?
@RayL Not all is homogeny, some comparisons are not true: homoplasy!
@Stammbaum Who cares. I have lots of stammbaume, one for every creature. All with homogeny, homoplasy and homology
@naefnotnaf @Stammbaum got it wrong. You can't mix phylogeny and systematics #Naef1919
@naefnotnaf homology is a systematic relationship separate from phylogeny
@angry_mayr Typologist!
@Zimmermann no it's not! homology is a transformational relationship.
@a.remane or a process #Remane1952
@willi Why not compromise? Use @naefnotnaf's systematics for taxa and @Zimmermann for their characters! #Hennig1950
@ggsimp what about ancestors? Homology is similarity between the bits of us and ancestors
@sokal_123 you mean overall similarity at a node? #SokalSneath63
@willi no, special similarity, that is synapomorphy #Hennig66
@angry_mayr Cladist!
@nelson_usa perhaps it's a non-transformational relationship? #NelsonPlat81
@beaty.boy Pattern Cladist!
@Colin82 non-transformational but based on similarity #Patterson82 
@ron.brady forget similarity, homology is simply an affinity. See @Goethe1824
@normlovesspiders homology is a three-item relationship regardless what is based on
@hennig_superstar %$#%! Homology is synapomorphy?
@k.nixon homology = synapomorphy + symplesiomorphy #NixonCarp11

Sunday 6 November 2011

The Autonomous Algorithm: Malpractice in Theory

In our last post we introduced the topic of the Autonomous Algorithm, 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.

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.

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.

Wednesday 24 August 2011

The Autonomous Algorithm

The 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.

The Timetree of Life: A product
of the Autonomous Algorithm?

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.