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).

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.

Wednesday, 20 April 2011

Willi Hennig (1913 - 1976)

The great entomologist Willi Hennig (1913—1976), founder of ‘Phylogenetic Systematics’, was born on this day. Had he lived, he’d be 98.

Friday, 4 February 2011

So Long, and Thanks for All the Fish

It’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.

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:

“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).

German logic? ‘Real’ evolution? Classification as ‘art’? Cavalier-Smith continues:

“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).

“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:

“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).

János Podani (2010) echoes the sentiment:

“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).

Non-evolutionary? Anti-evolutionary?

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)

The statements above, from Cavalier-Smith, Podani, Hörandl & Stuessy: Are any true, or even any part of them true?

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.

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

Hörandl, E. & Stuessy, T.F. 2010. Paraphyletic groups as natural units of biological classification. Taxon 59: 1641—1653

Podani, J. 2010. Monophyly and paraphyly: A discourse without end? Taxon 59: 1011—1015.

Wednesday, 2 February 2011

A Makeover

You like it? The Blogger Template Designer calls it "Simple". We like it and hope that it is easier on the eye.

Above you will see our new design, a 'Chtenopteryx ontogeny motif', and below that, an additional quote that will change from time-to-time (this month it's Darwin).

We hope to hear from you, dear Systematics & Biogeography reader, especially those can enlighten us on the ontogeny in the header above. You will be hearing from us.

Sunday, 23 January 2011

Adventures with my DNA Barcoder

"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" (Janzen, 2010, Biotropica, 42:540-542).

Thursday, 25th
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.

Friday, 26th
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.

Saturday, 27th
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?

Sunday, 28th
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.

Wednesday, 1st
Finally, a hot and sunny day! I tried to entice a bird with bread crumbs. No luck.

Thursday, 2nd
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 every time. There was only one plant sign in the whole park that was wrong!

Sunday, 5th
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!

Tuesday, 7th
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.

Sunday, 9 January 2011

Publications for 2010

Below is our list of publications for 2010. For those with no access to the links, will be happy to provide pdf copies on request.
      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.
      Ebach, M.C. (2010). Paleobiological Revolution: Essays on the Growth of Modern Paleontology. Systematic Biology, 59: 753-755.
      Ebach, M.C. (2010). A new book on biogeography. Cladistics, 26: 560-562.
      Ebach, M.C. and de Carvalho M.R. (2010). Anti-intellectualism and the DNA Barcoding Enterprise. Zoologia, 27: 165-178 [access free pdf here]. 
      Ebach, M.C. and Williams D.M. (2010). Aphyly: A Systematic Designation for a Taxonomic Problem. Evolutionary Biology, 37: 123-127.
      Ebach, M.C. and Williams D.M. (2010). Systematics and Biogeography: Cladistics and Vicariance. Systematic Biology, 59: 612-614.
      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.
      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.
      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.
      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.
        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.
            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.
            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. 
            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.
            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.
              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.